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arXiv · 0906.1992

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

Rajesh Ramaswamy·Nélido González-Segredo·Ivo F. Sbalzarini
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Abstract

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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Rajesh Ramaswamy, Nélido González-Segredo, Ivo F. Sbalzarini. 2009-06-10. A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. https://doi.org/10.1063/1.3154624

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