Exact Stochastic Simulation of Coupled Chemical Reactions

each of the M chemical reactions can be regarded as a … structures and rate constants of the M chemical reaction channels. These equations are called the …

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Exact Stochastic Simulation of Coupled Chemical Reactions
D anlel T. G illespie
Research Department, NaVal Weapons Center, China Lake, California 93555 (Received May 72, 1977) Publication costs assisted by the Naval Weapons Center
There are two formalisms for mathematically describing the time behavior of a spatially homogeneous chemical system: The deterministic approach regards the time evolution as a continuous, wholly predictable process which is governed by a set of coupled, ordinary differential equations (the \”reaction-rateequations\”);the stochastic approach regards the time evolution as a kind of random-walk process which is governed by a single differential-difference equation (the \”master equation\”). Fairly simple kinetic theory arguments show that the stochastic formulation of chemical kinetics has a firmer physical basis than the deterministic formulation, but unfortunately the stochastic master equation is often mathematically intractable. There is, however, a way to make exact numerical calculations within the framework of the stochastic formulation without having to deal with the master equation directly. It is a relatively simple digital computer algorithm which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of the given chemical system. Like the master equation, this \”stochastic simulation algorithm\” correctly accounts for the inherent fluctuations and correlations that are necessarily ignored in the deterministic formulation. In addition, unlike most procedures for numerically solving the deterministic reaction-rate equations, this algorithm never approximates infinitesimal time increments dt by finite time steps At. The feasibility and utility of the simulation algorithm are demonstrated by applying it to several well-known model chemical systems, including the Lotka model, the Brusselator, and the Oregonator.

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