title: Order reduction of the chemical master equation via balanced realisation.
abstract: 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 solving the chemical master equation directly. 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. Later, we obtain a reduced order model for a catalytic conversion of substrate to a product (a so-called Michaelis-Menten mechanism), and compare its dynamics with a rapid equilibrium approximation method. For this example, we highlight the savings on the computational load obtained by means of the reduced-order model. Furthermore, we revisit the substrate catalytic conversion by obtaining a lower-order model that approximates the probability of having predefined ranges of product molecules. In such an example, we obtain an approximation of the output of a model with 5151 states by a reduced model with 16 states. Finally, we obtain a reduced-order model of the Brusselator.
authors.affiliation: Integrative Systems Biology Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa, Japan.
authors.forename: Fernando
authors.initials: F
authors.lastname: López-Caamal
authors.affiliation: Integrative Systems Biology Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa, Japan.
authors.forename: Tatiana T
authors.initials: TT
authors.lastname: Marquez-Lago
mesh_terms: D000465:Algorithms; D002384:Catalysis; D003198:Computer Simulation; D007700:Kinetics; D008390:Markov Chains; D008956:Models, Chemical; D011336:Probability