Generalized Stochastic

nonspatial stochastic simulation (Gillespie/Gibson solver) now supports general kinetic laws.

• As before, reaction kinetics recognized as Mass Action are simulated using elementary forward and reverse stochastic processes.
• Now, non-mass action kinetics (e.g. enzyme kinetics) can be simulated stochastically where the propensity is derived from the effective net reaction rate.
  • Each reaction is still decomposed into forward and reverse stochastic processes,
  • but the forward rate propensity is driven by the net reaction rate (when its sign is positive),
  • and the reverse rate propensity is driven by the net reaction rate (when its sign is negative)
  • this approach results in reasonable mean trajectories, but may not capture rare events accurately and the noise characteristics of the underlying elementary processes (normally described by mass action kinetics) are not well represented.