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J Comput Biol. 2009 Sep;16(9):1195-208. doi: 10.1089/cmb.2008.0249.

Accurate stochastic simulation via the step anticipation tau-leaping (SAL) algorithm.

Author information

1
Department of Biomathematics, David Geffen School of Medicine, University of California , Los Angeles, Los Angeles, California 90095-1766, USA.

Abstract

Stochastic simulation methods are important in modeling chemical reactions, and biological and physical stochastic processes describable as continuous-time discrete-state Markov chains with a finite number of reactant species and reactions. The current algorithm of choice, tau-leaping, achieves fast and accurate stochastic simulation by taking large time steps that leap over individual reactions. During a leap interval (t, t + tau) in tau-leaping, each reaction channel operates as a Poisson process with a constant intensity. We modify tau-leaping to allow linear and quadratic changes in reaction intensities. Because our version of tau-leaping accurately anticipates how intensities change over time, we propose calling it the step anticipation tau-leaping (SAL) algorithm. We apply SAL to four examples: Kendall's process, a two-type branching process, Ehrenfest's model of diffusion, and Michaelis-Menten enzyme kinetics. In each case, SAL is more accurate than ordinary tau-leaping. The degree of improvement varies with the situation. Near stochastic equilibrium, reaction intensities are roughly constant, and SAL and ordinary tau-leaping perform about equally well.

PMID:
19772431
PMCID:
PMC3148118
DOI:
10.1089/cmb.2008.0249
[Indexed for MEDLINE]
Free PMC Article

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