Multi-variate Minimization Techniques and Molecular         Dynamics Simulations for Predicting 3-D Structures of DNA   and RNA on Supercomputers
{'Code': '05090000', 'Directorate': {'Abbreviation': 'CSE', 'LongName': 'Direct For Computer & Info Scie & Enginr'}, 'Division': {'Abbreviation': 'OAC', 'LongName': 'Office of Advanced Cyberinfrastructure (OAC)'}}
{'SignBlockName': 'Maxine Hynson', 'PO_EMAI': None, 'PO_PHON': None}
The goal for the research proposed here is to develop                           mathematical tools for computing three-dimensional structures of                large biological molecules.  In particular, modeling and large-                 scale minimization techniques will be devised to predict the                    conformations of single and doublestranded RNA and DNA molecules.                                                                                               The computational tools involve semi-empirical potential energy                 minimization and molecular dynamics, executed on the Cray X-MP                  and aided by interactive computer graphics on the Evans and                     Sutherland PS-330.  The plan is to work on the following four                   areas of program development:  (1) Global optimization                          strategies; test the determination Tunneling method of Levy and                 Gomez and a variant of the stochastic Simulated Annealing:  (2)                 Faster manipulation of the pairwise interactions in the energy                  function; investigate the new method recently proposed by                       Greengard and Rokhlin which could reduce the order O(N2)                        computational complexity for an N - particle system to order                    O(N):  (3) Implementation of molecular dynamics:  dynamics                      simulations will enable an examination of the dynamic                           trajectories of the structures obtained from minimization;                      and:  (4) Incorporation of solvent and metalions into the                       molecular model; this will provide a more realistic potential                   field to represent the molecular forces influencing the RNA and                 DNA in its natural milieu.  The developed computational tools                   will yield the ability to investigate some intriquing problems of               three-dimensional molecular structures.  These problems include                 the dependence of DNA conformation on the nucleic acid base                     sequence and the structure and the complex folding patterns of                  single-stranded RNA. The minimizations and dynamics results will                be used to make 16 mm films and videotapes that will reveal the                 dynamic range of  structures and permit us to relate                            conformational features with known biological functions.                                                                                                        This proposal projects to develop mathematical tools, using                     state-of-the-art optimization algorithms, for examination of                    dynamics simulation of solvent and metal-ion interaction in the                 biologically important molecular RNA and DNA.                                                                                                                   The Program Director for Computational Science and Engineering                  recommends support in the sum of $69,370 for a period of one year.
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