Order Reduction of the Chemical Master Equation via Balanced Realisation
  We consider a Markov process in continuous time with a finite number of discrete states. The time-dependent probabilities of being in any state of the Markov chain are governed by a set of ordinary differential equations, whose dimension might be large even for trivial systems. Here, we derive a reduced ODE set that accurately approximates the probabilities of subspaces of interest with a known error bound. Our methodology is based on model reduction by balanced truncation and can be considerably more computationally efficient than the Finite State Projection Algorithm (FSP) when used for obtaining transient responses. We show the applicability of our method by analysing stochastic chemical reactions. First, we obtain a reduced order model for the infinitesimal generator of a Markov chain that models a reversible, monomolecular reaction. In such an example, we obtain an approximation of the output of a model with 301 states by a reduced model with 10 states. Later, we obtain a reduced order model for a catalytic conversion of substrate to a product; and compare its dynamics with a stochastic Michaelis-Menten representation. For this example, we highlight the savings on the computational load obtained by means of the reduced-order model. Finally, we revisit the substrate catalytic conversion by obtaining a lower-order model that approximates the probability of having predefined ranges of product molecules. 
Fernando Lopez-Caamal and Tatiana T. Marquez-Lago
math.OC