fern.network

Class AbstractKineticConstantPropensityCalculator

java.lang.Object

fern.network.AbstractKineticConstantPropensityCalculator

All Implemented Interfaces:

KineticConstantPropensityCalculator, PartialDerivativePropensityCalculator, PropensityCalculator

Direct Known Subclasses:

ArrayKineticConstantPropensityCalculator

public abstract class AbstractKineticConstantPropensityCalculator
extends Object
implements KineticConstantPropensityCalculator, PartialDerivativePropensityCalculator

Base implementation of a PropensityCalculator. The propensity is simply a product of the populations of its reactant species and a specific reaction probability rate constant (which is related to the conventional deterministic rate constant and can be calculated by getConstantFromDeterministicRateConstant.

Some of the tau leap procedures need partial derivatives of the propensity function (and use therefore the method calculatePartialDerivative) so the use of this procedures is only possible when the network's PropensityCalculator is a AbstractKineticConstantPropensityCalculator.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
AbstractKineticConstantPropensityCalculator(int[][] reactants) Creates a AbstractKineticConstantPropensityCalculator by an array of adjacency arrays for the reaction's reactant species (which are the only one needed for the propensity calculation).

Method Summary

Modifier and Type	Method and Description
double	calculatePartialDerivative(int reaction, AmountManager amount, int reactantIndex, double volume) Calculates partial differentials of the propensity functions for the tau leaping methods.
double	calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for reaction by the formula h*c, where c is the kinetic constant for reaction and h is the number of distinct molecular reactant combinations for 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 class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fern.network.KineticConstantPropensityCalculator

getConstant

Constructor Detail

AbstractKineticConstantPropensityCalculator

public AbstractKineticConstantPropensityCalculator(int[][] reactants)

Creates a AbstractKineticConstantPropensityCalculator by an array of adjacency arrays for the reaction's reactant species (which are the only one needed for the propensity calculation).

Parameters:

reactants - array of adjacency arrays

Method Detail

calculatePropensity

public double calculatePropensity(int reaction,
                                  AmountManager amount,
                                  Simulator sim)

Calculates the propensity for reaction by the formula h*c, where c is the kinetic constant for reaction and h is the number of distinct molecular reactant combinations for reaction. If a positive value for volume is given, it is assumed that the constants are deterministic rate constants and are hence transformed to specific reaction rate constants.

Specified by:

calculatePropensity in interface PropensityCalculator

Parameters:

reaction - the index of the reaction

amount - the AmountManager

sim - the simulator

Returns:

the propensity for the reaction

calculatePartialDerivative

public double calculatePartialDerivative(int reaction,
                                         AmountManager amount,
                                         int reactantIndex,
                                         double volume)

Calculates partial differentials of the propensity functions for the tau leaping methods. If a positive value for volume is given, it is assumed that the constants are deterministic rate constants and are hence transformed to specific reaction rate constants.

Specified by:

calculatePartialDerivative in interface PartialDerivativePropensityCalculator

Parameters:

reaction - the reaction index

amount - the AmountManager

reactantIndex - the network index of the reactant to calculate the partial differential for

volume - the volume of the reaction space

Returns:

partial differential

getConstantFromDeterministicRateConstant

public 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) doi: 10.1016/0021-9991(76)90041-3

Specified by:

getConstantFromDeterministicRateConstant in interface KineticConstantPropensityCalculator

Parameters:

k - deterministic rate constant

reaction - the index of the constant's reaction

V - the fixed volume

Returns:

the specific reaction probability rate constant