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Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits
International Nuclear Information System (INIS)
Koseska, Aneta; Volkov, Evgenii; Kurths, Juergen
Synthetic biology is a relatively new research discipline that combines standard biology approaches with the constructive nature of engineering. Thus, recent efforts in the field of synthetic biology have given a perspective to consider cells as 'programmable matter'. Here, we address the possibility of using synthetic circuits to control protein dynamics. In particular, we show how intercellular communication and stochasticity can be used to manipulate the dynamical behavior of a population of coupled synthetic units and, in this manner, finely tune the expression of specific proteins of interest, e.g. in large bioreactors.
Protein complexes and cholesterol in the control of late endosomal dynamicsCholesterol and multi-protein complexes in the control of late endosomal dynamics
Kant, Rik Henricus Nicolaas van der
Late endosomal transport is disrupted in several diseases such as Niemann-Pick type C, ARC syndrome and Alzheimer's disease. This thesis describes the regulation of late endosomal dynamics by cholesterol and multi-protein complexes. We find that cholesterol acts as a cellular tomtom that steers the
The dynamic mechanism of presenilin-function: Sensitive gate dynamics and loop unplugging control protein access
DEFF Research Database (Denmark)
Somavarapu, Arun Kumar; Kepp, Kasper Planeta
There is no molecular explanation for the many presenilin 1 (PSEN1) mutations causing Alzheimer's disease, but both gain of function relating to amyloid production and loss of isolated PSEN1 function have been implied. We report here the first detailed dynamic all-atom model of mature PSEN1 from ...
Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression
Kojima, Shihoko; Sher-Chen, Elaine L.; Green, Carla B.
Green and colleagues perform a global analysis of circadian-controlled poly(A) tails and identify hundreds of mRNAs that display dynamic rhythmic polyadenylation states. They identify three distinct classes of mRNAs with rhythmic poly(A) tails. Interestingly, class III mRNAs are controlled not by transcription, but by rhythmic cytoplasmic polyadenylation, and are regulated by the components of the cytoplasmic polyadenylation machinery, CPEB2 in particular, which are themselves rhythmically ex...
DMPD: Protein kinase C epsilon: a new target to control inflammation andimmune-mediated disorders. [Dynamic Macrophage Pathway CSML Database
Lifescience Database Archive (English)
Full Text Available 14643884 Protein kinase C epsilon: a new target to control inflammation andimmune-m...g) (.html) (.csml) Show Protein kinase C epsilon: a new target to control inflammation andimmune-mediated di...sorders. PubmedID 14643884 Title Protein kinase C epsilon: a new target to contro
Transcellular tunnel dynamics: Control of cellular dewetting by actomyosin contractility and I-BAR proteins.
Lemichez, Emmanuel; Gonzalez-Rodriguez, David; Bassereau, Patricia; Brochard-Wyart, Françoise
Dewetting is the spontaneous withdrawal of a liquid film from a non-wettable surface by nucleation and growth of dry patches. Two recent reports now propose that the principles of dewetting explain the physical phenomena underpinning the opening of transendothelial cell macroaperture (TEM) tunnels, referred to as cellular dewetting. This was discovered by studying a group of bacterial toxins endowed with the property of corrupting actomyosin cytoskeleton contractility. For both liquid and cellular dewetting, the growth of holes is governed by a competition between surface forces and line tension. We also discuss how the dynamics of TEM opening and closure represent remarkable systems to investigate actin cytoskeleton regulation by sensors of plasma membrane curvature and investigate the impact on membrane tension and the role of TEM in vascular dysfunctions. Copyright © 2013 Soçiété Française des Microscopies and Soçiété de Biologie Cellulaire de France.
Rajamani, Rajesh
Vehicle Dynamics and Control provides a comprehensive coverage of vehicle control systems and the dynamic models used in the development of these control systems. The control system applications covered in the book include cruise control, adaptive cruise control, ABS, automated lane keeping, automated highway systems, yaw stability control, engine control, passive, active and semi-active suspensions, tire-road friction coefficient estimation, rollover prevention, and hybrid electric vehicle. In developing the dynamic model for each application, an effort is made to both keep the model simple enough for control system design but at the same time rich enough to capture the essential features of the dynamics. A special effort has been made to explain the several different tire models commonly used in literature and to interpret them physically. In the second edition of the book, chapters on roll dynamics, rollover prevention and hybrid electric vehicles have been added, and the chapter on electronic stability co...
Analysis of extended molecular dynamics (MD) simulations of lysozyme in vacuo and in aqueous solution reveals that it is possible to separate the configurational space into two subspaces: (1) an ''essential'' subspace containing only a few degrees of freedom in which anharmonic motion occurs that
Control of dynamical localization
International Nuclear Information System (INIS)
Gong Jiangbin; Woerner, Hans Jakob; Brumer, Paul
Control over the quantum dynamics of chaotic kicked rotor systems is demonstrated. Specifically, control over a number of quantum coherent phenomena is achieved by a simple modification of the kicking field. These include the enhancement of the dynamical localization length, the introduction of classical anomalous diffusion assisted control for systems far from the semiclassical regime, and the observation of a variety of strongly nonexponential line shapes for dynamical localization. The results provide excellent examples of controlled quantum dynamics in a system that is classically chaotic and offer opportunities to explore quantum fluctuations and correlations in quantum chaos
Controlling Uncertain Dynamical Systems
Indian Academy of Sciences (India)
Author Affiliations. N Ananthkrishnan1 Rashi Bansal2. Head, CAE Analysis & Design Zeus Numerix Pvt Ltd. M-03, SINE, IIT Bombay Powai Mumbai 400076, India. MTech (Aerospace Engineering) with specialization in Dynamics & Control from IIT Bombay.
Dynamic Systems and Control Engineering
International Nuclear Information System (INIS)
Kim, Jong Seok
This book deals with introduction of dynamic system and control engineering, frequency domain modeling of dynamic system, temporal modeling of dynamic system, typical dynamic system and automatic control device, performance and stability of control system, root locus analysis, analysis of frequency domain dynamic system, design of frequency domain dynamic system, design and analysis of space, space of control system and digital control system such as control system design of direct digital and digitalization of consecutive control system.
Dynamic Systems and Control Engineering
Energy Technology Data Exchange (ETDEWEB)
Kim, Jong Seok
This book deals with introduction of dynamic system and control engineering, frequency domain modeling of dynamic system, temporal modeling of dynamic system, typical dynamic system and automatic control device, performance and stability of control system, root locus analysis, analysis of frequency domain dynamic system, design of frequency domain dynamic system, design and analysis of space, space of control system and digital control system such as control system design of direct digital and digitalization of consecutive control system.
Protein kinesis: The dynamics of protein trafficking and stability
Energy Technology Data Exchange (ETDEWEB)
The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.
Fractional Dynamics and Control
Machado, José; Luo, Albert
Fractional Dynamics and Control provides a comprehensive overview of recent advances in the areas of nonlinear dynamics, vibration and control with analytical, numerical, and experimental results. This book provides an overview of recent discoveries in fractional control, delves into fractional variational principles and differential equations, and applies advanced techniques in fractional calculus to solving complicated mathematical and physical problems.Finally, this book also discusses the role that fractional order modeling can play in complex systems for engineering and science. Discusses how fractional dynamics and control can be used to solve nonlinear science and complexity issues Shows how fractional differential equations and models can be used to solve turbulence and wave equations in mechanics and gravity theories and Schrodinger's equation Presents factional relaxation modeling of dielectric materials and wave equations for dielectrics Develops new methods for control and synchronization of...
Aquatic degradation of Cry1Ab protein and decomposition dynamics of transgenic corn leaves under controlled conditions.
Böttger, Rita; Schaller, Jörg; Lintow, Sven; Gert Dudel, E
The increasing cultivation of genetically modified corn plants (Zea mays) during the last decades is suggested as a potential risk to the environment. One of these genetically modified variety expressed the insecticidal Cry1Ab protein originating from Bacillus thuringiensis (Bt), resulting in resistance against Ostrinia nubilalis, the European corn borer. Transgenic litter material is extensively studied regarding the decomposition in soils. However, only a few field studies analyzed the fate of the Cry1Ab protein and the impact of green and senescent leaf litter from corn on the decomposition rate and related ecosystem functions in aquatic environments. Consequently, a microbial litter decomposition experiment was conducted under controlled semi-natural conditions in batch culture using two maize varieties: one variety with Cry1Ab and another one with the appertaining Iso-line as control treatment. The results showed no significant differences between the treatment with Cry1Ab and the Iso-line regarding loss of total mass in dry weight of 43% for Iso-line and 45% for Bt-corn litter, lignin content increased to 137.5% (Iso-line) and 115.7% (Bt-corn), and phenol loss decreased by 53.6% (Iso-line), 62.2% (Bt-corn) during three weeks of the experiment. At the end of the experiment Cry1Ab protein was still detected with 6% of the initial concentration. A slightly but significant lower cellulose content was found for the Cry1Ab treatment compared to the Iso-line litter at the end of the experiment. The significant higher total protein (25%) and nitrogen (25%) content in Bt corn, most likely due to the additionally expression of the transgenic protein, may increase the microbial cellulose degradation and decrease microbial lignin degradation. In conclusion a relevant year by year input of protein and therefore nitrogen rich Bt corn litter into aquatic environments may affect the balanced nutrient turnover in aquatic ecosystems. Copyright © 2014 Elsevier Inc. All rights
How proteins modify water dynamics
Persson, Filip; Söderhjelm, Pär; Halle, Bertil
Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)—the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the
Bacterial Ice Crystal Controlling Proteins
Lorv, Janet S. H.; Rose, David R.; Glick, Bernard R.
Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions. PMID:24579057
Dynamic protein assembly by programmable DNA strand displacement
Chen, Rebecca P.; Blackstock, Daniel; Sun, Qing; Chen, Wilfred
Inspired by the remarkable ability of natural protein switches to sense and respond to a wide range of environmental queues, here we report a strategy to engineer synthetic protein switches by using DNA strand displacement to dynamically organize proteins with highly diverse and complex logic gate architectures. We show that DNA strand displacement can be used to dynamically control the spatial proximity and the corresponding fluorescence resonance energy transfer between two fluorescent proteins. Performing Boolean logic operations enabled the explicit control of protein proximity using multi-input, reversible and amplification architectures. We further demonstrate the power of this technology beyond sensing by achieving dynamic control of an enzyme cascade. Finally, we establish the utility of the approach as a synthetic computing platform that drives the dynamic reconstitution of a split enzyme for targeted prodrug activation based on the sensing of cancer-specific miRNAs.
Water-Protein Interactions: The Secret of Protein Dynamics
Directory of Open Access Journals (Sweden)
Silvia Martini
Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.
Hydration dynamics near a model protein surface
International Nuclear Information System (INIS)
Russo, Daniela; Hura, Greg; Head-Gordon, Teresa
The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering and molecular dynamics simulation for both the completely deuterated and completely hydrogenated leucine monomer. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational water dynamics are analyzed in a first approximation with a jump diffusion model. At the highest solute concentrations, the hydration water dynamics is significantly suppressed and characterized by a long residential time and a slow diffusion coefficient. The analysis of the more dilute concentration solutions takes into account the results of the 2.0M solution as a model of the first hydration shell. Subtracting the first hydration layer based on the 2.0M spectra, the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis shows spatially heterogeneous dynamics at high concentration that becomes homogeneous at more dilute concentrations. We discuss the hydration dynamics results of this model protein system in the context of glassy systems, protein function, and protein-protein interfaces
Dynamics of nonlinear feedback control
Snippe, H.P.; Hateren, J.H. van
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain
Inactivation of Tor proteins affects the dynamics of endocytic proteins ...
Indian Academy of Sciences (India)
Tor2 is an activator of the Rom2/Rho1 pathway that regulates -factor internalization. Since the recruitment of endocytic proteins such as actin-binding proteins and the amphiphysins precedes the internalization of -factor, we hypothesized that loss of Tor function leads to an alteration in the dynamics of the endocytic ...
Simultaneous determination of protein structure and dynamics
DEFF Research Database (Denmark)
Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.
at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...
Controlling proteins through molecular springs.
Zocchi, Giovanni
We argue that the mechanical control of proteins-the notion of controlling chemical reactions and processes by mechanics-is conceptually interesting. We give a brief review of the main accomplishments so far, leading to our present approach of using DNA molecular springs to exert controlled stresses on proteins. Our focus is on the physical principles that underlie both artificial mechanochemical devices and natural mechanisms of allostery.
Controlling Strange Attractor in Dynamics
Institute of Scientific and Technical Information of China (English)
A nonlinear system which exhibits a strange attractor is considered, with the goal of illustrating how to control the chaotic dynamical system and to obtain a desired attracting periodic orbit by the OGY control algorithm.
Functional dynamics of cell surface membrane proteins.
Nishida, Noritaka; Osawa, Masanori; Takeuchi, Koh; Imai, Shunsuke; Stampoulis, Pavlos; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio
Cell surface receptors are integral membrane proteins that receive external stimuli, and transmit signals across plasma membranes. In the conventional view of receptor activation, ligand binding to the extracellular side of the receptor induces conformational changes, which convert the structure of the receptor into an active conformation. However, recent NMR studies of cell surface membrane proteins have revealed that their structures are more dynamic than previously envisioned, and they fluctuate between multiple conformations in an equilibrium on various timescales. In addition, NMR analyses, along with biochemical and cell biological experiments indicated that such dynamical properties are critical for the proper functions of the receptors. In this review, we will describe several NMR studies that revealed direct linkage between the structural dynamics and the functions of the cell surface membrane proteins, such as G-protein coupled receptors (GPCRs), ion channels, membrane transporters, and cell adhesion molecules. Copyright © 2013 Elsevier Inc. All rights reserved.
Dynamics of nonlinear feedback control
Snippe, H.P.; Hateren, J.H. van
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain signal (resp. the attenuation signal) is obtained through a concatenation of an instantaneous nonlinearity and a linear low-pass filter operating on the output of the feedback loop. For input step...
Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis
Klinman, Judith P.; Kohen, Amnon
The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C–H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial. PMID:23746260
Genetic noise control via protein oligomerization
Energy Technology Data Exchange (ETDEWEB)
Ghim, C; Almaas, E
Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamical role of protein-protein associations. We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast protein binding-unbinding kinetics, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its intrinsic switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of phenotypically important toggle switches, and nested positive feedback loops in
Proteins with Novel Structure, Function and Dynamics
Pohorille, Andrew
Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.
Dynamics in electron transfer protein complexes
Bashir, Qamar
Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We have used paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize the ensemble of encounter orientations in the short-lived electron transfer complex of yeast Cc and CcP. The complete conformational space sampled by the protein molecules during the dynamic part of ...
Is a malleable protein necessarily highly dynamic?
DEFF Research Database (Denmark)
Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare
core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...
Molecular dynamics of surfactant protein C
DEFF Research Database (Denmark)
Ramírez, Eunice; Santana, Alberto; Cruz, Anthony
Surfactant protein C (SP-C) is a membrane-associated protein essential for normal respiration. It has been found that the alpha-helix form of SP-C can undergo, under certain conditions, a transformation from an alpha-helix to a beta-strand conformation that closely resembles amyloid fibrils, which...... are possible contributors to the pathogenesis of pulmonary alveolar proteinosis. Molecular dynamics simulations using the NAMD2 package were performed for systems containing from one to seven SP-C molecules to study their behavior in water. The results of our simulations show that unfolding of the protein...
International Nuclear Information System (INIS)
Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.
The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.
Stochastic dynamics and control
Sun, Jian-Qiao; Zaslavsky, George
This book is a result of many years of author's research and teaching on random vibration and control. It was used as lecture notes for a graduate course. It provides a systematic review of theory of probability, stochastic processes, and stochastic calculus. The feedback control is also reviewed in the book. Random vibration analyses of SDOF, MDOF and continuous structural systems are presented in a pedagogical order. The application of the random vibration theory to reliability and fatigue analysis is also discussed. Recent research results on fatigue analysis of non-Gaussian stress proc
Constraint theory and hierarchical protein dynamics
Energy Technology Data Exchange (ETDEWEB)
Phillips, J C [Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854-8019 (United States)
The complexity and functionality of proteins requires that they occupy an exponentially small fraction of configuration space (perhaps 10{sup -300}). How did evolution manage to create such unlikely objects? Thorpe has solved the static half of this problem (known in protein chemistry as Levinthal's paradox) by observing that for stress-free chain segments the complexity of optimally constrained elastic networks scales not with expN (where N {approx} 100-1000 is the number of amino acids in a protein), but only with N. Newman's results for diffusion in N-dimensional spaces provide suggestive insights into the dynamical half of the problem. He showed that the distribution of residence (or pausing) time between sign reversals changes qualitatively at N {approx}40. The overall sign of a protein can be defined in terms of a product of curvature and hydrophobic(philic) character over all amino acid residues. This construction agrees with the sizes of the smallest known proteins and prions, and it suggests a universal clock for protein molecular dynamics simulations.
Constraint theory and hierarchical protein dynamics
International Nuclear Information System (INIS)
Phillips, J C
The complexity and functionality of proteins requires that they occupy an exponentially small fraction of configuration space (perhaps 10 -300 ). How did evolution manage to create such unlikely objects? Thorpe has solved the static half of this problem (known in protein chemistry as Levinthal's paradox) by observing that for stress-free chain segments the complexity of optimally constrained elastic networks scales not with expN (where N ∼ 100-1000 is the number of amino acids in a protein), but only with N. Newman's results for diffusion in N-dimensional spaces provide suggestive insights into the dynamical half of the problem. He showed that the distribution of residence (or pausing) time between sign reversals changes qualitatively at N ∼40. The overall sign of a protein can be defined in terms of a product of curvature and hydrophobic(philic) character over all amino acid residues. This construction agrees with the sizes of the smallest known proteins and prions, and it suggests a universal clock for protein molecular dynamics simulations
Dynamics of nonlinear feedback control.
Snippe, H P; van Hateren, J H
Feedback control in neural systems is ubiquitous. Here we study the mathematics of nonlinear feedback control. We compare models in which the input is multiplied by a dynamic gain (multiplicative control) with models in which the input is divided by a dynamic attenuation (divisive control). The gain signal (resp. the attenuation signal) is obtained through a concatenation of an instantaneous nonlinearity and a linear low-pass filter operating on the output of the feedback loop. For input steps, the dynamics of gain and attenuation can be very different, depending on the mathematical form of the nonlinearity and the ordering of the nonlinearity and the filtering in the feedback loop. Further, the dynamics of feedback control can be strongly asymmetrical for increment versus decrement steps of the input. Nevertheless, for each of the models studied, the nonlinearity in the feedback loop can be chosen such that immediately after an input step, the dynamics of feedback control is symmetric with respect to increments versus decrements. Finally, we study the dynamics of the output of the control loops and find conditions under which overshoots and undershoots of the output relative to the steady-state output occur when the models are stimulated with low-pass filtered steps. For small steps at the input, overshoots and undershoots of the output do not occur when the filtering in the control path is faster than the low-pass filtering at the input. For large steps at the input, however, results depend on the model, and for some of the models, multiple overshoots and undershoots can occur even with a fast control path.
Dynamics of proteins aggregation. II. Dynamic scaling in confined media
Zheng, Size; Shing, Katherine S.; Sahimi, Muhammad
In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.
Dynamic Controllability and Dispatchability Relationships
Morris, Paul Henry
An important issue for temporal planners is the ability to handle temporal uncertainty. Recent papers have addressed the question of how to tell whether a temporal network is Dynamically Controllable, i.e., whether the temporal requirements are feasible in the light of uncertain durations of some processes. We present a fast algorithm for Dynamic Controllability. We also note a correspondence between the reduction steps in the algorithm and the operations involved in converting the projections to dispatchable form. This has implications for the complexity for sparse networks.
Protein Dynamics in the Plant Extracellular Space
Directory of Open Access Journals (Sweden)
Leonor Guerra-Guimarães
Full Text Available The extracellular space (ECS or apoplast is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF. The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in "cell wall organization and biogenesis", "response to stimulus" and "protein metabolism". It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.
Controlling dynamics in diatomic systems
Indian Academy of Sciences (India)
Abstract. Controlling molecular energetics using laser pulses is exemplified for nuclear motion in two different diatomic systems. The problem of finding the optimized field for maximizing a desired quantum dynamical target is formulated using an iterative method. The method is applied for two diatomic sys- tems, HF and OH.
Genetic noise control via protein oligomerization
Directory of Open Access Journals (Sweden)
Almaas Eivind
Full Text Available Abstract Background Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. Results We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch, integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast binding-unbinding kinetics among proteins, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced state from randomly being induced (uninduced. Conclusion The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of regulatory circuits
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.
Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark
The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.
Rho-associated coiled-coil kinase (ROCK) protein controls microtubule dynamics in a novel signaling pathway that regulates cell migration.
Schofield, Alice V; Steel, Rohan; Bernard, Ora
The two members of the Rho-associated coiled-coil kinase (ROCK1 and 2) family are established regulators of actin dynamics that are involved in the regulation of the cell cycle as well as cell motility and invasion. Here, we discovered a novel signaling pathway whereby ROCK regulates microtubule (MT) acetylation via phosphorylation of the tubulin polymerization promoting protein 1 (TPPP1/p25). We show that ROCK phosphorylation of TPPP1 inhibits the interaction between TPPP1 and histone deacetylase 6 (HDAC6), which in turn results in increased HDAC6 activity followed by a decrease in MT acetylation. As a consequence, we show that TPPP1 phosphorylation by ROCK increases cell migration and invasion via modulation of cellular acetyl MT levels. We establish here that the ROCK-TPPP1-HDAC6 signaling pathway is important for the regulation of cell migration and invasion.
Dynamic prestress in a globular protein.
Directory of Open Access Journals (Sweden)
Scott A Edwards
Full Text Available A protein at equilibrium is commonly thought of as a fully relaxed structure, with the intra-molecular interactions showing fluctuations around their energy minimum. In contrast, here we find direct evidence for a protein as a molecular tensegrity structure, comprising a balance of tensed and compressed interactions, a concept that has been put forward for macroscopic structures. We quantified the distribution of inter-residue prestress in ubiquitin and immunoglobulin from all-atom molecular dynamics simulations. The network of highly fluctuating yet significant inter-residue forces in proteins is a consequence of the intrinsic frustration of a protein when sampling its rugged energy landscape. In beta sheets, this balance of forces is found to compress the intra-strand hydrogen bonds. We estimate that the observed magnitude of this pre-compression is enough to induce significant changes in the hydrogen bond lifetimes; thus, prestress, which can be as high as a few 100 pN, can be considered a key factor in determining the unfolding kinetics and pathway of proteins under force. Strong pre-tension in certain salt bridges on the other hand is connected to the thermodynamic stability of ubiquitin. Effective force profiles between some side-chains reveal the signature of multiple, distinct conformational states, and such static disorder could be one factor explaining the growing body of experiments revealing non-exponential unfolding kinetics of proteins. The design of prestress distributions in engineering proteins promises to be a new tool for tailoring the mechanical properties of made-to-order nanomaterials.
Control algorithms for dynamic attenuators
Energy Technology Data Exchange (ETDEWEB)
Hsieh, Scott S., E-mail: firstname.lastname@example.com [Department of Radiology, Stanford University, Stanford, California 94305 and Department of Electrical Engineering, Stanford University, Stanford, California 94305 (United States); Pelc, Norbert J. [Department of Radiology, Stanford University, Stanford California 94305 and Department of Bioengineering, Stanford University, Stanford, California 94305 (United States)
Purpose: The authors describe algorithms to control dynamic attenuators in CT and compare their performance using simulated scans. Dynamic attenuators are prepatient beam shaping filters that modulate the distribution of x-ray fluence incident on the patient on a view-by-view basis. These attenuators can reduce dose while improving key image quality metrics such as peak or mean variance. In each view, the attenuator presents several degrees of freedom which may be individually adjusted. The total number of degrees of freedom across all views is very large, making many optimization techniques impractical. The authors develop a theory for optimally controlling these attenuators. Special attention is paid to a theoretically perfect attenuator which controls the fluence for each ray individually, but the authors also investigate and compare three other, practical attenuator designs which have been previously proposed: the piecewise-linear attenuator, the translating attenuator, and the double wedge attenuator. Methods: The authors pose and solve the optimization problems of minimizing the mean and peak variance subject to a fixed dose limit. For a perfect attenuator and mean variance minimization, this problem can be solved in simple, closed form. For other attenuator designs, the problem can be decomposed into separate problems for each view to greatly reduce the computational complexity. Peak variance minimization can be approximately solved using iterated, weighted mean variance (WMV) minimization. Also, the authors develop heuristics for the perfect and piecewise-linear attenuators which do not requirea priori knowledge of the patient anatomy. The authors compare these control algorithms on different types of dynamic attenuators using simulated raw data from forward projected DICOM files of a thorax and an abdomen. Results: The translating and double wedge attenuators reduce dose by an average of 30% relative to current techniques (bowtie filter with tube current
Control algorithms for dynamic attenuators
International Nuclear Information System (INIS)
Hsieh, Scott S.; Pelc, Norbert J.
Purpose: The authors describe algorithms to control dynamic attenuators in CT and compare their performance using simulated scans. Dynamic attenuators are prepatient beam shaping filters that modulate the distribution of x-ray fluence incident on the patient on a view-by-view basis. These attenuators can reduce dose while improving key image quality metrics such as peak or mean variance. In each view, the attenuator presents several degrees of freedom which may be individually adjusted. The total number of degrees of freedom across all views is very large, making many optimization techniques impractical. The authors develop a theory for optimally controlling these attenuators. Special attention is paid to a theoretically perfect attenuator which controls the fluence for each ray individually, but the authors also investigate and compare three other, practical attenuator designs which have been previously proposed: the piecewise-linear attenuator, the translating attenuator, and the double wedge attenuator. Methods: The authors pose and solve the optimization problems of minimizing the mean and peak variance subject to a fixed dose limit. For a perfect attenuator and mean variance minimization, this problem can be solved in simple, closed form. For other attenuator designs, the problem can be decomposed into separate problems for each view to greatly reduce the computational complexity. Peak variance minimization can be approximately solved using iterated, weighted mean variance (WMV) minimization. Also, the authors develop heuristics for the perfect and piecewise-linear attenuators which do not requirea priori knowledge of the patient anatomy. The authors compare these control algorithms on different types of dynamic attenuators using simulated raw data from forward projected DICOM files of a thorax and an abdomen. Results: The translating and double wedge attenuators reduce dose by an average of 30% relative to current techniques (bowtie filter with tube current
Control algorithms for dynamic attenuators.
Hsieh, Scott S; Pelc, Norbert J
The authors describe algorithms to control dynamic attenuators in CT and compare their performance using simulated scans. Dynamic attenuators are prepatient beam shaping filters that modulate the distribution of x-ray fluence incident on the patient on a view-by-view basis. These attenuators can reduce dose while improving key image quality metrics such as peak or mean variance. In each view, the attenuator presents several degrees of freedom which may be individually adjusted. The total number of degrees of freedom across all views is very large, making many optimization techniques impractical. The authors develop a theory for optimally controlling these attenuators. Special attention is paid to a theoretically perfect attenuator which controls the fluence for each ray individually, but the authors also investigate and compare three other, practical attenuator designs which have been previously proposed: the piecewise-linear attenuator, the translating attenuator, and the double wedge attenuator. The authors pose and solve the optimization problems of minimizing the mean and peak variance subject to a fixed dose limit. For a perfect attenuator and mean variance minimization, this problem can be solved in simple, closed form. For other attenuator designs, the problem can be decomposed into separate problems for each view to greatly reduce the computational complexity. Peak variance minimization can be approximately solved using iterated, weighted mean variance (WMV) minimization. Also, the authors develop heuristics for the perfect and piecewise-linear attenuators which do not require a priori knowledge of the patient anatomy. The authors compare these control algorithms on different types of dynamic attenuators using simulated raw data from forward projected DICOM files of a thorax and an abdomen. The translating and double wedge attenuators reduce dose by an average of 30% relative to current techniques (bowtie filter with tube current modulation) without
Protein electron transfer: is biology (thermo)dynamic?
International Nuclear Information System (INIS)
Matyushov, Dmitry V
Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic
Theory of controlled quantum dynamics
Energy Technology Data Exchange (ETDEWEB)
De Martino, Salvatore; De Siena, Silvio; Illuminati, Fabrizio [Dipartimento di Fisica, Universita di Salerno, and INFN, Sezione di Napoli, Gruppo collegato di Salerno, Baronissi (Italy)
We introduce a general formalism to obtain localized quantum wavepackets as dynamically controlled systems, in the framework of Nelson stochastic quantization. We show that in general the control is linear, and it amounts to introducing additional time-dependent terms in the potential. In this way one can construct for general systems either coherent packets following classical motion with constant dispersion, or coherent packets following classical motion whose time-dependent dispersion remains bounded for all times. We show that in the operatorial language our scheme amounts to introducing a suitable generalization to arbitrary potentials of the displacement and scaling operators that generate the coherent and squeezed states of the harmonic oscillator. (author)
Laser Controlled Molecular Orientation Dynamics
International Nuclear Information System (INIS)
Atabek, O.
Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation
Protein dynamics by neutron scattering: The protein dynamical transition and the fragile-to-strong dynamical crossover in hydrated lysozyme
International Nuclear Information System (INIS)
Magazù, Salvatore; Migliardo, Federica; Benedetto, Antonio; Vertessy, Beata
Highlights: • The role played by the instrumental energy resolution in neutron scattering is presented. • The effect of natural bioprotectants on protein dynamics is shown. • A connection between the protein dynamical transition and the fragile-to-strong dynamical crossover is formulated. - Abstract: In this work Elastic Incoherent Neutron Scattering (EINS) results on lysozyme water mixtures in absence and in presence of bioprotectant systems are presented. The EINS data have been collected by using the IN13 and the IN10 spectrometers at the Institut Laue-Langevin (ILL, Grenoble, France) allowing to evaluate the temperature behaviour of the mean square displacement and of the relaxation time for the investigated systems. The obtained experimental findings together with theoretical calculations allow to put into evidence the role played by the spectrometer resolution and to clarify the connexion between the registered protein dynamical transition, the system relaxation time, and the instrumental energy resolution
Protein-protein docking with dynamic residue protonation states.
Directory of Open Access Journals (Sweden)
Krishna Praneeth Kilambi
Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.
Voltage Controlled Dynamic Demand Response
DEFF Research Database (Denmark)
Bhattarai, Bishnu Prasad; Bak-Jensen, Birgitte; Mahat, Pukar
Future power system is expected to be characterized by increased penetration of intermittent sources. Random and rapid fluctuations in demands together with intermittency in generation impose new challenges for power balancing in the existing system. Conventional techniques of balancing by large...... central or dispersed generations might not be sufficient for future scenario. One of the effective methods to cope with this scenario is to enable demand response. This paper proposes a dynamic voltage regulation based demand response technique to be applied in low voltage (LV) distribution feeders....... An adaptive dynamic model has been developed to determine composite voltage dependency of an aggregated load on feeder level. Following the demand dispatch or control signal, optimum voltage setting at the LV substation is determined based on the voltage dependency of the load. Furthermore, a new technique...
Fuzzy control of pressurizer dynamic process
International Nuclear Information System (INIS)
Ming Zhedong; Zhao Fuyu
Considering the characteristics of pressurizer dynamic process, the fuzzy control system that takes the advantages of both fuzzy controller and PID controller is designed for the dynamic process in pressurizer. The simulation results illustrate this type of composite control system is with better qualities than those of single fuzzy controller and single PID controller. (authors)
Power system dynamics and control
Kwatny, Harry G
This monograph explores a consistent modeling and analytic framework that provides the tools for an improved understanding of the behavior and the building of efficient models of power systems. It covers the essential concepts for the study of static and dynamic network stability, reviews the structure and design of basic voltage and load-frequency regulators, and offers an introduction to power system optimal control with reliability constraints. A set of Mathematica tutorial notebooks providing detailed solutions of the examples worked-out in the text, as well as a package that will enable readers to work out their own examples and problems, supplements the text. A key premise of the book is that the design of successful control systems requires a deep understanding of the processes to be controlled; as such, the technical discussion begins with a concise review of the physical foundations of electricity and magnetism. This is followed by an overview of nonlinear circuits that include resistors, inductors, ...
Functional advantages of dynamic protein disorder.
Berlow, Rebecca B; Dyson, H Jane; Wright, Peter E
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
Directory of Open Access Journals (Sweden)
Ulf Hensen
Full Text Available Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.
The dynamic multisite interactions between two intrinsically disordered proteins
Wu, Shaowen; Wang, Dongdong; Liu, Jin; Feng, Yitao; Weng, Jingwei; Li, Yu; Gao, Xin; Liu, Jianwei; Wang, Wenning
Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
DEFF Research Database (Denmark)
Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.
In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...
Water dynamics clue to key residues in protein folding
International Nuclear Information System (INIS)
Gao, Meng; Zhu, Huaiqiu; Yao, Xin-Qiu; She, Zhen-Su
A computational method independent of experimental protein structure information is proposed to recognize key residues in protein folding, from the study of hydration water dynamics. Based on all-atom molecular dynamics simulation, two key residues are recognized with distinct water dynamical behavior in a folding process of the Trp-cage protein. The identified key residues are shown to play an essential role in both 3D structure and hydrophobic-induced collapse. With observations on hydration water dynamics around key residues, a dynamical pathway of folding can be interpreted.
Protein quality control in the nucleus
DEFF Research Database (Denmark)
Nielsen, Sofie V.; Poulsen, Esben Guldahl; Rebula, Caio A.
to aggregate, cells have evolved several elaborate quality control systems to deal with these potentially toxic proteins. First, various molecular chaperones will seize the misfolded protein and either attempt to refold the protein or target it for degradation via the ubiquitin-proteasome system...... to be particularly active in protein quality control. Thus, specific ubiquitin-protein ligases located in the nucleus, target not only misfolded nuclear proteins, but also various misfolded cytosolic proteins which are transported to the nucleus prior to their degradation. In comparison, much less is known about...... these mechanisms in mammalian cells. Here we highlight recent advances in our understanding of nuclear protein quality control, in particular regarding substrate recognition and proteasomal degradation....
Dynamics and Control of a Maglev Vehicle
Directory of Open Access Journals (Sweden)
Won ko
Full Text Available In this paper, dynamics of a Maglev vehicle was analyzed and controls utilizing an optimized damping and an LQR algorithms were designed to stabilize the vehicle. The dynamics of magnetically levitated and propelled Maglev vehicle are complex and inherently unstable. Moreover, 6-DOF system dynamics is highly nonlinear and coupled. The proposed control schemes provide the dynamic stability and controllability, which computer simulations confirmed the effectiveness.
Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
Directory of Open Access Journals (Sweden)
Lyngsø Rune
Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.
3D Protein Dynamics in the Cell Nucleus.
Singh, Anand P; Galland, Rémi; Finch-Edmondson, Megan L; Grenci, Gianluca; Sibarita, Jean-Baptiste; Studer, Vincent; Viasnoff, Virgile; Saunders, Timothy E
The three-dimensional (3D) architecture of the cell nucleus plays an important role in protein dynamics and in regulating gene expression. However, protein dynamics within the 3D nucleus are poorly understood. Here, we present, to our knowledge, a novel combination of 1) single-objective based light-sheet microscopy, 2) photoconvertible proteins, and 3) fluorescence correlation microscopy, to quantitatively measure 3D protein dynamics in the nucleus. We are able to acquire >3400 autocorrelation functions at multiple spatial positions within a nucleus, without significant photobleaching, allowing us to make reliable estimates of diffusion dynamics. Using this tool, we demonstrate spatial heterogeneity in Polymerase II dynamics in live U2OS cells. Further, we provide detailed measurements of human-Yes-associated protein diffusion dynamics in a human gastric cancer epithelial cell line. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Coherent control of plasma dynamics
He, Zhaohan
The concept of coherent control - precise measurement or determination of a process through control of the phase of an applied oscillating field - has been applied to numerous systems with great success. Here, we demonstrate the use of coherent control on plasma dynamics in a laser wakefield electron acceleration experiment. A tightly focused femtosecond laser pulse (10 mJ, 35 fs) was used to generate electron beams by plasma wakefield acceleration in the density down ramp. The technique is based on optimization of the electron beam using a deformable mirror adaptive optical system with an iterative evolutionary genetic algorithm. The image of the electrons on a scintillator screen was processed and used in a fitness function as direct feedback for the optimization algorithm. This coherent manipulation of the laser wavefront leads to orders of magnitude improvement to the electron beam properties such as the peak charge and beam divergence. The laser beam optimized to generate the best electron beam was not the one with the ``best'' focal spot. When a particular wavefront of laser light interacts with plasma, it can affect the plasma wave structures and trapping conditions of the electrons in a complex way. For example, Raman forward scattering, envelope self-modulation, relativistic self-focusing, and relativistic self-phase modulation and many other nonlinear interactions modify both the pulse envelope and phase as the pulse propagates, in a way that cannot be easily predicted and that subsequently dictates the formation of plasma waves. The optimal wavefront could be successfully determined via the heuristic search under laser-plasma conditions that were not known a priori. Control and shaping of the electron energy distribution was found to be less effective, but was still possible. Particle-in-cell simulations were performed to show that the mode structure of the laser beam can affect the plasma wave structure and trapping conditions of electrons, which
Organization and Dynamics of Receptor Proteins in a Plasma Membrane.
Koldsø, Heidi; Sansom, Mark S P
The interactions of membrane proteins are influenced by their lipid environment, with key lipid species able to regulate membrane protein function. Advances in high-resolution microscopy can reveal the organization and dynamics of proteins and lipids within living cells at resolutions membranes of in vivo-like complexity. We explore the dynamics of proteins and lipids in crowded and complex plasma membrane models, thereby closing the gap in length and complexity between computations and experiments. Our simulations provide insights into the mutual interplay between lipids and proteins in determining mesoscale (20-100 nm) fluctuations of the bilayer, and in enabling oligomerization and clustering of membrane proteins.
Organizing membrane-curving proteins: the emerging dynamical picture.
Simunovic, Mijo; Bassereau, Patricia; Voth, Gregory A
Lipid membranes play key roles in cells, such as in trafficking, division, infection, remodeling of organelles, among others. The key step in all these processes is creating membrane curvature, typically under the control of many anchored, adhered or included proteins. However, it has become clear that the membrane itself can mediate the interactions among proteins to produce highly ordered assemblies. Computer simulations are ideally suited to investigate protein organization and the dynamics of membrane remodeling at near-micron scales, something that is extremely challenging to tackle experimentally. We review recent computational efforts in modeling protein-caused membrane deformation mechanisms, specifically focusing on coarse-grained simulations. We highlight work that exposed the membrane-mediated ordering of proteins into lines, meshwork, spirals and other assemblies, in what seems to be a very generic mechanism driven by a combination of short and long-ranged forces. Modulating the mechanical properties of membranes is an underexplored signaling mechanism in various processes deserving of more attention in the near future. Copyright © 2018 Elsevier Ltd. All rights reserved.
Bacillus coagulans GBI-30, 6086 increases plant protein digestion in a dynamic, computer-controlled in vitro model of the small intestine (TIM-1).
Keller, D; Van Dinter, R; Cash, H; Farmer, S; Venema, K
The aim of this study was to assess the potential of the probiotic Bacillus coagulans GBI-30, 6086 [GanedenBC 30 ] (BC30) to aid in protein digestion of alimentary plant proteins. To test this, three plant proteins, from pea, soy and rice, were digested in a validated in vitro model of the stomach and small intestine (TIM-1) in the absence and in the presence of BC30. Samples were taken from the TIM-1 fractions that mimic uptake of amino acids by the host and analysed for α-amino nitrogen (AAN) and total nitrogen (TN). Both were increased by BC30 for all three plant proteins sources. The ratio of TN/AAN indicated that for pea protein digestion was increased by BC30, but the degree of polymerisation of the liberated small peptides and free amino acids was not changed. For soy and rice, however, BC30 showed a 2-fold reduction in the TN/AAN ratio, indicating that the liberated digestion products formed during digestion in the presence of BC30 were shorter peptides and more free amino acids, than those liberated in the absence of BC30. As BC30 increased protein digestion and uptake in the upper gastrointestinal (GI) tract, it consequently also reduced the amount of protein that would be delivered to the colon, which could there be fermented into toxic metabolites by the gut microbiota. Thus, the enhanced protein digestion by BC30 showed a dual benefit: enhanced amino acid bioavailability from plant proteins in the upper GI tract, and a healthier environment in the colon.
The dynamic multisite interactions between two intrinsically disordered proteins
Wu, Shaowen
Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a structured protein, while the Interaction between two IDPs is poorly understood. In this study, we combined NMR, smFRET, and molecular dynamics (MD) simulation to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by MD and mutagenesis studies. Our study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.
Protein synthesis controls phosphate homeostasis.
Pontes, Mauricio H; Groisman, Eduardo A
Phosphorus is an essential element assimilated largely as orthophosphate (Pi). Cells respond to Pi starvation by importing Pi from their surroundings. We now report that impaired protein synthesis alone triggers a Pi starvation response even when Pi is plentiful in the extracellular milieu. In the bacterium Salmonella enterica serovar Typhimurium , this response entails phosphorylation of the regulatory protein PhoB and transcription of PhoB-dependent Pi transporter genes and is eliminated upon stimulation of adenosine triphosphate (ATP) hydrolysis. When protein synthesis is impaired due to low cytoplasmic magnesium (Mg 2+ ), Salmonella triggers the Pi starvation response because ribosomes are destabilized, which reduces ATP consumption and thus free cytoplasmic Pi. This response is transient because low cytoplasmic Mg 2+ promotes an uptake in Mg 2+ and a decrease in ATP levels, which stabilizes ribosomes, resulting in ATP consumption and Pi increase, thus ending the response. Notably, pharmacological inhibition of protein synthesis also elicited a Pi starvation response in the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae Our findings identify a regulatory connection between protein synthesis and Pi homeostasis that is widespread in nature. © 2018 Pontes and Groisman; Published by Cold Spring Harbor Laboratory Press.
Core-shell microparticles for protein sequestration and controlled release of a protein-laden core.
Rinker, Torri E; Philbrick, Brandon D; Temenoff, Johnna S
Development of multifunctional biomaterials that sequester, isolate, and redeliver cell-secreted proteins at a specific timepoint may be required to achieve the level of temporal control needed to more fully regulate tissue regeneration and repair. In response, we fabricated core-shell heparin-poly(ethylene-glycol) (PEG) microparticles (MPs) with a degradable PEG-based shell that can temporally control delivery of protein-laden heparin MPs. Core-shell MPs were fabricated via a re-emulsification technique and the number of heparin MPs per PEG-based shell could be tuned by varying the mass of heparin MPs in the precursor PEG phase. When heparin MPs were loaded with bone morphogenetic protein-2 (BMP-2) and then encapsulated into core-shell MPs, degradable core-shell MPs initiated similar C2C12 cell alkaline phosphatase (ALP) activity as the soluble control, while non-degradable core-shell MPs initiated a significantly lower response (85+19% vs. 9.0+4.8% of the soluble control, respectively). Similarly, when degradable core-shell MPs were formed and then loaded with BMP-2, they induced a ∼7-fold higher C2C12 ALP activity than the soluble control. As C2C12 ALP activity was enhanced by BMP-2, these studies indicated that degradable core-shell MPs were able to deliver a bioactive, BMP-2-laden heparin MP core. Overall, these dynamic core-shell MPs have the potential to sequester, isolate, and then redeliver proteins attached to a heparin core to initiate a cell response, which could be of great benefit to tissue regeneration applications requiring tight temporal control over protein presentation. Tissue repair requires temporally controlled presentation of potent proteins. Recently, biomaterial-mediated binding (sequestration) of cell-secreted proteins has emerged as a strategy to harness the regenerative potential of naturally produced proteins, but this strategy currently only allows immediate amplification and re-delivery of these signals. The multifunctional, dynamic
Multibody system dynamics, robotics and control
Gerstmayr, Johannes
The volume contains 19 contributions by international experts in the field of multibody system dynamics, robotics and control. The book aims to bridge the gap between the modeling of mechanical systems by means of multibody dynamics formulations and robotics. In the classical approach, a multibody dynamics model contains a very high level of detail, however, the application of such models to robotics or control is usually limited. The papers aim to connect the different scientific communities in multibody dynamics, robotics and control. Main topics are flexible multibody systems, humanoid robots, elastic robots, nonlinear control, optimal path planning, and identification.
Polymer dynamics from synthetic polymers to proteins
Indian Academy of Sciences (India)
Keywords. Polymer dynamics; reptation; domain dynamics biomolecules. Abstract. Starting from the standard model of polymer motion - the Rouse model - we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the ...
On the dynamical incompleteness of the Protein Data Bank.
Marino-Buslje, Cristina; Monzon, Alexander Miguel; Zea, Diego Javier; Fornasari, María Silvina; Parisi, Gustavo
Major scientific challenges that are beyond the capability of individuals need to be addressed by multi-disciplinary and multi-institutional consortia. Examples of these endeavours include the Human Genome Project, and more recently, the Structural Genomics (SG) initiative. The SG initiative pursues the expansion of structural coverage to include at least one structural representative for each protein family to derive the remaining structures using homology modelling. However, biological function is inherently connected with protein dynamics that can be studied by knowing different structures of the same protein. This ensemble of structures provides snapshots of protein conformational diversity under native conditions. Thus, sequence redundancy in the Protein Data Bank (PDB) (i.e. crystallization of the same protein under different conditions) is therefore an essential input contributing to experimentally based studies of protein dynamics and providing insights into protein function. In this work, we show that sequence redundancy, a key concept for exploring protein dynamics, is highly biased and fundamentally incomplete in the PDB. Additionally, our results show that dynamical behaviour of proteins cannot be inferred using homologous proteins. Minor to moderate changes in sequence can produce great differences in dynamical behaviour. Nonetheless, the structural and dynamical incompleteness of the PDB is apparently unrelated concepts in SG. While the first could be reversed by promoting the extension of the structural coverage, we would like to emphasize that further focused efforts will be needed to amend the incompleteness of the PDB in terms of dynamical information content, essential to fully understand protein function. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.com.
Modelling Protein Dynamics on the Microsecond Time Scale
DEFF Research Database (Denmark)
Siuda, Iwona Anna
Recent years have shown an increase in coarse-grained (CG) molecular dynamics simulations, providing structural and dynamic details of large proteins and enabling studies of self-assembly of biological materials. It is not easy to acquire such data experimentally, and access is also still limited...... in atomistic simulations. During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger......ELNEDIN was therefore proposed as part of the work. Iwona Siuda's results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins...
Discriminating lysosomal membrane protein types using dynamic neural network.
Tripathi, Vijay; Gupta, Dwijendra Kumar
This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.
Dynamic optimization and adaptive controller design
Inamdar, S. R.
In this work I present a new type of controller which is an adaptive tracking controller which employs dynamic optimization for optimizing current value of controller action for the temperature control of nonisothermal continuously stirred tank reactor (CSTR). We begin with a two-state model of nonisothermal CSTR which are mass and heat balance equations and then add cooling system dynamics to eliminate input multiplicity. The initial design value is obtained using local stability of steady states where approach temperature for cooling action is specified as a steady state and a design specification. Later we make a correction in the dynamics where material balance is manipulated to use feed concentration as a system parameter as an adaptive control measure in order to avoid actuator saturation for the main control loop. The analysis leading to design of dynamic optimization based parameter adaptive controller is presented. The important component of this mathematical framework is reference trajectory generation to form an adaptive control measure.
Controlling the shape of membrane protein polyhedra
Li, Di; Kahraman, Osman; Haselwandter, Christoph A.
Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of membrane proteins and targeted drug delivery. We develop here a general analytic model of how MPPN self-assembly depends on bilayer-protein interactions and lipid bilayer mechanical properties. We find that the bilayer-protein hydrophobic thickness mismatch is a key molecular control parameter for MPPN shape that can be used to bias MPPN self-assembly towards highly symmetric and uniform MPPN shapes. Our results suggest strategies for optimizing MPPN shape for structural studies of membrane proteins and targeted drug delivery.
Molecular nonlinear dynamics and protein thermal uncertainty quantification
Xia, Kelin; Wei, Guo-Wei
This work introduces molecular nonlinear dynamics (MND) as a new approach for describing protein folding and aggregation. By using a mode system, we show that the MND of disordered proteins is chaotic while that of folded proteins exhibits intrinsically low dimensional manifolds (ILDMs). The stability of ILDMs is found to strongly correlate with protein energies. We propose a novel method for protein thermal uncertainty quantification based on persistently invariant ILDMs. Extensive comparison with experimental data and the state-of-the-art methods in the field validate the proposed new method for protein B-factor prediction. PMID:24697365
Strong field control of predissociation dynamics.
Corrales, María E; Balerdi, Garikoitz; Loriot, Vincent; de Nalda, Rebeca; Bañares, Luis
Strong field control scenarios are investigated in the CH3I predissociation dynamics at the origin of the second absorption B-band, in which state-selective electronic predissociation occurs through the crossing with a valence dissociative state. Dynamic Stark control (DSC) and pump-dump strategies are shown capable of altering both the predissociation lifetime and the product branching ratio.
Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin
Directory of Open Access Journals (Sweden)
Soichiro Kitazawa
Full Text Available Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics.
Simulation of Protein Structure, Dynamics and Function in Organic Media
National Research Council Canada - National Science Library
Daggett, Valerie
The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...
Protein dynamics in individual human cells: experiment and theory.
Directory of Open Access Journals (Sweden)
Ariel Aharon Cohen
Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.
Lee, Hui Sun; Qi, Yifei; Im, Wonpil
N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585
Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+.
Directory of Open Access Journals (Sweden)
Yosef Y Kuttner
Full Text Available Knowledge of the structural basis of protein-protein interactions (PPI is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM, whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+. Calmodulin is a regulatory protein that acts as an intracellular Ca(2+ sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+ and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+ binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.
Targeting protein-protein interactions for parasite control.
Directory of Open Access Journals (Sweden)
Christina M Taylor
Full Text Available Finding new drug targets for pathogenic infections would be of great utility for humanity, as there is a large need to develop new drugs to fight infections due to the developing resistance and side effects of current treatments. Current drug targets for pathogen infections involve only a single protein. However, proteins rarely act in isolation, and the majority of biological processes occur via interactions with other proteins, so protein-protein interactions (PPIs offer a realm of unexplored potential drug targets and are thought to be the next-generation of drug targets. Parasitic worms were chosen for this study because they have deleterious effects on human health, livestock, and plants, costing society billions of dollars annually and many sequenced genomes are available. In this study, we present a computational approach that utilizes whole genomes of 6 parasitic and 1 free-living worm species and 2 hosts. The species were placed in orthologous groups, then binned in species-specific orthologous groups. Proteins that are essential and conserved among species that span a phyla are of greatest value, as they provide foundations for developing broad-control strategies. Two PPI databases were used to find PPIs within the species specific bins. PPIs with unique helminth proteins and helminth proteins with unique features relative to the host, such as indels, were prioritized as drug targets. The PPIs were scored based on RNAi phenotype and homology to the PDB (Protein DataBank. EST data for the various life stages, GO annotation, and druggability were also taken into consideration. Several PPIs emerged from this study as potential drug targets. A few interactions were supported by co-localization of expression in M. incognita (plant parasite and B. malayi (H. sapiens parasite, which have extremely different modes of parasitism. As more genomes of pathogens are sequenced and PPI databases expanded, this methodology will become increasingly
Protein array staining methods for undefined protein content, manufacturing quality control, and performance validation.
Schabacker, Daniel S; Stefanovska, Ivana; Gavin, Igor; Pedrak, Casandra; Chandler, Darrell P
Methods to assess the quality and performance of protein microarrays fabricated from undefined protein content are required to elucidate slide-to-slide variability and interpolate resulting signal intensity values after an interaction assay. We therefore developed several simple total- and posttranslational modification-specific, on-chip staining methods to quantitatively assess the quality of gel element protein arrays manufactured with whole-cell lysate in vitro protein fractions derived from two-dimensional liquid-phase fractionation (PF2D) technology. A linear dynamic range of at least 3 logs was observed for protein stains and immobilized protein content, with a lower limit of detection at 8 pg of protein per gel element with Deep Purple protein stain and a field-portable microarray imager. Data demonstrate the successful isolation, separation, transfer, and immobilization of putative transmembrane proteins from Yersinia pestis KIM D27 with the combined PF2D and gel element array method. Internal bovine serum albumin standard curves provided a method to assess on-chip PF2D transfer and quantify total protein immobilized per gel element. The basic PF2D array fabrication and quality assurance/quality control methods described here therefore provide a standard operating procedure and basis for developing whole-proteome arrays for interrogating host-pathogen interactions, independent of sequenced genomes, affinity tags, or a priori knowledge of target cell composition.
Tools for controlling protein interactions with light
Tucker, Chandra L.; Vrana, Justin D.; Kennedy, Matthew J.
Genetically-encoded actuators that allow control of protein-protein interactions with light, termed 'optical dimerizers', are emerging as new tools for experimental biology. In recent years, numerous new and versatile dimerizer systems have been developed. Here we discuss the design of optical dimerizer experiments, including choice of a dimerizer system, photoexcitation sources, and coordinate use of imaging reporters. We provide detailed protocols for experiments using two dimerization systems we previously developed, CRY2/CIB and UVR8/UVR8, for use controlling transcription, protein localization, and protein secretion with light. Additionally, we provide instructions and software for constructing a pulse-controlled LED light device for use in experiments requiring extended light treatments. PMID:25181301
Dynamics of a Highly Flexible Protein
DEFF Research Database (Denmark)
Andersen, Lisbeth
malleability are the subject of this defense. Using nuclear magnetic resonance (NMR) spectroscopy, the dynamics of NCBD have been investigated on timescales ranging from picoseconds to milliseconds using relaxation dispersion experiments, residual dipolar couplings and methyl group deuterium relaxation. From...
Dynamics in electron transfer protein complexes
Bashir, Qamar
Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We have used paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize
A comparison of techniques for calculating protein essential dynamics
van Aalten, D.M.F.; de Groot, B.L.; Findlay, J.B.C.; Berendsen, H.J.C.; Amadei, A
Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to
Dynamic properties of motor proteins with two subunits
International Nuclear Information System (INIS)
Kolomeisky, Anatoly B; III, Hubert Phillips
The dynamics of motor protein molecules consisting of two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate states and conformations between the corresponding binding states of proteins. These models enable us to provide a detailed description and comparison of two different mechanisms of the motion of motor proteins along the linear tracks: the hand-over-hand mechanism, when the motion of subunits alternate; and the inchworm mechanism, when one subunit is always trailing another one. It is shown that the proteins in the hand-over-hand mechanism move faster and fluctuate more than the molecules in the inchworm mechanism. The effect of external forces on dynamic properties of motor proteins is also discussed. Finally, a quantitative method, based on experimental observations for single motor proteins, is proposed for distinguishing between two mechanisms of motion
Dynamic control of traffic lights
Haijema, Rene; Hendrix, Eligius M.T.; Wal, van der Jan
Traffic lights are put in place to dynamically change priority between traffic participants. Commonly, the duration of green intervals and the grouping, and ordering in which traffic flows are served are pre-fixed. In this chapter, the problem of minimizing vehicle delay at isolated intersections is
Hybrid Predictive Control for Dynamic Transport Problems
Núñez, Alfredo A; Cortés, Cristián E
Hybrid Predictive Control for Dynamic Transport Problems develops methods for the design of predictive control strategies for nonlinear-dynamic hybrid discrete-/continuous-variable systems. The methodology is designed for real-time applications, particularly the study of dynamic transport systems. Operational and service policies are considered, as well as cost reduction. The control structure is based on a sound definition of the key variables and their evolution. A flexible objective function able to capture the predictive behaviour of the system variables is described. Coupled with efficient algorithms, mainly drawn from the area of computational intelligence, this is shown to optimize performance indices for real-time applications. The framework of the proposed predictive control methodology is generic and, being able to solve nonlinear mixed-integer optimization problems dynamically, is readily extendable to other industrial processes. The main topics of this book are: ●hybrid predictive control (HPC) ...
Dynamics and control of technical systems
Balthazar, José M; Kaczmarczyk, Stefan
The main topics of this Special Issue are linear and, mainly, nonlinear dynamics, chaos and control of systems and structures and their applications in different field of science and engineering. According to the goal of the Special Issue, the selected contributions are divided into three major parts: ""Vibration Problems in Vertical Transportation Systems"", ""Nonlinear Dynamics, Chaos and Control of Elastic Structures"" and ""New Strategies and Challenges for Aerospace and Ocean Structures Dynamics and Control"". The discussion of real problems in aerospace and how these problems can be unde
PDB2CD visualises dynamics within protein structures.
Janes, Robert W
Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.
Robust control synthesis for uncertain dynamical systems
Byun, Kuk-Whan; Wie, Bong; Sunkel, John
This paper presents robust control synthesis techniques for uncertain dynamical systems subject to structured parameter perturbation. Both QFT (quantitative feedback theory) and H-infinity control synthesis techniques are investigated. Although most H-infinity-related control techniques are not concerned with the structured parameter perturbation, a new way of incorporating the parameter uncertainty in the robust H-infinity control design is presented. A generic model of uncertain dynamical systems is used to illustrate the design methodologies investigated in this paper. It is shown that, for a certain noncolocated structural control problem, use of both techniques results in nonminimum phase compensation.
Controllable Subspaces of Open Quantum Dynamical Systems
International Nuclear Information System (INIS)
Zhang Ming; Gong Erling; Xie Hongwei; Hu Dewen; Dai Hongyi
This paper discusses the concept of controllable subspace for open quantum dynamical systems. It is constructively demonstrated that combining structural features of decoherence-free subspaces with the ability to perform open-loop coherent control on open quantum systems will allow decoherence-free subspaces to be controllable. This is in contrast to the observation that open quantum dynamical systems are not open-loop controllable. To a certain extent, this paper gives an alternative control theoretical interpretation on why decoherence-free subspaces can be useful for quantum computation.
Dynamic Control Based Photovoltaic Illuminating System
Directory of Open Access Journals (Sweden)
Zhang Chengkai
Full Text Available Smart LED illumination system can use the power from whether the photovoltaic cell or the power grid automatically based on the SOC (State Of Charge of the photovoltaic cell. This paper proposes a feedback control of the photovoltaic cells and a dynamic control strategy for the Energy system. The dynamic control strategy is used to determine the switching state of the photovoltaic cell based on the illumination load in the past one hour and the battery capacity. These controls are manifested by experimental prototype that the control scheme is correct and effective.
Dynamic Algorithm for LQGPC Predictive Control
DEFF Research Database (Denmark)
Hangstrup, M.; Ordys, A.W.; Grimble, M.J.
In this paper the optimal control law is derived for a multi-variable state space Linear Quadratic Gaussian Predictive Controller (LQGPC). A dynamic performance index is utilized resulting in an optimal steady state controller. Knowledge of future reference values is incorporated into the control......In this paper the optimal control law is derived for a multi-variable state space Linear Quadratic Gaussian Predictive Controller (LQGPC). A dynamic performance index is utilized resulting in an optimal steady state controller. Knowledge of future reference values is incorporated...... into the controller design and the solution is derived using the method of Lagrange multipliers. It is shown how well-known GPC controller can be obtained as a special case of the LQGPC controller design. The important advantage of using the LQGPC framework for designing predictive, e.g. GPS is that LQGPC enables...
Hindered protein dynamics in the presence of a cryoprotecting agent
Energy Technology Data Exchange (ETDEWEB)
Koeper, I. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France); Physikdepartment E13, TU Muenchen, 85747 Garching (Germany); Bellissent-Funel, M.C. [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette (France)
We present a study of the influence of trehalose, a well-known cryoprotecting disaccharide, on the dynamics of a protein, the C-phycocyanin. The dynamics is investigated in a time range from some picoseconds to several nanoseconds using different neutron-scattering techniques. Data obtained on samples containing hydrated powders of the protein in the presence of trehalose are compared to that of the protein alone, studied by neutron-scattering techniques as well as by molecular dynamics simulations. The analysis of time-of-flight data gives access to the geometry of the observed motions. These motions can be described via a model of a particle diffusing inside a sphere. We observe a slowing down of the movements of the protein due to the presence of trehalose of one to two orders of magnitude, while the geometry of the motions is conserved. (orig.)
Dynamics of DNA conformations and DNA-protein interaction
DEFF Research Database (Denmark)
Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen
Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...... denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed...... in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent...
Coherent Protein Dynamics Explored at FELIX
Austin, Robert
We have discovered that there exists a very narrow (less than 0.02 microns) wide resonance in the amide I band of myoglobin and photoactive yellow protein that can be driven to greater than 30% saturation using very narrow linewidth pump-probe spectroscopy at FELIX. The extraordinary narrowness of this transition and the extraordinary ease of saturation inplies that this band is highly anharmonic and decoupled from the other oscillators in the amide I band. We will present detailed measurments on this discovery and implications for energy flow in proteins.
Dynamics and control of hybrid mechanical systems
Leonov, G.A.; Nijmeijer, H.; Pogromski, A.Y.; Fradkov, A.L.
The papers in this edited volume aim to provide a better understanding of the dynamics and control of a large class of hybrid dynamical systems that are described by different models in different state space domains. They not only cover important aspects and tools for hybrid systems analysis and
Controlling chaos in discontinuous dynamical systems
International Nuclear Information System (INIS)
Danca, Marius-F.
In this paper we consider the possibility to implement the technique of changes in the system variables to control the chaos introduced by Gueemez and Matias for continuous dynamical systems to a class of discontinuous dynamical systems. The approach is realized via differential inclusions following the Filippov theory. Three practical examples are considered
Flexible Access Control for Dynamic Collaborative Environments
Dekker, M.A.C.
Access control is used in computer systems to control access to confidential data. In this thesis we focus on access control for dynamic collaborative environments where multiple users and systems access and exchange data in an ad hoc manner. In such environments it is difficult to protect
State estimation for integrated vehicle dynamics control
Zuurbier, J.; Bremmer, P.
This paper discusses a vehicle controller and a state estimator that was implemented and tested in a vehicle equipped with a combined braking and chassis control system to improve handling. The vehicle dynamics controller consists of a feed forward body roll compensation and a feedback stability
Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation
International Nuclear Information System (INIS)
Dellerue, Serge
Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr
Bifurcation Control of Chaotic Dynamical Systems
National Research Council Canada - National Science Library
Wang, Hua O; Abed, Eyad H
A nonlinear system which exhibits bifurcations, transient chaos, and fully developed chaos is considered, with the goal of illustrating the role of two ideas in the control of chaotic dynamical systems...
Solved problems in dynamical systems and control
Tenreiro-Machado, J; Valério, Duarte; Galhano, Alexandra M
This book presents a collection of exercises on dynamical systems, modelling and control. Each topic covered includes a summary of the theoretical background, problems with solutions, and further exercises.
Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity
Directory of Open Access Journals (Sweden)
Elena ePapaleo
Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome
Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong
We constructed and simulated a 'minimal proteome' model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that 'proper' populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643
Enterprise Dynamic Access Control (EDAC)
National Research Council Canada - National Science Library
Fernandez, Richard
.... Resources can represent software applications, web services and even facility access. An effective access control model should be capable of evaluating resource access based on user characteristics and environmentals...
Stochastic control theory dynamic programming principle
Nisio, Makiko
This book offers a systematic introduction to the optimal stochastic control theory via the dynamic programming principle, which is a powerful tool to analyze control problems. First we consider completely observable control problems with finite horizons. Using a time discretization we construct a nonlinear semigroup related to the dynamic programming principle (DPP), whose generator provides the Hamilton–Jacobi–Bellman (HJB) equation, and we characterize the value function via the nonlinear semigroup, besides the viscosity solution theory. When we control not only the dynamics of a system but also the terminal time of its evolution, control-stopping problems arise. This problem is treated in the same frameworks, via the nonlinear semigroup. Its results are applicable to the American option price problem. Zero-sum two-player time-homogeneous stochastic differential games and viscosity solutions of the Isaacs equations arising from such games are studied via a nonlinear semigroup related to DPP (the min-ma...
Dynamic Frequency Control in Power Networks
Zhao, Changhong; Mallada Garcia, Enrique; Low, Steven H.
Node controllers in power distribution networks in accordance with embodiments of the invention enable dynamic frequency control. One embodiment includes a node controller comprising a network interface a processor; and a memory containing a frequency control application; and a plurality of node operating parameters describing the operating parameters of a node, where the node is selected from a group consisting of at least one generator node in a power distribution network wherein the proces...
Discrete Control Processes, Dynamic Games and Multicriterion Control Problems
Directory of Open Access Journals (Sweden)
Dumitru Lozovanu
Full Text Available The discrete control processes with state evaluation in time of dynamical system is considered. A general model of control problems with integral-time cost criterion by a trajectory is studied and a general scheme for solving such classes of problems is proposed. In addition the game-theoretical and multicriterion models for control problems are formulated and studied.
Collective dynamics of protein hydration water by brillouin neutron spectroscopy.
Orecchini, Andrea; Paciaroni, Alessandro; De Francesco, Alessio; Petrillo, Caterina; Sacchetti, Francesco
By a detailed experimental study of THz dynamics in the ribonuclease protein, we could detect the propagation of coherent collective density fluctuations within the protein hydration shell. The emerging picture indicates the presence of both a dispersing mode, traveling with a speed greater than 3000 m/s, and a nondispersing one, characterized by an almost constant energy of 6-7 meV. In agreement with molecular dynamics simulations [Phys. Rev. Lett. 2002, 89, 275501], the features of the dispersion curves closely resemble those observed in pure liquid water [Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2004, 69, 061203]. On the contrary, the observed damping factors are much larger than in bulk water, with the dispersing mode becoming overdamped at Q = 0.6 A(-1) already. Such novel experimental findings are discussed as a dynamic signature of the disordering effect induced by the protein surface on the local structure of water.
Hydration and temperature interdependence of protein picosecond dynamics.
Lipps, Ferdinand; Levy, Seth; Markelz, A G
We investigate the nature of the solvent motions giving rise to the rapid temperature dependence of protein picoseconds motions at 220 K, often referred to as the protein dynamical transition. The interdependence of picoseconds dynamics on hydration and temperature is examined using terahertz time domain spectroscopy to measure the complex permittivity in the 0.2-2.0 THz range for myoglobin. Both the real and imaginary parts of the permittivity over the frequency range measured have a strong temperature dependence at >0.27 h (g water per g protein), however the permittivity change is strongest for frequencies 1 THz, and 0.27 h for frequencies <1 THz. The data are consistent with the dynamical transition solvent fluctuations requiring only clusters of ~5 water molecules, whereas the enhancement of lowest frequency motions requires a fully spanning water network. This journal is © the Owner Societies 2012
Dynamic control of chaotic resonators
Di Falco, A.; Bruck, R.; Liu, C.; Muskens, O.; Fratalocchi, Andrea
We report on the all-optical control of chaotic optical resonators based on silicon on insulator (SOI) platform. We show that simple non-chaotic cavities can be tuned to exhibit chaotic behavior via intense optical pump- ing, inducing a local change of refractive index. To this extent we have fabricated a number of devices and demonstrated experimentally and theoretically that chaos can be triggered on demand on an optical chip. © 2016 SPIE.
Dynamic control of chaotic resonators
Di Falco, A.
We report on the all-optical control of chaotic optical resonators based on silicon on insulator (SOI) platform. We show that simple non-chaotic cavities can be tuned to exhibit chaotic behavior via intense optical pump- ing, inducing a local change of refractive index. To this extent we have fabricated a number of devices and demonstrated experimentally and theoretically that chaos can be triggered on demand on an optical chip. © 2016 SPIE.
Role of controllability in optimizing quantum dynamics
International Nuclear Information System (INIS)
Wu Rebing; Hsieh, Michael A.; Rabitz, Herschel
This paper reveals an important role that controllability plays in the complexity of optimizing quantum control dynamics. We show that the loss of controllability generally leads to multiple locally suboptimal controls when gate fidelity in a quantum control system is maximized, which does not happen if the system is controllable. Such local suboptimal controls may attract an optimization algorithm into a local trap when a global optimal solution is sought, even if the target gate can be perfectly realized. This conclusion results from an analysis of the critical topology of the corresponding quantum control landscape, which refers to the gate fidelity objective as a functional of the control fields. For uncontrollable systems, due to SU(2) and SU(3) dynamical symmetries, the control landscape corresponding to an implementable target gate is proven to possess multiple locally optimal critical points, and its ruggedness can be further increased if the target gate is not realizable. These results imply that the optimization of quantum dynamics can be seriously impeded when operating with local search algorithms under these conditions, and thus full controllability is demanded.
Contrasting the excited-state dynamics of the photoactive yellow protein chromophore: Protein versus solvent environments
Vengris, M.; Horst, M.A.; Zgrablic, G.; van Stokkum, I.H.M.; Haacke, S.; Chergui, M.; Hellingwerf, K.J.; van Grondelle, R.; Larsen, D.S.
Wavelength- and time-resolved fluorescence experiments have been performed on the photoactive yellow protein, the E46Q mutant, the hybrids of these proteins containing a nonisomerizing "locked" chromophore, and the native and locked chromophores in aqueous solution. The ultrafast dynamics of these
Time-resolved infrared studies of protein conformational dynamics
Energy Technology Data Exchange (ETDEWEB)
Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)
We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.
Enhancing protein adsorption simulations by using accelerated molecular dynamics.
Directory of Open Access Journals (Sweden)
Christian Mücksch
Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.
Dynamic organization of genetic recombination proteins and chromosomes
International Nuclear Information System (INIS)
Essers, J.; Van Cappellen, G.; Van Drunen, E.; Theil, A.; Jaspers, N.N.G.J.; Houtsmuller, A.B.; Vermeulen, W.; Kanaar, R.
Homologous recombination requires the co-ordinated action of the RAD52 group proteins, including Rad51, Rad52 and Rad54. Upon treatment of mammalian cells with ionizing radiation, these proteins accumulate into foci at sites of DSB induction. We probed the nature of the DNA damage-induced foci in living cells with the use of photobleaching techniques. These foci are not static assemblies of DNA repair proteins. Instead, they are dynamic structures of which Rad51 is a stable core component, while Rad52 and Rad54 reversibly interact with the structure. Furthermore, even though the RAD52 group proteins colocalize in the DNA damage-induced foci, the majority of the proteins are not part of the same multi-protein complex in the absence of DNA damage. Executing DNA transactions through dynamic multi-protein complexes, rather than stable holo-complexes, allows greater flexibility during the transaction. In case of DNA repair, for example, it allows cross talk between different DNA repair pathways and coupling to other DNA transactions, such as replication. In addition to the behavior of proteins in living cells, we have tracked chromosomes during cell division. Our results suggest that the relative position of chromosomes in the mother cell is conserved in its daughter cells
Solution structure and dynamics of melanoma inhibitory activity protein
International Nuclear Information System (INIS)
Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.
Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures
Role of protein dynamics in transmembrane receptor signalling
DEFF Research Database (Denmark)
Wang, Yong; Bugge, Katrine Østergaard; Kragelund, Birthe Brandt
Cells are dependent on transmembrane receptors to communicate and transform chemical and physical signals into intracellular responses. Because receptors transport 'information', conformational changes and protein dynamics play a key mechanistic role. We here review examples where experiment...... to function. Because the receptors function in a heterogeneous environment and need to be able to switch between distinct functional states, they may be particularly sensitive to small perturbations that complicate studies linking dynamics to function....
Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.
Directory of Open Access Journals (Sweden)
Eric A Yen
Full Text Available Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and
Experience with dynamic material control subsystems
International Nuclear Information System (INIS)
Severe, W.R.; Hagen, J.; Siebelist, R.; Wagner, R.P.; Olson, W.M.
Operation of a Dynamic Material Control (DYMAC) prototype system has yielded some useful information for installing the final system. We discovered a bias between two methods for measuring filtrates. Evaluation of a unit process dynamic balance brought to light an operating procedure that weakens the accountability goals of the DYMAC system. We were able to correct both situations for the final system and learned that we must regularly monitor the system once it is operational for similar discrepancies
Chaos control of Chen chaotic dynamical system
International Nuclear Information System (INIS)
Yassen, M.T.
This paper is devoted to study the problem of controlling chaos in Chen chaotic dynamical system. Two different methods of control, feedback and nonfeedback methods are used to suppress chaos to unstable equilibria or unstable periodic orbits (UPO). The Lyapunov direct method and Routh-Hurwitz criteria are used to study the conditions of the asymptotic stability of the steady states of the controlled system. Numerical simulations are presented to show these results
Evolutionary dynamics of protein domain architecture in plants
Directory of Open Access Journals (Sweden)
Zhang Xue-Cheng
Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing
Approaches to Learning to Control Dynamic Uncertainty
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Magda Osman
Full Text Available In dynamic environments, when faced with a choice of which learning strategy to adopt, do people choose to mostly explore (maximizing their long term gains or exploit (maximizing their short term gains? More to the point, how does this choice of learning strategy influence one's later ability to control the environment? In the present study, we explore whether people's self-reported learning strategies and levels of arousal (i.e., surprise, stress correspond to performance measures of controlling a Highly Uncertain or Moderately Uncertain dynamic environment. Generally, self-reports suggest a preference for exploring the environment to begin with. After which, those in the Highly Uncertain environment generally indicated they exploited more than those in the Moderately Uncertain environment; this difference did not impact on performance on later tests of people's ability to control the dynamic environment. Levels of arousal were also differentially associated with the uncertainty of the environment. Going beyond behavioral data, our model of dynamic decision-making revealed that, in actual fact, there was no difference in exploitation levels between those in the highly uncertain or moderately uncertain environments, but there were differences based on sensitivity to negative reinforcement. We consider the implications of our findings with respect to learning and strategic approaches to controlling dynamic uncertainty.
Non-interacting surface solvation and dynamics in protein-protein interactions
Visscher, Koen M.; Kastritis, Panagiotis L.|info:eu-repo/dai/nl/315886668; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238
Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo
Controlling Chemistry in Dynamic Nanoscale Systems
DEFF Research Database (Denmark)
Jesorka, Aldo; Lizana, Ludvig; Konkoli, Zoran
Spatial organization and shape dynamics are inherent properties of biological cells and cell interiors. There are strong indications that these features are important for the in vivo control of reaction parameters in biochemical transformations. Nanofluidic model devices founded on surfactant...... of the concept. Controlled release of chol-DNA molecules from SU-8 surfaces gives the possibility to dynamically change surface and/or solution properties in micro and nanoreactor applications, opening access to stable 2D chemistry on surface-based devices with potential for easy interfacing with conventional...
Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2
Directory of Open Access Journals (Sweden)
Laulumaa Saara
Full Text Available Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.
Neutron scattering studies on protein dynamics using the human myelin peripheral membrane protein P2
Laulumaa, Saara; Kursula, Petri; Natali, Francesca
Myelin is a multilayered proteolipid membrane structure surrounding selected axons in the vertebrate nervous system, which allows the rapid saltatory conduction of nerve impulses. Deficits in myelin formation and maintenance may lead to chronic neurological disease. P2 is an abundant myelin protein from peripheral nerves, binding between two apposing lipid bilayers. We studied the dynamics of the human myelin protein P2 and its mutated P38G variant in hydrated powders using elastic incoherent neutron scattering. The local harmonic vibrations at low temperatures were very similar for both samples, but the mutant protein had increased flexibility and softness close to physiological temperatures. The results indicate that a drastic mutation of proline to glycine at a functional site can affect protein dynamics, and in the case of P2, they may explain functional differences between the two proteins.
Progression of 3D Protein Structure and Dynamics Measurements
Sato-Tomita, Ayana; Sekiguchi, Hiroshi; Sasaki, Yuji C.
New measurement methodologies have begun to be proposed with the recent progress in the life sciences. Here, we introduce two new methodologies, X-ray fluorescence holography for protein structural analysis and diffracted X-ray tracking (DXT), to observe the dynamic behaviors of individual single molecules.
Unveiling protein functions through the dynamics of the interaction network.
Directory of Open Access Journals (Sweden)
Irene Sendiña-Nadal
Full Text Available Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.
Dynamic Surface Control and Its Application to Lateral Vehicle Control
Directory of Open Access Journals (Sweden)
Bongsob Song
Full Text Available This paper extends the design and analysis methodology of dynamic surface control (DSC in Song and Hedrick, 2011, for a more general class of nonlinear systems. When rotational mechanical systems such as lateral vehicle control and robot control are considered for applications, sinusoidal functions are easily included in the equation of motions. If such a sinusoidal function is used as a forcing term for DSC, the stability analysis faces the difficulty due to highly nonlinear functions resulting from the low-pass filter dynamics. With modification of input variables to the filter dynamics, the burden of mathematical analysis can be reduced and stability conditions in linear matrix inequality form to guarantee the quadratic stability via DSC are derived for the given class of nonlinear systems. Finally, the proposed design and analysis approach are applied to lateral vehicle control for forward automated driving and backward parallel parking at a low speed as well as an illustrative example.
Dynamic nuclear polarization of membrane proteins: covalently bound spin-labels at protein–protein interfaces
International Nuclear Information System (INIS)
Wylie, Benjamin J.; Dzikovski, Boris G.; Pawsey, Shane; Caporini, Marc; Rosay, Melanie; Freed, Jack H.; McDermott, Ann E.
We demonstrate that dynamic nuclear polarization of membrane proteins in lipid bilayers may be achieved using a novel polarizing agent: pairs of spin labels covalently bound to a protein of interest interacting at an intermolecular interaction surface. For gramicidin A, nitroxide tags attached to the N-terminal intermolecular interface region become proximal only when bimolecular channels forms in the membrane. We obtained signal enhancements of sixfold for the dimeric protein. The enhancement effect was comparable to that of a doubly tagged sample of gramicidin C, with intramolecular spin pairs. This approach could be a powerful and selective means for signal enhancement in membrane proteins, and for recognizing intermolecular interfaces
Controlling Complex Systems and Developing Dynamic Technology
Avizienis, Audrius Victor
In complex systems, control and understanding become intertwined. Following Ilya Prigogine, we define complex systems as having control parameters which mediate transitions between distinct modes of dynamical behavior. From this perspective, determining the nature of control parameters and demonstrating the associated dynamical phase transitions are practically equivalent and fundamental to engaging with complexity. In the first part of this work, a control parameter is determined for a non-equilibrium electrochemical system by studying a transition in the morphology of structures produced by an electroless deposition reaction. Specifically, changing the size of copper posts used as the substrate for growing metallic silver structures by the reduction of Ag+ from solution under diffusion-limited reaction conditions causes a dynamical phase transition in the crystal growth process. For Cu posts with edge lengths on the order of one micron, local forces promoting anisotropic growth predominate, and the reaction produces interconnected networks of Ag nanowires. As the post size is increased above 10 microns, the local interfacial growth reaction dynamics couple with the macroscopic diffusion field, leading to spatially propagating instabilities in the electrochemical potential which induce periodic branching during crystal growth, producing dendritic deposits. This result is interesting both as an example of control and understanding in a complex system, and as a useful combination of top-down lithography with bottom-up electrochemical self-assembly. The second part of this work focuses on the technological development of devices fabricated using this non-equilibrium electrochemical process, towards a goal of integrating a complex network as a dynamic functional component in a neuromorphic computing device. Self-assembled networks of silver nanowires were reacted with sulfur to produce interfacial "atomic switches": silver-silver sulfide junctions, which exhibit
Control theory of digitally networked dynamic systems
Lunze, Jan
The book gives an introduction to networked control systems and describes new modeling paradigms, analysis methods for event-driven, digitally networked systems, and design methods for distributed estimation and control. Networked model predictive control is developed as a means to tolerate time delays and packet loss brought about by the communication network. In event-based control the traditional periodic sampling is replaced by state-dependent triggering schemes. Novel methods for multi-agent systems ensure complete or clustered synchrony of agents with identical or with individual dynamic
Design and control of swarm dynamics
Bouffanais, Roland
The book is about the key elements required for designing, building and controlling effective artificial swarms comprised of multiple moving physical agents. Therefore this book presents the fundamentals of each of those key elements in the particular frame of dynamic swarming, specifically exposing the profound connections between these elements and establish some general design principles for swarming behaviors. This scientific endeavor requires an inter-disciplinary approach: biomimetic inspiration from ethology and ecology, study of social information flow, analysis of temporal and adaptive signaling network of interaction, considerations of control of networked real-time systems, and lastly, elements of complex adaptive dynamical systems. This book offers a completely new perspective on the scientific understanding of dynamic collective behaviors thanks to its multi-disciplinary approach and its focus on artificial swarm of physical agents. Two of the key problems in understanding the emergence of swarm ...
Dynamic Control of Kinematically Redundant Robotic Manipulators
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Erling Lunde
Full Text Available Several methods for task space control of kinematically redundant manipulators have been proposed in the literature. Most of these methods are based on a kinematic analysis of the manipulator. In this paper we propose a control algorithm in which we are especially concerned with the manipulator dynamics. The algorithm is particularly well suited for the class of redundant manipulators consisting of a relatively small manipulator mounted on a larger positioning part.
Cognitive Control: Dynamic, Sustained, and Voluntary Influences
Fernandez-Duque, Diego; Knight, MaryBeth
The cost of incongruent stimuli is reduced when conflict is expected. This series of experiments tested whether this improved performance is due to repetition priming or to enhanced cognitive control. Using a paradigm in which Word and Number Stroop alternated every trial, Experiment 1 assessed dynamic trial-to-trial changes. Incongruent trials…
A perspective on stage dynamics and control
Butler, H.
In the semiconductor industry, a wafer stepper is used to expose the pattern on a mask ('reticle') onto a wafer. Accurate positioning of the reticle and the wafer is of crucial importance for creating a working IC. This paper reflects on the stage dynamics and control design in Stepper technology,
Direct Optimal Control of Duffing Dynamics
Oz, Hayrani; Ramsey, John K.
The "direct control method" is a novel concept that is an attractive alternative and competitor to the differential-equation-based methods. The direct method is equally well applicable to nonlinear, linear, time-varying, and time-invariant systems. For all such systems, the method yields explicit closed-form control laws based on minimization of a quadratic control performance measure. We present an application of the direct method to the dynamics and optimal control of the Duffing system where the control performance measure is not restricted to a quadratic form and hence may include a quartic energy term. The results we present in this report also constitute further generalizations of our earlier work in "direct optimal control methodology." The approach is demonstrated for the optimal control of the Duffing equation with a softening nonlinear stiffness.
Conformational dynamics of amyloid proteins at the aqueous interface
Armbruster, Matthew; Horst, Nathan; Aoki, Brendy; Malik, Saad; Soto, Patricia
Amyloid proteins is a class of proteins that exhibit distinct monomeric and oligomeric conformational states hallmark of deleterious neurological diseases for which there are not yet cures. Our goal is to examine the extent of which the aqueous/membrane interface modulates the folding energy landscape of amyloid proteins. To this end, we probe the dynamic conformational ensemble of amyloids (monomer prion protein and Alzheimer's Ab protofilaments) interacting with model bilayers. We will present the results of our coarse grain molecular modeling study in terms of the existence of preferential binding spots of the amyloid to the bilayer and the response of the bilayer to the interaction with the amyloid. NSF Nebraska EPSCoR First Award
Dynamic gastric digestion of a commercial whey protein concentrate†.
Miralles, Beatriz; Del Barrio, Roberto; Cueva, Carolina; Recio, Isidra; Amigo, Lourdes
A dynamic gastrointestinal simulator, simgi ® , has been applied to assess the gastric digestion of a whey protein concentrate. Samples collected from the outlet of the stomach have been compared to those resulting from the static digestion protocol INFOGEST developed on the basis of physiologically inferred conditions. Progress of digestion was followed by SDS-PAGE and LC-MS/MS. By SDS-PAGE, serum albumin and α-lactalbumin were no longer detectable at 30 and 60 min, respectively. On the contrary, β-lactoglobulin was visible up to 120 min, although in decreasing concentrations in the dynamic model due to the gastric emptying and the addition of gastric fluids. Moreover, β-lactoglobulin was partly hydrolysed by pepsin probably due to the presence of heat-denatured forms and the peptides released using both digestion models were similar. Under dynamic conditions, a stepwise increase in number of peptides over time was observed, while the static protocol generated a high number of peptides from the beginning of digestion. Whey protein digestion products using a dynamic stomach are consistent with those generated with the static protocol but the kinetic behaviour of the peptide profile emphasises the effect of the sequential pepsin addition, peristaltic shaking, and gastric emptying on protein digestibility. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.
Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein
Directory of Open Access Journals (Sweden)
Michael T. Zimmermann
Full Text Available We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure.
Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions.
Delaforge, Elise; Milles, Sigrid; Huang, Jie-Rong; Bouvier, Denis; Jensen, Malene Ringkjøbing; Sattler, Michael; Hart, Darren J; Blackledge, Martin
Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions
Directory of Open Access Journals (Sweden)
Elise Delaforge
Full Text Available Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
Dynamics and Control of Chemical Reactors-Selectively Surveyed
DEFF Research Database (Denmark)
Jørgensen, S. B.; Jensen, N.
The chemical reactor or bioreactor is physically at a central position in a process, and often with a decisive role on the overall technical and economical performance. Even though application of feedback control on reactors is gaining momentum and on-line optimization has been implemented....... For bioreactors the theory and practice of reactor design, dynamics and control have to be adapted to the peculiarities of the biological catalysts. Enzymes, the protein catalysts, are the simplest ones, which have many common features with chemical catalysts. The living cells are much more complex, these growing...... in industry, many reactor control problems are still left unsolved or only partly solved using open loop strategies where disturbance rejection and model inaccuracies have to be handled through manual reactor control and feedback control of raw material preprocessing and product purification operations...
Markov dynamic models for long-timescale protein motion.
Chiang, Tsung-Han
Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.
Markov dynamic models for long-timescale protein motion.
Chiang, Tsung-Han; Hsu, David; Latombe, Jean-Claude
Molecular dynamics (MD) simulation is a well-established method for studying protein motion at the atomic scale. However, it is computationally intensive and generates massive amounts of data. One way of addressing the dual challenges of computation efficiency and data analysis is to construct simplified models of long-timescale protein motion from MD simulation data. In this direction, we propose to use Markov models with hidden states, in which the Markovian states represent potentially overlapping probabilistic distributions over protein conformations. We also propose a principled criterion for evaluating the quality of a model by its ability to predict long-timescale protein motions. Our method was tested on 2D synthetic energy landscapes and two extensively studied peptides, alanine dipeptide and the villin headpiece subdomain (HP-35 NleNle). One interesting finding is that although a widely accepted model of alanine dipeptide contains six states, a simpler model with only three states is equally good for predicting long-timescale motions. We also used the constructed Markov models to estimate important kinetic and dynamic quantities for protein folding, in particular, mean first-passage time. The results are consistent with available experimental measurements.
The dynamics of plant plasma membrane proteins: PINs and beyond.
Luschnig, Christian; Vert, Grégory
Plants are permanently situated in a fixed location and thus are well adapted to sense and respond to environmental stimuli and developmental cues. At the cellular level, several of these responses require delicate adjustments that affect the activity and steady-state levels of plasma membrane proteins. These adjustments involve both vesicular transport to the plasma membrane and protein internalization via endocytic sorting. A substantial part of our current knowledge of plant plasma membrane protein sorting is based on studies of PIN-FORMED (PIN) auxin transport proteins, which are found at distinct plasma membrane domains and have been implicated in directional efflux of the plant hormone auxin. Here, we discuss the mechanisms involved in establishing such polar protein distributions, focusing on PINs and other key plant plasma membrane proteins, and we highlight the pathways that allow for dynamic adjustments in protein distribution and turnover, which together constitute a versatile framework that underlies the remarkable capabilities of plants to adjust growth and development in their ever-changing environment. © 2014. Published by The Company of Biologists Ltd.
Indirect learning control for nonlinear dynamical systems
Ryu, Yeong Soon; Longman, Richard W.
In a previous paper, learning control algorithms were developed based on adaptive control ideas for linear time variant systems. The learning control methods were shown to have certain advantages over their adaptive control counterparts, such as the ability to produce zero tracking error in time varying systems, and the ability to eliminate repetitive disturbances. In recent years, certain adaptive control algorithms have been developed for multi-body dynamic systems such as robots, with global guaranteed convergence to zero tracking error for the nonlinear system euations. In this paper we study the relationship between such adaptive control methods designed for this specific class of nonlinear systems, and the learning control problem for such systems, seeking to converge to zero tracking error in following a specific command repeatedly, starting from the same initial conditions each time. The extension of these methods from the adaptive control problem to the learning control problem is seen to be trivial. The advantages and disadvantages of using learning control based on such adaptive control concepts for nonlinear systems, and the use of other currently available learning control algorithms are discussed.
Studying pressure denaturation of a protein by molecular dynamics simulations.
Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar
Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties
Strategies for the photo-control of endogenous protein activity.
Brechun, Katherine E; Arndt, Katja M; Woolley, G Andrew
Photo-controlled or 'optogenetic' effectors interfacing with endogenous protein machinery allow the roles of endogenous proteins to be probed. There are two main approaches being used to develop optogenetic effectors: (i) caging strategies using photo-controlled conformational changes, and (ii) protein relocalization strategies using photo-controlled protein-protein interactions. Numerous specific examples of these approaches have been reported and efforts to develop general methods for photo-control of endogenous proteins are a current focus. The development of improved screening and selection methods for photo-switchable proteins would advance the field. Copyright © 2016 Elsevier Ltd. All rights reserved.
Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics
DEFF Research Database (Denmark)
Papaleo, Elena
that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....
The Unfolded Protein Response and Cell Fate Control.
Hetz, Claudio; Papa, Feroz R
The secretory capacity of a cell is constantly challenged by physiological demands and pathological perturbations. To adjust and match the protein-folding capacity of the endoplasmic reticulum (ER) to changing secretory needs, cells employ a dynamic intracellular signaling pathway known as the unfolded protein response (UPR). Homeostatic activation of the UPR enforces adaptive programs that modulate and augment key aspects of the entire secretory pathway, whereas maladaptive UPR outputs trigger apoptosis. Here, we discuss recent advances into how the UPR integrates information about the intensity and duration of ER stress stimuli in order to control cell fate. These findings are timely and significant because they inform an evolving mechanistic understanding of a wide variety of human diseases, including diabetes mellitus, neurodegeneration, and cancer, thus opening up the potential for new therapeutic modalities to treat these diverse diseases. Copyright © 2017 Elsevier Inc. All rights reserved.
Bioluminescence resonance energy transfer system for measuring dynamic protein-protein interactions in bacteria.
Cui, Boyu; Wang, Yao; Song, Yunhong; Wang, Tietao; Li, Changfu; Wei, Yahong; Luo, Zhao-Qing; Shen, Xihui
Protein-protein interactions are important for virtually every biological process, and a number of elegant approaches have been designed to detect and evaluate such interactions. However, few of these methods allow the detection of dynamic and real-time protein-protein interactions in bacteria. Here we describe a bioluminescence resonance energy transfer (BRET) system based on the bacterial luciferase LuxAB. We found that enhanced yellow fluorescent protein (eYFP) accepts the emission from LuxAB and emits yellow fluorescence. Importantly, BRET occurred when LuxAB and eYFP were fused, respectively, to the interacting protein pair FlgM and FliA. Furthermore, we observed sirolimus (i.e., rapamycin)-inducible interactions between FRB and FKBP12 and a dose-dependent abolishment of such interactions by FK506, the ligand of FKBP12. Using this system, we showed that osmotic stress or low pH efficiently induced multimerization of the regulatory protein OmpR and that the multimerization induced by low pH can be reversed by a neutralizing agent, further indicating the usefulness of this system in the measurement of dynamic interactions. This method can be adapted to analyze dynamic protein-protein interactions and the importance of such interactions in bacterial processes such as development and pathogenicity. Real-time measurement of protein-protein interactions in prokaryotes is highly desirable for determining the roles of protein complex in the development or virulence of bacteria, but methods that allow such measurement are not available. Here we describe the development of a bioluminescence resonance energy transfer (BRET) technology that meets this need. The use of endogenous excitation light in this strategy circumvents the requirement for the sophisticated instrument demanded by standard fluorescence resonance energy transfer (FRET). Furthermore, because the LuxAB substrate decanal is membrane permeable, the assay can be performed without lysing the bacterial cells
Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation
Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project
Measuring protein dynamics with ultrafast two-dimensional infrared spectroscopy
International Nuclear Information System (INIS)
Adamczyk, Katrin; Candelaresi, Marco; Hunt, Neil T; Robb, Kirsty; Hoskisson, Paul A; Tucker, Nicholas P; Gumiero, Andrea; Walsh, Martin A; Parker, Anthony W
Recent advances in the methodology and application of ultrafast two-dimensional infrared (2D-IR) spectroscopy to biomolecular systems are reviewed. A description of the 2D-IR technique and the molecular contributions to the observed spectra are presented followed by a discussion of recent literature relating to the use of 2D-IR and associated approaches for measuring protein dynamics. In particular, these include the use of diatomic ligand groups for measuring haem protein dynamics, isotopic labelling strategies and the use of vibrational probe groups. The final section reports on the current state of the art regarding the use of 2D-IR methods to provide insights into biological reaction mechanisms. (topical review)
A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.
Schlecht, Ulrich; Liu, Zhimin; Blundell, Jamie R; St Onge, Robert P; Levy, Sasha F
Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.
Success Stories in Control: Nonlinear Dynamic Inversion Control
Bosworth, John T.
NASA plays an important role in advancing the state of the art in flight control systems. In the case of Nonlinear Dynamic Inversion (NDI) NASA supported initial implementation of the theory in an aircraft and demonstration in a space vehicle. Dr. Dale Enns of Honeywell Aerospace Advanced Technology performed this work in cooperation with NASA and under NASA contract. Honeywell and Lockheed Martin were subsequently contracted by AFRL to create "Design Guidelines for Multivariable Control Theory". This foundational work directly contributed to the advancement of the technology and the credibility of the control law as a design option. As a result Honeywell collaborated with Lockheed Martin to produce a Nonlinear Dynamic Inversion controller for the X-35 and subsequently Lockheed Martin did the same for the production Lockheed Martin F-35 vehicle. The theory behind NDI is to use a systematic generalized approach to controlling a vehicle. Using general aircraft nonlinear equations of motion and onboard aerodynamic, mass properties, and engine models specific to the vehicle, a relationship between control effectors and desired aircraft motion can be formulated. Using this formulation a control combination is used that provides a predictable response to commanded motion. Control loops around this formulation shape the response as desired and provide robustness to modeling errors. Once the control law is designed it can be used on a similar class of vehicle with only an update to the vehicle specific onboard models.
Picosecond Fluorescence Dynamics of Tryptophan and 5-Fluorotryptophan in Monellin : Slow Water-Protein Relaxation Unmasked
Xu, Jianhua; Chen, Binbin; Callis, Patrik Robert; Muiño, Pedro L; Rozeboom, Henriette J; Broos, Jaap; Toptygin, Dmitri; Brand, Ludwig; Knutson, Jay R
Time Dependent Fluorescence Stokes (emission wavelength) Shifts (TDFSS) from tryptophan (Trp) following sub-picosecond excitation are increasingly used to investigate protein dynamics, most recently enabling active research interest into water dynamics near the surface of proteins. Unlike many
Numerical Investigations of Dynamic Stall Control
Directory of Open Access Journals (Sweden)
Florin FRUNZULICA
Full Text Available In this paper we investigated numerically the dynamic stall phenomenon and the possibilities to control it, with application to vertical axis wind turbines (for urban users. The Phenomenon appear at low tip speed ratio (TSR<4 and it has a great impact on structural integrity of the wind turbine and power performances. For this reason we performed a computational study of dynamic stall around NACA 0012 airfoil in pitching motion at relative low Reynolds number (105. Also, we performed the same analysis for four flow control methods: two passive (Gurney flap and slot and two active (blowing jet on the rounded trailing edge and synthetic jet periodically activated. The Results are compared to those of an existing experimental case test.
Hybrid dynamical systems observation and control
Defoort, Michael
This book is a collection of contributions defining the state of current knowledge and new trends in hybrid systems – systems involving both continuous dynamics and discrete events – as described by the work of several well-known groups of researchers. Hybrid Dynamical Systems presents theoretical advances in such areas as diagnosability, observability and stabilization for various classes of system. Continuous and discrete state estimation and self-triggering control of nonlinear systems are advanced. The text employs various methods, among them, high-order sliding modes, Takagi–Sugeno representation and sampled-data switching to achieve its ends. The many applications of hybrid systems from power converters to computer science are not forgotten; studies of flexible-joint robotic arms and – as representative biological systems – the behaviour of the human heart and vasculature, demonstrate the wide-ranging practical significance of control in hybrid systems. The cross-disciplinary origins of study ...
Energy Management Dynamic Control Topology In MANET
Madhusudan, G.; Kumar, TNR
Topology management via per-node transmission power adjustment has been shown effective in extending network lifetime. The existing algorithms constructs static topologies which fail to take the residual energy of network nodes, and cannot balance energy consumption efficiently. To address this problem, a Light Weighted Distributed Topology Control algorithm EMDCT(Energy Management Dynamic Control Topology ) is proposed in this paper. Based on the link metric of the network, both the energy consumption rate level and residual energy levels at the two end nodes are considered. EMDCT generates a Dynamic Topology that changes with the variation of node energy without the aid of location information, each node determines its transmission power according to local network information, which reduces the overhead complexity of EMDCT greatly. The experiment results show that EMDCT preserves network connectivity and manitains minimum-cost property of the network also it can extend network lifetime more remarkably.
The Matrix exponential, Dynamic Systems and Control
DEFF Research Database (Denmark)
Poulsen, Niels Kjølstad
The matrix exponential can be found in various connections in analysis and control of dynamic systems. In this short note we are going to list a few examples. The matrix exponential usably pops up in connection to the sampling process, whatever it is in a deterministic or a stochastic setting...... or it is a tool for determining a Gramian matrix. This note is intended to be used in connection to the teaching post the course in Stochastic Adaptive Control (02421) given at Informatics and Mathematical Modelling (IMM), The Technical University of Denmark. This work is a result of a study of the litterature....
Neuromechanical tuning of nonlinear postural control dynamics
Ting, Lena H.; van Antwerp, Keith W.; Scrivens, Jevin E.; McKay, J. Lucas; Welch, Torrence D. J.; Bingham, Jeffrey T.; DeWeerth, Stephen P.
Postural control may be an ideal physiological motor task for elucidating general questions about the organization, diversity, flexibility, and variability of biological motor behaviors using nonlinear dynamical analysis techniques. Rather than presenting "problems" to the nervous system, the redundancy of biological systems and variability in their behaviors may actually be exploited to allow for the flexible achievement of multiple and concurrent task-level goals associated with movement. Such variability may reflect the constant "tuning" of neuromechanical elements and their interactions for movement control. The problem faced by researchers is that there is no one-to-one mapping between the task goal and the coordination of the underlying elements. We review recent and ongoing research in postural control with the goal of identifying common mechanisms underlying variability in postural control, coordination of multiple postural strategies, and transitions between them. We present a delayed-feedback model used to characterize the variability observed in muscle coordination patterns during postural responses to perturbation. We emphasize the significance of delays in physiological postural systems, requiring the modulation and coordination of both the instantaneous, "passive" response to perturbations as well as the delayed, "active" responses to perturbations. The challenge for future research lies in understanding the mechanisms and principles underlying neuromechanical tuning of and transitions between the diversity of postural behaviors. Here we describe some of our recent and ongoing studies aimed at understanding variability in postural control using physical robotic systems, human experiments, dimensional analysis, and computational models that could be enhanced from a nonlinear dynamics approach.
Chaos control applied to heart rhythm dynamics
Energy Technology Data Exchange (ETDEWEB)
Borem Ferreira, Bianca, E-mail: email@example.com [Universidade Federal do Rio de Janeiro, COPPE, Department of Mechanical Engineering, P.O. Box 68.503, 21.941.972 Rio de Janeiro, RJ (Brazil); Souza de Paula, Aline, E-mail: firstname.lastname@example.com [Universidade de Brasi' lia, Department of Mechanical Engineering, 70.910.900 Brasilia, DF (Brazil); Amorim Savi, Marcelo, E-mail: email@example.com [Universidade Federal do Rio de Janeiro, COPPE, Department of Mechanical Engineering, P.O. Box 68.503, 21.941.972 Rio de Janeiro, RJ (Brazil)
Highlights: > A natural cardiac pacemaker is modeled by a modified Van der Pol oscillator. > Responses related to normal and chaotic, pathological functioning of the heart are investigated. > Chaos control methods are applied to avoid pathological behaviors of heart dynamics. > Different approaches are treated: stabilization of unstable periodic orbits and chaos suppression. - Abstract: The dynamics of cardiovascular rhythms have been widely studied due to the key aspects of the heart in the physiology of living beings. Cardiac rhythms can be either periodic or chaotic, being respectively related to normal and pathological physiological functioning. In this regard, chaos control methods may be useful to promote the stabilization of unstable periodic orbits using small perturbations. In this article, the extended time-delayed feedback control method is applied to a natural cardiac pacemaker described by a mathematical model. The model consists of a modified Van der Pol equation that reproduces the behavior of this pacemaker. Results show the ability of the chaos control strategy to control the system response performing either the stabilization of unstable periodic orbits or the suppression of chaotic response, avoiding behaviors associated with critical cardiac pathologies.
Dynamic control of quadruped robot with hierarchical control structure
International Nuclear Information System (INIS)
Wang, Yu-Zhang; Furusho, Junji; Okajima, Yosuke.
For moving on irregular terrain, such as the inside of a nuclear power plant and outer space, it is generally recognized that the multilegged walking robot is suitable. This paper proposes a hierarchical control structure for the dynamic control of quadruped walking robots. For this purpose, we present a reduced order model which can approximate the original higher order model very well. Since this reduced order model does not require much computational time, it can be used in the real-time control of a quadruped walking robot. A hierarchical control experiment is shown in which the optimal control algorithm using a reduced order model is calculated by one microprocessor, and the other control algorithm is calculated by another microprocessor. (author)
Dynamic modeling and control of CFSTF
International Nuclear Information System (INIS)
Danesh, Y.; Jalali Farahani, F.
This paper deals with the modeling and control of a continuous-flow fermentation process for the production of alcohol: The dynamic behavior of ferment ors has been developed from mass balance and leads to nonlinear differential equations. Based on the proposed model, two computer algorithms are provided to control output alcohol concentration at the desired value by input flow rate manipulation. The first algorithm is based on a conventional Proportional-Integral-Derivative, in which its parameters are determined in a trial and error procedure. The second algorithm is based on optimal controllers. In this way, the difference between output alcohol concentration and desired value is minimized by flow rate manipulation. Minimization (optimization) is done based on the MARQYARDT procedure. The advantages of this method over the conventional Proportional-Integral-Derivative controller are its higher speed and lack of overshoot
Estimation and control of dynamical systems
Bensoussan, Alain
This book provides a comprehensive presentation of classical and advanced topics in estimation and control of dynamical systems with an emphasis on stochastic control. Many aspects which are not easily found in a single text are provided, such as connections between control theory and mathematical finance, as well as differential games. The book is self-contained and prioritizes concepts rather than full rigor, targeting scientists who want to use control theory in their research in applied mathematics, engineering, economics, and management science. Examples and exercises are included throughout, which will be useful for PhD courses and graduate courses in general. Dr. Alain Bensoussan is Lars Magnus Ericsson Chair at UT Dallas and Director of the International Center for Decision and Risk Analysis which develops risk management research as it pertains to large-investment industrial projects that involve new technologies, applications and markets. He is also Chair Professor at City University Hong Kong.
Dynamics and control in nuclear power stations
International Nuclear Information System (INIS)
Butterfield, M.H.
This volume presents a wide view of aspects of control of nuclear power stations by taking into consideration the plant as a whole and the protection systems employed therein. Authors with worldwide experience consider all aspects of dynamics and control in the context of both fast and thermal power stations. The topics discussed include the methods of development and applications within the analysis of plant behaviour, the validation of mathematical models, plant testing, and the design and implementation of controls. There are 27 papers all of which are indexed separately; steady states and model evolution (5 papers), control and protection systems (5 papers), transients (7 papers), testing and data (3 papers), model validation (6 papers) and commissioning and operation (1 paper). (author)
Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases
Directory of Open Access Journals (Sweden)
Juan A. González-Vera
Full Text Available Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
Aircraft Landing and Attitude Control Using Dynamic Matrix Control
Directory of Open Access Journals (Sweden)
George Cristian Calugaru
Full Text Available This paper proposes a method for an efficient control of the aircraft landing and attitude through Dynamic Matrix Control. The idea of MPC structures used in aircraft control has been well established during the last few years, but some aspects require further investigation. With this in mind, the paper proposes structures for aircraft landing and aircraft attitude control by using single DMC controllers for landing and respectively one DMC controller for each of the attitude axis (pitch attitude hold, bank angle hold and heading hold. The model used for analysis of the aircraft landing structure is based on the last phase of landing. Also, the model used to illustrate the attitude control is that of a pitch attitude hold system of a N250-100 aircraft. Simulations are performed for a variety of control and prediction horizons, taking into account the possibility of adding a weighting factor for the control actions. Apart from separate studies on step reference variations, for some use cases, a generic reference trajectory is provided as a control purpose of the system. Results show a better performance of the proposed method in terms of control surface transition and protection of the actuators involved and a better time response in stabilizing the aircraft attitude. Overall, the aspects shown ensure an improved aircraft attitude control and landing stabilization.
Polyubiquitin chain assembly and organisation determine the dynamics of protein activation and degradation
Directory of Open Access Journals (Sweden)
Lan K. Nguyen
Full Text Available Protein degradation via ubiquitination is a major proteolytic mechanism in cells. Once a protein is destined for degradation, it is tagged by multiple ubiquitin molecules. The synthesised polyubiquitin chains can be recognised by the 26S proteosome where proteins are degraded. These chains form through multiple ubiquitination cycles that are similar to multi-site phosphorylation cycles. As kinases and phosphatases, two opposing enzymes (E3 ligases and deubiquitinases DUBs catalyse (deubiquitination cycles. Although multi-ubiquitination cycles are fundamental mechanisms of controlling protein concentrations within a cell, their dynamics have never been explored. Here, we fill this knowledge gap. We show that under permissive physiological conditions, the formation of polyubiquitin chain of length greater than two and subsequent degradation of the ubiquitinated protein, which is balanced by protein synthesis, can display bistable, switch-like responses. Interestingly, the occurrence of bistability becomes pronounced, as the chain grows, giving rise to all-or-none regulation at the protein levels. We give predictions of protein distributions under bistable regime awaiting experimental verification. Importantly, we show for the first time that sustained oscillations can robustly arise in the process of formation of ubiquitin chain, largely due to the degradation of the target protein. This new feature is opposite to the properties of multi-site phosphorylation cycles, which are incapable of generating oscillation if the total abundance of interconverted protein forms is conserved. We derive structural and kinetic constraints for the emergence of oscillations, indicating that a competition between different substrate forms and the E3 and DUB is critical for oscillation. Our work provides the first detailed elucidation of the dynamical features brought about by different molecular setups of the polyubiquitin chain assembly process responsible for
ProteinAC: a frequency domain technique for analyzing protein dynamics
Bozkurt Varolgunes, Yasemin; Demir, Alper
It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.
A dual small-molecule rheostat for precise control of protein concentration in Mammalian cells.
Lin, Yu Hsuan; Pratt, Matthew R
One of the most successful strategies for controlling protein concentrations in living cells relies on protein destabilization domains (DD). Under normal conditions, a DD will be rapidly degraded by the proteasome. However, the same DD can be stabilized or "shielded" in a stoichiometric complex with a small molecule, enabling dose-dependent control of its concentration. This process has been exploited by several labs to post-translationally control the expression levels of proteins in vitro as well as in vivo, although the previous technologies resulted in permanent fusion of the protein of interest to the DD, which can affect biological activity and complicate results. We previously reported a complementary strategy, termed traceless shielding (TShld), in which the protein of interest is released in its native form. Here, we describe an optimized protein concentration control system, TTShld, which retains the traceless features of TShld but utilizes two tiers of small molecule control to set protein concentrations in living cells. These experiments provide the first protein concentration control system that results in both a wide range of protein concentrations and proteins free from engineered fusion constructs. The TTShld system has a greatly improved dynamic range compared to our previously reported system, and the traceless feature is attractive for elucidation of the consequences of protein concentration in cell biology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.
Choy, Meng S; Li, Yang; Machado, Luciana E S F; Kunze, Micha B A; Connors, Christopher R; Wei, Xingyu; Lindorff-Larsen, Kresten; Page, Rebecca; Peti, Wolfgang
Protein function originates from a cooperation of structural rigidity, dynamics at different timescales, and allostery. However, how these three pillars of protein function are integrated is still only poorly understood. Here we show how these pillars are connected in Protein Tyrosine Phosphatase 1B (PTP1B), a drug target for diabetes and cancer that catalyzes the dephosphorylation of numerous substrates in essential signaling pathways. By combining new experimental and computational data on WT-PTP1B and ≥10 PTP1B variants in multiple states, we discovered a fundamental and evolutionarily conserved CH/π switch that is critical for positioning the catalytically important WPD loop. Furthermore, our data show that PTP1B uses conformational and dynamic allostery to regulate its activity. This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function. Copyright © 2017 Elsevier Inc. All rights reserved.
The BOXES Methodology Black Box Dynamic Control
Russell, David W
Robust control mechanisms customarily require knowledge of the system's describing equations which may be of the high order differential type. In order to produce these equations, mathematical models can often be derived and correlated with measured dynamic behavior. There are two flaws in this approach one is the level of inexactness introduced by linearizations and the other when no model is apparent. Several years ago a new genre of control systems came to light that are much less dependent on differential models such as fuzzy logic and genetic algorithms. Both of these soft computing solutions require quite considerable a priori system knowledge to create a control scheme and sometimes complicated training program before they can be implemented in a real world dynamic system. Michie and Chambers' BOXES methodology created a black box system that was designed to control a mechanically unstable system with very little a priori system knowledge, linearization or approximation. All the method need...
Dynamic Parameter-Control Chaotic System.
Hua, Zhongyun; Zhou, Yicong
This paper proposes a general framework of 1-D chaotic maps called the dynamic parameter-control chaotic system (DPCCS). It has a simple but effective structure that uses the outputs of a chaotic map (control map) to dynamically control the parameter of another chaotic map (seed map). Using any existing 1-D chaotic map as the control/seed map (or both), DPCCS is able to produce a huge number of new chaotic maps. Evaluations and comparisons show that chaotic maps generated by DPCCS are very sensitive to their initial states, and have wider chaotic ranges, better unpredictability and more complex chaotic behaviors than their seed maps. Using a chaotic map of DPCCS as an example, we provide a field-programmable gate array design of this chaotic map to show the simplicity of DPCCS in hardware implementation, and introduce a new pseudo-random number generator (PRNG) to investigate the applications of DPCCS. Analysis and testing results demonstrate the excellent randomness of the proposed PRNG.
Adaptive Dynamic Surface Control for Generator Excitation Control System
Directory of Open Access Journals (Sweden)
Zhang Xiu-yu
Full Text Available For the generator excitation control system which is equipped with static var compensator (SVC and unknown parameters, a novel adaptive dynamic surface control scheme is proposed based on neural network and tracking error transformed function with the following features: (1 the transformation of the excitation generator model to the linear systems is omitted; (2 the prespecified performance of the tracking error can be guaranteed by combining with the tracking error transformed function; (3 the computational burden is greatly reduced by estimating the norm of the weighted vector of neural network instead of the weighted vector itself; therefore, it is more suitable for the real time control; and (4 the explosion of complicity problem inherent in the backstepping control can be eliminated. It is proved that the new scheme can make the system semiglobally uniformly ultimately bounded. Simulation results show the effectiveness of this control scheme.
Protein Availability and Satellite Cell Dynamics in Skeletal Muscle.
Shamim, Baubak; Hawley, John A; Camera, Donny M
Human skeletal muscle satellite cells are activated in response to both resistance and endurance exercise. It was initially proposed that satellite cell proliferation and differentiation were only required to support resistance exercise-induced hypertrophy. However, satellite cells may also play a role in muscle fibre remodelling after endurance-based exercise and extracellular matrix regulation. Given the importance of dietary protein, particularly branched chain amino acids, in supporting myofibrillar and mitochondrial adaptations to both resistance and endurance-based training, a greater understanding of how protein intake impacts satellite cell activity would provide further insight into the mechanisms governing skeletal muscle remodelling with exercise. While many studies have investigated the capacity for protein ingestion to increase post-exercise rates of muscle protein synthesis, few investigations have examined the role for protein ingestion to modulate satellite cell activity. Here we review the molecular mechanisms controlling the activation of satellite cells in response to mechanical stress and protein intake in both in vitro and in vivo models. We provide a mechanistic framework that describes how protein ingestion may enhance satellite activity and promote exercise adaptations in human skeletal muscle.
Fast dynamics perturbation analysis for prediction of protein functional sites
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Cohn Judith D
Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.
Wake flow control using a dynamically controlled wind turbine
Castillo, Ricardo; Wang, Yeqin; Pol, Suhas; Swift, Andy; Hussain, Fazle; Westergaard, Carsten; Texas Tech University Team
A wind tunnel based "Hyper Accelerated Wind Farm Kinematic-Control Simulator" (HAWKS) is being built at Texas Tech University to emulate controlled wind turbine flow physics. The HAWKS model turbine has pitch, yaw and speed control which is operated in real model time, similar to that of an equivalent full scale turbine. Also, similar to that of a full scale wind turbine, the controls are developed in a Matlab Simulink environment. The current diagnostic system consists of power, rotor position, rotor speed measurements and PIV wake characterization with four cameras. The setup allows up to 7D downstream of the rotor to be mapped. The purpose of HAWKS is to simulate control strategies at turnaround times much faster than CFD and full scale testing. The fundamental building blocks of the simulator have been tested, and demonstrate wake steering for both static and dynamic turbine actuation. Parameters which have been studied are yaw, rotor speed and combinations hereof. The measured wake deflections for static yaw cases are in agreement with previously reported research implying general applicability of the HAWKS platform for the purpose of manipulating the wake. In this presentation the general results will be introduced followed by an analysis of the wake turbulence and coherent structures when comparing static and dynamic flow cases. The outcome of such studies could ultimately support effective wind farm wake flow control strategies. Texas Emerging Technology Fund (ETF).
Dynamic principle for ensemble control tools.
Samoletov, A; Vasiev, B
Dynamical equations describing physical systems in contact with a thermal bath are commonly extended by mathematical tools called "thermostats." These tools are designed for sampling ensembles in statistical mechanics. Here we propose a dynamic principle underlying a range of thermostats which is derived using fundamental laws of statistical physics and ensures invariance of the canonical measure. The principle covers both stochastic and deterministic thermostat schemes. Our method has a clear advantage over a range of proposed and widely used thermostat schemes that are based on formal mathematical reasoning. Following the derivation of the proposed principle, we show its generality and illustrate its applications including design of temperature control tools that differ from the Nosé-Hoover-Langevin scheme.
Nonsmooth mechanics models, dynamics and control
Brogliato, Bernard
Now in its third edition, this standard reference is a comprehensive treatment of nonsmooth mechanical systems refocused to give more prominence to control and modelling. It covers Lagrangian and Newton–Euler systems, detailing mathematical tools such as convex analysis and complementarity theory. The ways in which nonsmooth mechanics influence and are influenced by well-posedness analysis, numerical analysis and simulation, modelling and control are explained. Contact/impact laws, stability theory and trajectory-tracking control are given in-depth exposition connected by a framework formed from complementarity systems and measure-differential inclusions. Links are established with electrical circuits with set-valued nonsmooth elements and with other nonsmooth dynamical systems like impulsive and piecewise linear systems. Nonsmooth Mechanics (third edition) has been substantially rewritten, edited and updated to account for the significant body of results that have emerged in the twenty-first century—incl...
Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.
Wako, Hiroshi; Endo, Shigeru
Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo- and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.
Application of Solution NMR Spectroscopy to Study Protein Dynamics
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Christoph Göbl
Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.
Duplicate retention in signalling proteins and constraints from network dynamics.
Soyer, O S; Creevey, C J
Duplications are a major driving force behind evolution. Most duplicates are believed to fix through genetic drift, but it is not clear whether this process affects all duplications equally or whether there are certain gene families that are expected to show neutral expansions under certain circumstances. Here, we analyse the neutrality of duplications in different functional classes of signalling proteins based on their effects on response dynamics. We find that duplications involving intermediary proteins in a signalling network are neutral more often than those involving receptors. Although the fraction of neutral duplications in all functional classes increase with decreasing population size and selective pressure on dynamics, this effect is most pronounced for receptors, indicating a possible expansion of receptors in species with small population size. In line with such an expectation, we found a statistically significant increase in the number of receptors as a fraction of genome size in eukaryotes compared with prokaryotes. Although not confirmative, these results indicate that neutral processes can be a significant factor in shaping signalling networks and affect proteins from different functional classes differently. © 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology.
A comparative molecular dynamics study on thermostability of human and chicken prion proteins
International Nuclear Information System (INIS)
Ji, Hong-Fang; Zhang, Hong-Yu
To compare the thermostabilities of human and chicken normal cellular prion proteins (HuPrP C and CkPrP C ), molecular dynamics (MD) simulations were performed for both proteins at an ensemble level (10 parallel simulations at 400 K and 5 parallel simulations at 300 K as a control). It is found that the thermostability of HuPrP C is comparable with that of CkPrP C , which implicates that the non-occurrence of prion diseases in non-mammals cannot be completely attributed to the thermodynamic properties of non-mammalian PrP C
Transformable ferroelectric control of dynamic magnetic permeability
Jiang, Changjun; Jia, Chenglong; Wang, Fenglong; Zhou, Cai; Xue, Desheng
Magnetic permeability, which measures the response of a material to an applied magnetic field, is crucial to the performance of magnetic devices and related technologies. Its dynamic value is usually a complex number with real and imaginary parts that describe, respectively, how much magnetic power can be stored and lost in the material. Control of permeability is therefore closely related to energy redistribution within a magnetic system or energy exchange between magnetic and other degrees of freedom via certain spin-dependent interactions. To avoid a high power consumption, direct manipulation of the permeability with an electric field through magnetoelectric coupling leads to high efficiency and simple operation, but remains a big challenge in both the fundamental physics and material science. Here we report unambiguous evidence of ferroelectric control of dynamic magnetic permeability in a Co /Pb (Mg1/3Nb2/3) 0.7Ti0.3O3 (Co/PMN-PT) heterostructure, in which the ferroelectric PMN-PT acts as an energy source for the ferromagnetic Co film via an interfacial linear magnetoelectric interaction. The electric field tuning of the magnitude and line shape of the permeability offers a highly localized means of controlling magnetization with ultralow power consumption. Additionally, the emergence of negative permeability promises a new way of realizing functional nanoscale metamaterials with adjustable refraction index.
Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)
Bergasa-Caceres, Fernando; Rabitz, Herschel A.
A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.
Vaccinia complement control protein: Multi-functional protein and a ...
Indian Academy of Sciences (India)
naturally occurring antagonist of the proinflammatory cytokine IL-18. Another strategy used by ... receptors or binding proteins for tumour necrosis factor. (TNF) ... immune regulators, such as the viral IL-10 and vascular endothelial growth factor ...
Advances in dynamical systems and control
Zgurovsky, Mikhail
Focused on recent advances, this book covers theoretical foundations as well as various applications. It presents modern mathematical modeling approaches to the qualitative and numerical analysis of solutions for complex engineering problems in physics, mechanics, biochemistry, geophysics, biology and climatology. Contributions by an international team of respected authors bridge the gap between abstract mathematical approaches, such as applied methods of modern analysis, algebra, fundamental and computational mechanics, nonautonomous and stochastic dynamical systems on the one hand, and practical applications in nonlinear mechanics, optimization, decision making theory and control theory on the other. As such, the book will be of interest to mathematicians and engineers working at the interface of these fields. .
Cardea: Dynamic Access Control in Distributed Systems
Lepro, Rebekah
Modern authorization systems span domains of administration, rely on many different authentication sources, and manage complex attributes as part of the authorization process. This . paper presents Cardea, a distributed system that facilitates dynamic access control, as a valuable piece of an inter-operable authorization framework. First, the authorization model employed in Cardea and its functionality goals are examined. Next, critical features of the system architecture and its handling of the authorization process are then examined. Then the S A M L and XACML standards, as incorporated into the system, are analyzed. Finally, the future directions of this project are outlined and connection points with general components of an authorization system are highlighted.
Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.
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Kei Moritsugu
Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.
Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein.
Sharma, V K; Hayes, Douglas G; Urban, Volker S; O'Neill, Hugh M; Tyagi, M; Mamontov, E
Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. Here we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates that surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants' hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. This study
Dynamics of proteins at low temperatures: fibrous vs. globular
Foucat, L.; Renou, J.-P.; Tengroth, C.; Janssen, S.; Middendorf, H. D.
We have measured quasielastic neutron scattering from H2O-hydrated collagen and haemoglobin at Tτ>10 ps. Relative to haemoglobin, the 200-K dynamic transition is shifted upward by 20-25 K in collagen, and the T-dependence of m.-sq. displacements derived from Sqe(Q;T) suggests that in triple-helical systems there are three rather than two regimes: one up to around 120K (probably purely harmonic), an intermediate quasiharmonic region with a linear dependence up to 240K, followed by a steeper nonlinear rise similar to that in globular proteins.
Studying protein assembly with reversible Brownian dynamics of patchy particles
International Nuclear Information System (INIS)
Klein, Heinrich C. R.; Schwarz, Ulrich S.
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly
Studying protein assembly with reversible Brownian dynamics of patchy particles
Energy Technology Data Exchange (ETDEWEB)
Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: firstname.lastname@example.com [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.
Dynamics of protein aggregation and oligomer formation governed by secondary nucleation
Energy Technology Data Exchange (ETDEWEB)
Michaels, Thomas C. T., E-mail: firstname.lastname@example.com; Lazell, Hamish W.; Arosio, Paolo; Knowles, Tuomas P. J., E-mail: email@example.com [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.
Dynamic Stall Control Using Plasma Actuators
Webb, Nathan; Singhal, Achal; Castaneda, David; Samimy, Mo
Dynamic stall occurs in many applications, including sharp maneuvers of fixed wing aircraft, wind turbines, and rotorcraft and produces large unsteady aerodynamic loads that can lead to flutter and mechanical failure. This work uses flow control to reduce the unsteady loads by excitation of instabilities in the shear layer over the separated region using nanosecond pulse driven dielectric barrier discharge (NS-DBD) plasma actuators. These actuators have been shown to effectively delay or mitigate static stall. A wide range of flow parameters were explored in the current work: Reynolds number (Re = 167,000 to 500,000), reduced frequency (k = 0.025 to 0.075), and excitation Strouhal number (Ste = 0 to 10). Based on the results, three major conclusions were drawn: (a) Low Strouhal number excitation (Ste <0.5) results in oscillatory aerodynamic loads in the stalled stage of dynamic stall; (b) All excitation resulted in earlier flow reattachment; and (c) Excitation at progressively higher Ste weakened and eventually eliminated the dynamic stall vortex (DSV), thereby dramatically reducing the unsteady loading. The decrease in the strength of the DSV is achieved by the formation of shear layer coherent structures that bleed the leading-edge vorticity prior to the ejection of the DSV.
Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins
Chun, Chan; Haohua, Wen; Lanyuan, Lu; Jun, Fan
Membrane curvature is no longer thought of as a passive property of the membrane; rather, it is considered as an active, regulated state that serves various purposes in the cell such as between cells and organelle definition. While transport is usually mediated by tiny membrane bubbles known as vesicles or membrane tubules, such communication requires complex interplay between the lipid bilayers and cytosolic proteins such as members of the Bin/Amphiphysin/Rvs (BAR) superfamily of proteins. With rapid developments in novel experimental techniques, membrane remodeling has become a rapidly emerging new field in recent years. Molecular dynamics (MD) simulations are important tools for obtaining atomistic information regarding the structural and dynamic aspects of biological systems and for understanding the physics-related aspects. The availability of more sophisticated experimental data poses challenges to the theoretical community for developing novel theoretical and computational techniques that can be used to better interpret the experimental results to obtain further functional insights. In this review, we summarize the general mechanisms underlying membrane remodeling controlled or mediated by proteins. While studies combining experiments and molecular dynamics simulations recall existing mechanistic models, concurrently, they extend the role of different BAR domain proteins during membrane remodeling processes. We review these recent findings, focusing on how multiscale molecular dynamics simulations aid in understanding the physical basis of BAR domain proteins, as a representative of membrane-remodeling proteins. Project supported by the National Natural Science Foundation of China (Grant No. 21403182) and the Research Grants Council of Hong Kong, China (Grant No. CityU 21300014).
Classical-driving-assisted entanglement dynamics control
Energy Technology Data Exchange (ETDEWEB)
Zhang, Ying-Jie, E-mail: email@example.com [Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, Department of Physics, Qufu Normal University, Qufu 273165 (China); Han, Wei [Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, Department of Physics, Qufu Normal University, Qufu 273165 (China); Xia, Yun-Jie, E-mail: firstname.lastname@example.com [Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, Department of Physics, Qufu Normal University, Qufu 273165 (China); Fan, Heng, E-mail: firstname.lastname@example.com [Beijing National Laboratory of Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing, 100190 (China)
We propose a scheme of controlling entanglement dynamics of a quantum system by applying the external classical driving field for two atoms separately located in a single-mode photon cavity. It is shown that, with a judicious choice of the classical-driving strength and the atom–photon detuning, the effective atom–photon interaction Hamiltonian can be switched from Jaynes–Cummings model to anti-Jaynes–Cummings model. By tuning the controllable atom–photon interaction induced by the classical field, we illustrate that the evolution trajectory of the Bell-like entanglement states can be manipulated from entanglement-sudden-death to no-entanglement-sudden-death, from no-entanglement-invariant to entanglement-invariant. Furthermore, the robustness of the initial Bell-like entanglement can be improved by the classical driving field in the leaky cavities. This classical-driving-assisted architecture can be easily extensible to multi-atom quantum system for scalability.
Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex
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Lisa M. Tuttle
Full Text Available Summary: Transcription activation domains (ADs are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. : Tuttle et al. report a "fuzzy free-for-all" interaction mechanism that explains how seemingly unrelated transcription activators converge on a limited number of coactivator targets. The mechanism provides a rationale for the observation that individually weak and low-specificity interactions can combine to produce biologically critical function without requiring highly ordered structure. Keywords: transcription activation, intrinsically disordered proteins, fuzzy binding
NASA Armstrong Flight Research Center Dynamics and Controls Branch
Jacobson, Steve
NASA Armstrong continues its legacy of exciting work in the area of Dynamics and Control of advanced vehicle concepts. This presentation describes Armstrongs research in control of flexible structures, peak seeking control and adaptive control in the Spring of 2015.
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
Directory of Open Access Journals (Sweden)
Aboul-Magd Mohammed O
Full Text Available Abstract Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures from primary sequence data which makes use of Parallel Cascade Identification (PCI, a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at http://bioinf.sce.carleton.ca/PCISS. In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input
Prediction of methyl-side Chain Dynamics in Proteins
International Nuclear Information System (INIS)
Ming Dengming; Brueschweiler, Rafael
A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S 2 order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S 2 order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S 2 values with an average correlation coefficient r-bar=0.65±0.14. For the unusually rigid cytochrome c 2 no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism
Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity
Digman, Michelle
Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.
Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex.
Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda; Luo, Jie; Ranish, Jeff; Hahn, Steven; Klevit, Rachel E
Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
Dynamic control of knee axial deformities
Directory of Open Access Journals (Sweden)
E. E. Malyshev
Full Text Available The authors have evaluated the clinical examination of the patients with axial malalignments in the knee by the original method and device which was named varovalgometer. The measurements were conducted by tension of the cord through the spina iliaca anterior superior and the middle of the lower pole of patella. The deviation of the center of the ankle estimated by metal ruler which was positioned perpendicular to the lower leg axis on the level of the ankle joint line. The results of comparison of our method and computer navigation in 53 patients during the TKA show no statistically significant varieties but they differ by average 5° of valgus in clinical examination in comparison with mechanical axis which was identified by computer navigation. The dynamic control of axial malalignment can be used in clinical practice for estimation of the results of treatment of pathology with axial deformities in the knee; for the control of reduction and secondary displacement of the fractures around the knee; for assessment of instability; in planning of correctional osteotomies and intraoperative control of deformity correction; for estimation of Q angle in subluxation and recurrent dislocation of patella; in planning of TKA; during the growth of child it allows to assess the progression of deformity.
Experimental targeting of chaos via controlled symbolic dynamics
International Nuclear Information System (INIS)
Corron, Ned J.; Pethel, Shawn D.
In this Letter, we report experimental targeting in a chaotic system by controlling symbolic dynamics. We acquire and control an electronic circuit using small perturbations to elicit a desired objective state starting from an arbitrary, uncontrolled state. The control perturbations are calculated using a symbolic targeting sequence and applied using dynamic limiting control
Dynamics and control of electrical drives
Energy Technology Data Exchange (ETDEWEB)
Wach, Piotr [Politechnika Opolska, Opole (Poland). Inst. of Electromechanical Systems and Applied Informatics
Dynamics is a science concerned with movement and changes. In the most general approach it relates to life processes as well as behavior in nature in rest. It governs small particles, technical objects, conversion of matter and materials but also concerns people, groups of people in their individual and, in particular, social dimension. In dynamics we always have to do with causes or stimuli for motion, the rules of reaction or behavior and its result in the form of trajectory of changes. This book is devoted to dynamics of a wide class of specific but very important objects such as electromechanical systems. This is a very rigorous discipline and has a long tradition, as its theoretical bases were formulated in the first half of the XIX century by d' Alembert, Lagrange, Hamilton, Maxwell and other prominent scientists, but their crucial results were based on previous pioneering research of others such as Copernicus, Galileo, Newton..This book in its theoretical foundations is based on the principle of least action which governs classical as well as relativistic mechanics and electromagnetism and leads to Lagrange's equations which are applied in the book as universal method to construct equations of motion of electromechanical systems. It gives common and coherent grounds to formulate mathematical models for all lumped parameters' electromechanical systems, which are vital in our contemporary industry and civilized everyday life. From these remarks it seems that the book is general and theoretical but in fact it is a very practical one concerning modern electrical drives in a broad sense, including electromechanical energy conversion, induction motor drives, brushless DC drives with a permanent magnet excitation and switched reluctance machines (SRM). And of course their control, which means shaping of their trajectories of motion using modern tools, their designed autonomy in keeping a track according to our programmed expectations. The problems
Dynamics of proteins and of their hydration layer studied by neutron scattering and additional biophysical methods
International Nuclear Information System (INIS)
Gallat, Francois-Xavier
This thesis work focused on the dynamics of proteins, surrounded by their hydration layer, a water shell around the protein vital for its biological function. Each of these components is accompanied by a specific dynamics which union reforms the complex energy landscape of the system. The joint implementation of selective deuteration, incoherent neutron scattering and tera-hertz spectroscopy allowed to explore the dynamics of proteins and that of the hydration shell. The influence of the folding state of protein on its dynamics has been studied by elastic neutron scattering. Globular proteins were less dynamic than its intrinsically disordered analogues. Themselves appear to be stiffer than non-physiological unfolded proteins. The oligomerization state and the consequences on the dynamics were investigated. Aggregates of a globular protein proved to be more flexible than the soluble form. In contrast, aggregates of a disordered protein showed lower average dynamics compared to the soluble form. These observations demonstrate the wide range of dynamics among the proteome. Incoherent neutron scattering experiences on the hydration layer of globular and disordered proteins have yielded information on the nature of water motion around these proteins. The measurements revealed the presence of translational motions concomitant with the onset of the transition dynamics of hydration layers, at 220 K. Measurements have also shown a stronger coupling between a disordered protein and its hydration water, compared to a globular protein and its hydration shell. The nature of the hydration layer and its influence on its dynamics has been explored with the use of polymers that mimic the water behavior and that act as a source of flexibility for the protein. Eventually, the dynamics of methyl groups involved in the dynamical changes observed at 150 and 220 K, was investigated. (author) [fr
Protein-membrane interaction: effect of myelin basic protein on the dynamics of oriented lipids
Energy Technology Data Exchange (ETDEWEB)
Natali, F.; Relini, A.; Gliozzi, A.; Rolandi, R.; Cavatorta, P.; Deriu, A.; Fasano, A.; Riccio, P
We have studied the effect of physiological amounts of myelin basic protein (MBP) on pure dimyristoyl L-{alpha}-phosphatidic acid (DMPA) oriented membranes. The investigation has been carried out using several complementary experimental methods to provide a detailed characterization of the proteo-lipid complexes. In particular, taking advantage of the power of the quasi-elastic neutron scattering (QENS) technique as optimal probe in biology, a significant effect is suggested to be induced by MBP on the anisotropy of lipid dynamics across the liquid-gel phase transition. Thus, the enhancement of the spatially restricted, vertical translation motion of DMPA is suggested to be the main responsible for the increased contribution of the out of plane lipid dynamics observed at 340 K.
Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin☆
Roche, Camille J.; Dantsker, David; Heller, Elizabeth R.; Sabat, Joseph E.; Friedman, Joel M.
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to mani...
Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5
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Inger Lindin
Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.
Mitogen-activated protein kinase (MAPK) dynamics determine cell fate in the yeast mating response.
Li, Yang; Roberts, Julie; AkhavanAghdam, Zohreh; Hao, Nan
In the yeast Saccharomyces cerevisiae , the exposure to mating pheromone activates a prototypic mitogen-activated protein kinase (MAPK) cascade and triggers a dose-dependent differentiation response. Whereas a high pheromone dose induces growth arrest and formation of a shmoo-like morphology in yeast cells, lower pheromone doses elicit elongated cell growth. Previous population-level analysis has revealed that the MAPK Fus3 plays an important role in mediating this differentiation switch. To further investigate how Fus3 controls the fate decision process at the single-cell level, we developed a specific translocation-based reporter for monitoring Fus3 activity in individual live cells. Using this reporter, we observed strikingly different dynamic patterns of Fus3 activation in single cells differentiated into distinct fates. Cells committed to growth arrest and shmoo formation exhibited sustained Fus3 activation. In contrast, most cells undergoing elongated growth showed either a delayed gradual increase or pulsatile dynamics of Fus3 activity. Furthermore, we found that chemically perturbing Fus3 dynamics with a specific inhibitor could effectively redirect the mating differentiation, confirming the causative role of Fus3 dynamics in driving cell fate decisions. MAPKs mediate proliferation and differentiation signals in mammals and are therapeutic targets in many cancers. Our results highlight the importance of MAPK dynamics in regulating single-cell responses and open up the possibility that MAPK signaling dynamics could be a pharmacological target in therapeutic interventions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Brownian dynamics of a protein-polymer chain complex in a solid-state nanopore
Wells, Craig C.; Melnikov, Dmitriy V.; Gracheva, Maria E.
We study the movement of a polymer attached to a large protein inside a nanopore in a thin silicon dioxide membrane submerged in an electrolyte solution. We use Brownian dynamics to describe the motion of a negatively charged polymer chain of varying lengths attached to a neutral protein modeled as a spherical bead with a radius larger than that of the nanopore, allowing the chain to thread the nanopore but preventing it from translocating. The motion of the protein-polymer complex within the pore is also compared to that of a freely translocating polymer. Our results show that the free polymer's standard deviations in the direction normal to the pore axis is greater than that of the protein-polymer complex. We find that restrictions imposed by the protein, bias, and neighboring chain segments aid in controlling the position of the chain in the pore. Understanding the behavior of the protein-polymer chain complex may lead to methods that improve molecule identification by increasing the resolution of ionic current measurements.
Dissecting the dynamic conformations of the metamorphic protein lymphotactin.
Harvey, Sophie R; Porrini, Massimiliano; Konijnenberg, Albert; Clarke, David J; Tyler, Robert C; Langridge-Smith, Patrick R R; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E
A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.
Biomolecular Modeling in a Process Dynamics and Control Course
Gray, Jeffrey J.
I present modifications to the traditional course entitled, "Process dynamics and control," which I renamed "Modeling, dynamics, and control of chemical and biological processes." Additions include the central dogma of biology, pharmacokinetic systems, population balances, control of gene transcription, and large-scale…
Steering the dynamics within reduced space through quantum learning control
International Nuclear Information System (INIS)
Kim, Young Sik
In quantum dynamics of many-body systems, to identify the Hamiltonian becomes more difficult very rapidly as the number of degrees of freedom increases. In order to simplify the dynamics and to deduce dynamically relevant Hamiltonian information, it is desirable to control the dynamics to lie within a reduced space. With a judicious choice for the cost functional, the closed loop optimal control experiments can be manipulated efficiently to steer the dynamics to lie within a subspace of the system eigenstates without requiring any prior detailed knowledge about the system Hamiltonian. The procedure is simulated for optimally controlled population transfer experiments in the system of two degrees of freedom. To show the feasibility of steering the dynamics to lie in a specified subspace, the learning algorithms guiding the dynamics are presented along with frequency filtering. The results demonstrate that the optimal control fields derive the system to the desired target state through the desired subspace
New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations
Directory of Open Access Journals (Sweden)
Yesylevskyy S. O.
Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed
Ubiquitin in signaling and protein quality control
DEFF Research Database (Denmark)
Al-Saoudi, Sofie Vincents
is related to the cancer-predisposition disease, Lynch syndrome. Of 24 different MSH2 variants, some of which have been linked to Lynch syndrome, we show that there is a strong correlation between the predicted structural stability and the protein half-life. We show that a predicted destabilization of 3 kcal....../mol is sufficient to cause proteasomal degradation of MSH2 variants. Importantly our calculations can, in addition to protein turnover, also predict pathogenicity of MSH2 variants, suggesting that this approach can be applied for Lynch syndrome diagnosis, and perhaps for other hereditary diseases....
Compressible dynamic stall vorticity flux control using a dynamic ...
Indian Academy of Sciences (India)
systems, such as a wind turbine, are prevented from ever entering dynamic stall, essentially disregarding potential ... future generations of such systems, an overwhelming need has developed to avail this benefit safely. ... approach must diffuse the vorticity prior to its coalescence, but keep the vorticity over the airfoil up to ...
Acetylation dynamics of human nuclear proteins during the ionizing radiation-induced DNA damage response
DEFF Research Database (Denmark)
Bennetzen, Martin; Andersen, J.S.; Lasen, D.H.
Genotoxic insults, such as ionizing radiation (IR), cause DNA damage that evokes a multifaceted cellular DNA damage response (DDR). DNA damage signaling events that control protein activity, subcellular localization, DNA binding, protein-protein interactions, etc. rely heavily on time...
Directory of Open Access Journals (Sweden)
Dechechi E.C.
Full Text Available A dynamic mathematical model, simulation and computer control of a Continuous Affinity Recycle Extraction (CARE process, a protein purification technique based on protein adsorption on solid-phase adsorbents is described in this work. This process, consisting of three reactors, is a multivariable process with considerable time delay in the on-line analyses of the controlled variable. An advanced predictive control configuration, specifically the Dynamic Matrix Control (DMC, was applied. The DMC algorithm was applied in process schemes where the aim was to maintain constant the enzyme concentration in the outlet of the third reactor. The performance of the DMC controller was analyzed in the feed-flow disturbances and the results are presented.
Dynamic cost control information system for nuclear power plant construction
International Nuclear Information System (INIS)
Wang Yongqing; Liu Wei
The authors first introduce the cost control functions of some overseas popular project management software at present and the specific ways of cost control of nuclear power plant construction in China. Then the authors stress the necessity of cost and schedule control integration and present the concept of dynamic cost control, the design scheme of dynamic cost control information system and the data structure modeling. Based on the above, the authors can develop the system which has the functions of dynamic estimate, cash flow management and cost optimization for nuclear engineering
Nitrogen control of photosynthetic protein synthesis
Energy Technology Data Exchange (ETDEWEB)
Schmidt, G.W.
Plant growth is severely affected by impaired photosynthesis resulting from nitrogen deficiency. The molecular aspects of this effect are being studied in the green alga Chlamydomonas grown in continuous culture systems. Photosynthetic membranes of nitrogen-limited cells are dramatically depleted in chlorophylls, xanthophylls and proteins of the light-harvesting complexes. In contrast, enzymes of the reductive pentose phosphate cycle and electron transport chain complexes are reduced only 40 to 65% on a per cell basis comparison with nitrogen-sufficient cultures. From analyses of mRNA levels by in vitro translation and hybridization analyses with cloned DNA sequences for photosynthetic proteins, we have found there are rather minor effects of nitrogen deficiency on nuclear or chloroplast gene transcription. Maturation of a transcript of the nuclear-encoded small subunit of ribulose 1,5-bisphosphate carboxylase is inhibited in nitrogen-deficient cells and causes accumulation of large amounts of mRNA precursors. Most of the effects of nitrogen deficiency on photosynthetic proteins appear to result from posttranscriptional regulatory processes: light-harvesting protein synthesis may be sustained but their import into chloroplasts or translocation to photosynthetic membranes is impaired. Nitrogen-deficient cells lack violaxanthin, a pigment that is essential for the structure, function and biogenesis of the major antenna complexes. The absence of this pigment may be a causative factor for the deficiency of light harvesting complexes. Finally, the accumulation of massive amounts of starch and triglycerides in nitrogen-limited cells indicate there are some genes whose maximal expression is dependent upon nitrogen-limiting conditions. 10 refs.
Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.
Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin
Roche, Camille J.; Dantsker, David; Heller, Elizabeth R.; Sabat, Joseph E.; Friedman, Joel M.
Hydration waters impact protein dynamics. Dissecting the interplay between hydration waters and dynamics requires a protein that manifests a broad range of dynamics. Proteins in reverse micelles (RMs) have promise as tools to achieve this objective because the water content can be manipulated. Hemoglobin is an appropriate tool with which to probe hydration effects. We describe both a protocol for hemoglobin encapsulation in reverse micelles and a facile method using PEG and cosolvents to manipulate water content. Hydration properties are probed using the water-sensitive fluorescence from Hb bound pyranine and covalently attached Badan. Protein dynamics are probed through ligand recombination traces derived from photodissociated carbonmonoxy hemoglobin on a log scale that exposes the potential role of both α and β solvent fluctuations in modulating protein dynamics. The results open the possibility of probing hydration level phenomena in this system using a combination of NMR and optical probes.
Control of striatal signaling by G protein regulators
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Keqiang eXie
Full Text Available Signaling via heterotrimeric G proteins plays a crucial role in modulating the responses of striatal neurons that ultimately shape core behaviors mediated by the basal ganglia circuitry, such as reward valuation, habit formation and movement coordination. Activation of G-protein-coupled receptors (GPCRs by extracellular signals activates heterotrimeric G proteins by promoting the binding of GTP to their α subunits. G proteins exert their effects by influencing the activity of key effector proteins in this region, including ion channels, second messenger enzymes and protein kinases. Striatal neurons express a staggering number of GPCRs whose activation results in the engagement of downstream signaling pathways and cellular responses with unique profiles but common molecular mechanisms. Studies over the last decade have revealed that the extent and duration of GPCR signaling are controlled by a conserved protein family named Regulator of G protein Signaling (RGS. RGS proteins accelerate GTP hydrolysis by the α subunits of G proteins, thus promoting deactivation of GPCR signaling. In this review, we discuss the progress made in understanding the roles of RGS proteins in controlling striatal G protein signaling and providing integration and selectivity of signal transmission. We review evidence on the formation of a macromolecular complex between RGS proteins and other components of striatal signaling pathways, their molecular regulatory mechanisms and impacts on GPCR signaling in the striatum obtained from biochemical studies and experiments involving genetic mouse models. Special emphasis is placed on RGS9-2, a member of the RGS family that is highly enriched in the striatum and plays critical roles in drug addiction and motor control.
Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein
International Nuclear Information System (INIS)
Asafi, M S; Tekpinar, M; Yildirim, A
Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)
Dynamic two-stage mechanism of versatile DNA damage recognition by xeroderma pigmentosum group C protein
Energy Technology Data Exchange (ETDEWEB)
Clement, Flurina C.; Camenisch, Ulrike; Fei, Jia; Kaczmarek, Nina; Mathieu, Nadine [Institute of Pharmacology and Toxicology, University of Zuerich-Vetsuisse, Winterthurerstrasse 260, CH-8057 Zuerich (Switzerland); Naegeli, Hanspeter, E-mail: email@example.com [Institute of Pharmacology and Toxicology, University of Zuerich-Vetsuisse, Winterthurerstrasse 260, CH-8057 Zuerich (Switzerland)
The recognition and subsequent repair of DNA damage are essential reactions for the maintenance of genome stability. A key general sensor of DNA lesions is xeroderma pigmentosum group C (XPC) protein, which recognizes a wide variety of helix-distorting DNA adducts arising from ultraviolet (UV) radiation, genotoxic chemicals and reactive metabolic byproducts. By detecting damaged DNA sites, this unique molecular sensor initiates the global genome repair (GGR) pathway, which allows for the removal of all the aforementioned lesions by a limited repertoire of excision factors. A faulty GGR activity causes the accumulation of DNA adducts leading to mutagenesis, carcinogenesis, neurological degeneration and other traits of premature aging. Recent findings indicate that XPC protein achieves its extraordinary substrate versatility by an entirely indirect readout strategy implemented in two clearly discernible stages. First, the XPC subunit uses a dynamic sensor interface to monitor the double helix for the presence of non-hydrogen-bonded bases. This initial screening generates a transient nucleoprotein intermediate that subsequently matures into the ultimate recognition complex by trapping undamaged nucleotides in the abnormally oscillating native strand, in a way that no direct contacts are made between XPC protein and the offending lesion itself. It remains to be elucidated how accessory factors like Rad23B, centrin-2 or the UV-damaged DNA-binding complex contribute to this dynamic two-stage quality control process.
Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control
Directory of Open Access Journals (Sweden)
Bing Li
Full Text Available In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.
Computational and biological characterization of fusion proteins of two insecticidal proteins for control of insect pests.
Javaid, Shaista; Naz, Sehrish; Amin, Imran; Jander, Georg; Ul-Haq, Zaheer; Mansoor, Shahid
Sucking pests pose a serious agricultural challenge, as available transgenic technologies such as Bacillus thuringiensis crystal toxins (Bt) are not effective against them. One approach is to produce fusion protein toxins for the control of these pests. Two protein toxins, Hvt (ω-atracotoxin from Hadronyche versuta) and onion leaf lectin, were translationally fused to evaluate the negative effects of fusion proteins on Phenacoccus solenopsis (mealybug), a phloem-feeding insect pest. Hvt was cloned both N-terminally (HL) and then C-terminally (LH) in the fusion protein constructs, which were expressed transiently in Nicotiana tabacum using a Potato Virus X (PVX) vector. The HL fusion protein was found to be more effective against P. solenopsis, with an 83% mortality rate, as compared to the LH protein, which caused 65% mortality. Hvt and lectin alone caused 42% and 45%, respectively, under the same conditions. Computational studies of both fusion proteins showed that the HL protein is more stable than the LH protein. Together, these results demonstrate that translational fusion of two insecticidal proteins improved the insecticidal activity relative to each protein individually and could be expressed in transgenic plants for effective control of sucking pests.
Anisotropic biodegradable lipid coated particles for spatially dynamic protein presentation.
Meyer, Randall A; Mathew, Mohit P; Ben-Akiva, Elana; Sunshine, Joel C; Shmueli, Ron B; Ren, Qiuyin; Yarema, Kevin J; Green, Jordan J
There has been growing interest in the use of particles coated with lipids for applications ranging from drug delivery, gene delivery, and diagnostic imaging to immunoengineering. To date, almost all particles with lipid coatings have been spherical despite emerging evidence that non-spherical shapes can provide important advantages including reduced non-specific elimination and increased target-specific binding. We combine control of core particle geometry with control of particle surface functionality by developing anisotropic, biodegradable ellipsoidal particles with lipid coatings. We demonstrate that these lipid coated ellipsoidal particles maintain advantageous properties of lipid polymer hybrid particles, such as the ability for modular protein conjugation to the particle surface using versatile bioorthogonal ligation reactions. In addition, they exhibit biomimetic membrane fluidity and demonstrate lateral diffusive properties characteristic of natural membrane proteins. These ellipsoidal particles simultaneously provide benefits of non-spherical particles in terms of stability and resistance to non-specific phagocytosis by macrophages as well as enhanced targeted binding. These biomaterials provide a novel and flexible platform for numerous biomedical applications. The research reported here documents the ability of non-spherical polymeric particles to be coated with lipids to form anisotropic biomimetic particles. In addition, we demonstrate that these lipid-coated biodegradable polymeric particles can be conjugated to a wide variety of biological molecules in a "click-like" fashion. This is of interest due to the multiple types of cellular mimicry enabled by this biomaterial based technology. These features include mimicry of the highly anisotropic shape exhibited by cells, surface presentation of membrane bound protein mimetics, and lateral diffusivity of membrane bound substrates comparable to that of a plasma membrane. This platform is demonstrated to
Magnetogenetic control of protein gradients inside living cells with high spatial and temporal resolution.
Etoc, Fred; Vicario, Chiara; Lisse, Domenik; Siaugue, Jean-Michel; Piehler, Jacob; Coppey, Mathieu; Dahan, Maxime
Tools for controlling the spatial organization of proteins are a major prerequisite for deciphering mechanisms governing the dynamic architecture of living cells. Here, we have developed a generic approach for inducing and maintaining protein gradients inside living cells by means of biofunctionalized magnetic nanoparticles (MNPs). For this purpose, we tailored the size and surface properties of MNPs in order to ensure unhindered mobility in the cytosol. These MNPs with a core diameter below 50 nm could be rapidly relocalized in living cells by exploiting biased diffusion at weak magnetic forces in the femto-Newton range. In combination with MNP surface functionalization for specific in situ capturing of target proteins as well as efficient delivery into the cytosplasm, we here present a comprehensive technology for controlling intracellular protein gradients with a temporal resolution of a few tens of seconds.
Coupled dynamic systems and Le Chatelier's principle in noise control
Maidanik, G.; Becker, K. J.
Investigation of coupling an externally driven dynamic system-a master dynamic system-to a passive one-an adjunct dynamic system-reveals that the response of the adjunct dynamic system affects the precoupled response of the master dynamic system. The responses, in the two dynamic systems when coupled, are estimated by the stored energies (Es) and (E0), respectively. Since the adjunct dynamic system, prior to coupling, was with zero (0) stored energy, E0s=0, the precoupled stored energy (E00) in the master dynamic system is expected to be reduced to (E0) when coupling is instituted; i.e., one expects E0
Advances in analysis and control of timedelayed dynamical systems
Sun, Jianqiao
Analysis and control of timedelayed systems have been applied in a wide range of applications, ranging from mechanical, control, economic, to biological systems. Over the years, there has been a steady stream of interest in timedelayed dynamic systems, this book takes a snap shot of recent research from the world leading experts in analysis and control of dynamic systems with time delay to provide a bird's eye view of its development. The topics covered in this book include solution methods, stability analysis and control of periodic dynamic systems with time delay, bifurcations, stochastic dy
Fragile X mental retardation protein: A paradigm for translational control by RNA-binding proteins.
Chen, Eileen; Joseph, Simpson
Translational control is a common mechanism used to regulate gene expression and occur in bacteria to mammals. Typically in translational control, an RNA-binding protein binds to a unique sequence in the mRNA to regulate protein synthesis by the ribosomes. Alternatively, a protein may bind to or modify a translation factor to globally regulate protein synthesis by the cell. Here, we review translational control by the fragile X mental retardation protein (FMRP), the absence of which causes the neurological disease, fragile X syndrome (FXS). Copyright © 2015 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.
Optimal control of HIV/AIDS dynamic: Education and treatment
Sule, Amiru; Abdullah, Farah Aini
A mathematical model which describes the transmission dynamics of HIV/AIDS is developed. The optimal control representing education and treatment for this model is explored. The existence of optimal Control is established analytically by the use of optimal control theory. Numerical simulations suggest that education and treatment for the infected has a positive impact on HIV/AIDS control.
Dynamic Primitives in the Control of Locomotion
Directory of Open Access Journals (Sweden)
Neville eHogan
Full Text Available Humans achieve locomotor dexterity that far exceeds the capability of modern robots, yet this is achieved despite slower actuators, imprecise sensors and vastly slower communication. We propose that this spectacular performance arises from encoding motor commands in terms of dynamic primitives. We propose three primitives as a foundation for a comprehensive theoretical framework that can embrace a wide range of upper- and lower-limb behaviors. Building on previous work that suggested discrete and rhythmic movements as elementary dynamic behaviors, we define submovements and oscillations: As discrete movements cannot be combined with sufficient flexibility, we argue that suitably-defined submovements are primitives. As the term rhythmic may be ambiguous, we define oscillations as the corresponding class of primitives. We further propose mechanical impedances as a third class of dynamic primitives, necessary for interaction with the physical environment. Combination of these three classes of primitive requires care. One approach is through a generalized equivalent network: a virtual trajectory composed of simultaneous and/or sequential submovements and/or oscillations that interacts with mechanical impedances to produce observable forces and motions. Reliable experimental identification of these dynamic primitives presents challenges: Identification of mechanical impedances is exquisitely sensitive to assumptions about their dynamic structure; identification of submovements and oscillations is sensitive to their assumed form and to details of the algorithm used to extract them. Some methods to address these challenges are presented. Some implications of this theoretical framework for locomotor rehabilitation are considered.
Dynamic primitives in the control of locomotion.
Hogan, Neville; Sternad, Dagmar
Humans achieve locomotor dexterity that far exceeds the capability of modern robots, yet this is achieved despite slower actuators, imprecise sensors, and vastly slower communication. We propose that this spectacular performance arises from encoding motor commands in terms of dynamic primitives. We propose three primitives as a foundation for a comprehensive theoretical framework that can embrace a wide range of upper- and lower-limb behaviors. Building on previous work that suggested discrete and rhythmic movements as elementary dynamic behaviors, we define submovements and oscillations: as discrete movements cannot be combined with sufficient flexibility, we argue that suitably-defined submovements are primitives. As the term "rhythmic" may be ambiguous, we define oscillations as the corresponding class of primitives. We further propose mechanical impedances as a third class of dynamic primitives, necessary for interaction with the physical environment. Combination of these three classes of primitive requires care. One approach is through a generalized equivalent network: a virtual trajectory composed of simultaneous and/or sequential submovements and/or oscillations that interacts with mechanical impedances to produce observable forces and motions. Reliable experimental identification of these dynamic primitives presents challenges: identification of mechanical impedances is exquisitely sensitive to assumptions about their dynamic structure; identification of submovements and oscillations is sensitive to their assumed form and to details of the algorithm used to extract them. Some methods to address these challenges are presented. Some implications of this theoretical framework for locomotor rehabilitation are considered.
Flux control through protein phosphorylation in yeast
DEFF Research Database (Denmark)
Chen, Yu; Nielsen, Jens
Protein phosphorylation is one of the most important mechanisms regulating metabolism as it can directly modify metabolic enzymes by the addition of phosphate groups. Attributed to such a rapid and reversible mechanism, cells can adjust metabolism rapidly in response to temporal changes. The yeast...... as well as identify mechanisms underlying human metabolic diseases. Here we collect functional phosphorylation events of 41 enzymes involved in yeast metabolism and demonstrate functional mechanisms and the application of this information in metabolic engineering. From a systems biology perspective, we...... describe the development of phosphoproteomics in yeast as well as approaches to analysing the phosphoproteomics data. Finally, we focus on integrated analyses with other omics data sets and genome-scale metabolic models. Despite the advances, future studies improving both experimental technologies...
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins
DEFF Research Database (Denmark)
Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P
. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...
Directory of Open Access Journals (Sweden)
Osama Elshazly
Full Text Available In this paper, development of a reduced order, augmented dynamics-drive model that combines both the dynamics and drive subsystems of the skid steering mobile robot (SSMR is presented. A Linear Quadratic Regulator (LQR control algorithm with feed-forward compensation of the disturbances part included in the reduced order augmented dynamics-drive model is designed. The proposed controller has many advantages such as its simplicity in terms of design and implementation in comparison with complex nonlinear control schemes that are usually designed for this system. Moreover, the good performance is also provided by the controller for the SSMR comparable with a nonlinear controller based on the inverse dynamics which depends on the availability of an accurate model describing the system. Simulation results illustrate the effectiveness and enhancement provided by the proposed controller.
Dynamic Intelligent Feedback Scheduling in Networked Control Systems
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Hui-ying Chen
Full Text Available For the networked control system with limited bandwidth and flexible workload, a dynamic intelligent feedback scheduling strategy is proposed. Firstly, a monitor is used to acquire the current available network bandwidth. Then, the new available bandwidth in the next interval is predicted by using LS_SVM approach. At the same time, the dynamic performance indices of all control loops are obtained with a two-dimensional fuzzy logic modulator. Finally, the predicted network bandwidth is dynamically allocated by the bandwidth manager and the priority allocator in terms of the loops' dynamic performance indices. Simulation results show that the sampling periods and priorities of control loops are adjusted timely according to the network workload condition and the dynamic performance of control loops, which make the system running in the optimal state all the time.
Dynamical control of chaos by slave-master feedback
International Nuclear Information System (INIS)
Behnia, S.; Akhshani, A.
Techniques for stabilizing unstable state in nonlinear dynamical systems using small perturbations fall into three general categories: feedback, non-feedback schemes, and a combination of feedback and non-feedback. However, the general problem of finding conditions for creation or suppression of chaos still remains open. We describe a method for dynamical control of chaos. This method is based on a definition of the hierarchy of solvable chaotic maps with dynamical parameter as a control parameter. In order to study the new mechanism of control of chaotic process, Kolmogorov-Sinai entropy of the chaotic map with dynamical parameter based on discussion the properties of invariant measure have been calculated and confirmed by calculation of Lyapunov exponents. The introduced chaotic maps can be used as dynamical control.
Belt conveyor dynamics in transient operation for speed control
He, D.; Pang, Y.; Lodewijks, G.
Belt conveyors play an important role in continuous dry bulk material transport, especially at the mining industry. Speed control is expected to reduce the energy consumption of belt conveyors. Transient operation is the operation of increasing or decreasing conveyor speed for speed control. According to literature review, current research rarely takes the conveyor dynamics in transient operation into account. However, in belt conveyor speed control, the conveyor dynamic behaviors are signifi...
Dynamics and Control of a Flexible Solar Sail
Jiafu Liu; Siyuan Rong; Fan Shen; Naigang Cui
Solar sail can merely make use of solar radiation pressure (SRP) force as the thrust for space missions. The attitude dynamics is obtained for the highly flexible solar sail with control vanes, sliding masses, and a gimbaled control boom. The vibration equations are derived considering the geometric nonlinearity of the sail structure subjected to the forces generated by the control vanes, solar radiation pressure (SRP), and sliding masses. Then the dynamic models for attitude/vibration contr...
Chaos control of chaotic dynamical systems using backstepping design
International Nuclear Information System (INIS)
Yassen, M.T.
This work presents chaos control of chaotic dynamical systems by using backstepping design method. This technique is applied to achieve chaos control for each of the dynamical systems Lorenz, Chen and Lue systems. Based on Lyapunov stability theory, control laws are derived. We used the same technique to enable stabilization of chaotic motion to a steady state as well as tracking of any desired trajectory to be achieved in a systematic way. Numerical simulations are shown to verify the results
A hybrid total internal reflection fluorescence and optical tweezers microscope to study cell adhesion and membrane protein dynamics of single living cells
Snijder-van As, M.I.; Rieger, B.; Joosten, B.; Subramaniam, Vinod; Figdor, Carl; Kanger, Johannes S.
The dynamics of cell surface membrane proteins plays an important role in cell–cell interactions. The onset of the interaction is typically not precisely controlled by current techniques, making especially difficult the visualization of early-stage dynamics. We have developed a novel method where
The Quadrotor Dynamic Modeling and Indoor Target Tracking Control Method
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Dewei Zhang
Full Text Available A reliable nonlinear dynamic model of the quadrotor is presented. The nonlinear dynamic model includes actuator dynamic and aerodynamic effect. Since the rotors run near a constant hovering speed, the dynamic model is simplified at hovering operating point. Based on the simplified nonlinear dynamic model, the PID controllers with feedback linearization and feedforward control are proposed using the backstepping method. These controllers are used to control both the attitude and position of the quadrotor. A fully custom quadrotor is developed to verify the correctness of the dynamic model and control algorithms. The attitude of the quadrotor is measured by inertia measurement unit (IMU. The position of the quadrotor in a GPS-denied environment, especially indoor environment, is estimated from the downward camera and ultrasonic sensor measurements. The validity and effectiveness of the proposed dynamic model and control algorithms are demonstrated by experimental results. It is shown that the vehicle achieves robust vision-based hovering and moving target tracking control.
Quality control methodology for high-throughput protein-protein interaction screening.
Vazquez, Alexei; Rual, Jean-François; Venkatesan, Kavitha
Protein-protein interactions are key to many aspects of the cell, including its cytoskeletal structure, the signaling processes in which it is involved, or its metabolism. Failure to form protein complexes or signaling cascades may sometimes translate into pathologic conditions such as cancer or neurodegenerative diseases. The set of all protein interactions between the proteins encoded by an organism constitutes its protein interaction network, representing a scaffold for biological function. Knowing the protein interaction network of an organism, combined with other sources of biological information, can unravel fundamental biological circuits and may help better understand the molecular basics of human diseases. The protein interaction network of an organism can be mapped by combining data obtained from both low-throughput screens, i.e., "one gene at a time" experiments and high-throughput screens, i.e., screens designed to interrogate large sets of proteins at once. In either case, quality controls are required to deal with the inherent imperfect nature of experimental assays. In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens.
On the control of ribosomal protein biosynthesis in Escherichia coli
International Nuclear Information System (INIS)
Pichon, J.; Marvaldi, J.; Coeroli, C.; Cozzone, A.; Marchis-Mouren, G.
The rate of individual ribosomal protein synthesis relative to total protein synthesis has been determined in Escherichia coli rel + and rel - cells, under valyl-tRNA deprivation. These strains have a temperature-sensitive valyl-tRNA synthetase. Starvation was obtained following transfer of the cells to non-permissive temperature. Ribosomal proteins were obtained by treatment of either total lysates of freeze-thawed lysozyme spheroplasts or ammonium sulphate precipitate of ribosomes, with acetic acid. Differential labelling of the ribosomal proteins was observed in both strains: proteins from the rel + strain appear more labelled than those from the rel - strain, the rate of labelling of individual proteins being about the same in both strains. Moreover ribosomal proteins were found as stable during starvation as total protein. It is thus concluded that in starving cells individual ribosomal proteins are not synthesized at equal rates. This indicates that the synthesis of ribosomal proteins is not only under the control of the rel gene
Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation
Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
The conformational diversity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.
Identification of hierarchy of dynamic domains in proteins: comparison of HDWA and HCCP techniques
Directory of Open Access Journals (Sweden)
Yesylevskyy S. O.
Full Text Available Aim. There are several techniques for the identification of hierarchy of dynamic domains in proteins. The goal of this work is to compare systematically two recently developed techniques, HCCP and HDWA,on a set of proteins from diverse structural classes. Methods. HDWA and HCCP techniques are used. The HDWA technique is designed to identify hierarchically organized dynamic domains in proteins using the Molecular Dynamics (MD trajectories, while HCCP utilizes the normal modes of simplified elastic network models. Results. It is shown that the dynamic domains found by HDWA are consistent with the domains identified by HCCP and other techniques. At the same time HDWA identifies flexible mobile loops of proteins correctly, which is hard to achieve with other model-based domain identification techniques. Conclusion. HDWA is shown to be a powerful method of analysis of MD trajectories, which can be used in various areas of protein science.
Antitumor Immunity Is Controlled by Tetraspanin Proteins
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Fleur Schaper
Full Text Available Antitumor immunity is shaped by the different types of immune cells that are present in the tumor microenvironment (TME. In particular, environmental signals (for instance, soluble factors or cell–cell contact transmitted through the plasma membrane determine whether immune cells are activated or inhibited. Tetraspanin proteins are emerging as central building blocks of the plasma membrane by their capacity to cluster immune receptors, enzymes, and signaling molecules into the tetraspanin web. Whereas some tetraspanins (CD81, CD151, CD9 are widely and broadly expressed, others (CD53, CD37, Tssc6 have an expression pattern restricted to hematopoietic cells. Studies using genetic mouse models have identified important immunological functions of these tetraspanins on different leukocyte subsets, and as such, may be involved in the immune response against tumors. While multiple studies have been performed with regards to deciphering the function of tetraspanins on cancer cells, the effect of tetraspanins on immune cells in the antitumor response remains understudied. In this review, we will focus on tetraspanins expressed by immune cells and discuss their potential role in antitumor immunity. New insights in tetraspanin function in the TME and possible prognostic and therapeutic roles of tetraspanins will be discussed.
Identifying protein complex by integrating characteristic of core-attachment into dynamic PPI network.
Directory of Open Access Journals (Sweden)
Xianjun Shen
Full Text Available How to identify protein complex is an important and challenging task in proteomics. It would make great contribution to our knowledge of molecular mechanism in cell life activities. However, the inherent organization and dynamic characteristic of cell system have rarely been incorporated into the existing algorithms for detecting protein complexes because of the limitation of protein-protein interaction (PPI data produced by high throughput techniques. The availability of time course gene expression profile enables us to uncover the dynamics of molecular networks and improve the detection of protein complexes. In order to achieve this goal, this paper proposes a novel algorithm DCA (Dynamic Core-Attachment. It detects protein-complex core comprising of continually expressed and highly connected proteins in dynamic PPI network, and then the protein complex is formed by including the attachments with high adhesion into the core. The integration of core-attachment feature into the dynamic PPI network is responsible for the superiority of our algorithm. DCA has been applied on two different yeast dynamic PPI networks and the experimental results show that it performs significantly better than the state-of-the-art techniques in terms of prediction accuracy, hF-measure and statistical significance in biology. In addition, the identified complexes with strong biological significance provide potential candidate complexes for biologists to validate.
Structure-based control of complex networks with nonlinear dynamics.
Zañudo, Jorge Gomez Tejeda; Yang, Gang; Albert, Réka
What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.
Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.
Zhang, Lei; Andersen, Eskil M E; Khajo, Abdelahad; Magliozzo, Richard S; Koder, Ronald L
We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7, this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities, and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime that may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when exposed to oxygen. Compared to that of HP7, the distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off rate. Electron paramagnetic resonance comparison of these ferric hemoproteins demonstrates that the mutation increases the level of disorder at the heme binding site. Nuclear magnetic resonance-detected deuterium exchange demonstrates that the mutation greatly increases the degree of penetration of water into the protein core. The inability of the mutant protein to bind oxygen may be due to an increased level of water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together, these data underline the importance of the control of protein dynamics in the design of functional artificial proteins.
Controlling chitosan-based encapsulation for protein and vaccine delivery
Koppolu, Bhanu prasanth; Smith, Sean G.; Ravindranathan, Sruthi; Jayanthi, Srinivas; Kumar, Thallapuranam K.S.; Zaharoff, David A.
Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, was inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters. PMID:24560459
Controlled release and intracellular protein delivery from mesoporous silica nanoparticles.
Deodhar, Gauri V; Adams, Marisa L; Trewyn, Brian G
Protein therapeutics are promising candidates for disease treatment due to their high specificity and minimal adverse side effects; however, targeted protein delivery to specific sites has proven challenging. Mesoporous silica nanoparticles (MSN) have demonstrated to be ideal candidates for this application, given their high loading capacity, biocompatibility, and ability to protect host molecules from degradation. These materials exhibit tunable pore sizes, shapes and volumes, and surfaces which can be easily functionalized. This serves to control the movement of molecules in and out of the pores, thus entrapping guest molecules until a specific stimulus triggers release. In this review, we will cover the benefits of using MSN as protein therapeutic carriers, demonstrating that there is great diversity in the ways MSN can be used to service proteins. Methods for controlling the physical dimensions of pores via synthetic conditions, applications of therapeutic protein loaded MSN materials in cancer therapies, delivering protein loaded MSN materials to plant cells using biolistic methods, and common stimuli-responsive functionalities will be discussed. New and exciting strategies for controlled release and manipulation of proteins are also covered in this review. While research in this area has advanced substantially, we conclude this review with future challenges to be tackled by the scientific community. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Practical synchronization on complex dynamical networks via optimal pinning control
Li, Kezan; Sun, Weigang; Small, Michael; Fu, Xinchu
We consider practical synchronization on complex dynamical networks under linear feedback control designed by optimal control theory. The control goal is to minimize global synchronization error and control strength over a given finite time interval, and synchronization error at terminal time. By utilizing the Pontryagin's minimum principle, and based on a general complex dynamical network, we obtain an optimal system to achieve the control goal. The result is verified by performing some numerical simulations on Star networks, Watts-Strogatz networks, and Barabási-Albert networks. Moreover, by combining optimal control and traditional pinning control, we propose an optimal pinning control strategy which depends on the network's topological structure. Obtained results show that optimal pinning control is very effective for synchronization control in real applications.
Protein quality control in organelles - AAA/FtsH story.
Janska, Hanna; Kwasniak, Malgorzata; Szczepanowska, Joanna
This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids. Copyright © 2012 Elsevier B.V. All rights reserved.
Robot-Arm Dynamic Control by Computer
Bejczy, Antal K.; Tarn, Tzyh J.; Chen, Yilong J.
Feedforward and feedback schemes linearize responses to control inputs. Method for control of robot arm based on computed nonlinear feedback and state tranformations to linearize system and decouple robot end-effector motions along each of cartesian axes augmented with optimal scheme for correction of errors in workspace. Major new feature of control method is: optimal error-correction loop directly operates on task level and not on joint-servocontrol level.
Control of the Protein Turnover Rates in Lemna minor
Trewavas, A.
The control of protein turnover in Lemna minor has been examined using a method described in the previous paper for determining the rate constants of synthesis and degradation of protein. If Lemna is placed on water, there is a reduction in the rate constants of synthesis of protein and an increase (3- to 6-fold) in the rate constant of degradation. The net effect is a loss of protein from the tissue. Omission of nitrate, phosphate, sulfate, magnesium, or calcium results in increases in the rate constant of degradation of protein. An unusual dual effect of benzyladenine on the turnover constants has been observed. Treatment of Lemna grown on sucrose-mineral salts with benzyladenine results in alterations only in the rate constant of synthesis. Treatment of Lemna grown on water with benzyladenine alters only the rate constant of degradation. Abscisic acid on the other hand alters both rate constants of synthesis and degradation of protein together. Inclusion of growth-inhibiting amino acids in the medium results in a reduction in the rate constants of synthesis and increases in the rate constant of degradation of protein. It is concluded that the rate of turnover of protein in Lemna is very dependent on the composition of the growth medium. Conditions which reduce growth rates also reduce the rates of synthesis of protein and increase those of degradation. PMID:16657895
Dynamics and Controls of Swarms of Femtosatellites
National Aeronautics and Space Administration — The proposed research activity is focused on the development of fuel and computationally efficient guidance and control algorithms for spacecraft swarms. The...
Satellite Dynamic Damping via Active Force Control Augmentation
Varatharajoo, Renuganth
An approach that incorporates the Active Force Control (AFC) technique into a conventional Proportional-Derivative (PD) controller is proposed for a satellite active dynamic damping towards a full attitude control. The AFC method has been established to facilitate a robust motion control of dynamical systems in the presence of disturbances, parametric uncertainties and changes that are commonly prevalent in the real-world environment. The usefulness of the method can be extended by introducing intelligent mechanisms to approximate the mass or inertia matrix of the dynamic system to trigger the compensation effect of the controller. AFC is a technique that relies on the appropriate estimation of the inertial or mass parameters of the dynamic system and the measurements of the acceleration and force signals induced by the system if practical implementation is ever considered. In AFC, it is shown that the system subjected to a number of disturbances remains stable and robust via the compensating action of the control strategy. We demonstrate that it is possible to design a spacecraft attitude feedback controller that will ensure the system dynamics set point remains unchanged even in the presence of the disturbances provided that the actual disturbances can be modeled effectively. In order to further facilitate this analysis, a combined energy and attitude control system (CEACS) is proposed as a model satellite attitude control actuator. All the governing equations are established and the proposed satellite attitude control architecture is made amenable to numerical treatments. The results show that the PD-AFC attitude damping performances are superiorly better than that of the solely PD type. It is also shown that the tunings of the AFC system gains are crucial to ensure a better attitude damping performance and this process is mandatory for AFC systems. Finally, the results demonstrate an important satellite dynamic damping enhancement capability using the AFC
Adaptive pseudolinear compensators of dynamic characteristics of automatic control systems
Skorospeshkin, M. V.; Sukhodoev, M. S.; Timoshenko, E. A.; Lenskiy, F. V.
Adaptive pseudolinear gain and phase compensators of dynamic characteristics of automatic control systems are suggested. The automatic control system performance with adaptive compensators has been explored. The efficiency of pseudolinear adaptive compensators in the automatic control systems with time-varying parameters has been demonstrated.
A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.
Directory of Open Access Journals (Sweden)
Brittany Burton
Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.
Exercise training restores cardiac protein quality control in heart failure.
Directory of Open Access Journals (Sweden)
Juliane C Campos
Full Text Available Exercise training is a well-known coadjuvant in heart failure treatment; however, the molecular mechanisms underlying its beneficial effects remain elusive. Despite the primary cause, heart failure is often preceded by two distinct phenomena: mitochondria dysfunction and cytosolic protein quality control disruption. The objective of the study was to determine the contribution of exercise training in regulating cardiac mitochondria metabolism and cytosolic protein quality control in a post-myocardial infarction-induced heart failure (MI-HF animal model. Our data demonstrated that isolated cardiac mitochondria from MI-HF rats displayed decreased oxygen consumption, reduced maximum calcium uptake and elevated H₂O₂ release. These changes were accompanied by exacerbated cardiac oxidative stress and proteasomal insufficiency. Declined proteasomal activity contributes to cardiac protein quality control disruption in our MI-HF model. Using cultured neonatal cardiomyocytes, we showed that either antimycin A or H₂O₂ resulted in inactivation of proteasomal peptidase activity, accumulation of oxidized proteins and cell death, recapitulating our in vivo model. Of interest, eight weeks of exercise training improved cardiac function, peak oxygen uptake and exercise tolerance in MI-HF rats. Moreover, exercise training restored mitochondrial oxygen consumption, increased Ca²⁺-induced permeability transition and reduced H₂O₂ release in MI-HF rats. These changes were followed by reduced oxidative stress and better cardiac protein quality control. Taken together, our findings uncover the potential contribution of mitochondrial dysfunction and cytosolic protein quality control disruption to heart failure and highlight the positive effects of exercise training in re-establishing cardiac mitochondrial physiology and protein quality control, reinforcing the importance of this intervention as a non-pharmacological tool for heart failure therapy.
Cognitive Models for Learning to Control Dynamic Systems
National Research Council Canada - National Science Library
Eberhart, Russ; Hu, Xiaohui; Chen, Yaobin
Report developed under STTR contract for topic "Cognitive models for learning to control dynamic systems" demonstrated a swarm intelligence learning algorithm and its application in unmanned aerial vehicle (UAV) mission planning...
Motor Control Research Requires Nonlinear Dynamics
Guastello, Stephen J.
The author comments on the original article "The Cinderella of psychology: The neglect of motor control in the science of mental life and behavior," by D. A. Rosenbaum. Rosenbaum draws attention to the study of motor control and evaluates seven possible explanations for why the topic has been relatively neglected. The point of this comment is that…
Study of the interaction of potassium ion channel protein with micelle by molecular dynamics simulation
Shantappa, Anil; Talukdar, Keka
Ion channels are proteins forming pore inside the body of all living organisms. This potassium ion channel known as KcsA channel and it is found in the each cell and nervous system. Flow of various ions is regulated by the function of the ion channels. The nerve ion channel protein with protein data bank entry 1BL8, which is basically an ion channel protein in Streptomyces Lividans and which is taken up to form micelle-protein system and the system is analyzed by using molecular dynamics simulation. Firstly, ion channel pore is engineered by CHARMM potential and then Micelle-protein system is subjected to molecular dynamics simulation. For some specific micelle concentration, the protein unfolding is observed.
Dynamical model of birdsong maintenance and control
Abarbanel, Henry D. I.; Talathi, Sachin S.; Mindlin, Gabriel; Rabinovich, Misha; Gibb, Leif
The neuroethology of song learning, production, and maintenance in songbirds presents interesting similarities to human speech. We have developed a biophysical model of the manner in which song could be maintained in adult songbirds. This model may inform us about the human counterpart to these processes. In songbirds, signals generated in nucleus High Vocal center (HVc) follow a direct route along a premotor pathway to the robust nucleus of the archistriatum (RA) as well as an indirect route to RA through the anterior forebrain pathway (AFP): the neurons of RA are innervated from both sources. HVc expresses very sparse bursts of spikes having interspike intervals of about 2ms . The expressions of these bursts arrive at the RA with a time difference ΔT≈50±10ms between the two pathways. The observed combination of AMPA and NMDA receptors at RA projection neurons suggests that long-term potentiation and long-term depression can both be induced by spike timing plasticity through the pairing of the HVc and AFP signals. We present a dynamical model that stabilizes this synaptic plasticity through a feedback from the RA to the AFP using known connections. The stabilization occurs dynamically and is absent when the RA→AFP connection is removed. This requires a dynamical selection of ΔT . The model does this, and ΔT lies within the observed range. Our model represents an illustration of a functional consequence of activity-dependent plasticity directly connected with neuroethological observations. Within the model the parameters of the AFP, and thus the magnitude of ΔT , can also be tuned to an unstable regime. This means that destabilization might be induced by neuromodulation of the AFP.
Analysis and control of complex dynamical systems robust bifurcation, dynamic attractors, and network complexity
Imura, Jun-ichi; Ueta, Tetsushi
This book is the first to report on theoretical breakthroughs on control of complex dynamical systems developed by collaborative researchers in the two fields of dynamical systems theory and control theory. As well, its basic point of view is of three kinds of complexity: bifurcation phenomena subject to model uncertainty, complex behavior including periodic/quasi-periodic orbits as well as chaotic orbits, and network complexity emerging from dynamical interactions between subsystems. Analysis and Control of Complex Dynamical Systems offers a valuable resource for mathematicians, physicists, and biophysicists, as well as for researchers in nonlinear science and control engineering, allowing them to develop a better fundamental understanding of the analysis and control synthesis of such complex systems.
Kinematics and Dynamics of Motion Control Based on Acceleration Control
Ohishi, Kiyoshi; Ohba, Yuzuru; Katsura, Seiichiro
The first IEEE International Workshop on Advanced Motion Control was held in 1990 pointed out the importance of physical interpretation of motion control. The software servoing technology is now common in machine tools, robotics, and mechatronics. It has been intensively developed for the numerical control (NC) machines. Recently, motion control in unknown environment will be more and more important. Conventional motion control is not always suitable due to the lack of adaptive capability to the environment. A more sophisticated ability in motion control is necessary for compliant contact with environment. Acceleration control is the key technology of motion control in unknown environment. The acceleration control can make a motion system to be a zero control stiffness system without losing the robustness. Furthermore, a realization of multi-degree-of-freedom motion is necessary for future human assistance. A human assistant motion will require various control stiffness corresponding to the task. The review paper focuses on the modal coordinate system to integrate the various control stiffness in the virtual axes. A bilateral teleoperation is a good candidate to consider the future human assistant motion and integration of decentralized systems. Thus the paper reviews and discusses the bilateral teleoperation from the control stiffness and the modal control design points of view.
Handbook of electrical power system dynamics modeling, stability, and control
Eremia, Mircea
Complete guidance for understanding electrical power system dynamics and blackouts This handbook offers a comprehensive and up-to-date treatment of power system dynamics. Addressing the full range of topics, from the fundamentals to the latest technologies in modeling, stability, and control, Handbook of Electrical Power System Dynamics provides engineers with hands-on guidance for understanding the phenomena leading to blackouts so they can design the most appropriate solutions for a cost-effective and reliable operation. Focusing on system dynamics, the book details
Architecture and dynamics of proteins and aqueous solvation complexes
Lotze, S.M.
For this thesis, the molecular dynamics of water and biological (model) systems have been studied with advanced nonlinear optical techniques. In chapters 4-5, the technique of femtosecond mid-infrared pump probe spectroscopy has been used to study the energy transfer and the reorientational dynamics
Protein damage and repair controlling seed vigor and longevity.
Ogé, Laurent; Broyart, Caroline; Collet, Boris; Godin, Béatrice; Jallet, Denis; Bourdais, Gildas; Job, Dominique; Grappin, Philippe
The formation of abnormal isoaspartyl residues derived from aspartyl or asparaginyl residues is a major source of spontaneous protein misfolding in cells. The repair enzyme protein L: -isoaspartyl methyltransferase (PIMT) counteracts such damage by catalyzing the conversion of abnormal isoaspartyl residues to their normal aspartyl forms. Thus, this enzyme contributes to the survival of many organisms, including plants. Analysis of the accumulation of isoaspartyl-containing proteins and its modulation by the PIMT repair pathway, using germination tests, immunodetection, enzymatic assays, and HPLC analysis, gives new insights in understanding controlling mechanisms of seed longevity and vigor.
Role of proteins in controlling selenium nanoparticle size
International Nuclear Information System (INIS)
Dobias, J; Suvorova, E I; Bernier-Latmani, R
This work investigates the potential for harnessing the association of bacterial proteins to biogenic selenium nanoparticles (SeNPs) to control the size distribution and the morphology of the resultant SeNPs. We conducted a proteomic study and compared proteins associated with biogenic SeNPs produced by E. coli to chemically synthesized SeNPs as well as magnetite nanoparticles. We identified four proteins (AdhP, Idh, OmpC, AceA) that bound specifically to SeNPs and observed a narrower size distribution as well as more spherical morphology when the particles were synthesized chemically in the presence of proteins. A more detailed study of AdhP (alcohol dehydrogenase propanol-preferring) confirmed the strong affinity of this protein for the SeNP surface and revealed that this protein controlled the size distribution of the SeNPs and yielded a narrow size distribution with a three-fold decrease in the median size. These results support the assertion that protein may become an important tool in the industrial-scale synthesis of SeNPs of uniform size and properties.
Structural Elements Regulating AAA+ Protein Quality Control Machines.
Chang, Chiung-Wen; Lee, Sukyeong; Tsai, Francis T F
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.
Initial photoinduced dynamics of the photoactive yellow protein
Larsen, D.S.; van Grondelle, R.
The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises
Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.
Cheng, Chi-Yuan; Han, Songi
Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.
Dynamics of domain coverage of the protein sequence universe
Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its "dark matter". Results Here we suggest that true size of "dark matter" is much larger than stated by current definitions. We propose an approach to reducing the size of "dark matter" by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of "dark matter"; however, its absolute size increases substantially with the growth of sequence data. PMID:23157439
Dynamics of domain coverage of the protein sequence universe
Directory of Open Access Journals (Sweden)
Rekapalli Bhanu
Full Text Available Abstract Background The currently known protein sequence space consists of millions of sequences in public databases and is rapidly expanding. Assigning sequences to families leads to a better understanding of protein function and the nature of the protein universe. However, a large portion of the current protein space remains unassigned and is referred to as its "dark matter". Results Here we suggest that true size of "dark matter" is much larger than stated by current definitions. We propose an approach to reducing the size of "dark matter" by identifying and subtracting regions in protein sequences that are not likely to contain any domain. Conclusions Recent improvements in computational domain modeling result in a decrease, albeit slowly, in the relative size of "dark matter"; however, its absolute size increases substantially with the growth of sequence data.
Fuzzy controller for an uncertain dynamical system
DEFF Research Database (Denmark)
Kulczycki, P.; Wisniewski, Rafal
The present paper deals with the time-optimal control for mechanical systems with uncertain load. A fuzzy approach is used in the design of suboptimal feedback controllers, robust with respect to the load. Statistical kernel estimators are used for the specification of crucial parameters. The met......The present paper deals with the time-optimal control for mechanical systems with uncertain load. A fuzzy approach is used in the design of suboptimal feedback controllers, robust with respect to the load. Statistical kernel estimators are used for the specification of crucial parameters....... The methodology proposed in this work may be easily adopted to other modeling uncertainties of mechanical systems, e.g. motion resistance....
Dynamic flow control strategies of vehicle SCR Urea Dosing System
Lin, Wei; Zhang, Youtong; Asif, Malik
Selective Catalyst Reduction(SCR) Urea Dosing System(UDS) directly affects the system accuracy and the dynamic response performance of a vehicle. However, the UDS dynamic response is hard to keep up with the changes of the engine's operating conditions. That will lead to low NO X conversion efficiency or NH3 slip. In order to optimize the injection accuracy and the response speed of the UDS in dynamic conditions, an advanced control strategy based on an air-assisted volumetric UDS is presented. It covers the methods of flow compensation and switching working conditions. The strategy is authenticated on an UDS and tested in different dynamic conditions. The result shows that the control strategy discussed results in higher dynamic accuracy and faster dynamic response speed of UDS. The inject deviation range is improved from being between -8% and 10% to -4% and 2% and became more stable than before, and the dynamic response time was shortened from 200 ms to 150 ms. The ETC cycle result shows that after using the new strategy the NH3 emission is reduced by 60%, and the NO X emission remains almost unchanged. The trade-off between NO X conversion efficiency and NH3 slip is mitigated. The studied flow compensation and switching working conditions can improve the dynamic performance of the UDS significantly and make the UDS dynamic response keep up with the changes of the engine's operating conditions quickly.
Controlling chaos in dynamical systems described by maps
International Nuclear Information System (INIS)
Crispin, Y.; Marduel, C.
The problem of suppressing chaotic behavior in dynamical systems is treated using a feedback control method with limited control effort. The proposed method is validated on archetypal systems described by maps, i.e. discrete-time difference equations. The method is also applicable to dynamical systems described by flows, i.e. by systems of ordinary differential equations. Results are presented for the one-dimensional logistic map and for a two-dimensional Lotka-Volterra map describing predator-prey population dynamics. It is shown that chaos can be suppressed and the system stabilized about a period-1 fixed point of the maps
LiGRO: a graphical user interface for protein-ligand molecular dynamics.
Kagami, Luciano Porto; das Neves, Gustavo Machado; da Silva, Alan Wilter Sousa; Caceres, Rafael Andrade; Kawano, Daniel Fábio; Eifler-Lima, Vera Lucia
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http://www.ufrgs.br/lasomfarmacia/ligro/ .
Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress
Directory of Open Access Journals (Sweden)
Eva Griesser
Full Text Available Reactive oxygen and nitrogen species (ROS/RNS play an important role in the regulation of cardiac function. Increase in ROS/RNS concentration results in lipid and protein oxidation and is often associated with onset and/or progression of many cardiovascular disorders. However, interplay between lipid and protein modifications has not been simultaneously studied in detail so far. Biomolecule carbonylation is one of the most common biomarkers of oxidative stress. Using a dynamic model of nitroxidative stress we demonstrated rapid changes in biomolecule carbonylation in rat cardiomyocytes. Levels of carbonylated species increased as early as 15 min upon treatment with the peroxynitrite donor, 3-morpholinosydnonimine (SIN-1, and decreased to values close to control after 16 h. Total (lipids+proteins vs. protein-specific carbonylation showed different dynamics, with a significant increase in protein-bound carbonyls at later time points. Treatment with SIN-1 in combination with inhibitors of proteasomal and autophagy/lysosomal degradation pathways allowed confirmation of a significant role of the proteasome in the degradation of carbonylated proteins, whereas lipid carbonylation increased in the presence of autophagy/lysosomal inhibitors. Electrophilic aldehydes and ketones formed by lipid peroxidation were identified and relatively quantified using LC-MS/MS. Molecular identity of reactive species was used for data-driven analysis of their protein targets. Combination of different enrichment strategies with LC-MS/MS analysis allowed identification of more than 167 unique proteins with 332 sites modified by electrophilic lipid peroxidation products. Gene ontology analysis of modified proteins demonstrated enrichment of several functional categories including proteins involved in cytoskeleton, extracellular matrix, ion channels and their regulation. Using calcium mobilization assays, the effect of nitroxidative stress on the activity of several ion
Complex systems and networks dynamics, controls and applications
Yu, Xinghuo; Chen, Guanrong; Yu, Wenwu
This elementary book provides some state-of-the-art research results on broad disciplinary sciences on complex networks. It presents an in-depth study with detailed description of dynamics, controls and applications of complex networks. The contents of this book can be summarized as follows. First, the dynamics of complex networks, for example, the cluster dynamic analysis by using kernel spectral methods, community detection algorithms in bipartite networks, epidemiological modeling with demographics and epidemic spreading on multi-layer networks, are studied. Second, the controls of complex networks are investigated including topics like distributed finite-time cooperative control of multi-agent systems by applying homogenous-degree and Lyapunov methods, composite finite-time containment control for disturbed second-order multi-agent systems, fractional-order observer design of multi-agent systems, chaos control and anticontrol of complex systems via Parrondos game and many more. Third, the applications of ...
Performance, Career Dynamics, and Span of Control
DEFF Research Database (Denmark)
Smeets, Valerie Anne Rolande; Waldman, Michael; Warzynski, Frederic Michel Patrick
that higher ability managers should supervise more subordinates, or equivalently, have a larger span of control. And although some of this theory's predictions have been empirically investigated, there has been little systematic investigation of the theory's predictions concerning span of control....... In this paper we first extend the theoretical literature on the scale-of-operations effect to allow firms' beliefs concerning a manager's ability to evolve over the manager's career, where much of our focus is the determinants of span of control. We then empirically investigate testable predictions from......There is an extensive theoretical literature based on what is called the scale-of-operations effect, i.e., the idea that the return to managerial ability is higher the more resources the manager influences with his or her decisions. This idea leads to various testable predictions including...
Dynamic Control of Airport Departures: Algorithm Development and Field Evaluation
Simaiakis, Ioannis; Balakrishnan, Hamsa
Surface congestion leads to significant increases in taxi times and fuel burn at major airports. In this paper, we formulate the airport surface congestion management problem as a dynamic control problem. We address two main challenges: the random delay between actuation (at the gate) and the server being controlled (the runway), and the need to develop control strategies that can be implemented in practice by human air traffic controllers. The second requirement necessitates a strategy that ...
Yaw control for active damping of structural dynamics
Energy Technology Data Exchange (ETDEWEB)
Ekelund, T. [Chalmers Univ. of Technology, Goeteborg (Sweden). Control Engineering Lab.
Yaw torque control for reduction of structural dynamic loads in a two-bladed wind turbine is investigated. The models are obtained using rigid-body mechanics. Linear quadratic control theory is utilized for design and analysis. The analysis of two simple examples, where the teeter angle and the tower lateral bending motion are regarded, shows that a time-varying controller has some advantages compared with a time-invariant controller. 6 refs, 9 figs
Feedback Linearized Aircraft Control Using Dynamic Cell Structure
Jorgensen, C. C.
A Dynamic Cell Structure (DCS ) Neural Network was developed which learns a topology representing network (TRN) of F-15 aircraft aerodynamic stability and control derivatives. The network is combined with a feedback linearized tracking controller to produce a robust control architecture capable of handling multiple accident and off-nominal flight scenarios. This paper describes network and its performance for accident scenarios including differential stabilator lock, soft sensor failure, control, stability derivative variation, and turbulence.
Dynamic performance enhancement of microgrids by advanced sliding mode controller
Energy Technology Data Exchange (ETDEWEB)
Sofla, Mohammadhassan Abdollahi [Electrical Engineering and Computer Science Dept., University of Toledo, Ohio (United States); Gharehpetian, Gevorg B. [Electrical Engineering Dept., Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)
Dynamics are the most important problems in the microgrid operation. In the islanded microgrid, the mismatch of parallel operations of inverters during dynamics can result in the instability. This paper considers severe dynamics which can occur in the microgrid. Microgrid can have different configurations with different load and generation dynamics which are facing voltage disturbances. As a result, microgrid has many uncertainties and is placed in the distribution network where is full of voltage disturbances. Moreover, characteristics of the distribution network and distributed energy resources in the islanded mode make microgrid vulnerable and easily lead to instability. The main aim of this paper is to discuss the suitable mathematical modeling based on microgrid characteristics and to design properly inner controllers to enhance the dynamics of microgrid with uncertain and changing parameters. This paper provides a method for inner controllers of inverter-based distributed energy resources to have a suitable response for different dynamics. Parallel inverters in distribution networks were considered to be controlled by nonlinear robust voltage and current controllers. Theoretical prove beyond simulation results, reveal evidently the effectiveness of the proposed controller. (author)
Dedicated EGR engine with dynamic load control
Hayman, Alan W.; McAlpine, Robert S.; Keating, Edward J.
An internal combustion engine comprises a first engine bank and a second engine bank. A first intake valve is disposed in an intake port of a cylinder of the first engine bank, and is configured for metering the first flow of combustion air by periodically opening and closing according to a first intake valve lift and duration characteristic. A variable valve train control mechanism is configured for affecting the first intake valve lift and duration characteristic. Either a lift or duration of the first intake valve is modulated so as to satisfy an EGR control criterion.
Solar Dynamic Power System Stability Analysis and Control
Momoh, James A.; Wang, Yanchun
The objective of this research is to conduct dynamic analysis, control design, and control performance test of solar power system. Solar power system consists of generation system and distribution network system. A bench mark system is used in this research, which includes a generator with excitation system and governor, an ac/dc converter, six DDCU's and forty-eight loads. A detailed model is used for modeling generator. Excitation system is represented by a third order model. DDCU is represented by a seventh order system. The load is modeled by the combination of constant power and constant impedance. Eigen-analysis and eigen-sensitivity analysis are used for system dynamic analysis. The effects of excitation system, governor, ac/dc converter control, and the type of load on system stability are discussed. In order to improve system transient stability, nonlinear ac/dc converter control is introduced. The direct linearization method is used for control design. The dynamic analysis results show that these controls affect system stability in different ways. The parameter coordination of controllers are recommended based on the dynamic analysis. It is concluded from the present studies that system stability is improved by the coordination of control parameters and the nonlinear ac/dc converter control stabilize system oscillation caused by the load change and system fault efficiently.
Parameters control in GAs for dynamic optimization
Directory of Open Access Journals (Sweden)
Khalid Jebari
Full Text Available The Control of Genetic Algorithms parameters allows to optimize the search process and improves the performance of the algorithm. Moreover it releases the user to dive into a game process of trial and failure to find the optimal parameters.
Neural network based adaptive control for nonlinear dynamic regimes
Shin, Yoonghyun
Adaptive control designs using neural networks (NNs) based on dynamic inversion are investigated for aerospace vehicles which are operated at highly nonlinear dynamic regimes. NNs play a key role as the principal element of adaptation to approximately cancel the effect of inversion error, which subsequently improves robustness to parametric uncertainty and unmodeled dynamics in nonlinear regimes. An adaptive control scheme previously named 'composite model reference adaptive control' is further developed so that it can be applied to multi-input multi-output output feedback dynamic inversion. It can have adaptive elements in both the dynamic compensator (linear controller) part and/or in the conventional adaptive controller part, also utilizing state estimation information for NN adaptation. This methodology has more flexibility and thus hopefully greater potential than conventional adaptive designs for adaptive flight control in highly nonlinear flight regimes. The stability of the control system is proved through Lyapunov theorems, and validated with simulations. The control designs in this thesis also include the use of 'pseudo-control hedging' techniques which are introduced to prevent the NNs from attempting to adapt to various actuation nonlinearities such as actuator position and rate saturations. Control allocation is introduced for the case of redundant control effectors including thrust vectoring nozzles. A thorough comparison study of conventional and NN-based adaptive designs for a system under a limit cycle, wing-rock, is included in this research, and the NN-based adaptive control designs demonstrate their performances for two highly maneuverable aerial vehicles, NASA F-15 ACTIVE and FQM-117B unmanned aerial vehicle (UAV), operated under various nonlinearities and uncertainties.
The consistency of large concerted motions in proteins in molecular dynamics simulations
de Groot, B.L.; van Aalten, D.M.F.; Amadei, A; Berendsen, H.J.C.
A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Fan, H; Mark, AE
The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to
Dynamic and bio-orthogonal protein assembly along a supramolecular polymer
Petkau - Milroy, K.; Uhlenheuer, D.A.; Spiering, A.J.H.; Vekemans, J.A.J.M.; Brunsveld, L.
Dynamic protein assembly along supramolecular columnar polymers has been achieved through the site-specific covalent attachment of different SNAP-tag fusion proteins to self-assembled benzylguanine-decorated discotics. The self-assembly of monovalent discotics into supramolecular polymers creates a
Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range.
Milles, Sigrid; Koehler, Christine; Gambin, Yann; Deniz, Ashok A; Lemke, Edward A
Single molecule observation of fluorescence resonance energy transfer can be used to provide insight into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins.
msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
Directory of Open Access Journals (Sweden)
Yuan Zhang
Full Text Available Dynamics of protein-protein interactions (PPIs reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process.
Quality control mechanisms of protein biogenesis: proteostasis dies hard
Directory of Open Access Journals (Sweden)
Timothy Jan Bergmann
Full Text Available The biosynthesis of proteins entails a complex series of chemical reactions that transform the information stored in the nucleic acid sequence into a polypeptide chain that needs to properly fold and reach its functional location in or outside the cell. It is of no surprise that errors might occur that alter the polypeptide sequence leading to a non-functional proteins or that impede delivery of proteins at the appropriate site of activity. In order to minimize such mistakes and guarantee the synthesis of the correct amount and quality of the proteome, cells have developed folding, quality control, degradation and transport mechanisms that ensure and tightly regulate protein biogenesis. Genetic mutations, harsh environmental conditions or attack by pathogens can subvert the cellular quality control machineries and perturb cellular proteostasis leading to pathological conditions. This review summarizes basic concepts of the flow of information from DNA to folded and active proteins and to the variable fidelity (from incredibly high to quite sloppy characterizing these processes. We will give particular emphasis on events that maintain or recover the homeostasis of the endoplasmic reticulum (ER, a major site of proteins synthesis and folding in eukaryotic cells. Finally, we will report on how cells can adapt to stressful conditions, how perturbation of ER homeostasis may result in diseases and how these can be treated.
The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease.
Stürner, Elisabeth; Behl, Christian
In neurons, but also in all other cells the complex proteostasis network is monitored and tightly regulated by the cellular protein quality control (PQC) system. Beyond folding of newly synthesized polypeptides and their refolding upon misfolding the PQC also manages the disposal of aberrant proteins either by the ubiquitin-proteasome machinery or by the autophagic-lysosomal system. Aggregated proteins are primarily degraded by a process termed selective macroautophagy (or aggrephagy). One such recently discovered selective macroautophagy pathway is mediated by the multifunctional HSP70 co-chaperone BAG3 ( BCL-2-associated athanogene 3 ). Under acute stress and during cellular aging, BAG3 in concert with the molecular chaperones HSP70 and HSPB8 as well as the ubiquitin receptor p62/SQSTM1 specifically targets aggregation-prone proteins to autophagic degradation. Thereby, BAG3-mediated selective macroautophagy represents a pivotal adaptive safeguarding and emergency system of the PQC which is activated under pathophysiological conditions to ensure cellular proteostasis. Interestingly, BAG3-mediated selective macroautophagy is also involved in the clearance of aggregated proteins associated with age-related neurodegenerative disorders, like Alzheimer's disease (tau-protein), Huntington's disease (mutated huntingtin/polyQ proteins), and amyotrophic lateral sclerosis (mutated SOD1). In addition, based on its initial description BAG3 is an anti-apoptotic protein that plays a decisive role in other widespread diseases, including cancer and myopathies. Therefore, in the search for novel therapeutic intervention avenues in neurodegeneration, myopathies and cancer BAG3 is a promising candidate.
Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. Ligand-induced changes in the protein motions
DEFF Research Database (Denmark)
Peters, Günther H. J.; Frimurer, T.M.; Andersen, J.N.
Activity of enzymes, such as protein tyrosine phosphatases (PTPs), is often associated with structural changes in the enzyme, resulting in selective and stereospecific reactions with the substrate. To investigate the effect of a substrate on the motions occurring in PTPs, we have performed...... molecular dynamics simulations of PTP1B and PTP1B complexed with a high-affinity peptide DADEpYL, where pY stands for phosphorylated tyrosine. The peptide sequence is derived from the epidermal growth factor receptor (EGFR(988-993)). Simulations were performed in water for 1 ns, and the concerted motions...... in the protein were analyzed using the essential dynamics technique. Our results indicate that the predominately internal motions in PTP1B occur in a subspace of only a few degrees of freedom. Upon substrate binding, the flexibility of the protein is reduced by similar to 10%. The largest effect is found...
Compressible dynamic stall control using high momentum microjets
Beahan, James J.; Shih, Chiang; Krothapalli, Anjaneyulu; Kumar, Rajan; Chandrasekhara, Muguru S.
Control of the dynamic stall process of a NACA 0015 airfoil undergoing periodic pitching motion is investigated experimentally at the NASA Ames compressible dynamic stall facility. Multiple microjet nozzles distributed uniformly in the first 12 % chord from the airfoil's leading edge are used for the dynamic stall control. Point diffraction interferometry technique is used to characterize the control effectiveness, both qualitatively and quantitatively. The microjet control has been found to be very effective in suppressing both the emergence of the dynamic stall vortex and the associated massive flow separation at the entire operating range of angles of attack. At the high Mach number ( M = 0.4), the use of microjets appears to eliminate the shock structures that are responsible for triggering the shock-induced separation, establishing the fact that the use of microjets is effective in controlling dynamic stall with a strong compressibility effect. In general, microjet control has an overall positive effect in terms of maintaining leading edge suction pressure and preventing flow separation.
Importance of the CMAP Correction to the CHARMM22 Protein Force Field: Dynamics of Hen Lysozyme
Buck, Matthias; Bouguet-Bonnet, Sabine; Pastor, Richard W.; MacKerell, Alexander D.
The recently developed CMAP correction to the CHARMM22 force field (C22) is evaluated from 25 ns molecular dynamics simulations on hen lysozyme. Substantial deviations from experimental backbone root mean-square fluctuations and N-H NMR order parameters obtained in the C22 trajectories (especially in the loops) are eliminated by the CMAP correction. Thus, the C22/CMAP force field yields improved dynamical and structural properties of proteins in molecular dynamics simulations.
Understanding the dynamical control of animal movement
Edwards, Donald
Over the last 50 years, neurophysiologists have described many neural circuits that transform sensory input into motor commands, while biomechanicians and behavioral biologists have described many patterns of animal movement that occur in response to sensory input. Attempts to link these two have been frustrated by our technical inability to record from the necessary neurons in a freely behaving animal. As a result, we don't know how these neural circuits function in the closed loop context of free behavior, where the sensory and motor context changes on a millisecond time-scale. To address this problem, we have developed a software package, AnimatLab (www.AnimatLab.com), that enables users to reconstruct an animal's body and its relevant neural circuits, to link them at the sensory and motor ends, and through simulation, to test their ability to reproduce appropriate patterns of the animal's movements in a simulated Newtonian world. A Windows-based program, AnimatLab consists of a neural editor, a body editor, a world editor, stimulus and recording facilities, neural and physics engines, and an interactive 3-D graphical display. We have used AnimatLab to study three patterns of behavior: the grasshopper jump, crayfish escape, and crayfish leg movements used in postural control, walking, reaching and grasping. In each instance, the simulation helped identify constraints on both nervous function and biomechanical performance that have provided the basis for new experiments. Colleagues elsewhere have begun to use AnimatLab to study control of paw movements in cats and postural control in humans. We have also used AnimatLab simulations to guide the development of an autonomous hexapod robot in which the neural control circuitry is downloaded to the robot from the test computer.
Dynamics and chaos control of gyrostat satellite
International Nuclear Information System (INIS)
Aslanov, Vladimir; Yudintsev, Vadim
Highlights: ► Free dual-spin gyrostat with a small rotor asymmetry is considered. ► Equations in Andoyer-Deprit canonical dimensionless variables are obtained. ► Phase space heteroclinic and homoclinic trajectories are written in closed form. ► Modified Melnikov function is used to construct the control that eliminates chaos. - Abstract: We consider the chaotic motion of the free gyrostat consisting of a platform with a triaxial inertia ellipsoid and a rotor with a small asymmetry with respect to the axis of rotation. Dimensionless equations of motion of the system with perturbations caused by small asymmetries of the rotor are written in Andoyer-Deprit variables. These perturbations lead to separatrix chaos. For gyrostats with different ratios of moments of inertia heteroclinic and homoclinic trajectories are written in closed-form. These trajectories are used for constructing modified Melnikov function, which is used for determine the control that eliminates separatrix chaos. Melnikov function and phase space trajectory are built to show the effectiveness of the control.
An experimental and computational framework to build a dynamic protein atlas of human cell division
Kavur, Marina; Kavur, Marina; Kavur, Marina; Ellenberg, Jan; Peters, Jan-Michael; Ladurner, Rene; Martinic, Marina; Kueblbeck, Moritz; Nijmeijer, Bianca; Wachsmuth, Malte; Koch, Birgit; Walther, Nike; Politi, Antonio; Heriche, Jean-Karim; Hossain, M.
Essential biological functions of human cells, such as division, require the tight coordination of the activity of hundreds of proteins in space and time. While live cell imaging is a powerful tool to study the distribution and dynamics of individual proteins after fluorescence tagging, it has not yet been used to map protein networks due to the lack of systematic and quantitative experimental and computational approaches. Using the cell and nuclear boundaries as landmarks, we generated a 4D ...
SU-E-J-61: Electrodynamics and Nano-Scale Fluid Dynamics in Protein Localization of Nuclear Pore Complexes
International Nuclear Information System (INIS)
Cunningham, J; Gatenby, R
Purpose: To develop a simulation to catalyze a reevaluation of common assumptions about 3 dimensional diffusive processes and help cell biologists gain a more nuanced, intuitive understanding of the true physical hurdles of protein signaling cascades. Furthermore, to discuss the possibility of intracellular electrodynamics as a critical, unrecognized component of cellular biology and protein dynamics that is necessary for optimal information flow from the cell membrane to the nucleus. Methods: The Unity 3D gaming physics engine was used to build an accurate virtual scale model of the cytoplasm within a few hundred nanometers of the nuclear membrane. A cloud of simulated pERK proteins is controlled by the physics simulation, where diffusion is based on experimentally measured values and the electrodynamics are based on theoretical nano-fluid dynamics. The trajectories of pERK within the cytoplasm and through the 1250 nuclear pores on the nuclear surface is recorded and analyzed. Results: The simulation quickly demonstrates that pERKs moving solely by diffusion will rarely locate and come within capture distance of a nuclear pore. The addition of intracellular electrodynamics between charges on the nuclear pore complexes and on pERKs increases the number of successful translocations by allowing the electro-physical attractive effects to draw in pERKs from the cytoplasm. The effects of changes in intracellular shielding ion concentrations allowed for estimation of the "capture radius" under varying conditions. Conclusion: The simulation allows a shift in perspective that is paramount in attempting to communicate the scale and dynamics of intracellular protein cascade mechanics. This work has allowed researchers to more fully understand the parameters involved in intracellular electrodynamics, such as shielding anion concentration and protein charge. As these effects are still far below the spatial resolution of currently available measurement technology this
SU-E-J-61: Electrodynamics and Nano-Scale Fluid Dynamics in Protein Localization of Nuclear Pore Complexes
Energy Technology Data Exchange (ETDEWEB)
Cunningham, J; Gatenby, R [Moffitt Cancer Research Institute, Tampa, FL (United States)
Purpose: To develop a simulation to catalyze a reevaluation of common assumptions about 3 dimensional diffusive processes and help cell biologists gain a more nuanced, intuitive understanding of the true physical hurdles of protein signaling cascades. Furthermore, to discuss the possibility of intracellular electrodynamics as a critical, unrecognized component of cellular biology and protein dynamics that is necessary for optimal information flow from the cell membrane to the nucleus. Methods: The Unity 3D gaming physics engine was used to build an accurate virtual scale model of the cytoplasm within a few hundred nanometers of the nuclear membrane. A cloud of simulated pERK proteins is controlled by the physics simulation, where diffusion is based on experimentally measured values and the electrodynamics are based on theoretical nano-fluid dynamics. The trajectories of pERK within the cytoplasm and through the 1250 nuclear pores on the nuclear surface is recorded and analyzed. Results: The simulation quickly demonstrates that pERKs moving solely by diffusion will rarely locate and come within capture distance of a nuclear pore. The addition of intracellular electrodynamics between charges on the nuclear pore complexes and on pERKs increases the number of successful translocations by allowing the electro-physical attractive effects to draw in pERKs from the cytoplasm. The effects of changes in intracellular shielding ion concentrations allowed for estimation of the "capture radius" under varying conditions. Conclusion: The simulation allows a shift in perspective that is paramount in attempting to communicate the scale and dynamics of intracellular protein cascade mechanics. This work has allowed researchers to more fully understand the parameters involved in intracellular electrodynamics, such as shielding anion concentration and protein charge. As these effects are still far below the spatial resolution of currently available measurement technology this
Tracing control of chaos for the coupled dynamos dynamical system
International Nuclear Information System (INIS)
Wang Xuedi; Tian Lixin
This paper introduces a new method for the coupled dynamos dynamical system, which can be applied to the decision of the chaotic behavior of the system. And research the tracing control of the chaos for the coupled dynamos dynamical system by gradually changing the driving parameter for the chaos. With the different design of controllers, the numerical simulation results show the relation between the chaotic behavior and the changes of the parameter value. Furthermore, the result shows the difference of the controllers. In the mean time, it reveals the process of the orbit's gradual changing with the parameter value
Dynamic modeling, simulation and control of energy generation
Vepa, Ranjan
This book addresses the core issues involved in the dynamic modeling, simulation and control of a selection of energy systems such as gas turbines, wind turbines, fuel cells and batteries. The principles of modeling and control could be applied to other non-convention methods of energy generation such as solar energy and wave energy.A central feature of Dynamic Modeling, Simulation and Control of Energy Generation is that it brings together diverse topics in thermodynamics, fluid mechanics, heat transfer, electro-chemistry, electrical networks and electrical machines and focuses on their appli
Dynamic, electronically switchable surfaces for membrane protein microarrays.
Tang, C S; Dusseiller, M; Makohliso, S; Heuschkel, M; Sharma, S; Keller, B; Vörös, J
Microarray technology is a powerful tool that provides a high throughput of bioanalytical information within a single experiment. These miniaturized and parallelized binding assays are highly sensitive and have found widespread popularity especially during the genomic era. However, as drug diagnostics studies are often targeted at membrane proteins, the current arraying technologies are ill-equipped to handle the fragile nature of the protein molecules. In addition, to understand the complex structure and functions of proteins, different strategies to immobilize the probe molecules selectively onto a platform for protein microarray are required. We propose a novel approach to create a (membrane) protein microarray by using an indium tin oxide (ITO) microelectrode array with an electronic multiplexing capability. A polycationic, protein- and vesicle-resistant copolymer, poly(l-lysine)-grafted-poly(ethylene glycol) (PLL-g-PEG), is exposed to and adsorbed uniformly onto the microelectrode array, as a passivating adlayer. An electronic stimulation is then applied onto the individual ITO microelectrodes resulting in the localized release of the polymer thus revealing a bare ITO surface. Different polymer and biological moieties are specifically immobilized onto the activated ITO microelectrodes while the other regions remain protein-resistant as they are unaffected by the induced electrical potential. The desorption process of the PLL-g-PEG is observed to be highly selective, rapid, and reversible without compromising on the integrity and performance of the conductive ITO microelectrodes. As such, we have successfully created a stable and heterogeneous microarray of biomolecules by using selective electronic addressing on ITO microelectrodes. Both pharmaceutical diagnostics and biomedical technology are expected to benefit directly from this unique method.
Distributed dynamic simulations of networked control and building performance applications.
Yahiaoui, Azzedine
The use of computer-based automation and control systems for smart sustainable buildings, often so-called Automated Buildings (ABs), has become an effective way to automatically control, optimize, and supervise a wide range of building performance applications over a network while achieving the minimum energy consumption possible, and in doing so generally refers to Building Automation and Control Systems (BACS) architecture. Instead of costly and time-consuming experiments, this paper focuses on using distributed dynamic simulations to analyze the real-time performance of network-based building control systems in ABs and improve the functions of the BACS technology. The paper also presents the development and design of a distributed dynamic simulation environment with the capability of representing the BACS architecture in simulation by run-time coupling two or more different software tools over a network. The application and capability of this new dynamic simulation environment are demonstrated by an experimental design in this paper.
Dual Role of Ancient Ubiquitous Protein 1 (AUP1) in Lipid Droplet Accumulation and Endoplasmic Reticulum (ER) Protein Quality Control
Klemm, Elizabeth J.; Spooner, Eric; Ploegh, Hidde L.
Quality control of endoplasmic reticulum proteins involves the identification and engagement of misfolded proteins, dislocation of the misfolded protein across the endoplasmic reticulum (ER) membrane, and ubiquitin-mediated targeting to the proteasome for degradation. Ancient ubiquitous protein 1 (AUP1) physically associates with the mammalian HRD1-SEL1L complex, and AUP1 depletion impairs degradation of misfolded ER proteins. One of the functions of AUP1 in ER quality control is to recruit t...
Dynamic protein S-palmitoylation mediates parasite life cycle progression and diverse mechanisms of virulence.
Brown, Robert W B; Sharma, Aabha I; Engman, David M
Eukaryotic parasites possess complex life cycles and utilize an assortment of molecular mechanisms to overcome physical barriers, suppress and/or bypass the host immune response, including invading host cells where they can replicate in a protected intracellular niche. Protein S-palmitoylation is a dynamic post-translational modification in which the fatty acid palmitate is covalently linked to cysteine residues on proteins by the enzyme palmitoyl acyltransferase (PAT) and can be removed by lysosomal palmitoyl-protein thioesterase (PPT) or cytosolic acyl-protein thioesterase (APT). In addition to anchoring proteins to intracellular membranes, functions of dynamic palmitoylation include - targeting proteins to specific intracellular compartments via trafficking pathways, regulating the cycling of proteins between membranes, modulating protein function and regulating protein stability. Recent studies in the eukaryotic parasites - Plasmodium falciparum, Toxoplasma gondii, Trypanosoma brucei, Cryptococcus neoformans and Giardia lamblia - have identified large families of PATs and palmitoylated proteins. Many palmitoylated proteins are important for diverse aspects of pathogenesis, including differentiation into infective life cycle stages, biogenesis and tethering of secretory organelles, assembling the machinery powering motility and targeting virulence factors to the plasma membrane. This review aims to summarize our current knowledge of palmitoylation in eukaryotic parasites, highlighting five exemplary mechanisms of parasite virulence dependent on palmitoylation.
Dynamics and control of nuclear power plants
International Nuclear Information System (INIS)
Tomsic, M.; Mavko, B.; Aleksic, U.; Stritar, A.; Adrinek, R.
A mathematical model of the power plant with a pressurized water reactor has been prepared and tested. The model is intended for a schematic simulator based on a digital computer. The results of the simulation run for various normal transients are in good agreement with literature data. Equipment for computer control of the experimental reactor TRIGA has been completed. The equipment includes two microcomputers and associated interface circuits. Presently, only data logging is performed. The analyses of random signals on the TRIGA reactor have been continued. Measurements of neutron flux, fuel temperature and cooling water duct have been performed
On protein quality control, myofibrillar myopathies, and neurodegeneration
Meister, Melanie
Eiwitten zijn bouwstenen van de cel en het is noodzakelijk dat zij in specifieke -vooraf bepaalde – 3-dimensionale vormen 'gevouwen' worden om hun functies binnen de cel te kunnen vervullen. De cel heeft een speciaal netwerk (Protein Quality Control [PQC] netwerk) die de kwaliteit van dergelijke
Study on dynamic lifting characteristics of control rod drive mechanism
International Nuclear Information System (INIS)
Shen Xiaoyao
Based on the equations of the electric circuit and the magnetic circuit and analysis of the dynamic lifting process for the control rod drive mechanism (CRDM), coupled magnetic-electric-mechanical equations both for the static status and the dynamic status are derived. The analytical method is utilized to obtain the current and the time when the lift starts. The numerical simulation method of dynamic analysis recommended by ASME Code is utilized to simulate the dynamic lifting process of CRDM, and the dynamic features of the system with different design gaps are studied. Conclusions are drawn as: (1) the lifting-start time increases with the design gap, and the time for the lifting process is longer with larger gaps; (2) the lifting velocity increases with time; (3) the lifting acceleration increases with time, and with smaller gaps, the impact acceleration is larger. (author)
Structure and Dynamic Properties of Membrane Proteins using NMR
DEFF Research Database (Denmark)
Rösner, Heike; Kragelund, Birthe
conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....
Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics
Hirokawa, N.; Takemura, R.
Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.
Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics
DEFF Research Database (Denmark)
Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.
Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...
Group performance and group learning at dynamic system control tasks
International Nuclear Information System (INIS)
Drewes, Sylvana
Proper management of dynamic systems (e.g. cooling systems of nuclear power plants or production and warehousing) is important to ensure public safety and economic success. So far, research has provided broad evidence for systematic shortcomings in individuals' control performance of dynamic systems. This research aims to investigate whether groups manifest synergy (Larson, 2010) and outperform individuals and if so, what processes lead to these performance advantages. In three experiments - including simulations of a nuclear power plant and a business setting - I compare the control performance of three-person-groups to the average individual performance and to nominal groups (N = 105 groups per experiment). The nominal group condition captures the statistical advantage of aggregated group judgements not due to social interaction. First, results show a superior performance of groups compared to individuals. Second, a meta-analysis across all three experiments shows interaction-based process gains in dynamic control tasks: Interacting groups outperform the average individual performance as well as the nominal group performance. Third, group interaction leads to stable individual improvements of group members that exceed practice effects. In sum, these results provide the first unequivocal evidence for interaction-based performance gains of groups in dynamic control tasks and imply that employers should rely on groups to provide opportunities for individual learning and to foster dynamic system control at its best.
Dynamical Aperture Control in Accelerator Lattices With Multipole Potentials
Morozov, I
We develop tools for symbolic representation of a non-linear accelerator model and analytical methods for description of non-linear dynamics. Information relevant to the dynamic aperture (DA) is then obtained from this model and can be used for indirect DA control or as a complement to direct numerical optimization. We apply two analytical methods and use multipole magnets to satisfy derived analytical constraints. The accelerator model is represented as a product of unperturbed and perturbed exponential operators with the exponent of the perturbed operator given as a power series in the perturbation parameter. Normal forms can be applied to this representation and the lattice parameters are used to control the normal form Hamiltonian and normal form transformation. Hamiltonian control is used to compute a control term or controlled operator. Lattice parameters are then fitted to satisfy the imposed control constraints. Theoretical results, as well as illustrative examples, are presented.
Offset Free Tracking Predictive Control Based on Dynamic PLS Framework
Directory of Open Access Journals (Sweden)
Jin Xin
Full Text Available This paper develops an offset free tracking model predictive control based on a dynamic partial least square (PLS framework. First, state space model is used as the inner model of PLS to describe the dynamic system, where subspace identification method is used to identify the inner model. Based on the obtained model, multiple independent model predictive control (MPC controllers are designed. Due to the decoupling character of PLS, these controllers are running separately, which is suitable for distributed control framework. In addition, the increment of inner model output is considered in the cost function of MPC, which involves integral action in the controller. Hence, the offset free tracking performance is guaranteed. The results of an industry background simulation demonstrate the effectiveness of proposed method.
Adaptive Dynamic Programming for Control Algorithms and Stability
Zhang, Huaguang; Luo, Yanhong; Wang, Ding
There are many methods of stable controller design for nonlinear systems. In seeking to go beyond the minimum requirement of stability, Adaptive Dynamic Programming for Control approaches the challenging topic of optimal control for nonlinear systems using the tools of adaptive dynamic programming (ADP). The range of systems treated is extensive; affine, switched, singularly perturbed and time-delay nonlinear systems are discussed as are the uses of neural networks and techniques of value and policy iteration. The text features three main aspects of ADP in which the methods proposed for stabilization and for tracking and games benefit from the incorporation of optimal control methods: • infinite-horizon control for which the difficulty of solving partial differential Hamilton–Jacobi–Bellman equations directly is overcome, and proof provided that the iterative value function updating sequence converges to the infimum of all the value functions obtained by admissible control law sequences; • finite-...
High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes
Martinez, N.
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.
High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes
Martinez, N.; Michoud, Gregoire; Cario, A.; Ollivier, J.; Franzetti, B.; Jebbar, M.; Oger, P.; Peters, J.
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.
Molecular modeling of the conformational dynamics of the cellular prion protein
Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia
Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.
Position Control of Linear Synchronous Motor Drives with Exploitation of Forced Dynamics Control Principles
Directory of Open Access Journals (Sweden)
Jan Vittek
Full Text Available Closed-loop position control of mechanisms directly driven by linear synchronous motors with permanent magnets is presented. The control strategy is based on forced dynamic control, which is a form of feedback linearisation, yielding a non-liner multivariable control law to obtain a prescribed linear speed dynamics together with the vector control condition of mutal orthogonality between the stator current and magnetic flux vectors (assuming perfect estimates of the plant parameters. Outer position control loop is closed via simple feedback with proportional gain. Simulations of the design control sysstem, including the drive with power electronic switching, predict the intended drive performance.
Morphing methods to visualize coarse-grained protein dynamics.
Weiss, Dahlia R; Koehl, Patrice
Morphing was initially developed as a cinematic effect, where one image is seamlessly transformed into another image. The technique was widely adopted by biologists to visualize the transition between protein conformational states, generating an interpolated pathway from an initial to a final protein structure. Geometric morphing seeks to create visually suggestive movies that illustrate structural changes between conformations but do not necessarily represent a biologically relevant pathway, while minimum energy path (MEP) interpolations aim at describing the true transition state between the crystal structure minima in the energy landscape.
Dynamic Evolution Analysis of Stock Price Fluctuation and Its Control
Directory of Open Access Journals (Sweden)
Yuhua Xu
Full Text Available This paper studies a simple dynamical system of stock price fluctuation time series based on the rule of stock market. When the stock price fluctuation system is disturbed by external excitations, the system exhibits obviously chaotic phenomena, and its basic dynamic properties are analyzed. At the same time, a new fixed-time convergence theorem is proposed for achieving fixed-time control of stock price fluctuation system. Finally, the effectiveness of the method is verified by numerical simulation.
Dynamics and control of Lorentz-augmented spacecraft relative motion
Yan, Ye; Yang, Yueneng
This book develops a dynamical model of the orbital motion of Lorentz spacecraft in both unperturbed and J2-perturbed environments. It explicitly discusses three kinds of typical space missions involving relative orbital control: spacecraft hovering, rendezvous, and formation flying. Subsequently, it puts forward designs for both open-loop and closed-loop control schemes propelled or augmented by the geomagnetic Lorentz force. These control schemes are entirely novel and represent a significantly departure from previous approaches.
Using dynamic input allocation for elongation control at FTU
International Nuclear Information System (INIS)
Boncagni, L.; Galeani, S.; Granucci, G.; Varano, G.; Vitale, V.; Zaccarian, L.
In this paper we exploit the dynamic allocation scheme for input redundant control systems proposed in to achieve elongation control on FTU (Frascati Tokamak Upgrade). The scheme first serves as a means for regulating the current in the F coils. Then, due to the quasi-static relationship between the plasma elongation and the F coils current, elongation control is achieved by suitably generalizing the allocation scheme. Both simulation and experimental results are reported.
Isolated sub-100-attosecond pulse generation via controlling electron dynamics
Lan, Pengfei; Lu, Peixiang; Cao, Wei; Li, Yuhua; Wang, Xinlin
A new method to coherently control the electron dynamics is proposed using a few-cycle laser pulse in combination with a controlling field. It is shown that this method not only broadens the attosecond pulse bandwidth, but also reduces the chirp, then an isolated 80-as pulse is straightforwardly obtained and even shorter pulse is achievable by increasing the intensity of the controlling field. Such ultrashort pulses allow one to investigate ultrafast electronic processes which have never be a...
A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.
Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar
Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.
Is dynamic heterogeneity of water in presence of a protein ...
Indian Academy of Sciences (India)
Abstract. Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been inves- tigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutions.
Static and dynamic properties of proteins adsorbed at liquid interfaces
Benjamins, J.
The aim of the investigation described in this thesis was to increase the level of understanding of the role that proteins play in the preparation and subsequent stabilisation of foams and emulsions. One aspect of this role is facilitation of break-up, due to surface tension lowering. A
Cell fate reprogramming by control of intracellular network dynamics
Zanudo, Jorge G. T.; Albert, Reka
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Although the topic of controlling the dynamics of a system has a long history in control theory, most of this work is not directly applicable to intracellular networks. Here we present a network control method that integrates the structural and functional information available for intracellular networks to predict control targets. Formulated in a logical dynamic scheme, our control method takes advantage of certain function-dependent network components and their relation to steady states in order to identify control targets, which are guaranteed to drive any initial state to the target state with 100% effectiveness and need to be applied only transiently for the system to reach and stay in the desired state. We illustrate our method's potential to find intervention targets for cancer treatment and cell differentiation by applying it to a leukemia signaling network and to the network controlling the differentiation of T cells. We find that the predicted control targets are effective in a broad dynamic framework. Moreover, several of the predicted interventions are supported by experiments. This work was supported by NSF Grant PHY 1205840.
Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.
Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.
Proteomics in quality control: Whey protein-based supplements.
Garrido, Bruno Carius; Souza, Gustavo H M F; Lourenço, Daniela C; Fasciotti, Maíra
The growing consumption of nutritional supplements might represent a problem, given the concern about the quality of these supplements. One of the most used supplements is whey protein (WP); because of its popularity, it has been a target of adulteration with substitute products, such as cheaper proteins with lower biological value. To investigate this type of adulteration, this study used shotgun proteomics analyses by MS(E) (multiplexed, low- and high-collision energy, data-independent acquisition) of WP-based supplements. Seventeen WP-based supplement samples were evaluated. Chicken, maize, rice, potato, soybean, and wheat proteins were considered as probable sources of bovine whey adulteration. Collectively, 523 proteins were identified across all 16 samples and replicates, with 94% of peptides inside a normal distribution within 10ppm of maximum error. In 10 of the 16 samples analyzed, only proteins from bovine whey could be detected, while in the other samples several other protein sources were detected in high concentrations, especially soybean, wheat, and rice. These results point out a probable adulteration and/or sample contamination during manufacturing that could only be detected using this proteomic approach. The present work shows how shotgun proteomics can be used to provide reliable answers in quality control matters, especially focusing on Whey Protein nutritional supplements which are a very popular subject in food and nutrition. In order to achieve an appropriate methodology, careful evaluation was performed applying extremely rigorous quality criteria, established for the proteomic analysis. These criteria and the methodological approach used in this work might serve as a guide for other authors seeking to use proteomics in quality control. Copyright © 2016 Elsevier B.V. All rights reserved.
Material-controlled dynamic vacuum insulation
Benson, D.K.; Potter, T.F.
A compact vacuum insulation panel is described comprising a chamber enclosed by two sheets of metal, glass-like spaces disposed in the chamber between the sidewalls, and a high-grade vacuum in the chamber includes apparatus and methods for enabling and disabling, or turning ``on`` and ``off`` the thermal insulating capability of the panel. One type of enabling and disabling apparatus and method includes a metal hydride for releasing hydrogen gas into the chamber in response to heat, and a hydrogen grate between the metal hydride and the chamber for selectively preventing and allowing return of the hydrogen gas to the metal hydride. Another type of enabling and disabling apparatus and method includes a variable emissivity coating on the sheets of metal in which the emissivity is controllably variable by heat or electricity. Still another type of enabling and disabling apparatus and method includes metal-to-metal contact devices that can be actuated to establish or break metal-to-metal heat paths or thermal short circuits between the metal sidewalls. 25 figs.
Radiation-controlled dynamic vacuum insulation
Benson, D.K.; Potter, T.F.
A compact vacuum insulation panel is described comprising a chamber enclosed by two sheets of metal, glass-like spaces disposed in the chamber between the sidewalls, and a high-grade vacuum in the chamber that includes apparatus and methods for enabling and disabling, or turning ``on`` and ``off`` the thermal insulating capability of the panel. One type of enabling and disabling apparatus and method includes a metal hydride for releasing hydrogen gas into the chamber in response to heat, and a hydrogen grate between the metal hydride and the chamber for selectively preventing and allowing return of the hydrogen gas to the metal hydride. Another type of enabling and disabling apparatus and method includes a variable emissivity coating on the sheets of metal in which the emissivity is controllably variable by heat or electricity. Still another type of enabling and disabling apparatus and method includes metal-to-metal contact devices that can be actuated to establish or break metal-to-metal heat paths or thermal short circuits between the metal sidewalls. 25 figs.
Chaotic dynamics and chaos control in nonlinear laser systems
International Nuclear Information System (INIS)
Fang Jinqing; Yao Weiguang
Chaotic dynamics and chaos control have become a great challenge in nonlinear laser systems and its advances are reviewed mainly based on the ring cavity laser systems. The principle and stability conditions for time-delay feedback control are analyzed and applied to chaos control in the laser systems. Other advanced methods of chaos control, such as weak spatial perturbation and occasional proportional feedback technique, are discussed. Prospects of chaos control for application (such as improvement of laser power and performance, synchronized chaos secure communication and information processing) are pointed out finally
Control of chemical dynamics by lasers: theoretical considerations.
Kondorskiy, Alexey; Nanbu, Shinkoh; Teranishi, Yoshiaki; Nakamura, Hiroki
Theoretical ideas are proposed for laser control of chemical dynamics. There are the following three elementary processes in chemical dynamics: (i) motion of the wave packet on a single adiabatic potential energy surface, (ii) excitation/de-excitation or pump/dump of wave packet, and (iii) nonadiabatic transitions at conical intersections of potential energy surfaces. A variety of chemical dynamics can be controlled, if we can control these three elementary processes as we desire. For (i) we have formulated the semiclassical guided optimal control theory, which can be applied to multidimensional real systems. The quadratic or periodic frequency chirping method can achieve process (ii) with high efficiency close to 100%. Concerning process (iii) mentioned above, the directed momentum method, in which a predetermined momentum vector is given to the initial wave packet, makes it possible to enhance the desired transitions at conical intersections. In addition to these three processes, the intriguing phenomenon of complete reflection in the nonadiabatic-tunneling-type of potential curve crossing can also be used to control a certain class of chemical dynamics. The basic ideas and theoretical formulations are provided for the above-mentioned processes. To demonstrate the effectiveness of these controlling methods, numerical examples are shown by taking the following processes: (a) vibrational photoisomerization of HCN, (b) selective and complete excitation of the fine structure levels of K and Cs atoms, (c) photoconversion of cyclohexadiene to hexatriene, and (d) photodissociation of OHCl to O + HCl.
Effective control of complex turbulent dynamical systems through statistical functionals.
Majda, Andrew J; Qi, Di
Turbulent dynamical systems characterized by both a high-dimensional phase space and a large number of instabilities are ubiquitous among complex systems in science and engineering, including climate, material, and neural science. Control of these complex systems is a grand challenge, for example, in mitigating the effects of climate change or safe design of technology with fully developed shear turbulence. Control of flows in the transition to turbulence, where there is a small dimension of instabilities about a basic mean state, is an important and successful discipline. In complex turbulent dynamical systems, it is impossible to track and control the large dimension of instabilities, which strongly interact and exchange energy, and new control strategies are needed. The goal of this paper is to propose an effective statistical control strategy for complex turbulent dynamical systems based on a recent statistical energy principle and statistical linear response theory. We illustrate the potential practical efficiency and verify this effective statistical control strategy on the 40D Lorenz 1996 model in forcing regimes with various types of fully turbulent dynamics with nearly one-half of the phase space unstable.
Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.
Anfinrud, Philip
Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.
Dynamic changes in protein functional linkage networks revealed by integration with gene expression data.
Directory of Open Access Journals (Sweden)
Shubhada R Hegde
Full Text Available Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.
Molecular Dynamics and Monte Carlo simulations resolve apparent diffusion rate differences for proteins confined in nanochannels
Energy Technology Data Exchange (ETDEWEB)
Tringe, J.W., E-mail: firstname.lastname@example.com [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)
Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations
Directory of Open Access Journals (Sweden)
Guimarães Katia S
Full Text Available Abstract Background Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. Results We propose a new method for identifying and representing overlapping protein complexes (or larger units called functional groups within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. We illustrate the effectiveness of our method by applying it to TNFα/NF-κB and pheromone signaling pathways. Conclusion The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks.
Efficient control of mechatronic systems in dynamic motion tasks
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Despotova Desislava
Full Text Available Robots and powered exoskeletons have often complex and non-linear dynamics due to friction, elasticity, and changing load. The proposed study addresses various-type robots that have to perform dynamic point-to-point motion tasks (PTPMT. The performance demands are for faster motion, higher positioning accuracy, and lower energy consumption. With given motion task, it is of primary importance to study the structure and controllability of the corresponding controlled system. The following natural decentralized controllability condition is assumed: the signs of any control input and the corresponding output (the acceleration are the same, at least when the control input is at its maximum absolute value. Then we find explicit necessary and sufficient conditions on the control transfer matrix that can guarantee robust controllability in the face of arbitrary, but bounded disturbances. Further on, we propose a generic optimisation approach for control learning synthesis of various type robotic systems in PTPMT. Our procedure for iterative learning control (LC has the following main steps: (1 choose a set of appropriate test control functions; (2 define the most relevant input-output pairs; and (3 solve shooting equations and perform control parameter optimisation. We will give several examples to explain our controllability and optimisation concepts.
Controllability of Weighted and Directed Networks with Nonidentical Node Dynamics
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Linying Xiang
Full Text Available The concept of controllability from control theory is applied to weighted and directed networks with heterogenous linear or linearized node dynamics subject to exogenous inputs, where the nodes are grouped into leaders and followers. Under this framework, the controllability of the controlled network can be decomposed into two independent problems: the controllability of the isolated leader subsystem and the controllability of the extended follower subsystem. Some necessary and/or sufficient conditions for the controllability of the leader-follower network are derived based on matrix theory and graph theory. In particular, it is shown that a single-leader network is controllable if it is a directed path or cycle, but it is uncontrollable for a complete digraph or a star digraph in general. Furthermore, some approaches to improving the controllability of a heterogenous network are presented. Some simulation examples are given for illustration and verification.
Contribution to control of robotics structures and dynamic behaviour
International Nuclear Information System (INIS)
Gilliot, Jean-Marie
The scope of this thesis is the simulation of the dynamics of complex rigid multi-body systems involved in robotics, in order to control them. In the first stage, methods for obtaining equations and models required for simulation and control purposes are proposed and discussed: - determination of constraint equations using the jacobian matrices, - elaboration of direct and inverse dynamics of manipulators. The second part of this thesis deals with the different concepts and components involved in the setting of simulation systems for Robotics Application Programs: models, emulators and the software development environment. The control algorithms are then introduced as a particular class of robotics application programs. A simulator has been developed, allowing the calculation and the visualisation of robot motions, driven by generalized torques. Some examples of control programs generating such control torques are then presented to illustrate the use of the simulator. (author) [fr
Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.
Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal
Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Individual dynamic lighting control in a daylit space
DEFF Research Database (Denmark)
Logadóttir, Asta; Christoffersen, Jens
in combination with daylight. Subjects performed office work for one day in a simulated office environment. Every 30 minutes the subjects were invited to use the dimmer controls to change the lighting conditions to their preferred level. Measurements were made of illuminance, luminance, CCT and energy use......The objectives of the study are to observe individual preferences for dynamic lighting, individual control and possibly achieve energy savings in a daylit space. The dynamics in this study are modifications of light level and correlated colour temperature (CCT) from the electric lighting system...
Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding
Nucleotide Base pairs Hydrogen bonds FIG. 1: Ladder structure of DNA showing the Watson - Crick bonding of the bases A, T, G, and C which are suspended by a...protected against unwanted action of chemicals and proteins. The three-dimensional structure of DNA is the famed Watson - Crick double-helix, the equilibrium...quantitative analysis [88]. [1] A. Kornberg and T. A. Baker, DNA Replication (W. H. Freeman, New York, 1992). [2] J. D. Watson and F. H. C. Crick
Controlling uncertain neutral dynamic systems with delay in control input
International Nuclear Information System (INIS)
Park, Ju H.; Kwon, O.
This article gives a novel criterion for the asymptotic stabilization of the zero solutions of a class of neutral systems with delays in control input. By constructing Lyapunov functionals, we have obtained the criterion which is expressed in terms of matrix inequalities. The solutions of the inequalities can be easily solved by efficient convex optimization algorithms. A numerical example is included to illustrate the design procedure of the proposed method
A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
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Mingyuan Xu
Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.
Altered dynamics of a lipid raft associated protein in a kidney model of Fabry disease.
Labilloy, Anatália; Youker, Robert T; Bruns, Jennifer R; Kukic, Ira; Kiselyov, Kirill; Halfter, Willi; Finegold, David; do Monte, Semiramis Jamil Hadad; Weisz, Ora A
Accumulation of globotriaosylceramide (Gb3) and other neutral glycosphingolipids with galactosyl residues is the hallmark of Fabry disease, a lysosomal storage disorder caused by deficiency of the enzyme alpha-galactosidase A (α-gal A). These lipids are incorporated into the plasma membrane and intracellular membranes, with a preference for lipid rafts. Disruption of raft mediated cell processes is implicated in the pathogenesis of several human diseases, but little is known about the effects of the accumulation of glycosphingolipids on raft dynamics in the context of Fabry disease. Using siRNA technology, we have generated a polarized renal epithelial cell model of Fabry disease in Madin-Darby canine kidney cells. These cells present increased levels of Gb3 and enlarged lysosomes, and progressively accumulate zebra bodies. The polarized delivery of both raft-associated and raft-independent proteins was unaffected by α-gal A knockdown, suggesting that accumulation of Gb3 does not disrupt biosynthetic trafficking pathways. To assess the effect of α-gal A silencing on lipid raft dynamics, we employed number and brightness (N&B) analysis to measure the oligomeric status and mobility of the model glycosylphosphatidylinositol (GPI)-anchored protein GFP-GPI. We observed a significant increase in the oligomeric size of antibody-induced clusters of GFP-GPI at the plasma membrane of α-gal A silenced cells compared with control cells. Our results suggest that the interaction of GFP-GPI with lipid rafts may be altered in the presence of accumulated Gb3. The implications of our results with respect to the pathogenesis of Fabry disease are discussed. © 2013 Elsevier Inc. All rights reserved.
Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy
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Oyang Yen-Jen
Full Text Available Abstract Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy.
Inferior olive mirrors joint dynamics to implement an inverse controller.
Alvarez-Icaza, Rodrigo; Boahen, Kwabena
To produce smooth and coordinated motion, our nervous systems need to generate precisely timed muscle activation patterns that, due to axonal conduction delay, must be generated in a predictive and feedforward manner. Kawato proposed that the cerebellum accomplishes this by acting as an inverse controller that modulates descending motor commands to predictively drive the spinal cord such that the musculoskeletal dynamics are canceled out. This and other cerebellar theories do not, however, account for the rich biophysical properties expressed by the olivocerebellar complex's various cell types, making these theories difficult to verify experimentally. Here we propose that a multizonal microcomplex's (MZMC) inferior olivary neurons use their subthreshold oscillations to mirror a musculoskeletal joint's underdamped dynamics, thereby achieving inverse control. We used control theory to map a joint's inverse model onto an MZMC's biophysics, and we used biophysical modeling to confirm that inferior olivary neurons can express the dynamics required to mirror biomechanical joints. We then combined both techniques to predict how experimentally injecting current into the inferior olive would affect overall motor output performance. We found that this experimental manipulation unmasked a joint's natural dynamics, as observed by motor output ringing at the joint's natural frequency, with amplitude proportional to the amount of current. These results support the proposal that the cerebellum-in particular an MZMC-is an inverse controller; the results also provide a biophysical implementation for this controller and allow one to make an experimentally testable prediction.
Dynamics and Control of Distillation Columns - A Critical Survey
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Sigurd Skogestad
Full Text Available Distillation column dynamics and control have been viewed by many as a very mature or even dead field. However, as is discussed in this paper significant new results have appeared over the last 5-10 years. These results include multiple steady states and instability in simple columns with ideal thermodynamics (which was believed to be impossible, the understanding of the difference between various control configurations and the systematic transformation between these, the feasibility of using the distillate-bottom structure, for control (which was believed to be impossible, the importance of flow dynamics for control studies, the fundamental problems in identifying models from open-loops responses, the use of simple regression estimators to estimate composition from temperatures, and an improved general understanding of the dynamic behavior of distillation columns which includes a better understanding of the fundamental difference between internal and external flow, simple formulas for estimating the dominant time constant, and a derivation of the linearizing effect of logarithmic transformations. These issues apply to all columns, even for ideal mixtures and simple columns with only two products. In addition, there have been significant advances for cases with complex thermodynamics and complex column configurations. These include the behavior and control of azeotropic distillation columns, and the possible complex dynamics of nonideal mixtures and of interlinked columns. However, both for the simple and more complex cases there are still a number of areas where further research is needed.
Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*
Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc
During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433
Nonlinear systems techniques for dynamical analysis and control
Lefeber, Erjen; Arteaga, Ines
This treatment of modern topics related to the control of nonlinear systems is a collection of contributions celebrating the work of Professor Henk Nijmeijer and honoring his 60th birthday. It addresses several topics that have been the core of Professor Nijmeijer's work, namely: the control of nonlinear systems, geometric control theory, synchronization, coordinated control, convergent systems and the control of underactuated systems. The book presents recent advances in these areas, contributed by leading international researchers in systems and control. In addition to the theoretical questions treated in the text, particular attention is paid to a number of applications including (mobile) robotics, marine vehicles, neural dynamics and mechanical systems generally. This volume provides a broad picture of the analysis and control of nonlinear systems for scientists and engineers with an interest in the interdisciplinary field of systems and control theory. The reader will benefit from the expert participan...
Linear dynamical quantum systems analysis, synthesis, and control
Nurdin, Hendra I
This monograph provides an in-depth treatment of the class of linear-dynamical quantum systems. The monograph presents a detailed account of the mathematical modeling of these systems using linear algebra and quantum stochastic calculus as the main tools for a treatment that emphasizes a system-theoretic point of view and the control-theoretic formulations of quantum versions of familiar problems from the classical (non-quantum) setting, including estimation and filtering, realization theory, and feedback control. Both measurement-based feedback control (i.e., feedback control by a classical system involving a continuous-time measurement process) and coherent feedback control (i.e., feedback control by another quantum system without the intervention of any measurements in the feedback loop) are treated. Researchers and graduates studying systems and control theory, quantum probability and stochastics or stochastic control whether from backgrounds in mechanical or electrical engineering or applied mathematics ...
Dynamic control of biped locomotion robot using optimal regulator
International Nuclear Information System (INIS)
Sano, Akihito; Furusho, Junji
For moving in indoor space, it is generally recognized that biped locomotion is suitable. This paper proposes a hierarchical control strategy for the lower level where the position control or the force control at each joint is implemented. In the upper level control, the robot motion is divided into a sagittal plane and a lateral plane. We applied the optimal control algorithm to the motion control in the lateral plane in order to improve the robustness of the control system. The effects of these control schemes are shown by the experiments using the new walking robot BLR-G 1 and the parallel calculation system. BLR-G 1 has 9 degrees of freedom and equips the foot-pressure-sensors and a rate gyroscope. Complete dynamic walking is realized, in which the cycle for each step is about 1.0 second. (author)
Development and comparison of integrated dynamics control systems with fuzzy logic control and sliding mode control
International Nuclear Information System (INIS)
Song, Jeong Hoon
In this study, four integrated dynamics control (IDC) systems abbreviated as IDCB, IDCS, IDCF, and IDCR are developed, evaluated and compared. IDC systems were integrated with brake and steer control systems to enhance lateral stability and handling performance. To construct the IDC systems, a vehicle model with fourteen degrees of freedom, a fuzzy logic controller, and a sliding mode ABS controller were used. They were tested with various steering inputs when excessive full brake pressure or no brake pressure was applied on dry asphalt, wet asphalt, a snow-covered paved road, and a split-µ road. The results showed that an IDC-equipped vehicle improved lateral stability and controllability in every driving condition compared to an ABS-equipped vehicle. Under all road conditions, IDC controllers enabled the yaw rate to follow the reference yaw rate almost perfectly and reduced the body slip angle. On a split-µ road, IDCB, IDCS, IDCF, and IDCR vehicles drove straight ahead with only very small deviations.
Dynamical analysis of yeast protein interaction network during the sake brewing process.
Mirzarezaee, Mitra; Sadeghi, Mehdi; Araabi, Babak N
Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.
Dynamics and Control of a Flexible Solar Sail
Directory of Open Access Journals (Sweden)
Jiafu Liu
Full Text Available Solar sail can merely make use of solar radiation pressure (SRP force as the thrust for space missions. The attitude dynamics is obtained for the highly flexible solar sail with control vanes, sliding masses, and a gimbaled control boom. The vibration equations are derived considering the geometric nonlinearity of the sail structure subjected to the forces generated by the control vanes, solar radiation pressure (SRP, and sliding masses. Then the dynamic models for attitude/vibration controller design and dynamic simulation are obtained, respectively. The linear quadratic regulator (LQR based and optimal proportional-integral (PI based controllers are designed for the coupled attitude/vibration models with constant disturbance torques caused by the center-of-mass (cm/center-of-pressure (cp offset, respectively. It can be concluded from the theoretical analysis and simulation results that the optimal PI based controller performs better than the LQR based controller from the view of eliminating the steady-state errors. The responses with and without the geometrical nonlinearity are performed, and the differences are observed and analyzed. And some suggestions are also presented.
Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation
International Nuclear Information System (INIS)
Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA
Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation
Energy Technology Data Exchange (ETDEWEB)
Matsushita, Y., E-mail: firstname.lastname@example.com; Murakawa, T., E-mail: firstname.lastname@example.com; Shimamura, K., E-mail: firstname.lastname@example.com; Oishi, M., E-mail: email@example.com; Ohyama, T., E-mail: firstname.lastname@example.com; Kurita, N., E-mail: email@example.com [Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
The Role of the Multifunctional BAG3 Protein in Cellular Protein Quality Control and in Disease
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Elisabeth Stürner
Full Text Available In neurons, but also in all other cells the complex proteostasis network is monitored and tightly regulated by the cellular protein quality control (PQC system. Beyond folding of newly synthesized polypeptides and their refolding upon misfolding the PQC also manages the disposal of aberrant proteins either by the ubiquitin-proteasome machinery or by the autophagic-lysosomal system. Aggregated proteins are primarily degraded by a process termed selective macroautophagy (or aggrephagy. One such recently discovered selective macroautophagy pathway is mediated by the multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3. Under acute stress and during cellular aging, BAG3 in concert with the molecular chaperones HSP70 and HSPB8 as well as the ubiquitin receptor p62/SQSTM1 specifically targets aggregation-prone proteins to autophagic degradation. Thereby, BAG3-mediated selective macroautophagy represents a pivotal adaptive safeguarding and emergency system of the PQC which is activated under pathophysiological conditions to ensure cellular proteostasis. Interestingly, BAG3-mediated selective macroautophagy is also involved in the clearance of aggregated proteins associated with age-related neurodegenerative disorders, like Alzheimer's disease (tau-protein, Huntington's disease (mutated huntingtin/polyQ proteins, and amyotrophic lateral sclerosis (mutated SOD1. In addition, based on its initial description BAG3 is an anti-apoptotic protein that plays a decisive role in other widespread diseases, including cancer and myopathies. Therefore, in the search for novel therapeutic intervention avenues in neurodegeneration, myopathies and cancer BAG3 is a promising candidate.
Controlling the dynamics of multi-state neural networks
International Nuclear Information System (INIS)
Jin, Tao; Zhao, Hong
In this paper, we first analyze the distribution of local fields (DLF) which is induced by the memory patterns in the Q-Ising model. It is found that the structure of the DLF is closely correlated with the network dynamics and the system performance. However, the design rule adopted in the Q-Ising model, like the other rules adopted for multi-state neural networks with associative memories, cannot be applied to directly control the DLF for a given set of memory patterns, and thus cannot be applied to further study the relationships between the structure of the DLF and the dynamics of the network. We then extend a design rule, which was presented recently for designing binary-state neural networks, to make it suitable for designing general multi-state neural networks. This rule is able to control the structure of the DLF as expected. We show that controlling the DLF not only can affect the dynamic behaviors of the multi-state neural networks for a given set of memory patterns, but also can improve the storage capacity. With the change of the DLF, the network shows very rich dynamic behaviors, such as the 'chaos phase', the 'memory phase', and the 'mixture phase'. These dynamic behaviors are also observed in the binary-state neural networks; therefore, our results imply that they may be the universal behaviors of feedback neural networks
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.
Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: firstname.lastname@example.com, E-mail: email@example.com [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
Conformational dynamics of a protein in the folded and the unfolded state
Energy Technology Data Exchange (ETDEWEB)
Fitter, Joerg
In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.
Dynamically polarized samples for neutron protein crystallography at the Spallation Neutron Source
International Nuclear Information System (INIS)
Zhao, Jinkui; Pierce, Josh; Robertson, J. L.; Herwig, Kenneth W.; Myles, Dean; Cuneo, Matt; Li, Le; Meilleur, Flora; Standaert, Bob
To prepare for the next generation neutron scattering instruments for the planned second target station at the Spallation Neutron Source (SNS) and to broaden the scientific impact of neutron protein crystallography at the Oak Ridge National Laboratory, we have recently ramped up our efforts to develop a dynamically polarized target for neutron protein crystallography at the SNS. Proteins contain a large amount of hydrogen which contributes to incoherent diffraction background and limits the sensitivity of neutron protein crystallography. This incoherent background can be suppressed by using polarized neutron diffraction, which in the same time also improves the coherent diffraction signal. Our plan is to develop a custom Dynamic Nuclear Polarization (DNP) setup tailored to neutron protein diffraction instruments. Protein crystals will be polarized at a magnetic field of 5 T and temperatures of below 1 K. After the dynamic polarization process, the sample will be brought to a frozen-spin mode in a 0.5 T holding field and at temperatures below 100 mK. In a parallel effort, we are also investigating various ways of incorporating polarization agents needed for DNP, such as site specific spin labels, into protein crystals. (paper)
Periplasmic quality control in biogenesis of outer membrane proteins.
Lyu, Zhi Xin; Zhao, Xin Sheng
The β-barrel outer membrane proteins (OMPs) are integral membrane proteins that reside in the outer membrane of Gram-negative bacteria and perform a diverse range of biological functions. Synthesized in the cytoplasm, OMPs must be transported across the inner membrane and through the periplasmic space before they are assembled in the outer membrane. In Escherichia coli, Skp, SurA and DegP are the most prominent factors identified to guide OMPs across the periplasm and to play the role of quality control. Although extensive genetic and biochemical analyses have revealed many basic functions of these periplasmic proteins, the mechanism of their collaboration in assisting the folding and insertion of OMPs is much less understood. Recently, biophysical approaches have shed light on the identification of the intricate network. In the present review, we summarize recent advances in the characterization of these key factors, with a special emphasis on the multifunctional protein DegP. In addition, we present our proposed model on the periplasmic quality control in biogenesis of OMPs.
Fixed-bed Reactor Dynamics and Control - A Review
DEFF Research Database (Denmark)
Jørgensen, S. B.
The industrial diversity of fixed bed reactors offers a challenging and relevant set of control problems. These intricate problems arise due to the rather complex dynamics of fixed bed reactors and to the complexity of actual reactor configurations. Many of these control problems are nonlinear...... and multi-variable. During the last decade fixed bed reactor control strategies have been proposed and investigated experimentally. This paper reviews research on these complex control problems with an emphasis upon solutions which have been demon-strated to work in the laboratory and hold promise...
Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.
Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L
Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.
Survey of orbital dynamics and control of space rendezvous
Directory of Open Access Journals (Sweden)
Luo Yazhong
Full Text Available Rendezvous orbital dynamics and control (RODC is a key technology for operating space rendezvous and docking missions. This paper surveys the studies on RODC. Firstly, the basic relative dynamics equation set is introduced and its improved versions are evaluated. Secondly, studies on rendezvous trajectory optimization are commented from three aspects: the linear rendezvous, the nonlinear two-body rendezvous, and the perturbed and constrained rendezvous. Thirdly, studies on relative navigation are briefly reviewed, and then close-range control methods including automated control, manual control, and telecontrol are analyzed. Fourthly, advances in rendezvous trajectory safety and robust analysis are surveyed, and their applications in trajectory optimization are discussed. Finally, conclusions are drawn and prospects of studies on RODC are presented.
Dynamics and control of molten-salt breeder reactor
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Vikram Singh
Full Text Available Preliminary results of the dynamic analysis of a two-fluid molten-salt breeder reactor (MSBR system are presented. Based on an earlier work on the preliminary dynamic model of the concept, the model presented here is nonlinear and has been revised to accurately reflect the design exemplified in ORNL-4528. A brief overview of the model followed by results from simulations performed to validate the model is presented. Simulations illustrate stable behavior of the reactor dynamics and temperature feedback effects to reactivity excursions. Stable and smooth changes at various nodal temperatures are also observed. Control strategies for molten-salt reactor operation are discussed, followed by an illustration of the open-loop load-following capability of the molten-salt breeder reactor system. It is observed that the molten-salt breeder reactor system exhibits "self-regulating" behavior, minimizing the need for external controller action for load-following maneuvers.
Dynamics and control of molten-salt breeder reactor
Energy Technology Data Exchange (ETDEWEB)
Sing, Vikram; Lish, Matthew R.; Chvala, Ondrej; Upadhyaya, Belle R. [Dept. of Nuclear Engineering, University of Tennessee, Knoxville (United States)
Preliminary results of the dynamic analysis of a two-fluid molten-salt breeder reactor (MSBR) system are presented. Based on an earlier work on the preliminary dynamic model of the concept, the model presented here is nonlinear and has been revised to accurately reflect the design exemplified in ORNL-4528. A brief overview of the model followed by results from simulations performed to validate the model is presented. Simulations illustrate stable behavior of the reactor dynamics and temperature feedback effects to reactivity excursions. Stable and smooth changes at various nodal temperatures are also observed. Control strategies for molten-salt reactor operation are discussed, followed by an illustration of the open-loop load-following capability of the molten-salt breeder reactor system. It is observed that the molten-salt breeder reactor system exhibits "self-regulating" behavior, minimizing the need for external controller action for load-following maneuvers.
Optimized controllers for enhancing dynamic performance of PV interface system
Directory of Open Access Journals (Sweden)
Mahmoud A. Attia
Full Text Available The dynamic performance of PV interface system can be improved by optimizing the gains of the Proportional–Integral (PI controller. In this work, gravitational search algorithm and harmony search algorithm are utilized to optimal tuning of PI controller gains. Performance comparison between the PV system with optimized PI gains utilizing different techniques are carried out. Finally, the dynamic behavior of the system is studied under hypothetical sudden variations in irradiance. The examination of the proposed techniques for optimal tuning of PI gains is conducted using MATLAB/SIMULINK software package. The main contribution of this work is investigating the dynamic performance of PV interfacing system with application of gravitational search algorithm and harmony search algorithm for optimal PI parameters tuning. Keywords: Photovoltaic power systems, Gravitational search algorithm, Harmony search algorithm, Genetic algorithm, Artificial intelligence
Non-destructive Faraday imaging of dynamically controlled ultracold atoms
Gajdacz, Miroslav; Pedersen, Poul; Mørch, Troels; Hilliard, Andrew; Arlt, Jan; Sherson, Jacob
We investigate non-destructive measurements of ultra-cold atomic clouds based on dark field imaging of spatially resolved Faraday rotation. In particular, we pursue applications to dynamically controlled ultracold atoms. The dependence of the Faraday signal on laser detuning, atomic density and temperature is characterized in a detailed comparison with theory. In particular the destructivity per measurement is extremely low and we illustrate this by imaging the same cloud up to 2000 times. The technique is applied to avoid the effect of shot-to-shot fluctuations in atom number calibration. Adding dynamic changes to system parameters, we demonstrate single-run vector magnetic field imaging and single-run spatial imaging of the system's dynamic behavior. The method can be implemented particularly easily in standard imaging systems by the insertion of an extra polarizing beam splitter. These results are steps towards quantum state engineering using feedback control of ultracold atoms.
Major urinary protein (MUP) profiles show dynamic changes rather than individual 'barcode' signatures
Thoß, M.; Luzynski, K.C.; Ante, M.; Miller, I.; Penn, D.J.
House mice (Mus musculus) produce a variable number of major urinary proteins (MUPs), and studies suggest that each individual produces a unique MUP profile that provides a distinctive odor signature controlling individual and kin recognition. This 'barcode hypothesis' requires that MUP urinary profiles show high individual variability within populations and also high individual consistency over time, but tests of these assumptions are lacking. We analyzed urinary MUP profiles of 66 wild-caught house mice from eight populations using isoelectric focusing. We found that MUP profiles of wild male house mice are not individually unique, and though they were highly variable, closer inspection revealed that the variation strongly depended on MUP band type. The prominent ('major) bands were surprisingly homogenous (and hence most MUPs are not polymorphic), but we also found inconspicuous ('minor') bands that were highly variable and therefore potential candidates for individual fingerprints. We also examined changes in urinary MUP profiles of 58 males over time (from 6 to 24 weeks of age), and found that individual MUP profiles and MUP concentration were surprisingly dynamic, and showed significant changes after puberty and during adulthood. Contrary to what we expected, however, the minor bands were the most variable over time, thus no good candidates for individual fingerprints. Although MUP profiles do not provide individual fingerprints, we found that MUP profiles were more similar among siblings than non-kin despite considerable fluctuation. Our findings show that MUP profiles are not highly stable over time, they do not show strong individual clustering, and thus challenge the barcode hypothesis. Within-individual dynamics of MUP profiles indicate a different function of MUPs in individual recognition than previously assumed and advocate an alternative hypothesis ('dynamic changes' hypothesis). PMID:26973837
Major urinary protein (MUP) profiles show dynamic changes rather than individual 'barcode' signatures.
Thoß, M; Luzynski, K C; Ante, M; Miller, I; Penn, D J
House mice ( Mus musculus) produce a variable number of major urinary proteins (MUPs), and studies suggest that each individual produces a unique MUP profile that provides a distinctive odor signature controlling individual and kin recognition. This 'barcode hypothesis' requires that MUP urinary profiles show high individual variability within populations and also high individual consistency over time, but tests of these assumptions are lacking. We analyzed urinary MUP profiles of 66 wild-caught house mice from eight populations using isoelectric focusing. We found that MUP profiles of wild male house mice are not individually unique, and though they were highly variable, closer inspection revealed that the variation strongly depended on MUP band type. The prominent ('major) bands were surprisingly homogenous (and hence most MUPs are not polymorphic), but we also found inconspicuous ('minor') bands that were highly variable and therefore potential candidates for individual fingerprints. We also examined changes in urinary MUP profiles of 58 males over time (from 6 to 24 weeks of age), and found that individual MUP profiles and MUP concentration were surprisingly dynamic, and showed significant changes after puberty and during adulthood. Contrary to what we expected, however, the minor bands were the most variable over time, thus no good candidates for individual fingerprints. Although MUP profiles do not provide individual fingerprints, we found that MUP profiles were more similar among siblings than non-kin despite considerable fluctuation. Our findings show that MUP profiles are not highly stable over time, they do not show strong individual clustering, and thus challenge the barcode hypothesis. Within-individual dynamics of MUP profiles indicate a different function of MUPs in individual recognition than previously assumed and advocate an alternative hypothesis ('dynamic changes' hypothesis).
Developing a dynamic control system for mine compressed air networks
Van Heerden, S.W.; Pelzer, R.; Marais, J.H.
Mines in general, make use of compressed air systems for daily operational activities. Compressed air on mines is traditionally distributed via compressed air ring networks where multiple shafts are supplied with compressed air from an integral system. These compressed air networks make use of a number of compressors feeding the ring from various locations in the network. While these mines have sophisticated control systems to control these compressors, they are not dynamic systems. Compresso...
Dynamic pipe control with a multiple digit automatic measuring device
International Nuclear Information System (INIS)
Jenzer, P.
With the flow rotating method, thin-walled pipes can be produced with very tight tolerances and high mechanical sturdiness. The measuring device permits a dynamic control of these pipes, the outer diameter of which can lie between 70 and 300 mm, the length between 500 and 2000 mm and the wall thickness between 0,5 and 10 mm. Depending on the pipe type, up to 27 measurements in a maximum of 5 measuring levels are to be controlled. (orig.) [de
Directory of Open Access Journals (Sweden)
D. Jeya Sundara Sharmila1 *
Full Text Available Molecular interactions are key aspects in biological recognitions applicable in nano/micro systems. Bacterial nanowires are pilus filament based structures that can conduct electrons. The transport of electron is proposed to be facilitated by filamentous fibers made up of polymeric assemblies of proteins called pilin. Geobacter sulfurreducens is capable of delivering electrons through extracellular electron transport (EET by employing conductive nanowires, which are pilin proteins composed of type IV subunit PilA. Protein-protein interactions play an important role in the stabilization of the pilin nanowire assembly complex and it contains transmembrane (TM domain. In current study, protein-protein docking and multiple molecular dynamic (MD simulations were performed to understand the binding mode of pilin nanowires. The MD result explains the conformational behavior and folding of pilin nanowires in water environment in different time scale duration 20, 5, 5, 10 and 20ns (total of 60ns. Direct hydrogen bonds and water mediated hydrogen bonds that play a crucial role during the simulation were investigated. The conformational state, folding, end-toend distance profile and hydrogen bonding behavior had indicated that the Geobacter sulfurreducens pilin nanowires have electrical conductivity properties.
QM/MM Molecular Dynamics Studies of Metal Binding Proteins
Directory of Open Access Journals (Sweden)
Pietro Vidossich
Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
General problems of dynamics and control of vibratory gyroscopes
CSIR Research Space (South Africa)
Shatalov, MY
Full Text Available A general model of operation of vibratory gyroscopes, which is applicable to a broad class of instruments, including cylindrical, disc and micro-machined gyros, is formulated on the basis of analysis of dynamics and control of a hemispherical...
Dynamically tuned magnetostrictive spring with electrically controlled stiffness
Scheidler, Justin J.; Asnani, Vivake M.; Dapino, Marcelo J.
This paper presents the design and testing of an electrically controllable magnetostrictive spring that has a dynamically tunable stiffness (i.e., a magnetostrictive Varispring). The device enables in situ stiffness tuning or stiffness switching for vibration control applications. Using a nonlinear electromechanical transducer model and an analytical solution of linear, mechanically induced magnetic diffusion, Terfenol-D is shown to have a faster rise time to stepped voltage inputs and a significantly higher magnetic diffusion cut-off frequency relative to Galfenol. A Varispring is manufactured using a laminated Terfenol-D rod. Further rise time reductions are achieved by minimizing the rod's diameter and winding the electromagnet with larger wire. Dynamic tuning of the Varispring's stiffness is investigated by measuring the Terfenol-D rod's strain response to dynamic, compressive, axial forces in the presence of sinusoidal or square wave control currents. The Varispring's rise time is \\lt 1 ms for 1 A current switches. Continuous modulus changes up to 21.9 GPa and 500 Hz and square wave modulus changes (dynamic {{Δ }}E effect) up to 12.3 GPa and 100 Hz are observed. Stiffness tunability and tuning bandwidth can be considerably increased by operating about a more optimal bias stress and improving the control of the electrical input.
Population dynamics and population control of Galium aparine L.
Weide, van der R.Y.
The population biology of Galium aparine L. needs to be better understood, in order to be able to rationalize decisions about the short- and long-term control of this weed species for different cropping practices.
A population dynamics model was developed to
Integrated vehicle dynamics control using State Dependent Riccati Equations
Bonsen, B.; Mansvelders, R.; Vermeer, E.
In this paper we discuss a State Dependent Riccati Equations (SDRE) solution for Integrated Vehicle Dynamics Control (IVDC). The SDRE approach is a nonlinear variant of the well known Linear Quadratic Regulator (LQR) and implements a quadratic cost function optimization. A modified version of this
The potential value of dynamic materials control in international safeguards
International Nuclear Information System (INIS)
Keepin, G.R.; Lovett, J.E.
The difficulties inherent in conventional materials accountancy based on semi-annual or annual shutdown cleanout physical inventories have been recognized for many years. The increasing importance of international nuclear materials safeguards, coupled with the availability of advanced non-destructive measurement technology which could be installed on or near process lines, has led to the development of the concept of advanced or dynamic materials control. The potential benefits of dynamic materials control in terms of significantly improved detection capabilities (ranging from a few kilograms of plutonium down to perhaps a few hundred grams, even for large-scale bulk processing facilities), and even more dramatically improved detection timeliness (typically a few days, and potentially only a few hours, in advanced facilities), are reviewed. At least twelve major dynamic material control systems already in existence or in the process of being installed are noted, and some of the essential characteristics are discussed. Some currently unresolved questions are explored, and future prospects for the concept of dynamic material control in international safeguards are reviewed. (author)
Dynamic Positioning of Ships : A nonlinear control design study
Muhammad, S.
Dynamic positioning (DP) is relatively a new technique used to maintain the position and heading of ships in various offshore operations. Due to the features like better safety and operating efficiency, DP systems are becoming more and more popular. This thesis mainly focusses on the control system
Optimal control of peridinin excited-state dynamics
Czech Academy of Sciences Publication Activity Database
Dietzek, B.; Chábera, P.; Hanf, R.; Tschierlei, S.; Popp, J.; Pascher, T.; Yartsev, A.; Polívka, Tomáš
Roč. 373, 1-2 (2010), s. 129-136 ISSN 0301-0104 Institutional research plan: CEZ:AV0Z50510513 Keywords : peridin * excited-state dynamics * coherent control Subject RIV: BO - Biophysics Impact factor: 2.017, year: 2010
Graphene: A Dynamic Platform for Electrical Control of Plasmonic Resonance
DEFF Research Database (Denmark)
Emani, Naresh Kumar; Kildishev, Alexander V.; Shalaev, Vladimir M.
Graphene has recently emerged as a viable platform for integrated optoelectronic and hybrid photonic devices because of its unique properties. The optical properties of graphene can be dynamically controlled by electrical voltage and have been used to modulate the plasmons in noble metal nanostru...
Dynamically Authorized Role-Based Access Control for Grid Applications
Institute of Scientific and Technical Information of China (English)
YAO Hanbing; HU Heping; LU Zhengding; LI Ruixuan
Grid computing is concerned with the sharing and coordinated use of diverse resources in distributed "virtual organizations". The heterogeneous, dynamic and multi-domain nature of these environments makes challenging security issues that demand new technical approaches. Despite the recent advances in access control approaches applicable to Grid computing, there remain issues that impede the development of effective access control models for Grid applications. Among them there are the lack of context-based models for access control, and reliance on identity or capability-based access control schemes. An access control scheme that resolve these issues is presented, and a dynamically authorized role-based access control (D-RBAC) model extending the RBAC with context constraints is proposed. The D-RABC mechanisms dynamically grant permissions to users based on a set of contextual information collected from the system and user's environments, while retaining the advantages of RBAC model. The implementation architecture of D-RBAC for the Grid application is also described.
Approximate Dynamic Programming in Tracking Control of a Robotic Manipulator
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Marcin Szuster
Full Text Available This article focuses on the implementation of an approximate dynamic programming algorithm in the discrete tracking control system of the three-degrees of freedom Scorbot-ER 4pc robotic manipulator. The controlled system is included in an articulated robots group which uses rotary joints to access their work space. The main part of the control system is a dual heuristic dynamic programming algorithm that consists of two structures designed in the form of neural networks: an actor and a critic. The actor generates the suboptimal control law while the critic approximates the difference of the value function from Bellman's equation with respect to the state. The residual elements of the control system are the PD controller, the supervisory term and an additional control signal. The structure of the supervisory term derives from the stability analysis performed using the Lyapunov stability theorem. The control system works online, the neural networks' weights-adaptation procedure is performed in every iteration step, and the neural networks' preliminary learning process is not required. The performance of the control system was verified by a series of computer simulations and experiments performed using the Scorbot-ER 4pc robotic manipulator.
Nonlinear Dynamics of Controlled Synchronizations of Manipulator System
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Qingkai Han
Full Text Available The nonlinear dynamics of the manipulator system which is controlled to achieve the synchronization motions is investigated in the paper. Firstly, the control strategies and modeling approaches of the manipulator system are given, in which the synchronization goal is defined by both synchronization errors and its derivatives. The synchronization controllers applied on the manipulator system include neuron synchronization controller, improved OPCL synchronization controller, and MRAC-PD synchronization controller. Then, an improved adaptive synchronized control strategy is proposed in order to estimate online the unknown structure parameters and state variables of the manipulator system and to realize the needed synchronous compensation. Furthermore, a robust adaptive synchronization controller is also researched to guarantee the dynamic stability of the system. Finally, the stability of motion synchronizations of the manipulator system possessing nonlinear component is discussed, together with the effect of control parameters and joint friction and others. Some typical motions such as motion bifurcations and the loss of synchronization of it are obtained and illustrated as periodic, multiperiodic, and/or chaotic motion patterns.
Walking Robots Dynamic Control Systems on an Uneven Terrain
Directory of Open Access Journals (Sweden)
Full Text Available The paper presents ZPM dynamic control of walking robots, developing an open architecture real time control multiprocessor system, in view of obtaining new capabilities for walking robots. The complexity of the movement mechanism of a walking robot was taken into account, being a repetitive tilting process with numerous instable movements and which can lead to its turnover on an uneven terrain. The control system architecture for the dynamic robot walking is presented in correlation with the control strategy which contains three main real time control loops: balance robot control using sensorial feedback, walking diagram control with periodic changes depending on the sensorial information during each walk cycle, predictable movement control based on a quick decision from the previous experimental data. The results obtained through simulation and experiments show an increase in mobility, stability in real conditions and obtaining of high performances related to the possibility of moving walking robots on terrains with a configuration as close as possible to real situations, respectively developing new technological capabilities of the walking robot control systems for slope movement and walking by overtaking or going around obstacles.
A nonlinear optimal control approach for chaotic finance dynamics
Rigatos, G.; Siano, P.; Loia, V.; Tommasetti, A.; Troisi, O.
A new nonlinear optimal control approach is proposed for stabilization of the dynamics of a chaotic finance model. The dynamic model of the financial system, which expresses interaction between the interest rate, the investment demand, the price exponent and the profit margin, undergoes approximate linearization round local operating points. These local equilibria are defined at each iteration of the control algorithm and consist of the present value of the systems state vector and the last value of the control inputs vector that was exerted on it. The approximate linearization makes use of Taylor series expansion and of the computation of the associated Jacobian matrices. The truncation of higher order terms in the Taylor series expansion is considered to be a modelling error that is compensated by the robustness of the control loop. As the control algorithm runs, the temporary equilibrium is shifted towards the reference trajectory and finally converges to it. The control method needs to compute an H-infinity feedback control law at each iteration, and requires the repetitive solution of an algebraic Riccati equation. Through Lyapunov stability analysis it is shown that an H-infinity tracking performance criterion holds for the control loop. This implies elevated robustness against model approximations and external perturbations. Moreover, under moderate conditions the global asymptotic stability of the control loop is proven.
Short-Range Electron Transfer in Reduced Flavodoxin: Ultrafast Nonequilibrium Dynamics Coupled with Protein Fluctuations.
Kundu, Mainak; He, Ting-Fang; Lu, Yangyi; Wang, Lijuan; Zhong, Dongping
Short-range electron transfer (ET) in proteins is an ultrafast process on the similar timescales as local protein-solvent fluctuations thus the two dynamics are coupled. Here, we use semiquinone flavodoxin and systematically characterized the photoinduced redox cycle with eleven mutations of different aromatic electron donors (tryptophan and tyrosine) and local residues to change redox properties. We observed the forward and backward ET dynamics in a few picoseconds, strongly following a stretched behavior resulting from a coupling between local environment relaxations and these ET processes. We further observed the hot vibrational-state formation through charge recombination and the subsequent cooling dynamics also in a few picoseconds. Combined with the ET studies in oxidized flavodoxin, these results coherently reveal the evolution of the ET dynamics from single to stretched exponential behaviors and thus elucidate critical timescales for the coupling. The observed hot vibration-state formation is robust and should be considered in all photoinduced back ET processes in flavoproteins.
Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation*
Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert
trafficking, enhancement of metabolic activity, and Wnt signaling pathway during the steep phase of memory formation; and (3) cytoskeleton organization proteins. Taken together, this study clearly demonstrates dynamic assembly and disassembly of protein-protein interaction networks depending on the stage of memory formation engrams. PMID:26598641
Dynamics of Hippocampal Protein Expression During Long-term Spatial Memory Formation.
Borovok, Natalia; Nesher, Elimelech; Levin, Yishai; Reichenstein, Michal; Pinhasov, Albert; Michaelevski, Izhak
trafficking, enhancement of metabolic activity, and Wnt signaling pathway during the steep phase of memory formation; and (3) cytoskeleton organization proteins. Taken together, this study clearly demonstrates dynamic assembly and disassembly of protein-protein interaction networks depending on the stage of memory formation engrams. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Flatness-based adaptive fuzzy control of chaotic finance dynamics
Rigatos, G.; Siano, P.; Loia, V.; Tommasetti, A.; Troisi, O.
A flatness-based adaptive fuzzy control is applied to the problem of stabilization of the dynamics of a chaotic finance system, describing interaction between the interest rate, the investment demand and the price exponent. By proving that the system is differentially flat and by applying differential flatness diffeomorphisms, its transformation to the linear canonical (Brunovsky) is performed. For the latter description of the system, the design of a stabilizing state feedback controller becomes possible. A first problem in the design of such a controller is that the dynamic model of the finance system is unknown and thus it has to be identified with the use neurofuzzy approximators. The estimated dynamics provided by the approximators is used in the computation of the control input, thus establishing an indirect adaptive control scheme. The learning rate of the approximators is chosen from the requirement the system's Lyapunov function to have always a negative first-order derivative. Another problem that has to be dealt with is that the control loop is implemented only with the use of output feedback. To estimate the non-measurable state vector elements of the finance system, a state observer is implemented in the control loop. The computation of the feedback control signal requires the solution of two algebraic Riccati equations at each iteration of the control algorithm. Lyapunov stability analysis demonstrates first that an H-infinity tracking performance criterion is satisfied. This signifies elevated robustness against modelling errors and external perturbations. Moreover, the global asymptotic stability is proven for the control loop.
Self-Organized Biological Dynamics and Nonlinear Control
Walleczek, Jan
The frontiers and challenges of biodynamics research Jan Walleczek; Part I. Nonlinear Dynamics in Biology and Response to Stimuli: 1. External signals and internal oscillation dynamics - principal aspects and response of stimulated rhythmic processes Friedemann Kaiser; 2. Nonlinear dynamics in biochemical and biophysical systems: from enzyme kinetics to epilepsy Raima Larter, Robert Worth and Brent Speelman; 3. Fractal mechanisms in neural control: human heartbeat and gait dynamics in health and disease Chung-Kang Peng, Jeffrey M. Hausdorff and Ary L. Goldberger; 4. Self-organising dynamics in human coordination and perception Mingzhou Ding, Yanqing Chen, J. A. Scott Kelso and Betty Tuller; 5. Signal processing in biochemical reaction networks Adam P. Arkin; Part II. Nonlinear Sensitivity of Biological Systems to Electromagnetic Stimuli: 6. Electrical signal detection and noise in systems with long-range coherence Paul C. Gailey; 7. Oscillatory signals in migrating neutrophils: effects of time-varying chemical and electrical fields Howard R. Petty; 8. Enzyme kinetics and nonlinear biochemical amplification in response to static and oscillating magnetic fields Jan Walleczek and Clemens F. Eichwald; 9. Magnetic field sensitivity in the hippocampus Stefan Engström, Suzanne Bawin and W. Ross Adey; Part III. Stochastic Noise-Induced Dynamics and Transport in Biological Systems: 10. Stochastic resonance: looking forward Frank Moss; 11. Stochastic resonance and small-amplitude signal transduction in voltage-gated ion channels Sergey M. Bezrukov and Igor Vodyanoy; 12. Ratchets, rectifiers and demons: the constructive role of noise in free energy and signal transduction R. Dean Astumian; 13. Cellular transduction of periodic and stochastic energy signals by electroconformational coupling Tian Y. Tsong; Part IV. Nonlinear Control of Biological and Other Excitable Systems: 14. Controlling chaos in dynamical systems Kenneth Showalter; 15. Electromagnetic fields and biological
Protein dynamics associated with failed and rescued learning in the Ts65Dn mouse model of Down syndrome.
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Md Mahiuddin Ahmed
Full Text Available Down syndrome (DS is caused by an extra copy of human chromosome 21 (Hsa21. Although it is the most common genetic cause of intellectual disability (ID, there are, as yet, no effective pharmacotherapies. The Ts65Dn mouse model of DS is trisomic for orthologs of ∼55% of Hsa21 classical protein coding genes. These mice display many features relevant to those seen in DS, including deficits in learning and memory (L/M tasks requiring a functional hippocampus. Recently, the N-methyl-D-aspartate (NMDA receptor antagonist, memantine, was shown to rescue performance of the Ts65Dn in several L/M tasks. These studies, however, have not been accompanied by molecular analyses. In previous work, we described changes in protein expression induced in hippocampus and cortex in control mice after exposure to context fear conditioning (CFC, with and without memantine treatment. Here, we extend this analysis to Ts65Dn mice, measuring levels of 85 proteins/protein modifications, including components of MAP kinase and MTOR pathways, and subunits of NMDA receptors, in cortex and hippocampus of Ts65Dn mice after failed learning in CFC and after learning was rescued by memantine. We show that, compared with wild type littermate controls, (i of the dynamic responses seen in control mice in normal learning, >40% also occur in Ts65Dn in failed learning or are compensated by baseline abnormalities, and thus are considered necessary but not sufficient for successful learning, and (ii treatment with memantine does not in general normalize the initial protein levels but instead induces direct and indirect responses in approximately half the proteins measured and results in normalization of the endpoint protein levels. Together, these datasets provide a first view of the complexities associated with pharmacological rescue of learning in the Ts65Dn. Extending such studies to additional drugs and mouse models of DS will aid in identifying pharmacotherapies for effective
Zaccai neutron resilience and site-specific hydration dynamics in a globular protein
Energy Technology Data Exchange (ETDEWEB)
Miao, Yinglong [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hong, Liang [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yi, Zheng [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
A discussion is presented of contributions of the Zaccai group to the understanding of flexibility in biological macromolecules using dynamic neutron scattering. The concept of resilience as introduced by Zaccai is discussed and investigated using molecular dynamics simulation on camphor-bound cytochrome P450. The resilience of hydrophilic residues is found to be more strongly affected by hydration than that of hydrophobic counterparts. The hydration-induced softening of protein propagates from the surface into the dry core. Furthermore, buried hydrophilic residues behave more like those exposed on the protein surface, and are different from their hydrophobic counterparts.
Exploration of Protein Conformational Change with PELE and Meta-Dynamics.
Cossins, Benjamin P; Hosseini, Ali; Guallar, Victor
Atomistic molecular simulation methods are now able to explore complex protein or protein-ligand dynamical space in a tractable way with methods such as meta-dynamics or adaptive biasing force. However, many of these methods either require a careful selection of reaction coordinates or the knowledge of an initial pathway of some kind. Thus, it is important that effective methods are developed to produce this pathway data in an efficient fashion. PELE, a proven protein-ligand sampling code, has been developed to provide rapid protein sampling in highly flexible cases, using a reduced network model eigen problem approach. The resulting method is able to rapidly sample configuration space with very general driving information. When applied to ubiquitin, PELE was able to reproduce RMSD and average force data found in molecular dynamics simulations. PELE was also applied to explore the opening/closing transition of T4 lysozyme. A meta-dynamics exploration using a low energy pathway validated that the configurations explored by PELE represent the most populated regions of phase space. PELE and meta-dynamics explorations also discovered a low free energy region where a large cross-domain helix of T4 lysozyme is broken in two. There is previous NMR evidence for the validity of this unfolded helix region.
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.
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Samuel Hertig
Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.
A dynamic study of protein secretion and aggregation in the secretory pathway.
Mossuto, Maria Francesca; Sannino, Sara; Mazza, Davide; Fagioli, Claudio; Vitale, Milena; Yoboue, Edgar Djaha; Sitia, Roberto; Anelli, Tiziana
Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.
A dynamic study of protein secretion and aggregation in the secretory pathway.
Directory of Open Access Journals (Sweden)
Maria Francesca Mossuto
Full Text Available Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC is key for cell physiology. As a consequence, disturbances in these processes underlie many genetic and chronic diseases. Dynamic imaging methods are needed to follow the fate of cargo proteins and their interactions with resident enzymes and folding assistants. Here we applied the Halotag labelling system to study the behavior of proteins with different fates and roles in ESC: a chaperone, an ERAD substrate and an aggregation-prone molecule. Exploiting the Halo property of binding covalently ligands labelled with different fluorochromes, we developed and performed non-radioactive pulse and chase assays to follow sequential waves of proteins in ESC, discriminating between young and old molecules at the single cell level. In this way, we could monitor secretion and degradation of ER proteins in living cells. We can also follow the biogenesis, growth, accumulation and movements of protein aggregates in the ESC. Our data show that protein deposits within ESC grow by sequential apposition of molecules up to a given size, after which novel seeds are detected. The possibility of using ligands with distinct optical and physical properties offers a novel possibility to dynamically follow the fate of proteins in the ESC.
Reaction dynamics of inflammation proteins and T lymphocytes during radon balneotherapy
International Nuclear Information System (INIS)
Peter, A.; Vulpe, B.
During a three-week radon treatment with daily administration of baths a periodical course of reaction with antidromic dynamics of inflammation proteins and T lymphocytes could be shown. A conspicuous reaction of the organism (moment of the treatment reaction) is to be observed one week after the beginning of the treatment. At the end of the cure a decrease of the activity of inflammation as well as of individual acute-phase proteins and immunoglobulins it to be proved. (author)
Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.
Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.
Dynamic Colloidal Molecules Maneuvered by Light-Controlled Janus Micromotors.
Gao, Yirong; Mou, Fangzhi; Feng, Yizheng; Che, Shengping; Li, Wei; Xu, Leilei; Guan, Jianguo
In this work, we propose and demonstrate a dynamic colloidal molecule that is capable of moving autonomously and performing swift, reversible, and in-place assembly dissociation in a high accuracy by manipulating a TiO 2 /Pt Janus micromotor with light irradiation. Due to the efficient motion of the TiO 2 /Pt Janus motor and the light-switchable electrostatic interactions between the micromotor and colloidal particles, the colloidal particles can be captured and assembled one by one on the fly, subsequently forming into swimming colloidal molecules by mimicking space-filling models of simple molecules with central atoms. The as-demonstrated dynamic colloidal molecules have a configuration accurately controlled and stabilized by regulating the time-dependent intensity of UV light, which controls the stop-and-go motion of the colloidal molecules. The dynamic colloidal molecules are dissociated when the light irradiation is turned off due to the disappearance of light-switchable electrostatic interaction between the motor and the colloidal particles. The strategy for the assembly of dynamic colloidal molecules is applicable to various charged colloidal particles. The simulated optical properties of a dynamic colloidal molecule imply that the results here may provide a novel approach for in-place building functional microdevices, such as microlens arrays, in a swift and reversible manner.
Dynamical sensitivity control of a single-spin quantum sensor.
Lazariev, Andrii; Arroyo-Camejo, Silvia; Rahane, Ganesh; Kavatamane, Vinaya Kumar; Balasubramanian, Gopalakrishnan
The Nitrogen-Vacancy (NV) defect in diamond is a unique quantum system that offers precision sensing of nanoscale physical quantities at room temperature beyond the current state-of-the-art. The benchmark parameters for nanoscale magnetometry applications are sensitivity, spectral resolution, and dynamic range. Under realistic conditions the NV sensors controlled by conventional sensing schemes suffer from limitations of these parameters. Here we experimentally show a new method called dynamical sensitivity control (DYSCO) that boost the benchmark parameters and thus extends the practical applicability of the NV spin for nanoscale sensing. In contrast to conventional dynamical decoupling schemes, where π pulse trains toggle the spin precession abruptly, the DYSCO method allows for a smooth, analog modulation of the quantum probe's sensitivity. Our method decouples frequency selectivity and spectral resolution unconstrained over the bandwidth (1.85 MHz-392 Hz in our experiments). Using DYSCO we demonstrate high-accuracy NV magnetometry without |2π| ambiguities, an enhancement of the dynamic range by a factor of 4 · 10 3 , and interrogation times exceeding 2 ms in off-the-shelf diamond. In a broader perspective the DYSCO method provides a handle on the inherent dynamics of quantum systems offering decisive advantages for NV centre based applications notably in quantum information and single molecule NMR/MRI.
System dynamics and control with bond graph modeling
Kypuros, Javier
Part I Dynamic System ModelingIntroduction to System DynamicsIntroductionSystem Decomposition and Model ComplexityMathematical Modeling of Dynamic SystemsAnalysis and Design of Dynamic SystemsControl of Dynamic SystemsDiagrams of Dynamic SystemsA Graph-Centered Approach to ModelingSummaryPracticeExercisesBasic Bond Graph ElementsIntroductionPower and Energy VariablesBasic 1-Port ElementsBasic 2-Ports ElementsJunction ElementsSimple Bond Graph ExamplesSummaryPracticeExercisesBond Graph Synthesis and Equation DerivationIntroductionGeneral GuidelinesMechanical TranslationMechanical RotationElectrical CircuitsHydraulic CircuitsMixed SystemsState Equation DerivationState-Space RepresentationsAlgebraic Loops and Derivative CausalitySummaryPracticeExercisesImpedance Bond GraphsIntroductionLaplace Transform of the State-Space EquationBasic 1-Port ImpedancesImpedance Bond Graph SynthesisJunctions, Transformers, and GyratorsEffort and Flow DividersSign ChangesTransfer Function DerivationAlternative Derivation of Transf...
Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
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Zheng-Yu Jiang
Full Text Available Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1, a substrate adaptor component of the Cullin3 (Cul3-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2 and IκB kinase β (IKKβ, which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI, the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.
Integrated health management and control of complex dynamical systems
Tolani, Devendra K.
A comprehensive control and health management strategy for human-engineered complex dynamical systems is formulated for achieving high performance and reliability over a wide range of operation. Results from diverse research areas such as Probabilistic Robust Control (PRC), Damage Mitigating/Life Extending Control (DMC), Discrete Event Supervisory (DES) Control, Symbolic Time Series Analysis (STSA) and Health and Usage Monitoring System (HUMS) have been employed to achieve this goal. Continuous-domain control modules at the lower level are synthesized by PRC and DMC theories, whereas the upper-level supervision is based on DES control theory. In the PRC approach, by allowing different levels of risk under different flight conditions, the control system can achieve the desired trade off between stability robustness and nominal performance. In the DMC approach, component damage is incorporated in the control law to reduce the damage rate for enhanced structural durability. The DES controller monitors the system performance and, based on the mission requirements (e.g., performance metrics and level of damage mitigation), switches among various lower-level controllers. The core idea is to design a framework where the DES controller at the upper-level, mimics human intelligence and makes appropriate decisions to satisfy mission requirements, enhance system performance and structural durability. Recently developed tools in STSA have been used for anomaly detection and failure prognosis. The DMC deals with the usage monitoring or operational control part of health management, where as the issue of health monitoring is addressed by the anomaly detection tools. The proposed decision and control architecture has been validated on two test-beds, simulating the operations of rotorcraft dynamics and aircraft propulsion.
Model-based dynamic control and optimization of gas networks
Energy Technology Data Exchange (ETDEWEB)
Hofsten, Kai
This work contributes to the research on control, optimization and simulation of gas transmission systems to support the dispatch personnel at gas control centres for the decision makings in the daily operation of the natural gas transportation systems. Different control and optimization strategies have been studied. The focus is on the operation of long distance natural gas transportation systems. Stationary optimization in conjunction with linear model predictive control using state space models is proposed for supply security, the control of quality parameters and minimization of transportation costs for networks offering transportation services. The result from the stationary optimization together with a reformulation of a simplified fluid flow model formulates a linear dynamic optimization model. This model is used in a finite time control and state constrained linear model predictive controller. The deviation from the control and the state reference determined from the stationary optimization is penalized quadratically. Because of the time varying status of infrastructure, the control space is also generally time varying. When the average load is expected to change considerably, a new stationary optimization is performed, giving a new state and control reference together with a new dynamic model that is used for both optimization and state estimation. Another proposed control strategy is a control and output constrained nonlinear model predictive controller for the operation of gas transmission systems. Here, the objective is also the security of the supply, quality control and minimization of transportation costs. An output vector is defined, which together with a control vector are both penalized quadratically from their respective references in the objective function. The nonlinear model predictive controller can be combined with a stationary optimization. At each sampling instant, a non convex nonlinear programming problem is solved giving a local minimum
Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.
Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing
Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.
On some control problems of dynamic of reactor
Baskakov, A. V.; Volkov, N. P.
The paper analyzes controllability of the transient processes in some problems of nuclear reactor dynamics. In this case, the mathematical model of nuclear reactor dynamics is described by a system of integro-differential equations consisting of the non-stationary anisotropic multi-velocity kinetic equation of neutron transport and the balance equation of delayed neutrons. The paper defines the formulation of the linear problem on control of transient processes in nuclear reactors with application of spatially distributed actions on internal neutron sources, and the formulation of the nonlinear problems on control of transient processes with application of spatially distributed actions on the neutron absorption coefficient and the neutron scattering indicatrix. The required control actions depend on the spatial and velocity coordinates. The theorems on existence and uniqueness of these control actions are proved in the paper. To do this, the control problems mentioned above are reduced to equivalent systems of integral equations. Existence and uniqueness of the solution for this system of integral equations is proved by the method of successive approximations, which makes it possible to construct an iterative scheme for numerical analyses of transient processes in a given nuclear reactor with application of the developed mathematical model. Sufficient conditions for controllability of transient processes are also obtained. In conclusion, a connection is made between the control problems and the observation problems, which, by to the given information, allow us to reconstruct either the function of internal neutron sources, or the neutron absorption coefficient, or the neutron scattering indicatrix....
Determination of Dynamics of Plant Plasma Membrane Proteins with Fluorescence Recovery and Raster Image Correlation Spectroscopy.
Laňková, Martina; Humpolíčková, Jana; Vosolsobě, Stanislav; Cit, Zdeněk; Lacek, Jozef; Čovan, Martin; Čovanová, Milada; Hof, Martin; Petrášek, Jan
A number of fluorescence microscopy techniques are described to study dynamics of fluorescently labeled proteins, lipids, nucleic acids, and whole organelles. However, for studies of plant plasma membrane (PM) proteins, the number of these techniques is still limited because of the high complexity of processes that determine the dynamics of PM proteins and the existence of cell wall. Here, we report on the usage of raster image correlation spectroscopy (RICS) for studies of integral PM proteins in suspension-cultured tobacco cells and show its potential in comparison with the more widely used fluorescence recovery after photobleaching method. For RICS, a set of microscopy images is obtained by single-photon confocal laser scanning microscopy (CLSM). Fluorescence fluctuations are subsequently correlated between individual pixels and the information on protein mobility are extracted using a model that considers processes generating the fluctuations such as diffusion and chemical binding reactions. As we show here using an example of two integral PM transporters of the plant hormone auxin, RICS uncovered their distinct short-distance lateral mobility within the PM that is dependent on cytoskeleton and sterol composition of the PM. RICS, which is routinely accessible on modern CLSM instruments, thus represents a valuable approach for studies of dynamics of PM proteins in plants.
Dynamic Modelling and Adaptive Traction Control for Mobile Robots
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A. Albagul
Full Text Available Mobile robots have received a great deal of research in recent years. A significant amount of research has been published in many aspects related to mobile robots. Most of the research is devoted to design and develop some control techniques for robot motion and path planning. A large number of researchers have used kinematic models to develop motion control strategy for mobile robots. Their argument and assumption that these models are valid if the robot has low speed, low acceleration and light load. However, dynamic modelling of mobile robots is very important as they are designed to travel at higher speed and perform heavy duty work. This paper presents and discusses a new approach to develop a dynamic model and control strategy for wheeled mobile robot which I modelled as a rigid body that roles on two wheels and a castor. The motion control strategy consists of two levels. The first level is dealing with the dynamic of the system and denoted as 'Low' level controller. The second level is developed to take care of path planning and trajectory generation.
Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.
Gnanasekaran, Ramachandran; Xu, Yao; Leitner, David M
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
Quantized Passive Dynamic Output Feedback Control with Actuator Failure
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Zu-Xin Li
Full Text Available This paper investigates the problem of passive dynamic output feedback control for fuzzy discrete nonlinear systems with quantization and actuator failures, where the measurement output of the system is quantized by a logarithmic quantizer before being transferred to the fuzzy controller. By employing the fuzzy-basis-dependent Lyapunov function, sufficient condition is established to guarantee the closed-loop system to be mean-square stable and the prescribed passive performance. Based on the sufficient condition, the fuzzy dynamic output feedback controller is proposed for maintaining acceptable performance levels in the case of actuator failures and quantization effects. Finally, a numerical example is given to show the usefulness of the proposed method.
Dynamic Characteristics Analysis of Power Shift Control Valve
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Feng Ren
Full Text Available In order to study the influence that dynamic performance of shift control valve has on shifting process of construction machinery, the paper introduces working principle of the shift control valve and sets up the dynamically mathematical model and corresponding simulation model with simulation software LMS Imagine. Lab AMESim. Based on simulation, the paper analyzes the influence of pressure variation characteristics and buffering characteristics acting on vehicle performance during the process of shifting, meanwhile conducting experiments to verify the simulation. The results indicate that the simulation model is accurate and credible; the performance of the valve is satisfactory, which indeed reduces impact during shifting. Furthermore, the valve can meet the demand of other construction machineries in better degree by suitable matching between control spring stiffness and damping holes diameter.
Control of articulated snake robot under dynamic active constraints.
Kwok, Ka-Wai; Vitiello, Valentina; Yang, Guang-Zhong
Flexible, ergonomically enhanced surgical robots have important applications to transluminal endoscopic surgery, for which path-following and dynamic shape conformance are essential. In this paper, kinematic control of a snake robot for motion stabilisation under dynamic active constraints is addressed. The main objective is to enable the robot to track the visual target accurately and steadily on deforming tissue whilst conforming to pre-defined anatomical constraints. The motion tracking can also be augmented with manual control. By taking into account the physical limits in terms of maximum frequency response of the system (manifested as a delay between the input of the manipulator and the movement of the end-effector), we show the importance of visual-motor synchronisation for performing accurate smooth pursuit movements. Detailed user experiments are performed to demonstrate the practical value of the proposed control mechanism.
Dynamic control of a bistable wing under aerodynamic loading
International Nuclear Information System (INIS)
Bilgen, Onur; Arrieta, Andres F; Friswell, Michael I; Hagedorn, Peter
The aerodynamic evaluation of a dynamic control technique applied to a bistable unsymmetrical cross-ply composite plate with surface bonded piezoelectric actuators is presented. The plate is clamped on one end to form a low-aspect-ratio wing. A previously proposed dynamic control method, utilizing bending resonance in different stable equilibrium positions, is used to induce snap-through between the two equilibrium states. Compared to quasi-static actuation, driving the bistable plate near resonance using surface bonded piezoelectric materials requires, theoretically, a lower peak excitation voltage to achieve snap-through. First, a set of extensive wind tunnel experiments are conducted on the passive bistable wing to understand the change in the dynamic behavior under various aerodynamic conditions. The passive wing demonstrated sufficient bending stiffness to sustain its shape under aerodynamic loading while preserving the desired bistable behavior. Next, by the use of the resonant control technique, the plate is turned into an effectively monostable structure, or alternatively, both stable equilibrium positions can be reached actively from the other stable equilibrium. Dynamic forward and reverse snap-through is demonstrated in the wind tunnel which shows both the effectiveness of the piezoelectric actuation as well as the load carrying capability of both states of the bistable wing. (paper)
Predictive control and identification: Applications to steering dynamics
DEFF Research Database (Denmark)
Hansen, Anca Daniela
and of the loss function, which defines the optimality of the control. Some guidelines on how to choose the design parameters, depending on the type of process to be controlled and on the required control performance, are presented. A predictive track keeping system for a Mariner Class Vessel is formulated based...... the under- standing of the connection between identification and control, analysed in Chapter 7. Chapter 7 focuses on how to make the on-line identification for predictive control more robust towards unmodelled dynamics. The theory is verified via simulation studies on a Mariner Class Vessel. The effects...... and the need of a prefilter in the estimation are analysed and illustrated. Based on the idea that the control criterion must be dual to the estimation criterion, an iterative optimal prefilter is designed. This seems to be an appealing way to tune the model towards the objective for which the model...
Dynamic coordinated control laws in multiple agent models
International Nuclear Information System (INIS)
Morgan, David S.; Schwartz, Ira B.
We present an active control scheme of a kinetic model of swarming. It has been shown previously that the global control scheme for the model, presented in [Systems Control Lett. 52 (2004) 25], gives rise to spontaneous collective organization of agents into a unified coherent swarm, via steering controls and utilizing long-range attractive and short-range repulsive interactions. We extend these results by presenting control laws whereby a single swarm is broken into independently functioning subswarm clusters. The transition between one coordinated swarm and multiple clustered subswarms is managed simply with a homotopy parameter. Additionally, we present as an alternate formulation, a local control law for the same model, which implements dynamic barrier avoidance behavior, and in which swarm coherence emerges spontaneously
Importance of Dynamic Inflow Model Predictive Control of Wind Turbines
DEFF Research Database (Denmark)
Odgaard, Peter Fogh; Knudsen, Torben; Overgaard, Anders
The efficiency of including dynamic inflow in the model based design of wind turbine controller has been discussed for many years in the wind energy community with out getting to a safe conclusion. This paper delivers a good argument in favor of including dynamic inflow. The main contributions...... pronounces. For this the well accepted NREL 5MW reference turbine simulated with FAST is used. The main result is a reduction in tower fatigue load at 22% while power error, rotor speed error, generator torque and pitch rate is improved from 2 to 33%....
A dynamic model of the greenhouse effect and its control
International Nuclear Information System (INIS)
Perman, R.; Nisbet, R.; Ma, Y.
A dynamic model is developed for the analysis of programmes to control the greenhouse effect. The model uses simplified representations of physical processes determining climate change, linked to an economic model of emissions and emissions abatement. Feedbacks between physical and economic processes are incorporated, and the costs of emissions reduction are compared with the benefits through averted damage. Simulation analyses explore the relative merits of several intervention scenarios, each of which is compared with non intervention. Throughout the paper, emphasis is placed upon the long term consequences of behaviour, and the patterns of dynamic adjustment over time. (author)
Adaptive control of structural balance for complex dynamical networks based on dynamic coupling of nodes
Gao, Zilin; Wang, Yinhe; Zhang, Lili
In the existing research results of the complex dynamical networks controlled, the controllers are mainly used to guarantee the synchronization or stabilization of the nodes' state, and the terms coupled with connection relationships may affect the behaviors of nodes, this obviously ignores the dynamic common behavior of the connection relationships between the nodes. In fact, from the point of view of large-scale system, a complex dynamical network can be regarded to be composed of two time-varying dynamic subsystems, which can be called the nodes subsystem and the connection relationships subsystem, respectively. Similar to the synchronization or stabilization of the nodes subsystem, some characteristic phenomena can be also emerged in the connection relationships subsystem. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. This paper focuses on the structural balance in dynamic complex networks. Generally speaking, the state of the connection relationships subsystem is difficult to be measured accurately in practical applications, and thus it is not easy to implant the controller directly into the connection relationships subsystem. It is noted that the nodes subsystem and the relationships subsystem are mutually coupled, which implies that the state of the connection relationships subsystem can be affected by the controllable state of nodes subsystem. Inspired by this observation, by using the structural balance theory of triad, the controller with the parameter adaptive law is proposed for the nodes subsystem in this paper, which may ensure the connection relationship matrix to approximate a given structural balance matrix in the sense of the uniformly ultimately bounded (UUB). That is, the structural balance may be obtained by employing the controlling state of the nodes subsystem. Finally, the simulations are used to show the validity of the method in this paper.
Isolated sub-100-as pulse generation via controlling electron dynamics
International Nuclear Information System (INIS)
Lan Pengfei; Lu Peixiang; Cao Wei; Li Yuhua; Wang Xinlin
A method to coherently control electron dynamics is proposed using a few-cycle laser pulse in combination with a controlling field. It is shown that this method not only broadens the attosecond pulse bandwidth, but also reduces the chirp; thus an isolated 80-as pulse is straightforwardly obtained, and even shorter pulses are achievable by increasing the intensity of the controlling field. Such ultrashort pulses allow one to investigate ultrafast electronic processes. In addition, the few-cycle synthesized pulse is expected to be useful for manipulating a wide range of laser-atom interactions
Directory of Open Access Journals (Sweden)
Andrey Borisovich Nikolaev
Full Text Available The article considers the issues of traffic management using intelligent system "Car-Road" (IVHS, which consist of interacting intelligent vehicles (IV and intelligent roadside controllers. Vehicles are organized in convoy with small distances between them. All vehicles are assumed to be fully automated (throttle control, braking, steering. Proposed approaches for determining speed limits for traffic cars on the motorway using a model predictive control (MPC. The article proposes an approach to dynamic speed limit to minimize the downtime of vehicles in traffic.
Decentralized control and filtering in interconnected dynamical systems
Mahmoud, Magdi S
Based on the many approaches available for dealing with large-scale systems (LSS), Decentralized Control and Filtering in Interconnected Dynamical Systems supplies a rigorous framework for studying the analysis, stability, and control problems of LSS. Providing an overall assessment of LSS theories, it addresses model order reduction, parametric uncertainties, time delays, and control estimator gain perturbations. Taking readers on a guided tour through LSS, the book examines recent trends and approaches and reviews past methods and results from a contemporary perspective. It traces the progre
Advanced WEC Dynamics & Controls FY16 Testing Report
Energy Technology Data Exchange (ETDEWEB)
Coe, Ryan Geoffrey [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bacelli, Giorgio [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wilson, David G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Patterson, David Charles [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
A model-scale wave tank test was conducted in the interest of improving control systems design of wave energy converters (WECs). The success of most control strategies is based directly upon the availability of a reduced-order model with the ability to capture the dynamics of the system with sufficient accuracy. For this reason, the test described in this report, which is the first in a series of planned tests on WEC controls, focused on system identification (system ID) and model validation.
Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn.
Directory of Open Access Journals (Sweden)
Yongbin Dong
Full Text Available The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.
Adaptive and neuroadaptive control for nonnegative and compartmental dynamical systems
Volyanskyy, Kostyantyn Y.
Neural networks have been extensively used for adaptive system identification as well as adaptive and neuroadaptive control of highly uncertain systems. The goal of adaptive and neuroadaptive control is to achieve system performance without excessive reliance on system models. To improve robustness and the speed of adaptation of adaptive and neuroadaptive controllers several controller architectures have been proposed in the literature. In this dissertation, we develop a new neuroadaptive control architecture for nonlinear uncertain dynamical systems. The proposed framework involves a novel controller architecture with additional terms in the update laws that are constructed using a moving window of the integrated system uncertainty. These terms can be used to identify the ideal system weights of the neural network as well as effectively suppress system uncertainty. Linear and nonlinear parameterizations of the system uncertainty are considered and state and output feedback neuroadaptive controllers are developed. Furthermore, we extend the developed framework to discrete-time dynamical systems. To illustrate the efficacy of the proposed approach we apply our results to an aircraft model with wing rock dynamics, a spacecraft model with unknown moment of inertia, and an unmanned combat aerial vehicle undergoing actuator failures, and compare our results with standard neuroadaptive control methods. Nonnegative systems are essential in capturing the behavior of a wide range of dynamical systems involving dynamic states whose values are nonnegative. A sub-class of nonnegative dynamical systems are compartmental systems. These systems are derived from mass and energy balance considerations and are comprised of homogeneous interconnected microscopic subsystems or compartments which exchange variable quantities of material via intercompartmental flow laws. In this dissertation, we develop direct adaptive and neuroadaptive control framework for stabilization, disturbance
COFS 1: Beam dynamics and control technology overview
Allen, John L.
The Control of Flexible Structures (COFS) 1 Project provides the invaluable opportunity to test, validate, and measure the effectiveness of theories, structural concepts, control systems, and flight certification processes for future missions through a research program focusing on multiple issues in large flexible structures, dynamics, and controls. The COFS 1 Project consists of a series of ground and flight activities building progressively from modeling and dynamic characterization of large space systems to the more complex issues of flexible-body control. The program objectives are to: determine the degree to which theory and ground testing can predict flight performance of next-generation low-frequency structures; evaluate structural fidelity of representative next-generation large deployable precision structure; assess math modeling requirements for large lightweight complex systems on which ground test results are questionable; determine degree to which scale model analysis and tests can be correlated to full-scale performance; evaluate system identification and state estimation algorithms on complex lightweight structures in the space environment; evaluate and verify controls/structures modeling capability; evaluate control laws and control systems; and evaluate damping effects in micro-g environment.
Machine learning control taming nonlinear dynamics and turbulence
Duriez, Thomas; Noack, Bernd R
This is the first book on a generally applicable control strategy for turbulence and other complex nonlinear systems. The approach of the book employs powerful methods of machine learning for optimal nonlinear control laws. This machine learning control (MLC) is motivated and detailed in Chapters 1 and 2. In Chapter 3, methods of linear control theory are reviewed. In Chapter 4, MLC is shown to reproduce known optimal control laws for linear dynamics (LQR, LQG). In Chapter 5, MLC detects and exploits a strongly nonlinear actuation mechanism of a low-dimensional dynamical system when linear control methods are shown to fail. Experimental control demonstrations from a laminar shear-layer to turbulent boundary-layers are reviewed in Chapter 6, followed by general good practices for experiments in Chapter 7. The book concludes with an outlook on the vast future applications of MLC in Chapter 8. Matlab codes are provided for easy reproducibility of the presented results. The book includes interviews with leading r...
Designing sequence to control protein function in an EF-hand protein.
Bunick, Christopher G; Nelson, Melanie R; Mangahas, Sheryll; Hunter, Michael J; Sheehan, Jonathan H; Mizoue, Laura S; Bunick, Gerard J; Chazin, Walter J
The extent of conformational change that calcium binding induces in EF-hand proteins is a key biochemical property specifying Ca(2+) sensor versus signal modulator function. To understand how differences in amino acid sequence lead to differences in the response to Ca(2+) binding, comparative analyses of sequence and structures, combined with model building, were used to develop hypotheses about which amino acid residues control Ca(2+)-induced conformational changes. These results were used to generate a first design of calbindomodulin (CBM-1), a calbindin D(9k) re-engineered with 15 mutations to respond to Ca(2+) binding with a conformational change similar to that of calmodulin. The gene for CBM-1 was synthesized, and the protein was expressed and purified. Remarkably, this protein did not exhibit any non-native-like molten globule properties despite the large number of mutations and the nonconservative nature of some of them. Ca(2+)-induced changes in CD intensity and in the binding of the hydrophobic probe, ANS, implied that CBM-1 does undergo Ca(2+) sensorlike conformational changes. The X-ray crystal structure of Ca(2+)-CBM-1 determined at 1.44 A resolution reveals the anticipated increase in hydrophobic surface area relative to the wild-type protein. A nascent calmodulin-like hydrophobic docking surface was also found, though it is occluded by the inter-EF-hand loop. The results from this first calbindomodulin design are discussed in terms of progress toward understanding the relationships between amino acid sequence, protein structure, and protein function for EF-hand CaBPs, as well as the additional mutations for the next CBM design.
Dynamics and control of quadcopter using linear model predictive control approach
Islam, M.; Okasha, M.; Idres, M. M.
This paper investigates the dynamics and control of a quadcopter using the Model Predictive Control (MPC) approach. The dynamic model is of high fidelity and nonlinear, with six degrees of freedom that include disturbances and model uncertainties. The control approach is developed based on MPC to track different reference trajectories ranging from simple ones such as circular to complex helical trajectories. In this control technique, a linearized model is derived and the receding horizon method is applied to generate the optimal control sequence. Although MPC is computer expensive, it is highly effective to deal with the different types of nonlinearities and constraints such as actuators' saturation and model uncertainties. The MPC parameters (control and prediction horizons) are selected by trial-and-error approach. Several simulation scenarios are performed to examine and evaluate the performance of the proposed control approach using MATLAB and Simulink environment. Simulation results show that this control approach is highly effective to track a given reference trajectory.
Effect of dynamic high pressure homogenization on the aggregation state of soy protein.
Keerati-U-Rai, Maneephan; Corredig, Milena
Although soy proteins are often employed as functional ingredients in oil-water emulsions, very little is known about the aggregation state of the proteins in solution and whether any changes occur to soy protein dispersions during homogenization. The effect of dynamic high pressure homogenization on the aggregation state of the proteins was investigated using microdifferential scanning calorimetry and high performance size exclusion chromatography coupled with multiangle laser light scattering. Soy protein isolates as well as glycinin and beta-conglycinin fractions were prepared from defatted soy flakes and redispersed in 50 mM sodium phosphate buffer at pH 7.4. The dispersions were then subjected to homogenization at two different pressures, 26 and 65 MPa. The results demonstrated that dynamic high pressure homogenization causes changes in the supramolecular structure of the soy proteins. Both beta-conglycinin and glycinin samples had an increased temperature of denaturation after homogenization. The chromatographic elution profile showed a reduction in the aggregate concentration with homogenization pressure for beta-conglycinin and an increase in the size of the soluble aggregates for glycinin and soy protein isolate.
The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Moye Wang
Full Text Available As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.
Ultrafast quantum control of ionization dynamics in krypton.
Hütten, Konrad; Mittermair, Michael; Stock, Sebastian O; Beerwerth, Randolf; Shirvanyan, Vahe; Riemensberger, Johann; Duensing, Andreas; Heider, Rupert; Wagner, Martin S; Guggenmos, Alexander; Fritzsche, Stephan; Kabachnik, Nikolay M; Kienberger, Reinhard; Bernhardt, Birgitta
Ultrafast spectroscopy with attosecond resolution has enabled the real time observation of ultrafast electron dynamics in atoms, molecules and solids. These experiments employ attosecond pulses or pulse trains and explore dynamical processes in a pump-probe scheme that is selectively sensitive to electronic state of matter via photoelectron or XUV absorption spectroscopy or that includes changes of the ionic state detected via photo-ion mass spectrometry. Here, we demonstrate how the implementation of combined photo-ion and absorption spectroscopy with attosecond resolution enables tracking the complex multidimensional excitation and decay cascade of an Auger auto-ionization process of a few femtoseconds in highly excited krypton. In tandem with theory, our study reveals the role of intermediate electronic states in the formation of multiply charged ions. Amplitude tuning of a dressing laser field addresses different groups of decay channels and allows exerting temporal and quantitative control over the ionization dynamics in rare gas atoms.
A mathematical perspective on flight dynamics and control
L'Afflitto, Andrea
This brief presents several aspects of flight dynamics, which are usually omitted or briefly mentioned in textbooks, in a concise, self-contained, and rigorous manner. The kinematic and dynamic equations of an aircraft are derived starting from the notion of the derivative of a vector and then thoroughly analysed, interpreting their deep meaning from a mathematical standpoint and without relying on physical intuition. Moreover, some classic and advanced control design techniques are presented and illustrated with meaningful examples. Distinguishing features that characterize this brief include a definition of angular velocity, which leaves no room for ambiguities, an improvement on traditional definitions based on infinitesimal variations. Quaternion algebra, Euler parameters, and their role in capturing the dynamics of an aircraft are discussed in great detail. After having analyzed the longitudinal- and lateral-directional modes of an aircraft, the linear-quadratic regulator, the linear-quadratic Gaussian r...
Direct observation of TALE protein dynamics reveals a two-state search mechanism.
Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M
Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process-a search state and a recognition state-facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state.
Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.
Visone, Valeria; Vettone, Antonella; Serpe, Mario; Valenti, Anna; Perugino, Giuseppe; Rossi, Mosè; Ciaramella, Maria
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea
Directory of Open Access Journals (Sweden)
Valeria Visone
Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
Dynamics and control of mechanical systems in offshore engineering
He, Wei; How, Bernard Voon Ee; Choo, Yoo Sang
Dynamics and Control of Mechanical Systems in Offshore Engineering is a comprehensive treatment of marine mechanical systems (MMS) involved in processes of great importance such as oil drilling and mineral recovery. Ranging from nonlinear dynamic modeling and stability analysis of flexible riser systems, through advanced control design for an installation system with a single rigid payload attached by thrusters, to robust adaptive control for mooring systems, it is an authoritative reference on the dynamics and control of MMS. Readers will gain not only a complete picture of MMS at the system level, but also a better understanding of the technical considerations involved and solutions to problems that commonly arise from dealing with them. The text provides: ...
Coevolving residues of (beta/alpha)(8)-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics.
Shen, Hongbo; Xu, Feng; Hu, Hairong; Wang, Feifei; Wu, Qi; Huang, Qiang; Wang, Honghai
Indole-3-glycerol phosphate synthase (IGPS) is a representative of (beta/alpha)(8)-barrel proteins-the most common enzyme fold in nature. To better understand how the constituent amino-acids work together to define the structure and to facilitate the function, we investigated the evolutionary and dynamical coupling of IGPS residues by combining statistical coupling analysis (SCA) and molecular dynamics (MD) simulations. The coevolving residues identified by the SCA were found to form a network which encloses the active site completely. The MD simulations showed that these coevolving residues are involved in the correlated and anti-correlated motions. The correlated residues are within van der Waals contact and appear to maintain the active site architecture; the anti-correlated residues are mainly distributed on opposite sides of the catalytic cavity and coordinate the motions likely required for the substrate entry and product release. Our findings might have broad implications for proteins with the highly conserved (betaalpha)(8)-barrel in assessing the roles of amino-acids that are moderately conserved and not directly involved in the active site of the (beta/alpha)(8)-barrel. The results of this study could also provide useful information for further exploring the specific residue motions for the catalysis and protein design based on the (beta/alpha)(8)-barrel scaffold.
Structure and dynamics of interfacial water. Role of hydratation water in the globular proteins dynamics
International Nuclear Information System (INIS)
Zanotti, J.M.
This memoir includes five chapters. In the first chapter, are given the elements of the neutrons scattering theory that is used in this study. the second chapter is devoted to a general presentation of the interaction between biological macro molecule and water. The third part is dedicated to the study of the structure and the dynamics of interfacial water in the neighbouring of model systems, the vycor and the amorphous carbon. The results presented in this part are compared with these one relative to water dynamics at the C-phycocyanin surface. This study makes the object of the fourth chapter. Then, in the fifth and last chapter are discussed the results relative to the role of hydratation on the parv-albumin dynamics for which have been combined the neutron quasi elastic incoherent scattering and the nuclear magnetic resonance of the carbon 13 solid in natural abundance
Getting the ion-protein interactions right in molecular dynamics simulations
Czech Academy of Sciences Publication Activity Database
Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel
Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics
Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering.
Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel
A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).
How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.
The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ
Multicompartment lipid cubic nanoparticles with high protein upload: millisecond dynamics of formation
Czech Academy of Sciences Publication Activity Database
Angelov, Borislav; Angelova, A.; Filippov, Sergey K.; Drechsler, M.; Štěpánek, Petr; Lesieur, S.
Roč. 8, č. 5 (2014), s. 5216-5226 ISSN 1936-0851 R&D Projects: GA ČR GAP208/10/1600 Institutional support: RVO:61389013 Keywords : lipid- protein nanoassembly * dynamic membrane curvature * amphiphile nanoarchitectonics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 12.881, year: 2014
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions
Wassenaar, T.A.; Mark, A.E.
The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard
Changes in the anisotropy of oriented membrane dynamics induced by myelin basic protein
Energy Technology Data Exchange (ETDEWEB)
Natali, F. [OGG-INFM, Grenoble (France); Gliozzi, A.; Rolandi, R.; Relini, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Genova (Italy); Cavatorta, P.; Deriu, A. [Dipartimento di Fisica and Istituto Nazionale per la Fisica della Materia, Universita di Parma (Italy); Fasano, A. [Dipartimento di Biochimica e Biologia Molecolare, Universita di Bari (Italy); Riccio, P. [Dipartimento di Biologia D.B.A.F., Universita della Basilicata, Potenza (Italy)
We report recent results showing the evidence of the effect induced by physiological amounts of myelin basic protein (MBP) on the dynamics of dimyristoyl L-a-phosphatidic acid (DMPA) membranes. Incoherent elastic neutron scattering scans, performed over a wide temperature range, have shown that the anisotropy of motions in oriented membranes is significantly enhanced by the presence of MBP. (orig.)
Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies
Directory of Open Access Journals (Sweden)
Krutika Bavishi
Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.
A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.
Saha, Tanumoy; Rathmann, Isabel; Galic, Milos
Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.
A general theory of non-equilibrium dynamics of lipid-protein fluid membranes
DEFF Research Database (Denmark)
Lomholt, Michael Andersen; Hansen, Per Lyngs; Miao, L.
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of statistical physics and designed to be a meso...
Dynamic strength of the interaction between lung surfactant protein D (SP-D) and saccharide ligands
DEFF Research Database (Denmark)
Thormann, Esben; Dreyer, Jakob K; Simonsen, Adam C
In order to investigate the dynamic strength of the interaction between lung surfactant protein D (SP-D) and different sugars, maltose, mannose, glucose, and galactose, we have used an atomic force microscope to monitor the interaction on a single molecule scale. The experiment is performed...
Pyrenebutanoate as a dynamic protein modifier for fluorometric detection in capillary zone electrophoresis
Czech Academy of Sciences Publication Activity Database
Horká, Marie; Šlais, Karel
Roč. 23, 7-8 (2002), s. 1090-1095 ISSN 0173-0835 R&D Projects: GA AV ČR IAA4031901 Institutional research plan: CEZ:AV0Z4031919 Keywords : pyrenebutanoate * dynamic protein modifier * CZE Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 4.325, year: 2002
Flexible spacecraft dynamics, control and guidance technologies by giovanni campolo
Mazzini, Leonardo
This book is an up-to-date compendium on spacecraft attitude and orbit control (AOC) that offers a systematic and complete treatment of the subject with the aim of imparting the theoretical and practical knowledge that is required by designers, engineers, and researchers. After an introduction on the kinematics of the flexible and agile space vehicles, the modern architecture and functions of an AOC system are described and the main AOC modes reviewed with possible design solutions and examples. The dynamics of the flexible body in space are then considered using an original Lagrangian approach suitable for the control applications of large space flexible structures. Subsequent chapters address optimal control theory, attitude control methods, and orbit control applications, including the optimal orbital transfer with finite and infinite thrust. The theory is integrated with a description of current propulsion systems, with the focus especially on the new electric propulsion systems and state of the art senso...
Directory of Open Access Journals (Sweden)
Cemal YILMAZ
Full Text Available In this study, dynamic lighting control inside of buildings has been implemented over the Profibus-DP network. Automatically adjustable luminaries were used to adjust lighting level to desired values. The data received from sensors measuring illuminance levels inside building are transferred to central control unit over the Profibus-DP network. These data are evaluated in the control unit and then control signals related to evaluation results are sent to the luminaries over the Profibus-DP network. As a reason of this design, optimum energy usage has been supplied by controlling the lighting remotely. Moreover, a healthy lighting environment has been obtained by means of adjusting the illuminance level related to lighting variations occurred in the various hours of a day.
Direct Adaptive Aircraft Control Using Dynamic Cell Structure Neural Networks
Jorgensen, Charles C.
A Dynamic Cell Structure (DCS) Neural Network was developed which learns topology representing networks (TRNS) of F-15 aircraft aerodynamic stability and control derivatives. The network is integrated into a direct adaptive tracking controller. The combination produces a robust adaptive architecture capable of handling multiple accident and off- nominal flight scenarios. This paper describes the DCS network and modifications to the parameter estimation procedure. The work represents one step towards an integrated real-time reconfiguration control architecture for rapid prototyping of new aircraft designs. Performance was evaluated using three off-line benchmarks and on-line nonlinear Virtual Reality simulation. Flight control was evaluated under scenarios including differential stabilator lock, soft sensor failure, control and stability derivative variations, and air turbulence.
Nonlinear Dynamic Inversion Baseline Control Law: Architecture and Performance Predictions
Miller, Christopher J.
A model reference dynamic inversion control law has been developed to provide a baseline control law for research into adaptive elements and other advanced flight control law components. This controller has been implemented and tested in a hardware-in-the-loop simulation; the simulation results show excellent handling qualities throughout the limited flight envelope. A simple angular momentum formulation was chosen because it can be included in the stability proofs for many basic adaptive theories, such as model reference adaptive control. Many design choices and implementation details reflect the requirements placed on the system by the nonlinear flight environment and the desire to keep the system as basic as possible to simplify the addition of the adaptive elements. Those design choices are explained, along with their predicted impact on the handling qualities.
Submodularity in dynamics and control of networked systems
Clark, Andrew; Bushnell, Linda; Poovendran, Radha
This book presents a framework for the control of networked systems utilizing submodular optimization techniques. The main focus is on selecting input nodes for the control of networked systems, an inherently discrete optimization problem with applications in power system stability, social influence dynamics, and the control of vehicle formations. The first part of the book is devoted to background information on submodular functions, matroids, and submodular optimization, and presents algorithms for distributed submodular optimization that are scalable to large networked systems. In turn, the second part develops a unifying submodular optimization approach to controlling networked systems based on multiple performance and controllability criteria. Techniques are introduced for selecting input nodes to ensure smooth convergence, synchronization, and robustness to environmental and adversarial noise. Submodular optimization is the first unifying approach towards guaranteeing both performance and controllabilit...
Controlling the flux dynamics in superconductors by nanostructured magnetic arrays
Kapra, Andrey
In this thesis we investigate theoretically how the critical current jc of nano-engineered mesoscopic superconducting film can be improved and how one can control the dynamics of the magnetic flux, e.g., the transition from flux-pinned to flux-flow regime, using arrays of magnetic nanostructures. In particularly we investigate: (1) Vortex transport phenomena in superconductors with deposited ferromagnetic structures on top, and the influence of the sample geometry on the critical parameters and on the vortex configurations. Changing geometry of the magnetic bars and magnetization of the bars will affect the critical current jc of the superconducting film. Such nanostructured ferromagnets strongly alter the vortex structure in its neighborhood. The influence of geometry, position and magnetization of the ferromagnet (single bar or regular lattice of the bars) on the critical parameters of the superconductor is investigated. (2) Effect of flux confinement in narrow superconducting channels with zigzag-shaped banks: the flux motion is confined in the transverse (perpendicular) direction of a diamond-cell-shape channel. The matching effect for the magnetic flux is found in the system relevantless of boundary condition. We discuss the dynamics of vortices in the samples and vortex pattern formation in the channel. We show how the inclusion of higher-Tc superconductor into the sample can lead to enhanced properties of the system. By adding an external driving force, we study the vortex dynamics. The different dynamic regimes are discussed. They allowed an effective control of magnetic flux in superconductors.
Control of chaotic dynamics in an OLG economic model
International Nuclear Information System (INIS)
Mendes, Diana A; Mendes, Vivaldo
This paper deals with the control of chaotic economic motion. We show that very complicated dynamics arising, e.g., from an overlapping generations model (OLG) with production and an endogenous intertemporal decision between labour and leisure, which produces chaos, can in fact be controlled with relative simplicity. The aperiodic and very complicated motion that stems from this model can be subject to control by small perturbations in its parameters and turned into a stable steady state or into a regular cycle. Therefore, the system can be controlled without changing of its original properties. To perform the control of the totally unstable equilibrium (both eigenvalues with modulus greater than unity) in this economic model we apply the pole-placement technique, developed by Romeiras, Grebogi, Ott and Dayawansa (1992). The application of control methods to chaotic economic dynamics may raise serious reservations, at least on mathematical and logical grounds, to some recent views on economics which have argued that economic policy becomes useless in the presence of chaotic motion (and thus, that the performance of the economic system cannot be improved by public intervention, i.e., that the amplitude of cycles can not be controlled or reduced). In fact, the fine tuning of the system (that is, the control) can be performed without having to rely only on infinitesimal accuracy in the perturbation to the system, because the control can be performed with larger or smaller perturbations, but neither too large (because these would lead to a different fixed point of the system, therefore modifying its original nature), nor too small because the control becomes too inefficient
Close-loop Dynamic Stall Control on a Pitching Airfoil
Giles, Ian; Corke, Thomas
A closed-loop control scheme utilizing a plasma actuator to control dynamic stall is presented. The plasma actuator is located at the leading-edge of a pitching airfoil. It initially pulses at an unsteady frequency that perturbs the boundary layer flow over the suction surface of the airfoil. As the airfoil approaches and enters stall, the amplification of the unsteady disturbance is detected by an onboard pressure sensor also located near the leading edge. Once detected, the actuator is switched to a higher voltage control state that in static airfoil experiments would reattach the flow. The threshold level of the detection is a parameter in the control scheme. Three stall regimes were examined: light, medium, and deep stall, that were defined by their stall penetration angles. The results showed that in general, the closed-loop control scheme was effective at controlling dynamic stall. The cycle-integrated lift improved in all cases, and increased by as much as 15% at the lowest stall penetration angle. As important, the cycle-integrated aerodynamic damping coefficient also increased in all cases, and was made to be positive at the light stall regime where it traditionally is negative. The latter is important in applications where negative damping can lead to stall flutter.
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele
It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.
Dynamic Event Tree advancements and control logic improvements
International Nuclear Information System (INIS)
Alfonsi, Andrea; Rabiti, Cristian; Mandelli, Diego; Sen, Ramazan Sonat; Cogliati, Joshua Joseph
The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN is currently equipped with three different sampling categories: Forward samplers (Monte Carlo, Latin Hyper Cube, Stratified, Grid Sampler, Factorials, etc.), Adaptive Samplers (Limit Surface search, Adaptive Polynomial Chaos, etc.) and Dynamic Event Tree (DET) samplers (Deterministic and Adaptive Dynamic Event Trees). The main subject of this document is to report the activities that have been done in order to: start the migration of the RAVEN/RELAP-7 control logic system into MOOSE, and develop advanced dynamic sampling capabilities based on the Dynamic Event Tree approach. In order to provide to all MOOSE-based applications a control logic capability, in this Fiscal Year an initial migration activity has been initiated, moving the control logic system, designed for RELAP-7 by the RAVEN team, into the MOOSE framework. In this document, a brief explanation of what has been done is going to be reported. The second and most important subject of this report is about the development of a Dynamic Event Tree (DET) sampler named 'Hybrid Dynamic Event Tree' (HDET) and its Adaptive variant 'Adaptive Hybrid Dynamic Event Tree' (AHDET). As other authors have already reported, among the different types of uncertainties, it is possible to discern two principle types: aleatory and epistemic uncertainties. The classical Dynamic Event Tree is in charge of treating the first class (aleatory) uncertainties; the dependence of the probabilistic risk assessment and analysis on the epistemic uncertainties are treated by an initial Monte Carlo sampling (MCDET). From each Monte Carlo sample, a DET analysis is run (in total, N trees). The Monte Carlo employs a pre
Dynamic Event Tree advancements and control logic improvements
Energy Technology Data Exchange (ETDEWEB)
Alfonsi, Andrea [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mandelli, Diego [Idaho National Lab. (INL), Idaho Falls, ID (United States); Sen, Ramazan Sonat [Idaho National Lab. (INL), Idaho Falls, ID (United States); Cogliati, Joshua Joseph [Idaho National Lab. (INL), Idaho Falls, ID (United States)
The RAVEN code has been under development at the Idaho National Laboratory since 2012. Its main goal is to create a multi-purpose platform for the deploying of all the capabilities needed for Probabilistic Risk Assessment, uncertainty quantification, data mining analysis and optimization studies. RAVEN is currently equipped with three different sampling categories: Forward samplers (Monte Carlo, Latin Hyper Cube, Stratified, Grid Sampler, Factorials, etc.), Adaptive Samplers (Limit Surface search, Adaptive Polynomial Chaos, etc.) and Dynamic Event Tree (DET) samplers (Deterministic and Adaptive Dynamic Event Trees). The main subject of this document is to report the activities that have been done in order to: start the migration of the RAVEN/RELAP-7 control logic system into MOOSE, and develop advanced dynamic sampling capabilities based on the Dynamic Event Tree approach. In order to provide to all MOOSE-based applications a control logic capability, in this Fiscal Year an initial migration activity has been initiated, moving the control logic system, designed for RELAP-7 by the RAVEN team, into the MOOSE framework. In this document, a brief explanation of what has been done is going to be reported. The second and most important subject of this report is about the development of a Dynamic Event Tree (DET) sampler named "Hybrid Dynamic Event Tree" (HDET) and its Adaptive variant "Adaptive Hybrid Dynamic Event Tree" (AHDET). As other authors have already reported, among the different types of uncertainties, it is possible to discern two principle types: aleatory and epistemic uncertainties. The classical Dynamic Event Tree is in charge of treating the first class (aleatory) uncertainties; the dependence of the probabilistic risk assessment and analysis on the epistemic uncertainties are treated by an initial Monte Carlo sampling (MCDET). From each Monte Carlo sample, a DET analysis is run (in total, N trees). The Monte Carlo employs a pre-sampling of the
Identification of dynamic changes in proteins associated with the cellular cytoskeleton after exposure to okadaic acid
DEFF Research Database (Denmark)
Opsahl, Jill A; Ljostveit, Sonja; Solstad, Therese
be combined with control cells before the isolation of lipid rafts. Protein phosphorylation events and translocations induced by okadaic acid were identified by mass spectrometry. Okadaic acid was shown to regulate the phosphorylation status and location of proteins associated with the actin cytoskeleton...... of the cortical actin cytoskeleton and cell detachment....
Molecular Dynamics Simulations of a Flexible Polyethylene: A Protein-Like Behaviour in a Water Solvent
Kretov, D A
We used molecular dynamics (MD) simulations to study the density and the temperature behaviour of a flexible polyethylene (PE) subjected to various heating conditions and to investigate the PE chain conformational changes in a water solvent. First, we have considered the influence of the heating process on the final state of the polymeric system and the sensitivity of its thermodynamic characteristics (density, energy, etc.) for different heating regimes. For this purpose three different simulations were performed: fast, moderate, and slow heating. Second, we have investigated the PE chain conformational dynamics in water solvent for various simulation conditions and various configurations of the environment. From the obtained results we have got the pictures of the PE dynamical motions in water. We have observed a protein-like behaviour of the PE chain, like that of the DNA and the proteins in water, and have also estimated the rates of the conformational changes. For the MD simulations we used the optimized...
Dynamic Coupling and Allosteric Networks in the α Subunit of Heterotrimeric G Proteins.
Yao, Xin-Qiu; Malik, Rabia U; Griggs, Nicholas W; Skjærven, Lars; Traynor, John R; Sivaramakrishnan, Sivaraj; Grant, Barry J
G protein α subunits cycle between active and inactive conformations to regulate a multitude of intracellular signaling cascades. Important structural transitions occurring during this cycle have been characterized from extensive crystallographic studies. However, the link between observed conformations and the allosteric regulation of binding events at distal sites critical for signaling through G proteins remain unclear. Here we describe molecular dynamics simulations, bioinformatics analysis, and experimental mutagenesis that identifies residues involved in mediating the allosteric coupling of receptor, nucleotide, and helical domain interfaces of Gαi. Most notably, we predict and characterize novel allosteric decoupling mutants, which display enhanced helical domain opening, increased rates of nucleotide exchange, and constitutive activity in the absence of receptor activation. Collectively, our results provide a framework for explaining how binding events and mutations can alter internal dynamic couplings critical for G protein function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle
DEFF Research Database (Denmark)
Grabon, Aby; Orłowski, Adam; Tripathi, Ashutosh
. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical...... analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability......Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling...
Applying dynamic mold temperature control to cosmetic package design
Directory of Open Access Journals (Sweden)
Hsiao Shih-Wen
Full Text Available Owing to the fashion trend and the market needs, this study developed the eco-cushion compact. Through the product design and the advanced process technology, many issues have improved, for instance, the inconvenience of transportation, the lack of multiuse capability, the increase of costs, and the low yield rate. The eco-cushion compact developed in this study was high quality, low cost, and meets the requirements of the eco market. The study aimed at developing a reusable container. Dynamic mold temperature control was introduced in the injection modeling process. The innovation in the product was its multi-functional formula invention, eco-product design, one-piece powder case design, and multifunctional design in the big powder case, mold flow and development of dynamic mold temperature control. Finally, through 3D drawing and modeling, and computer assistance for mold flow and verification to develop and produce models. During the manufacturing process, in order to solve the problems of tightness and warping, development and manufacture of dynamic mold temperature control were introduced. This decreased the injection cycle and residual stress, and deformation of the products has reduced to less than 0.2 mm, and the air tightness increased. In addition, air leakage was less than 2% and the injection cycle decreased to at least 10%. The results of the study can be extended and applied on the future design on cosmetic package and an alternative can be proposed to solve the problems of air tightness and warping. In this study, dynamic mold temperature control is considered as a design with high price-performance ratio, which can be adopted on industrial application for practical benefit and improvement.