Syntax:
app_style chemistry
Examples:
app_style chemistry
Description:
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 |
Restrictions: none
Related commands: none
Default: none
(Gillepsie) Gillespie, J Chem Phys, 22, 403-434 (1976); Gillespie, J Phys Chem, 81, 2340-2361 (1977).