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J Chem Phys. 2009 Apr 14;130(14):144110. doi: 10.1063/1.3078490.

An exact accelerated stochastic simulation algorithm.

Author information

1
Department of Computer Science, University of California, Irvine, U.C. Irvine, California 92697, USA. emj@uci.edu

Abstract

An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 23 power of the number of reaction events in a Galton-Watson process.

PMID:
19368432
PMCID:
PMC2852436
DOI:
10.1063/1.3078490
[Indexed for MEDLINE]
Free PMC Article
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