Stochastic Simulation Algorithms for Chemical Reactions

In various biochemical systems, discrete and stochastic approaches are more appropriate than continuous and deterministic approaches when the system has small numbers of molecules. Before the emergence of the stochastic simulation algorithm (SSA) by Gillespie, chemical master equations were used to stochastically model. Solving the master equations is often mathematically intractable. Therefore, it is reasonable to investigate the SSA in order to understand stochastic processes for biochemical systems. Ever since the SSA emerged, there have been many papers to improve the computational efficiency of the SSA. This paper explains and compares various stochastic simulation algorithms for chemical reactions, with particular attention to the Gillespie algorithm.

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