Discrete-time stochastic modeling and simulation of biochemical networks

Abstract

Since inherent randomness in chemically reacting systems is evident, stochastic modeling and simulation are exceedingly important for investigating complex biological networks. Within the most common stochastic approach a network is modeled by a continuous-time Markov chain governed by the chemical master equation. We show how the continuous-time Markov chain can be converted to a stochastically identical discrete-time Markov chain and obtain a discrete-time version of the chemical master equation. Simulating the discrete-time Markov chain is equivalent to the Gillespie algorithm but requires less effort in that it eliminates the generation of exponential random variables. Thus, exactness as possessed by the Gillespie algorithm is preserved while the simulation can be performed more efficiently.