fern.network
Interface KineticConstantPropensityCalculator

All Superinterfaces:
PropensityCalculator
All Known Implementing Classes:
AbstractKineticConstantPropensityCalculator, ArrayKineticConstantPropensityCalculator

public interface KineticConstantPropensityCalculator
extends PropensityCalculator


Method Summary
 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