A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

Details A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

2006-01-30

arxiv.org/abs/physics/0601217v4

J. Chem. Phys. 125 (2006) 144107

Physics

Chemical Physics

v4: 12 pages, 5 figures, final accepted version. Error found and fixed in Appendix

Scientific paper

10.1063/1.2354085

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.

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