Tae-Hyuk Ahn1, Layne T. Watson1,2, Yang Cao1,1, Clifford A. Shaffer1, William T. Baumann3
CMES-Computer Modeling in Engineering & Sciences, Vol.51, No.1, pp. 27-52, 2009, DOI:10.3970/cmes.2009.051.027
Abstract For biochemical systems, where some chemical species are represented by small numbers of molecules, discrete and stochastic approaches are more appropriate than continuous and deterministic approaches. The continuous deterministic approach using ordinary differential equations is adequate for understanding the average behavior of cells, while the discrete stochastic approach accurately captures noisy events in the growth-division cycle. Since the emergence of the stochastic simulation algorithm (SSA) by Gillespie, alternative algorithms have been developed whose goal is to improve the computational efficiency of the SSA. This paper explains and empirically compares the performance of some of these SSA alternatives on a realistic… More >
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