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

摘要

We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) forsampling trajectories of the chemical master equation for a well-stirred system of coupled chemicalreactions. Our formulation is based on factored-out, partial reaction propensities. This novel exactSSA, called the partial-propensity direct method (PDM), is highly efficient and has a computationalcost that scales at most linearly with the number of chemical species, irrespective of the degree ofcoupling of the reaction network. In addition, we propose a sorting variant, SPDM, which isespecially efficient for multiscale reaction networks.