Publication: 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.
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Ramaswamy, R., González-Segredo, N., & Sbalzarini, I. F. (2009). A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of Chemical Physics, 130, 244104. https://doi.org/10.1063/1.3154624
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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 additi
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- Ramaswamy, Rajesh
- González-Segredo, Nélido
- Sbalzarini, Ivo F
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Ramaswamy, R., González-Segredo, N., & Sbalzarini, I. F. (2009). A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of Chemical Physics, 130, 244104. https://doi.org/10.1063/1.3154624
