5 - Efficient Stochastic Modelling of Chemical Reactions

Summary

This chapter presents approaches for efficient modelling of stochastic chemical systems. These methods are useful when a computational model based on the Gillespie stochastic simulation algorithm (SSA), introduced in Chapter 1, cannot be executed in a reasonably short time. Scenarios in which the Gillespie SSA can be computationally intensive are discussed, starting with an example involving fast and slow chemical reactions. This example is used to introduce the multiscale SSA, which speeds up simulations by assuming that the fast processes are at equilibrium, and other approximate approaches for problems with multiple time scales. Exact approaches to decrease the computational intensity of the Gillespie SSA are then discussed, including the next-reaction SSA.