Comment on “Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates” [J. Chem. Phys.123, 194107 (2005)]
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(a) An exact SSA simulation of reactions (1) for the parameter values (2). is the molecular population of species , etc. The populations were plotted after the occurrence of each slow reaction, or ; these slow reactions comprised one out of every reactions that were simulated to get this plot. Simulations using the ssSSA (Ref. 2) and the nSSA (Ref. 3), the latter with parameter , produced plotted trajectories that were statistically indistinguishable from these. Compared to the SSA run, the ssSSA run was times faster, and the nSSA run was times faster. (b) A simulation run of the nSSA with . Differences in the textures of the trajectories from the exact run in (a) are apparent with this smaller , yet this nSSA run was times slower than the ssSSA run.
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