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J Chem Phys. 2009 Jun 28;130(24):244104. doi: 10.1063/1.3154624.

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

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Institute of Theoretical Computer Science, ETH Zurich, CH-8092 Zurich, Switzerland.


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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