AbstractRushLarsenCardiacCell Class Reference

#include <AbstractRushLarsenCardiacCell.hpp>

Collaboration diagram for AbstractRushLarsenCardiacCell:

Public Member Functions
	AbstractRushLarsenCardiacCell (unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual	~AbstractRushLarsenCardiacCell ()
OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)
void	ComputeExceptVoltage (double tStart, double tEnd)
void	SolveAndUpdateState (double tStart, double tEnd)
Protected Member Functions
virtual void	ComputeOneStepExceptVoltage (const std::vector< double > &rDY, const std::vector< double > &rAlphaOrTau, const std::vector< double > &rBetaOrInf)=0
void	UpdateTransmembranePotential (const std::vector< double > &rDY)
virtual void	EvaluateEquations (double time, std::vector< double > &rDY, std::vector< double > &rAlphaOrTau, std::vector< double > &rBetaOrInf)=0
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
Friends
class	boost::serialization::access

Detailed Description

This is the base class for cardiac cells solved using the Rush-Larsen method. It is based on code contributed by Megan Lewis, University of Saskatchewan

The basic approach to solving such models is:

Compute alpha & beta values for gating variables, and derivatives for other state variables.
Update the transmembrane potential, either from solving an external PDE, or using a forward Euler step.
Update any elligible gating variables (or similar) with Rush-Larsen scheme.
Update the remaining state variables using a forward Euler step.

Definition at line 51 of file AbstractRushLarsenCardiacCell.hpp.

Constructor & Destructor Documentation

AbstractRushLarsenCardiacCell::AbstractRushLarsenCardiacCell	(	unsigned	numberOfStateVariables,
		unsigned	voltageIndex,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Standard constructor for a cell.

Parameters:

	numberOfStateVariables	the size of the ODE system
	voltageIndex	the index of the variable representing the transmembrane potential within the state variable vector
	pIntracellularStimulus	the intracellular stimulus function

Some notes for future reference:

It's a pity that inheriting from AbstractCardiacCell forces us to store a null pointer (for the unused ODE solver) in every instance. We may want to revisit this design decision at a later date.

Definition at line 38 of file AbstractRushLarsenCardiacCell.cpp.

AbstractRushLarsenCardiacCell::~AbstractRushLarsenCardiacCell ( ) [virtual]

Virtual destructor

Definition at line 47 of file AbstractRushLarsenCardiacCell.cpp.

Member Function Documentation

OdeSolution AbstractRushLarsenCardiacCell::Compute	(	double	tStart,
		double	tEnd,
		double	tSamp = `0.0`
	)			`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. Uses a forward Euler step to update the transmembrane potential at each timestep.

The length of the time interval must be a multiple of the timestep.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate
	tSamp	sampling interval for returned results (defaults to mDt)

Returns:: the values of each state variable, at intervals of tSamp.

Reimplemented from AbstractCardiacCell.

Definition at line 50 of file AbstractRushLarsenCardiacCell.cpp.

References ComputeOneStepExceptVoltage(), EvaluateEquations(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractUntemplatedParameterisedSystem::mpSystemInfo, OdeSolution::rGetSolutions(), AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

void AbstractRushLarsenCardiacCell::ComputeExceptVoltage	(	double	tStart,
		double	tEnd
	)			`[virtual]`

Simulates this cell's behaviour between the time interval [tStart, tEnd], with timestep mDt. The transmembrane potential is kept fixed throughout, but the other state variables are updated.

The length of the time interval must be a multiple of the timestep.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 99 of file AbstractRushLarsenCardiacCell.cpp.

References TimeStepper::AdvanceOneTimeStep(), ComputeOneStepExceptVoltage(), EvaluateEquations(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractCardiacCellInterface::mSetVoltageDerivativeToZero, and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

virtual void AbstractRushLarsenCardiacCell::ComputeOneStepExceptVoltage	(	const std::vector< double > &	rDY,
		const std::vector< double > &	rAlphaOrTau,
		const std::vector< double > &	rBetaOrInf
	)			`[protected, pure virtual]`

Update the values of elligible gating variables using the Rush-Larsen method, and of other non-V variables using forward Euler, for a single timestep.

Note:: This method must be provided by subclasses.

Parameters:

	rDY	vector containing dy/dt values
	rAlphaOrTau	vector containing alpha or tau values, depending on the formulation
	rBetaOrInf	vector containing beta or inf values, depending on the formulation

Referenced by Compute(), ComputeExceptVoltage(), and SolveAndUpdateState().

virtual void AbstractRushLarsenCardiacCell::EvaluateEquations	(	double	time,
		std::vector< double > &	rDY,
		std::vector< double > &	rAlphaOrTau,
		std::vector< double > &	rBetaOrInf
	)			`[protected, pure virtual]`

Compute dy/dt and alpha and beta values.

Note:: This method must be provided by subclasses.

Parameters:

	time	start of this timestep
	rDY	vector to fill in with dy/dt values
	rAlphaOrTau	vector to fill in with alpha or tau values, depending on the formulation
	rBetaOrInf	vector to fill in with beta or inf values, depending on the formulation

Referenced by Compute(), ComputeExceptVoltage(), and SolveAndUpdateState().

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

This function should never be called - the cell class incorporates its own solver.

Parameters:

	time
	rY
	rDY

Implements AbstractOdeSystem.

Definition at line 135 of file AbstractRushLarsenCardiacCell.hpp.

References NEVER_REACHED.

template<class Archive >

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

Archive the member variables.

Parameters:

	archive
	version

Reimplemented from AbstractCardiacCell.

Definition at line 63 of file AbstractRushLarsenCardiacCell.hpp.

void AbstractRushLarsenCardiacCell::SolveAndUpdateState	(	double	tStart,
		double	tEnd
	)			`[virtual]`

Simulate this cell's behaviour between the time interval [tStart, tEnd], with timestemp mDt, updating the internal state variable values.

Parameters:

	tStart	beginning of the time interval to simulate
	tEnd	end of the time interval to simulate

Reimplemented from AbstractCardiacCell.

Definition at line 123 of file AbstractRushLarsenCardiacCell.cpp.

References TimeStepper::AdvanceOneTimeStep(), ComputeOneStepExceptVoltage(), EvaluateEquations(), TimeStepper::GetTime(), TimeStepper::IsTimeAtEnd(), AbstractCardiacCell::mDt, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, UpdateTransmembranePotential(), and AbstractParameterisedSystem< std::vector< double > >::VerifyStateVariables().

void AbstractRushLarsenCardiacCell::UpdateTransmembranePotential ( const std::vector< double > & rDY ) [protected]

Perform a forward Euler step to update the transmembrane potential.

Parameters:

rDY

vector containing dy/dt values

Definition at line 142 of file AbstractRushLarsenCardiacCell.cpp.

References AbstractCardiacCellInterface::GetVoltageIndex(), AbstractCardiacCell::mDt, and AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables().

Referenced by Compute(), and SolveAndUpdateState().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCardiacCell.

Definition at line 55 of file AbstractRushLarsenCardiacCell.hpp.

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

heart/src/odes/AbstractRushLarsenCardiacCell.hpp
heart/src/odes/AbstractRushLarsenCardiacCell.cpp

AbstractRushLarsenCardiacCell Class Reference

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation