Accelerated Stochastic simulation of large chemical systems

For efficient simulation of chemical systems with large number of reactions, we report a fast and exact algorithm for direct simulation of chemical discrete Markov processes. The approach adopts the scheme of organizing the reactions into hierarchical groups. By generating a random number, the selection of the next reaction that actually occurs is accomplished by a few successive selections in the hierarchical groups. The algorithm which is suited for simulating systems with large number of reactions is much faster than the direct method or the optimized direct method. For a demonstration of its efficiency, the accelerated algorithm is applied to simulate the reaction-diffusion Brusselator model on a discretized space.