期刊
JOURNAL OF CHEMICAL PHYSICS
卷 130, 期 24, 页码 -出版社
AIP Publishing
DOI: 10.1063/1.3154624
关键词
reaction kinetics theory; reaction rate constants
资金
- Swiss SystemsX.ch initiative
- Swiss National Science Foundation
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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