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app_style chemistry command


app_style chemistry 


app_style chemistry 


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).