Exact Stochastic Simulation of Coupled Chemical Reactions
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Daniel T. Gillespie
The Journal of Physical Chemistry 81(25), pages 23402361
December 1977
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 "reactionrate equations"); the ~stochastic approach~ regards the time evolution as a kind of randomwalk process which is governed by a single differentialdifference 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 reactionrate equations, this algorithm never approximates infinitesimal time increments d~t~ by finite time steps Δ~t~. The feasibility and utility of the simulation algorithm are demonstrated by applying it to several wellknown model chemical systems, including the Lotka model, the Brusselator, and the Oregonator. 
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Daniel T. Gillespie
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December 1977
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The Journal of Physical Chemistry
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81
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25
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23402361
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