Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation

Abstract

MotivationThe Chemical Master Equation is the most comprehensive stochastic approach to describe the evolution of a (bio-)chemical reaction system. Its solution is a time-dependent probability distribution on all possible configurations of the system. As the number of possible configurations is typically very large, the Master Equation is often practically unsolvable. The Method of Moments reduces the system to the evolution of a few moments of this distribution, which are described by a system of ordinary differential equations. Those equations are not closed, since lower order moments generally depend on higher order moments. Various closure schemes have been suggested to solve this problem, with different advantages and limitations. Two major problems with these approaches are first that they are open loop systems, which can diverge from the true solution, and second, some of them are computationally expensive. ResultsHere we introduce Quasi-Entropy Closure, a moment closure scheme for the Method of Moments which estimates higher order moments by reconstructing the distribution that minimizes the distance to a uniform distribution subject to lower order moment constraints. Quasi-Entropy closure is similar to Zero-Information closure, which maximizes the information entropy. Results show that both approaches outperform truncation schemes. Moreover, Quasi-Entropy Closure is computationally much faster than Zero-Information Closure. Finally, our scheme includes a plausibility check for the existence of a distribution satisfying a given set of moments on the feasible set of configurations. Results are evaluated on different benchmark problems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/470753v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@8c2beforg.highwire.dtl.DTLVardef@9876f7org.highwire.dtl.DTLVardef@1aa5db7org.highwire.dtl.DTLVardef@1eed4b4_HPS_FORMAT_FIGEXP M_FIG C_FIG