Captures the fitness cost associated with the carriage of a plasmid. More...

Inheritance diagram for simulator.reaction.ReactionGrowthFitness:

Public Member Functions
void	init (Simulator aSim, XMLParser xmlRoot)
	Initialises the reaction by setting relevant parameters to values contained in the simulation protocol file. More...

void	initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser aReactionRoot)
	Use the reaction class to fill the parameters fields of the agent. More...

int	getTotalParam ()
	Return the total number of parameters needed to describe the kinetic of this reaction (muMax included) More...

void	updateMarginalMu (double[] s)
	Update the Marginal Mu data matrix. More...

void	computeUptakeRate (double[] s, double mass, double tdel)
	Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1. More...

double	computeSpecRate (double[] s)
	Compute the specific growth rate. More...

void	computeSpecificGrowthRate (double[] s)
	Compute specific growth rate in function to concentrations sent. More...

double[]	getMarginalDiffMu ()
	Return the marginalDiffMu array. More...

Matrix	calcdMUdS (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix. More...

Matrix	calcdMUdT (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to time. More...

double[]	computeMarginalDiffMu (double[] s)
	Compute the marginal difference array. More...

double	computeMassGrowthRate (ActiveAgent anAgent)

double	computeSpecGrowthRate (ActiveAgent anAgent)
	Compute the specific growth rate. More...

void	computeSpecificGrowthRate (double[] s, ActiveAgent anAgent)

void	computeSpecificGrowthRate (ActiveAgent anAgent)
	Return the specific reaction rate for a given agent. More...

ArrayList< Double >	setYield (ActiveAgent anAgent)

Public Member Functions inherited from simulator.reaction.Reaction
void	init (Simulator aSim, XMLParser aReactionRoot)
	Initialises a reaction object, giving the object the properties stated in the protocol file. More...

void	initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser xmlRoot)
	Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes. More...

void	register (String aReactionName, Simulator aSimulator)
	End of the initialization procedure. Store the name and simulation dictionary index for this reaction. More...

LinkedList< String >	declareSolutes ()
	Utilised by a solver instance to know the solutes affected by this reaction. More...

void	fillParameters (Simulator aSim, XMLParser xmlRoot)
	Reads the reaction information (name, solute yield, particle yield etc) from the XML file and initialises this reaction. More...

void	addAgent (ActiveAgent anAgent)
	Register an agent among the guild of this pathway. More...

void	removeAgent (ActiveAgent anAgent)
	Remove an agent among the guild of this pathway. More...

void	applyReaction (SpatialGrid[] concGrid, SpatialGrid[] reacGrid, SpatialGrid[] diffReacGrid, SpatialGrid biomassGrid)
	Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild. More...

void	fitAgentMassOnGrid (SpatialGrid aSpG)
	Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION. More...

double[]	readConcentrationSeen (ActiveAgent anAgent, SoluteGrid[] concGrid)
	Return a double array with all concentration seen by an agent on the default solute grid. More...

void	writeReport (ResultFile bufferState, ResultFile bufferSum) throws Exception
	Write reaction information to the result file stream. More...

void	fitGuildOnGrid ()
	Build a grid with mass and mass-growth-rate of all agents of the guild. More...

double[]	getSoluteYield ()
	Return the solute yield. More...

int[]	getSoluteIndex ()
	Return the solute index. More...

double[]	getParticulateYield ()
	Return the particulate yield. More...

double[]	getKinetic ()
	Return the kinetic parameters used in this reaction. More...

LinkedList< ActiveAgent >	getGuild ()
	Return the guild of this pathway. More...

Additional Inherited Members
Public Attributes inherited from simulator.reaction.Reaction
String	reactionName

int	reactionIndex

int	_catalystIndex

int[]	_mySoluteIndex

boolean	autocatalytic

double[]	totalUptake

double	Dil

Protected Attributes inherited from simulator.reaction.Reaction
LinkedList< ActiveAgent >	_guild = new LinkedList<ActiveAgent>()

SoluteGrid[]	_soluteList

SoluteGrid	_reacGrid

SoluteGrid	_guildGrid

double	_specRate

double[]	_diffUptakeRate

double[]	_uptakeRate

double[]	_soluteYield

double[]	_kineticParam

double[]	_particleYield

String[]	_particleNameYield

Detailed Description

Captures the fitness cost associated with the carriage of a plasmid.

This class deals with the fitness cost associated with the carriage of a plasmid. A cell carrying a plasmid will have its biomass yield reduced due to the metabolic burden conferred by the plasmid, which indirectly impacts its growth rate output. Here we assume that plasmid cost decreases exponentially with the time spent in the host, until it reaches a minimum value. The assumption behind this approach is that plasmid and host coevolve. We also assume that the individuals from a species don't mutate, thus a plasmid that has evolved in a host of a certain species if transferred to another individual of the same species, will have the "evolved" cost for its new recipient.

Author: SoniaMartins

Member Function Documentation

Matrix simulator.reaction.ReactionGrowthFitness.calcdMUdS	(	Matrix	S,
		double	biomass
	)

virtual

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix.

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns: Matrix containing rate of change of each uptake rate with respect to each solute

Implements simulator.reaction.Reaction.

Matrix simulator.reaction.ReactionGrowthFitness.calcdMUdT	(	Matrix	S,
		double	biomass
	)

virtual

Calculate the rate of change of each uptake rate with respect to time.

Calculate the rate of change of each uptake rate with respect to time. dMUdT = catalyticBiomass*specificGrowthRate*soluteYield. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns: Matrix containing rate of change of each uptake rate with respect to time

Implements simulator.reaction.Reaction.

double [] simulator.reaction.ReactionGrowthFitness.computeMarginalDiffMu ( double[] s )

virtual

Compute the marginal difference array.

Compute the marginal difference array. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns: Marginal diff array

Implements simulator.reaction.Reaction.

double simulator.reaction.ReactionGrowthFitness.computeMassGrowthRate ( ActiveAgent anAgent )

virtual

Parameters

anAgent

Returns: the marginal growth rate (i.e the specific growth rate times the mass of the particle which is mediating this reaction)

Implements simulator.reaction.Reaction.

double simulator.reaction.ReactionGrowthFitness.computeSpecGrowthRate ( ActiveAgent anAgent )

virtual

Compute the specific growth rate.

Compute the specific growth rate

Parameters

anAgent Specific growth rate for this ActiveAgent

Returns: The specific growth rate

Implements simulator.reaction.Reaction.

void simulator.reaction.ReactionGrowthFitness.computeSpecificGrowthRate ( double[] s )

virtual

Compute specific growth rate in function to concentrations sent.

Compute specific growth rate in function to concentrations sent

Parameters

s	Array of solute concentration

Implements simulator.reaction.Reaction.

void simulator.reaction.ReactionGrowthFitness.computeSpecificGrowthRate	(	double[]	s,
		ActiveAgent	anAgent
	)

virtual

Compute specific growth rate in function to concentrations sent

Parameters

s	: array of solute concentration
anAgent	Parameters used are those defined for THIS agent

Implements simulator.reaction.Reaction.

void simulator.reaction.ReactionGrowthFitness.computeSpecificGrowthRate ( ActiveAgent anAgent )

virtual

Return the specific reaction rate for a given agent.

Return the specific reaction rate for a given agent

Parameters

anAgent Agent to use to determine solute concentration and calculate reaction rate

See Also: ActiveAgent.grow(); Episome.computeRate(EpiBac)

Implements simulator.reaction.Reaction.

double simulator.reaction.ReactionGrowthFitness.computeSpecRate ( double[] s )

virtual

Compute the specific growth rate.

Compute the specific growth rate. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns: The specific growth rate

Implements simulator.reaction.Reaction.

void simulator.reaction.ReactionGrowthFitness.computeUptakeRate	(	double[]	s,
		double	mass,
		double	tdel
	)

virtual

Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1.

Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1

Parameters

s	The concentration of solute locally observed
mass	Mass of the catalyst (cell...)
tdel	Time

Implements simulator.reaction.Reaction.

double [] simulator.reaction.ReactionGrowthFitness.getMarginalDiffMu ( )

Return the marginalDiffMu array.

Return the marginalDiffMu array. Rob (25/8/2011): added this so that Reaction.applyChemostatReaction() can see marginalDiffMu

Returns: marginalDiffMu array

int simulator.reaction.ReactionGrowthFitness.getTotalParam ( )

Return the total number of parameters needed to describe the kinetic of this reaction (muMax included)

Returns: Integer stating the total number of parameters needed to describe the kinetic

void simulator.reaction.ReactionGrowthFitness.init	(	Simulator	aSim,
		XMLParser	xmlRoot
	)

Initialises the reaction by setting relevant parameters to values contained in the simulation protocol file.

Initialises the reaction by setting relevant parameters to values contained in the simulation protocol file

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
xmlRoot	The XML object containing the definition of one reaction in the protocol file

See Also: Simulator.createReaction()

void simulator.reaction.ReactionGrowthFitness.initFromAgent	(	ActiveAgent	anAgent,
		Simulator	aSim,
		XMLParser	aReactionRoot
	)

Use the reaction class to fill the parameters fields of the agent.

Use the reaction class to fill the parameters fields of the agent. Uses information in the agent and protocol file to achieve this

Parameters

anAgent	The ActiveAgent which parameters are being populated
aSim	The simulation object used to simulate the conditions specified in the protocol file
aReactionRoot	The XML object containing the definition of one reaction in the protocol file

See Also: Simulator.createReaction()

ArrayList<Double> simulator.reaction.ReactionGrowthFitness.setYield ( ActiveAgent anAgent )

Sonia Here we calculate the fitness cost of each of the plasmid types the host carries. For that we need the time the plasmid has spent in this cell since its reception or creation (for that we created a specific field for the plasmid: timeSpentInHost).

Parameters

anAgent

void simulator.reaction.ReactionGrowthFitness.updateMarginalMu ( double[] s )

virtual

Update the Marginal Mu data matrix.

Update the Marginal Mu data matrix

Parameters

s	Temporary container for solute concentration

Implements simulator.reaction.Reaction.

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/reaction/ReactionGrowthFitness.java

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation