#include <Nash2004ContractionModel.hpp>

Inheritance diagram for Nash2004ContractionModel:

Collaboration diagram for Nash2004ContractionModel:

Public Member Functions
	Nash2004ContractionModel ()

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

void	SetInputParameters (ContractionModelInputParameters &rInputParameters)

void	SetStretchAndStretchRate (double stretch, double stretchRate)

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)

Private Attributes
double	mScaledVoltage

Static Private Attributes
static const double	kTa = 47.9

static const double	e0ByT0 = 1.0/100

Additional Inherited Members
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 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

Detailed Description

Nash2004 contraction model - Nash & Panfilov "Electromechanical mode of excitable tissue to study reentrant cardiac arrthrymias", Progress in Biophysics and Molecular Biology, 2004.

A simple, stretch- and stretch-rate-independent contraction model, just dependent on the voltage. If v is the non-dimensionalised voltage, Ta is given by dTa/dt = eps(v) (kTa*v - Ta); where eps(v) = e0 if v < 0.05, = 10*e0 v >= 0.05.

We use the non-dimensionalisation: V in [-85,40] —> v in [0,1], ie v=(V+85)/125

Not sure what the appropriate value of e0 is: as the paper uses non-dimensionalised time the e0 above corresponds to "eps0/t0", where eps0 is value used in the paper (1.0) and t0 is the characteristic time. The paper suggests using t0=25.9 (?), which gives Ta growing too quickly at the beginning (as rapidly as the voltage). t0 = 100 coded at the moment..

Definition at line 60 of file Nash2004ContractionModel.hpp.

Constructor & Destructor Documentation

Nash2004ContractionModel::Nash2004ContractionModel ( )

inline

Constructor

Definition at line 73 of file Nash2004ContractionModel.hpp.

References OdeSystemInformation< ODE_SYSTEM >::Instance(), AbstractUntemplatedParameterisedSystem::mpSystemInfo, mScaledVoltage, and AbstractParameterisedSystem< std::vector< double > >::mStateVariables.

Member Function Documentation

void Nash2004ContractionModel::EvaluateYDerivatives	(	double	time,
		const std::vector< double > &	rY,
		std::vector< double > &	rDY
	)

inlinevirtual

Calculate the derivative of the Ta (the state variable)

Parameters

time	time
rY	1D vector containing Ta
rDY	1D vector in which dTa/dt is set

Implements AbstractOdeSystem.

Definition at line 87 of file Nash2004ContractionModel.hpp.

References e0ByT0, kTa, and mScaledVoltage.

double Nash2004ContractionModel::GetActiveTension ( )

inlinevirtual

Returns: the current active tension

Implements AbstractContractionModel.

Definition at line 115 of file Nash2004ContractionModel.hpp.

References AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables().

double Nash2004ContractionModel::GetNextActiveTension ( )

inlinevirtual

Returns: the active tension corresponding to the temporary stored state variables produced by calling RunDoNotUpdate (and before calling UpdateStateVariables())

Implements AbstractContractionModel.

Definition at line 124 of file Nash2004ContractionModel.hpp.

References AbstractOdeBasedContractionModel::mTemporaryStateVariables.

bool Nash2004ContractionModel::IsStretchDependent ( )

inlinevirtual