Permanent URL to this publication: http://dx.doi.org/10.5167/uzh-39864
Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F (2009). A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of chemical physics, 130(24):244104.
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We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on factored-out, partial reaction propensities. This novel exact SSA, called the partial-propensity direct method (PDM), is highly efficient and has a computational cost that scales at most linearly with the number of chemical species, irrespective of the degree of coupling of the reaction network. In addition, we propose a sorting variant, SPDM, which is especially efficient for multiscale reaction networks.
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|Item Type:||Journal Article, refereed, original work|
|Communities & Collections:||Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > LipidX
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|Dewey Decimal Classification:||570 Life sciences; biology|
|Deposited On:||08 Dec 2010 13:12|
|Last Modified:||05 Apr 2016 14:27|
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