This is a general application which evolves a set of coupled chemical reactions stochastically, producing a time trace of species concentrations. Chemical species are treated as counts of individual molecules reacting within a reaction volume in a well-mixed fashion. Individual reactions are chosen via the direct method variant of the Stochastic Simulation Algorithm (SSA) of (Gillespie).
A prototypical example is to use this model to simulate the execution of a protein signaling network in a biological cell.
This application can only be evolved using a kinetic Monte Carlo (KMC) algorithm. You must thus define a KMC solver to be used with the application via the solve_style command
The following additional commands are defined by this application:
|add_reaction||define a chemical reaction|
|add_species||define a chemical species|
|count||specify molecular count of a species|
|volume||specify volume of the chemical reactor|
Related commands: none
(Gillepsie) Gillespie, J Chem Phys, 22, 403-434 (1976); Gillespie, J Phys Chem, 81, 2340-2361 (1977).