Model a reaction using a monod kinetic factor. More...

Inheritance diagram for simulator.reaction.kinetic.MonodKinetic:

Public Member Functions
void	init (Element defMarkUp)
	Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation. More...

void	initFromAgent (Element defMarkUp, double[] kineticParam, int paramIndex)
	Initialise the reaction from a parent of the agent. More...

double	kineticValue (double solute, double[] paramTable, int index)
	Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array. More...

double	kineticValue (double solute)
	Calculate the value of the kinetic for a given level of solute. More...

double	kineticDiff (double solute, double[] paramTable, int index)
	Used to compute marginal difference kinetic values for a given solute level. More...

double	kineticDiff (double solute)
	Used to compute marginal difference kinetic values for a given solute level. More...

Additional Inherited Members
Public Attributes inherited from simulator.reaction.kinetic.IsKineticFactor
int	nParam

Detailed Description

Model a reaction using a monod kinetic factor.

Model a reaction using a monod kinetic factor. From Wikipedia: The Monod equation is a mathematical model for the growth of microorganisms. It is named for Jacques Monod who proposed using an equation of this form to relate microbial growth rates in an aqueous environment to the concentration of a limiting nutrient. The Monod equation has the same form as the Michaelis-Menten equation, but differs in that it is empirical while the latter is based on theoretical considerations.

Member Function Documentation

void simulator.reaction.kinetic.MonodKinetic.init ( Element defMarkUp )

virtual

Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation.

Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation

Parameters

defMarkUp XML tags that define this kinetic in the protocol file

Implements simulator.reaction.kinetic.IsKineticFactor.

void simulator.reaction.kinetic.MonodKinetic.initFromAgent	(	Element	defMarkUp,
		double[]	kineticParam,
		int	paramIndex
	)

virtual

Initialise the reaction from a parent of the agent.

Initialise the reaction from a parent of the agent

Parameters

defMarkUp	XML tags that define this kinetic in the protocol file
kineticParam	Array of parameters associated with this reaction
paramIndex	An index to the parameter array

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.MonodKinetic.kineticDiff	(	double	solute,
		double[]	paramTable,
		int	index
	)

virtual

Used to compute marginal difference kinetic values for a given solute level.

Used to compute marginal difference kinetic values for a given solute level

Parameters

solute	Solute level
paramTable	Array of parameters relating to this reaction
index	An index to the parameter array

Returns: Level of the reaction kinetic

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.MonodKinetic.kineticDiff ( double solute )

virtual

Used to compute marginal difference kinetic values for a given solute level.

Used to compute marginal difference kinetic values for a given solute level

Parameters

solute Solute level

Returns: Level of the reaction kinetic

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.MonodKinetic.kineticValue	(	double	solute,
		double[]	paramTable,
		int	index
	)

virtual

Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array.

Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array

Parameters

solute	Double stating the level of that solute
paramTable	Array of parameters relating to this reaction
index	An index to the parameter array

Returns: Double value stating the value of the kinetic for this level of solute

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.MonodKinetic.kineticValue ( double solute )

virtual

Calculate the value of the kinetic for a given level of solute.

Calculate the value of the kinetic for a given level of solute

Parameters

solute Double stating the level of that solute

Returns: Double value stating the value of the kinetic for this level of solute

Implements simulator.reaction.kinetic.IsKineticFactor.

The documentation for this class was generated from the following file:

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/reaction/kinetic/MonodKinetic.java

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation