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

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

2009-06-10

arxiv.org/abs/0906.1992v1

Biology

Quantitative Biology

Quantitative Methods

23 pages, 3 figures, 4 tables; accepted by J. Chem. Phys

Scientific paper

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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