Gillespie's Direct Method Stochastic Simulation Algorithm

Code to stochastically simulate coupled chemical reactions.

This code implements the Stochastic Simulation Algorithm (direct method) published by D.T. Gillespie in 1977 in the Journal of Physical Chemistry.

Default reactions and analytical solutions correspond to a simple model of gene expression for a single cell (Kaern et al.,Nat.Rev.Genet.,2005): Pro-->M-->P, with mRNA (M-->0) and protein (P-->0) decay, when the gene is assumed to be constantly expressed (Pro denotes the promoter of the gene) and cell volume is constant and set to unity. The mRNA and protein time series and probability histograms are plotted.