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Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-39542

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.



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.

Item Type:Journal Article, refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > WingX
DDC:570 Life sciences; biology
Deposited On:26 Nov 2010 16:00
Last Modified:28 Nov 2013 01:36
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:10.1063/1.3078490
PubMed ID:19368432
Citations:Web of Science®. Times Cited: 8
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Scopus®. Citation Count: 10

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