TysonNovak2001OdeSystem Class Reference

#include <TysonNovak2001OdeSystem.hpp>

Inheritance diagram for TysonNovak2001OdeSystem:

Collaboration diagram for TysonNovak2001OdeSystem:

List of all members.

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 43 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 32 of file TysonNovak2001OdeSystem.cpp.

References Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), AbstractParameterisedSystem< std::vector< double > >::mpSystemInfo, and AbstractOdeSystem::SetStateVariables().

TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem ( )

Destructor.

Definition at line 45 of file TysonNovak2001OdeSystem.cpp.

Member Function Documentation

template<class Archive>

void TysonNovak2001OdeSystem::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Definition at line 136 of file TysonNovak2001OdeSystem.hpp.

void TysonNovak2001OdeSystem::Init ( )

Initialise parameter values.

Definition at line 50 of file TysonNovak2001OdeSystem.cpp.

References mCycB_threshold, mJ15, mJ16, mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK11, mK12d, mK12dd, mK12ddd, mK13, mK14, mK15d, mK15dd, mK16d, mK16dd, mK2d, mK2dd, mK2ddd, mK3d, mK3dd, mK4, mK4d, mK5d, mK5dd, mK6, mK7, mK8, mK9, mKeq, mMad, mMstar, mMu, and mN.

Referenced by TysonNovak2001OdeSystem().

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 93 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.

Referenced by CalculateRootFunction(), and CalculateStoppingEvent().

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 216 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

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 226 of file TysonNovak2001OdeSystem.cpp.

References EvaluateYDerivatives(), and mCycB_threshold.

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 153 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.

Member Data Documentation

double TysonNovak2001OdeSystem::mK1 [private]

Parameters for the Tyson & Novak (2001) model. Dimensional parameter k_1.

Definition at line 52 of file TysonNovak2001OdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2d [private]

Dimensional parameter k_2'.

Definition at line 54 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2dd [private]

Dimensional parameter k_2''.

Definition at line 56 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK2ddd [private]

Dimensional parameter k_2'''.

Definition at line 58 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mCycB_threshold [private]

Dimensionless parameter [CycB]_threshold.

Definition at line 60 of file TysonNovak2001OdeSystem.hpp.

Referenced by CalculateRootFunction(), CalculateStoppingEvent(), and Init().

double TysonNovak2001OdeSystem::mK3d [private]

Dimensional parameter k_3'.

Definition at line 62 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK3dd [private]

Dimensional parameter k_3''.

Definition at line 64 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK4d [private]

Dimensional parameter k_4'.

Definition at line 66 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK4 [private]

Dimensional parameter k_4.

Definition at line 68 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ3 [private]

Dimensionless parameter J_3.

Definition at line 70 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ4 [private]

Dimensionless parameter J_4.

Definition at line 72 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK5d [private]

Dimensional parameter k_5'.

Definition at line 74 of file TysonNovak2001OdeSystem.hpp.

Referenced by EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK5dd [private]

Dimensional parameter k_5''.

Definition at line 76 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK6 [private]

Dimensional parameter k_6.

Definition at line 78 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ5 [private]

Dimensionless parameter J_5.

Definition at line 80 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

unsigned TysonNovak2001OdeSystem::mN [private]

Dimensionless parameter n.

Definition at line 82 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK7 [private]

Dimensional parameter k_7.

Definition at line 84 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK8 [private]

Dimensional parameter k_8.

Definition at line 86 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ7 [private]

Dimensionless parameter J_7.

Definition at line 88 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mJ8 [private]

Dimensionless parameter J_8.

Definition at line 90 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mMad [private]

Dimensionless parameter [Mad].

Definition at line 92 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK9 [private]

Dimensional parameter k_9.

Definition at line 94 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK10 [private]

Dimensional parameter k_10.

Definition at line 96 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mK11 [private]

Dimensional parameter k_11.

Definition at line 98 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12d [private]

Dimensional parameter k_12'.

Definition at line 100 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12dd [private]

Dimensional parameter k_12''.

Definition at line 102 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK12ddd [private]

Dimensional parameter k_12'''.

Definition at line 104 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mKeq [private]

Dimensionless parameter K_eq.

Definition at line 106 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK13 [private]

Dimensional parameter k_13.

Definition at line 108 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK14 [private]

Dimensional parameter k_14.

Definition at line 110 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK15d [private]

Dimensional parameter k_15'.

Definition at line 112 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK15dd [private]

Dimensional parameter k_15''.

Definition at line 114 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK16d [private]

Dimensional parameter k_16'.

Definition at line 116 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mK16dd [private]

Dimensional parameter k_16''.

Definition at line 118 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mJ15 [private]

Dimensionless parameter J_15.

Definition at line 120 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mJ16 [private]

Dimensionless parameter J_16.

Definition at line 122 of file TysonNovak2001OdeSystem.hpp.

Referenced by Init().

double TysonNovak2001OdeSystem::mMu [private]

Dimensional parameter mu.

Definition at line 124 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

double TysonNovak2001OdeSystem::mMstar [private]

Dimensionless parameter m_star.

Definition at line 126 of file TysonNovak2001OdeSystem.hpp.

Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().

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

cell_based/src/odes/TysonNovak2001OdeSystem.hpp
cell_based/src/odes/TysonNovak2001OdeSystem.cpp


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