#include <NhsContractionModel.hpp>

Inheritance diagram for NhsContractionModel:

Collaboration diagram for NhsContractionModel:

Public Member Functions
	NhsContractionModel ()

void	SetStretchAndStretchRate (double lambda, double dlambdaDt)

void	SetInputParameters (ContractionModelInputParameters &rInputParameters)

void	SetIntracellularCalciumConcentration (double calciumConcentration)

double	GetCalciumTroponinValue ()

void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)

double	GetActiveTension ()

double	GetNextActiveTension ()

bool	IsStretchDependent ()

bool	IsStretchRateDependent ()

Public Member Functions inherited from AbstractOdeBasedContractionModel
	AbstractOdeBasedContractionModel (unsigned numStateVariables)

virtual void	RunDoNotUpdate (double startTime, double endTime, double timeStep)

void	UpdateStateVariables ()

void	RunAndUpdate (double startTime, double endTime, double timeStep)

Public Member Functions inherited from AbstractOdeSystem
	AbstractOdeSystem (unsigned numberOfStateVariables)

virtual	~AbstractOdeSystem ()

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

virtual double	CalculateRootFunction (double time, const std::vector< double > &rY)

bool	GetUseAnalyticJacobian ()

const std::vector< double > &	rGetConstStateVariables () const

Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
	AbstractParameterisedSystem (unsigned numberOfStateVariables)

std::vector< double > &	rGetStateVariables ()

std::vector< double >	GetStateVariables ()

void	SetStateVariables (const std::vector< double > &rStateVariables)

double	GetStateVariable (unsigned index) const

double	GetStateVariable (const std::string &rName) const

void	SetStateVariable (unsigned index, double newValue)

void	SetStateVariable (const std::string &rName, double newValue)

virtual void	VerifyStateVariables ()

void	SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

std::vector< double >	GetInitialConditions () const

void	ResetToInitialConditions ()

double	GetParameter (unsigned index) const

double	GetParameter (const std::string &rName) const

void	SetParameter (const std::string &rName, double value)

void	SetParameter (unsigned index, double value)

double	GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)

double	GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)

void	SetAnyVariable (unsigned index, double value)

void	SetAnyVariable (const std::string &rName, double value)

virtual std::vector< double >	ComputeDerivedQuantities (double time, const std::vector< double > &rState)

std::vector< double >	ComputeDerivedQuantitiesFromCurrentState (double time)

Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
	AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)

virtual	~AbstractUntemplatedParameterisedSystem ()

boost::shared_ptr< const AbstractOdeSystemInformation >	GetSystemInformation () const

std::string	GetSystemName () const

unsigned	GetNumberOfAttributes () const

bool	HasAttribute (const std::string &rName) const

double	GetAttribute (const std::string &rName) const

unsigned	GetNumberOfStateVariables () const

const std::vector< std::string > &	rGetStateVariableNames () const

const std::vector< std::string > &	rGetStateVariableUnits () const

unsigned	GetStateVariableIndex (const std::string &rName) const

bool	HasStateVariable (const std::string &rName) const

std::string	GetStateVariableUnits (unsigned index) const

unsigned	GetNumberOfParameters () const

const std::vector< std::string > &	rGetParameterNames () const

const std::vector< std::string > &	rGetParameterUnits () const

unsigned	GetParameterIndex (const std::string &rName) const

bool	HasParameter (const std::string &rName) const

std::string	GetParameterUnits (unsigned index) const

unsigned	GetNumberOfDerivedQuantities () const

const std::vector< std::string > &	rGetDerivedQuantityNames () const

const std::vector< std::string > &	rGetDerivedQuantityUnits () const

unsigned	GetDerivedQuantityIndex (const std::string &rName) const

bool	HasDerivedQuantity (const std::string &rName) const

std::string	GetDerivedQuantityUnits (unsigned index) const

unsigned	GetAnyVariableIndex (const std::string &rName) const

bool	HasAnyVariable (const std::string &rName) const

std::string	GetAnyVariableUnits (unsigned index) const

std::string	GetAnyVariableUnits (const std::string &rName) const

Public Member Functions inherited from AbstractContractionModel
	AbstractContractionModel ()

virtual	~AbstractContractionModel ()

void	SetStretch (double stretch)

Protected Member Functions
void	CalculateCalciumTrop50 ()

double	CalculateT0 (double z)

Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > >
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y)

std::string	DumpState (const std::string &rMessage, std::vector< double >Y, double time)

void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)

Protected Attributes
double	mLambda

double	mDLambdaDt

double	mCalciumI

double	mCalciumTrop50

double	mK1

double	mK2

Protected Attributes inherited from AbstractOdeBasedContractionModel
std::vector< double >	mTemporaryStateVariables

double	mTime

Protected Attributes inherited from AbstractOdeSystem
bool	mUseAnalyticJacobian

Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > >
std::vector< double >	mStateVariables

std::vector< double >	mParameters

Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned	mNumberOfStateVariables

boost::shared_ptr < AbstractOdeSystemInformation >	mpSystemInfo

Static Protected Attributes
static const double	mKon = 100

static const double	mKrefoff = 0.2

static const double	mGamma = 2

static const double	mCalciumTroponinMax = 0.07

static const double	mAlphaR1 = 0.002

static const double	mAlphaR2 = 0.0017

static const double	mKZ = 0.15

static const unsigned	mNr = 3u

static const double	mBeta1 = -4

static const double	mAlpha0 = 0.008

static const unsigned	mN = 3u

static const double	mZp = 0.85

static const double	mCalcium50ref = 0.00105

static const double	mTref = 56.2

static const double	mBeta0 = 4.9

static const double	mA = 0.35

static const double	mA1 = -29

static const double	mA2 = 138

static const double	mA3 = 129

static const double	mAlpha1 = 0.03

static const double	mAlpha2 = 0.130

static const double	mAlpha3 = 0.625

Friends
class	TestContractionModels

Detailed Description

NHS (Niederer, Hunter, Smith) model of active tension in cardiac cells.

A system of ODEs which determines the active potential, given the intracellular calcium concentration, the stretch (lambda) of the cell, and the stretch rate (dlambda_dt) of the cell.

The state variables are, in order: Calcium_troponin, z, Q1, Q2, Q3

Reference: S.A. Niederer, N.P. Smith, P.J. Hunter, "New developments in a strongly coupled cardiac electro-mechanical model" Europace 7, S118-S127

The active tension is returned in KPa.

Definition at line 56 of file NhsContractionModel.hpp.

Constructor & Destructor Documentation

NhsContractionModel::NhsContractionModel ( )

Constructor. Initialises all state variables to zero, lambda to 1, dlambda_dt to 0 and intracellular calcium concentration to 0

Definition at line 100 of file NhsContractionModel.cpp.

References CalculateCalciumTrop50(), OdeSystemInformation< ODE_SYSTEM >::Instance(), mAlphaR2, mCalciumI, mDLambdaDt, mK1, mK2, mKZ, mLambda, mNr, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mZp, AbstractParameterisedSystem< std::vector< double > >::ResetToInitialConditions(), and SmallPow().

Member Function Documentation

void NhsContractionModel::CalculateCalciumTrop50 ( )

protected

Compute the calcium_trop50 concentration. This is a function of constants and lambda, so only needs to be called in the constructor or when lambda is set

Definition at line 74 of file NhsContractionModel.cpp.

References mBeta0, mBeta1, mCalcium50ref, mCalciumTrop50, mCalciumTroponinMax, mGamma, mKon, mKrefoff, and mLambda.

Referenced by NhsContractionModel(), and SetStretchAndStretchRate().

double NhsContractionModel::CalculateT0 ( double z )

protected

Returns: T0. This is a function of constants, lambda and z

Parameters

z

Definition at line 84 of file NhsContractionModel.cpp.

References mAlpha0, mAlphaR1, mBeta0, mCalciumTrop50, mCalciumTroponinMax, mK1, mK2, mLambda, mN, mTref, and SmallPow().

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), GetActiveTension(), and NhsModelWithBackwardSolver::GetNextActiveTension().

void NhsContractionModel::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)

virtual

Evaluate the derivatives of the state variables

Parameters

time	the current time, in milliseconds
rY	current values of the state variables
rDY	to be filled in with derivatives

Implements AbstractOdeSystem.

Definition at line 149 of file NhsContractionModel.cpp.

References CalculateT0(), EXCEPTION, mA, mA1, mA2, mA3, mAlpha0, mAlpha1, mAlpha2, mAlpha3, mAlphaR1, mAlphaR2, mCalciumI, mCalciumTrop50, mCalciumTroponinMax, mDLambdaDt, mGamma, mKon, mKrefoff, mKZ, mN, mNr, mTref, and SmallPow().

double NhsContractionModel::GetActiveTension ( )

virtual

Returns: the active tension, which is a function of the constants and current state variables. KILOPASCALS

Implements AbstractContractionModel.

Definition at line 207 of file NhsContractionModel.cpp.

References CalculateT0(), mA, and AbstractParameterisedSystem< std::vector< double > >::mStateVariables.

double NhsContractionModel::GetCalciumTroponinValue ( )

Returns: the current Calcium Troponin (one of the state variables) value. This may be needed if the cell model has Calcium troponin and might need overwriting

Definition at line 144 of file NhsContractionModel.cpp.

References AbstractParameterisedSystem< std::vector< double > >::mStateVariables.

double NhsContractionModel::GetNextActiveTension ( )

inlinevirtual

Returns: GetNextActiveTension() normally returns the active tension corresponding to the state variables that have been computed in RunDoNotUpdate. However, this only applies to when an implicit cardiac mechanics solver is used, in which case the NhsModelWithBackwardSolver should be used.

Implements AbstractContractionModel.

Reimplemented in NhsModelWithBackwardSolver.

Definition at line 211 of file NhsContractionModel.hpp.

References EXCEPTION.

bool NhsContractionModel::IsStretchDependent ( )

inlinevirtual

Returns: whether model is stretch-dependent

Implements AbstractContractionModel.

Definition at line 219 of file NhsContractionModel.hpp.

bool NhsContractionModel::IsStretchRateDependent ( )

inlinevirtual

Returns: whether model is stretch-rate-dependent

Implements AbstractContractionModel.

Definition at line 227 of file NhsContractionModel.hpp.

void NhsContractionModel::SetInputParameters ( ContractionModelInputParameters & rInputParameters )

virtual

Set the current intracellular calcium concentration

Parameters

rInputParameters input parameters (calcium, voltage, time, of which only calcium is used)

Implements AbstractContractionModel.

Definition at line 131 of file NhsContractionModel.cpp.

References DOUBLE_UNSET, ContractionModelInputParameters_::intracellularCalciumConcentration, and mCalciumI.

void NhsContractionModel::SetIntracellularCalciumConcentration ( double calciumConcentration )

Directly set the intracellular calcium concentration.

Parameters

calciumConcentration calcium concentration.

Definition at line 138 of file NhsContractionModel.cpp.

References mCalciumI.

void NhsContractionModel::SetStretchAndStretchRate	(	double	lambda,
		double	dlambdaDt
	)

virtual

Set the current stretch and the stretch rate of the cell/fibre

Parameters

lambda	current stretch
dlambdaDt	current stretch rate

Implements AbstractContractionModel.

Definition at line 122 of file NhsContractionModel.cpp.

References CalculateCalciumTrop50(), mDLambdaDt, and mLambda.

Member Data Documentation

const double NhsContractionModel::mA = 0.35

staticprotected

See reference. Dimensionless

Definition at line 125 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), GetActiveTension(), and NhsModelWithBackwardSolver::GetNextActiveTension().

const double NhsContractionModel::mA1 = -29

staticprotected

See reference. Dimensionless

Definition at line 128 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mA2 = 138

staticprotected

See reference. Dimensionless

Definition at line 131 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mA3 = 129

staticprotected

See reference. Dimensionless

Definition at line 134 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mAlpha0 = 0.008

staticprotected

See reference. (ms)^-1

Definition at line 107 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

const double NhsContractionModel::mAlpha1 = 0.03

staticprotected

See reference. (ms)^-1

Definition at line 137 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mAlpha2 = 0.130

staticprotected

See reference. (ms)^-1

Definition at line 140 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mAlpha3 = 0.625

staticprotected

See reference. (ms)^-1

Definition at line 143 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), and NhsModelWithBackwardSolver::ImplicitSolveForQ().

const double NhsContractionModel::mAlphaR1 = 0.002

staticprotected

See reference. (ms)^-1

Definition at line 92 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

const double NhsContractionModel::mAlphaR2 = 0.0017

staticprotected

See reference. (ms)^-1

Definition at line 95 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), and NhsContractionModel().

const double NhsContractionModel::mBeta0 = 4.9

staticprotected

See reference. Dimensionless

Definition at line 122 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), and CalculateT0().

const double NhsContractionModel::mBeta1 = -4

staticprotected

See reference. Dimensionless

Definition at line 104 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50().

const double NhsContractionModel::mCalcium50ref = 0.00105

staticprotected

See reference. mMols

Definition at line 116 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50().

double NhsContractionModel::mCalciumI

protected

The intracellular calcium concentration. To be specified by the caller

Definition at line 66 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), NhsContractionModel(), SetInputParameters(), and SetIntracellularCalciumConcentration().

double NhsContractionModel::mCalciumTrop50

protected

A parameter only dependent on constants and lambda, so updated whenever lambda is updated

Definition at line 70 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

const double NhsContractionModel::mCalciumTroponinMax = 0.07

staticprotected

See reference. mMols

Definition at line 89 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

double NhsContractionModel::mDLambdaDt

protected

The stretch rate. To be specified by the caller

Definition at line 64 of file NhsContractionModel.hpp.

Referenced by EvaluateYDerivatives(), NhsModelWithBackwardSolver::ImplicitSolveForQ(), NhsContractionModel(), and SetStretchAndStretchRate().

const double NhsContractionModel::mGamma = 2

staticprotected

See reference. Dimensionless

Definition at line 86 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().

double NhsContractionModel::mK1

protected

A constant determined from the other constrants. Set up in the constructor

Definition at line 73 of file NhsContractionModel.hpp.

Referenced by CalculateT0(), and NhsContractionModel().

double NhsContractionModel::mK2

protected

A constant determined from the other constrants. Set up in the constructor

Definition at line 75 of file NhsContractionModel.hpp.

Referenced by CalculateT0(), and NhsContractionModel().

const double NhsContractionModel::mKon = 100

staticprotected

See reference. (mMols)^-1 (ms)^-1

Definition at line 80 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().

const double NhsContractionModel::mKrefoff = 0.2

staticprotected

See reference. (ms)^-1

Definition at line 83 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), and EvaluateYDerivatives().

const double NhsContractionModel::mKZ = 0.15

staticprotected

See reference. Dimensionless

Definition at line 98 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), and NhsContractionModel().

double NhsContractionModel::mLambda

protected

The stretch. To be specified by the caller

Definition at line 62 of file NhsContractionModel.hpp.

Referenced by CalculateCalciumTrop50(), CalculateT0(), NhsContractionModel(), and SetStretchAndStretchRate().

const unsigned NhsContractionModel::mN = 3u

staticprotected

See reference. Dimensionless

Definition at line 110 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

const unsigned NhsContractionModel::mNr = 3u

staticprotected

See reference. Dimensionless

Definition at line 101 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), EvaluateYDerivatives(), and NhsContractionModel().

const double NhsContractionModel::mTref = 56.2

staticprotected

See reference. kPa

Definition at line 119 of file NhsContractionModel.hpp.

Referenced by NhsModelWithBackwardSolver::CalculateCaTropAndZDerivatives(), CalculateT0(), and EvaluateYDerivatives().

const double NhsContractionModel::mZp = 0.85

staticprotected

See reference. Dimensionless

Definition at line 113 of file NhsContractionModel.hpp.

Referenced by NhsContractionModel().

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

heart/src/odes/contractionmodels/NhsContractionModel.hpp
heart/src/odes/contractionmodels/NhsContractionModel.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation