TysonNovak2001OdeSystem Class Reference

#include <TysonNovak2001OdeSystem.hpp>

Inherits AbstractOdeSystemWithAnalyticJacobian.

Collaboration diagram for TysonNovak2001OdeSystem:

Public Member Functions
	TysonNovak2001OdeSystem (std::vector< double > stateVariables=std::vector< double >())
	~TysonNovak2001OdeSystem ()
void	Init ()
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
bool	CalculateStoppingEvent (double time, const std::vector< double > &rY)
double	CalculateRootFunction (double time, const std::vector< double > &rY)
virtual void	AnalyticJacobian (const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mK1
double	mK2d
double	mK2dd
double	mK2ddd
double	mCycB_threshold
double	mK3d
double	mK3dd
double	mK4d
double	mK4
double	mJ3
double	mJ4
double	mK5d
double	mK5dd
double	mK6
double	mJ5
unsigned	mN
double	mK7
double	mK8
double	mJ7
double	mJ8
double	mMad
double	mK9
double	mK10
double	mK11
double	mK12d
double	mK12dd
double	mK12ddd
double	mKeq
double	mK13
double	mK14
double	mK15d
double	mK15dd
double	mK16d
double	mK16dd
double	mJ15
double	mJ16
double	mMu
double	mMstar
Friends
class	boost::serialization::access

Detailed Description

Represents the Tyson & Novak (2001) system of ODEs. [doi:10.1006/jtbi.2001.2293]

Definition at line 44 of file TysonNovak2001OdeSystem.hpp.

Constructor & Destructor Documentation

TysonNovak2001OdeSystem::TysonNovak2001OdeSystem ( std::vector< double > stateVariables = std::vector<double>() )

Constructor.

Parameters:

stateVariables

optional initial conditions for state variables (only used in archiving)

Definition at line 33 of file TysonNovak2001OdeSystem.cpp.

References Init(), AbstractUntemplatedParameterisedSystem::mpSystemInfo, and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().

TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem ( )

Destructor.

Definition at line 46 of file TysonNovak2001OdeSystem.cpp.

Member Function Documentation

void TysonNovak2001OdeSystem::AnalyticJacobian	(	const std::vector< double > &	rSolutionGuess,
		double **	jacobian,
		double	time,
		double	timeStep
	)			`[virtual]`

Compute the Jacobian of the ODE system.

Parameters:

	rSolutionGuess	initial guess for the solution vector.
	jacobian	the Jacobian of the ODE system.
	time	at which to calculate the Jacobian.
	timeStep	used to calculate the Jacobian.

Implements AbstractOdeSystemWithAnalyticJacobian.

Definition at line 154 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.

double TysonNovak2001OdeSystem::CalculateRootFunction	(	double	time,
		const std::vector< double > &	rY
	)			`[virtual]`

Calculate whether the conditions for the cell cycle to finish have been met. (Used by CVODE solver to find exact stopping position)

Parameters:

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

Returns:: How close we are to the root of the stopping condition

Reimplemented from AbstractOdeSystem.

Definition at line 227 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

bool TysonNovak2001OdeSystem::CalculateStoppingEvent	(	double	time,
		const std::vector< double > &	rY
	)			`[virtual]`

Calculate whether the conditions for the cell cycle to finish have been met. (Used by Chaste solvers to find whether or not to stop solving)

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 217 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

void TysonNovak2001OdeSystem::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).

1. [CycB] 2. [Cdh1] 3. [Cdc20T] 4. [Cdc20A] 5. [IEP] 6. m - mass of the cell

Implements AbstractOdeSystem.

Definition at line 94 of file TysonNovak2001OdeSystem.cpp.

References mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5d, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.