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Exact Stochastic Simulation of Chemical Reactions with Cycle Leaping

Riedel, Marc D. and Bruck, Jehoshua (2006) Exact Stochastic Simulation of Chemical Reactions with Cycle Leaping. California Institute of Technology , Pasadena, CA. (Unpublished) http://resolver.caltech.edu/CaltechPARADISE:2006.ETR077

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Abstract

The stochastic simulation algorithm (SSA), first proposed by Gillespie, has become the workhorse of computational biology. It tracks integer quantities of the molecular species, executing reactions at random based on propensity calculations. An estimate for the resulting quantities of the different species is obtained by averaging the results of repeated trials. Unfortunately, for models with many reaction channels and many species, the algorithm requires a prohibitive amount of computation time. Many trials must be performed, each forming a lengthy trajectory through the state space. With coupled or reversible reactions, the simulation often loops through the same sequence of states repeatedly, consuming computing time, but making no forward progress. We propose a algorithm that reduces the simulation time through cycle leaping: when cycles are encountered, the exit probabilities are calculated. Then, in a single bound, the simulation leaps directly to one of the exit states. The technique is exact, sampling the state space with the expected probability distribution. It is a component of a general framework that we have developed for stochastic simulation based on probabilistic analysis and caching.


Item Type:Report or Paper (Technical Report)
Additional Information:This work is supported by the "Alpha Project" at the Center for Genomic Experimentation and Computation, a National Institutes of Health Center of Excellence in Genomic Sciences (grant no. P50 HG02370). Also available online: http://www.paradise.caltech.edu/papers/etr077.pdf
Group:Parallel and Distributed Systems Group
Record Number:CaltechPARADISE:2006.ETR077
Persistent URL:http://resolver.caltech.edu/CaltechPARADISE:2006.ETR077
Usage Policy:You are granted permission for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any format.
ID Code:26108
Collection:CaltechPARADISE
Deposited By: Imported from CaltechPARADISE
Deposited On:22 Dec 2006
Last Modified:25 Feb 2014 22:00

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