#include <Alarcon2004OxygenBasedCellCycleOdeSystem.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Collaboration diagram for Alarcon2004OxygenBasedCellCycleOdeSystem:

Public Member Functions
	Alarcon2004OxygenBasedCellCycleOdeSystem (double oxygenConcentration, bool isLabelled, std::vector< double > stateVariables=std::vector< double >())
	~Alarcon2004OxygenBasedCellCycleOdeSystem ()
void	Init ()
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)
void	SetIsLabelled (bool isLabelled)
bool	IsLabelled () const
double	GetOxygenConcentration () const
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	ma1
double	ma2
double	ma3
double	ma4
double	mb3
double	mb4
double	mc1
double	mc2
double	md1
double	md2
double	mJ3
double	mJ4
double	mEta
double	mMstar
double	mB
double	mxThreshold
double	myThreshold
double	mOxygenConcentration
bool	mIsLabelled
Friends
class	boost::serialization::access

Detailed Description

Represents the Alarcon et al. (2004) system of ODEs (see ticket #461). [doi:10.1016/j.jtbi.2004.04.016]

The variables are

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. P = oxygen concentration

Definition at line 59 of file Alarcon2004OxygenBasedCellCycleOdeSystem.hpp.

Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem	(	double	oxygenConcentration,
		bool	isLabelled,
		std::vector< double >	stateVariables = `std::vector<double>()`
	)

Constructor.

Parameters:

oxygenConcentration	is a non-dimensional oxygen concentration value between 0 and 1
isLabelled	whether the cell associated with this cell cycle ODE system is labelled (this affects the ODE system)
stateVariables	optional initial conditions for state variables (only used in archiving)

State variables

0. x = Cdh1-APC complexes 1. y = cyclin-CDK 2. z = p27 3. m = mass 4. u = RBNP 5. oxygenConcentration

Definition at line 39 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References Init(), ma1, mc1, mIsLabelled, mMstar, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mxThreshold, myThreshold, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

Alarcon2004OxygenBasedCellCycleOdeSystem::~Alarcon2004OxygenBasedCellCycleOdeSystem ( )

Destructor.

Definition at line 86 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

Member Function Documentation

bool Alarcon2004OxygenBasedCellCycleOdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)		`[virtual]`

Calculate whether the conditions for the cell cycle to finish have been met.

Parameters:

time	at which to calculate whether the stopping event has occurred
rY	value of the solution vector used to evaluate the RHS.

Returns:: whether or not stopping conditions have been met

Reimplemented from AbstractOdeSystem.

Definition at line 158 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References mxThreshold, and myThreshold.

void Alarcon2004OxygenBasedCellCycleOdeSystem::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)		`[virtual]`

Compute the RHS of the Alarcon et al. (2004) system of ODEs.

Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].

Parameters:

time	used to evaluate the RHS.
rY	value of the solution vector used to evaluate the RHS.
rDY	filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations).

Implements AbstractOdeSystem.

Definition at line 109 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References ma1, ma2, ma3, ma4, mB, mb3, mb4, mc1, mc2, md1, md2, mEta, mIsLabelled, mJ3, mJ4, and mMstar.