fern.network

Interface KineticConstantPropensityCalculator

All Superinterfaces:

PropensityCalculator

All Known Implementing Classes:

AbstractKineticConstantPropensityCalculator, ArrayKineticConstantPropensityCalculator

public interface KineticConstantPropensityCalculator
extends PropensityCalculator

Method Summary

Modifier and Type	Method and Description
double	getConstant(int reaction) Gets the constant for a reaction
double	getConstantFromDeterministicRateConstant(double k, int reaction, double V) Calculates the specific reaction probability rate constant c from the conventional deterministic rate constant k in some fixed volume v by the formula c=|reactants| !

Methods inherited from interface fern.network.PropensityCalculator

calculatePropensity

Method Detail

getConstant

double getConstant(int reaction)

Gets the constant for a reaction

Parameters:

reaction - index of the reaction

Returns:

constant for the reaction

getConstantFromDeterministicRateConstant

double getConstantFromDeterministicRateConstant(double k,
                                                int reaction,
                                                double V)

Calculates the specific reaction probability rate constant c from the conventional deterministic rate constant k in some fixed volume v by the formula c=|reactants| ! * k / V^(|reactants|-1)

For references see Daniel T. Gillespie, A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions, Journal of Computational Physics 22, 403-434 (1976)

Parameters:

k - deterministic rate constant

reaction - the index of the constant's reaction

V - the fixed volume

Returns:

the specific reaction probability rate constant