Trade-off between simulation time and resolution.
Illustration of events within a time step in -SSSA as compared with NSM ( stands for reaction event and for diffusion event).
Relative difference in time to reach a chemical steady state: Different numbers of subvolumes, with and without time scaling.
Solutions of the bistable system. (a) Deterministic solutions for molecular species and . (b) Sample single run using the NSM in 64 subvolumes, portraying the case where . (c) Sample single run using the NSM in 64 subvolumes, portraying the case where .
Average over ten independent runs in which after , for both NSM and -SSSA in 64 subvolumes (with ).
Description of the matrices and vectors used in the NSM method and .
Reaction propensities (diffusion propensities are calculated the same way as unary reaction propensities).
Comparison of CPU times in NSM and -SSSA, first reaction set, uniform distribution of molecules as initial condition.
Comparison of CPU times in NSM and -SSSA, second reaction set, clusters of molecules (“hotspots”) as initial condition.
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