#include <CorriasBuistSMCModified.hpp>

Inheritance diagram for CorriasBuistSMCModified:

Collaboration diagram for CorriasBuistSMCModified:

Public Member Functions
	CorriasBuistSMCModified (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

	~CorriasBuistSMCModified ()

void	VerifyStateVariables ()

double	GetIIonic (const std::vector< double > *pStateVariables=NULL)

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

void	SetFakeIccStimulusPresent (bool present)

bool	GetFakeIccStimulusPresent ()

double	SetCarbonMonoxideScaleFactor ()

void	SetCarbonMonoxideScaleFactor (double scaleFactor)

double	GetCarbonMonoxideScaleFactor ()

Public Member Functions inherited from AbstractCardiacCell
	AbstractCardiacCell (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

virtual	~AbstractCardiacCell ()

void	Init ()

void	SetTimestep (double dt)

virtual void	SolveAndUpdateState (double tStart, double tEnd)

virtual OdeSolution	Compute (double tStart, double tEnd, double tSamp=0.0)

virtual void	ComputeExceptVoltage (double tStart, double tEnd)

void	SetVoltage (double voltage)

double	GetVoltage ()

unsigned	GetNumberOfStateVariables () const

unsigned	GetNumberOfParameters () const

std::vector< double >	GetStdVecStateVariables ()

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

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

void	SetStateVariable (unsigned index, double newValue)

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

double	GetAnyVariable (const std::string &rName, double time=0.0)

double	GetParameter (const std::string &rParameterName)

double	GetParameter (unsigned parameterIndex)

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

virtual void	SetState (CellModelState state)

virtual void	SetSlowValues (const std::vector< double > &rSlowValues)

virtual void	GetSlowValues (std::vector< double > &rSlowValues)

virtual bool	IsFastOnly ()

virtual void	AdjustOutOfRangeSlowValues (std::vector< double > &rSlowValues)

virtual unsigned	GetNumSlowValues ()

Public Member Functions inherited from AbstractCardiacCellInterface
	AbstractCardiacCellInterface (boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)

virtual	~AbstractCardiacCellInterface ()

unsigned	GetVoltageIndex ()

void	SetStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)

double	GetStimulus (double time)

void	SetIntracellularStimulusFunction (boost::shared_ptr< AbstractStimulusFunction > pStimulus)

double	GetIntracellularStimulus (double time)

double	GetIntracellularAreaStimulus (double time)

void	SetUsedInTissueSimulation (bool tissue=true)

virtual boost::shared_ptr < RegularStimulus >	UseCellMLDefaultStimulus ()

bool	HasCellMLDefaultStimulus ()

virtual AbstractLookupTableCollection *	GetLookupTableCollection ()

boost::shared_ptr < AbstractStimulusFunction >	GetStimulusFunction ()

const boost::shared_ptr < AbstractStimulusFunction >	GetStimulusFunction () const

const boost::shared_ptr < AbstractIvpOdeSolver >	GetSolver () const

void	SetSolver (boost::shared_ptr< AbstractIvpOdeSolver > pSolver)

virtual void	SetVoltageDerivativeToZero (bool clamp=true)

void	SetFixedVoltage (double voltage)

virtual void	SetStretch (double stretch)

virtual double	GetIntracellularCalciumConcentration ()

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)

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

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Private Attributes
double	mScaleFactorCarbonMonoxide

bool	mFakeIccStimulusPresent

double	Cm

double	Asurf_in_cm_square

double	Asurf

double	VolCell

double	hCa

double	sCa

double	Ki

double	Nai

double	ACh

double	CaiRest

double	gLVA_max

double	gCaL_max

double	gBK_max

double	gKb_max

double	gKA_max

double	gKr_max

double	gNa_max

double	gnsCC_max

double	gcouple

double	JCaExt_max

double	Q10Ca

double	Q10K

double	Q10Na

double	Texp

double	T_correct_Ca

double	T_correct_K

double	T_correct_Na

double	T_correct_gBK

double	EK

double	ENa

double	EnsCC

double	Ca_o

double	K_o

double	Na_o

double	R

double	T

double	F

double	FoRT

double	RToF

Friends
class	boost::serialization::access

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 AbstractCardiacCell
double	mDt

Protected Attributes inherited from AbstractCardiacCellInterface
unsigned	mVoltageIndex

boost::shared_ptr < AbstractIvpOdeSolver >	mpOdeSolver

boost::shared_ptr < AbstractStimulusFunction >	mpIntracellularStimulus

bool	mSetVoltageDerivativeToZero

bool	mIsUsedInTissue

bool	mHasDefaultStimulusFromCellML

double	mFixedVoltage

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

This class is a modified version of the model of a gastric Smooth Muscle Cell.

Reference publication is:

Corrias A, Buist ML. "A quantitative model of gastric smooth muscle cellular activation." Ann Biomed Eng. 2007 Sep;35(9):1595-607. Epub 2007 May 8.

Modifications include:

ability to include/exclude built-in fake ICC stimulus
ability to set K+ channels-affecting CO concentrations

Definition at line 58 of file CorriasBuistSMCModified.hpp.

Constructor & Destructor Documentation

CorriasBuistSMCModified::CorriasBuistSMCModified	(	boost::shared_ptr< AbstractIvpOdeSolver >	pSolver,
		boost::shared_ptr< AbstractStimulusFunction >	pIntracellularStimulus
	)

Constructor

Parameters

pSolver	is a pointer to the ODE solver
pIntracellularStimulus	is a pointer to the intracellular stimulus

Definition at line 46 of file CorriasBuistSMCModified.cpp.

References ACh, Asurf, Asurf_in_cm_square, Ca_o, CaiRest, Cm, EK, ENa, EnsCC, F, FoRT, gBK_max, gCaL_max, gcouple, HeartConfig::GetCapacitance(), gKA_max, gKb_max, gKr_max, gLVA_max, gNa_max, gnsCC_max, hCa, AbstractCardiacCell::Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), HeartConfig::Instance(), JCaExt_max, K_o, Ki, mFakeIccStimulusPresent, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mScaleFactorCarbonMonoxide, Na_o, Nai, Q10Ca, Q10K, Q10Na, R, RToF, sCa, T, T_correct_Ca, T_correct_gBK, T_correct_K, T_correct_Na, Texp, and VolCell.

CorriasBuistSMCModified::~CorriasBuistSMCModified ( )

Destructor

Definition at line 117 of file CorriasBuistSMCModified.cpp.

Member Function Documentation

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

virtual

Compute the RHS of the FitHugh-Nagumo system of ODEs

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 191 of file CorriasBuistSMCModified.cpp.

References ACh, Asurf, Ca_o, CaiRest, EK, ENa, EnsCC, F, gCaL_max, gcouple, AbstractCardiacCellInterface::GetStimulus(), gKA_max, gKb_max, gKr_max, gLVA_max, gNa_max, gnsCC_max, hCa, JCaExt_max, mFakeIccStimulusPresent, mScaleFactorCarbonMonoxide, AbstractCardiacCellInterface::mSetVoltageDerivativeToZero, RToF, sCa, T_correct_Ca, T_correct_gBK, T_correct_K, T_correct_Na, and VolCell.

double CorriasBuistSMCModified::GetCarbonMonoxideScaleFactor ( )

Returns: the Carbon Monoxide scale factor

Definition at line 139 of file CorriasBuistSMCModified.cpp.

References mScaleFactorCarbonMonoxide.

bool CorriasBuistSMCModified::GetFakeIccStimulusPresent ( )

Returns: true if the fake ICC stimulus is present

Definition at line 134 of file CorriasBuistSMCModified.cpp.

References mFakeIccStimulusPresent.

double CorriasBuistSMCModified::GetIIonic ( const std::vector< double > * pStateVariables = NULL )

virtual

Calculates the ionic current

Parameters

pStateVariables the state variables of this model

Returns: the total ionic current

Now convert to microA over cm^2, the units that Chaste needs

Implements AbstractCardiacCellInterface.

Definition at line 144 of file CorriasBuistSMCModified.cpp.

References ACh, Asurf, Ca_o, EK, ENa, EnsCC, F, gCaL_max, gKA_max, gKb_max, gKr_max, gLVA_max, gNa_max, gnsCC_max, JCaExt_max, mScaleFactorCarbonMonoxide, AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), RToF, T_correct_gBK, and VolCell.

template<class Archive >

void CorriasBuistSMCModified::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 69 of file CorriasBuistSMCModified.hpp.

double CorriasBuistSMCModified::SetCarbonMonoxideScaleFactor ( )

Returns: the Carbon Monoxide scale for

void CorriasBuistSMCModified::SetCarbonMonoxideScaleFactor ( double scaleFactor )

Set the carbon monoxide scale factor. This will multiply the following currents: I_kr, I_Ka, Ibk

Parameters

scaleFactor the scale factor that multiply the currents.

Definition at line 124 of file CorriasBuistSMCModified.cpp.

References mScaleFactorCarbonMonoxide.

void CorriasBuistSMCModified::SetFakeIccStimulusPresent ( bool present )

Set whether we want the fake ICC stimulus or not. It changes the member variable mFakeIccStimulusPresent (which is true by default).

Parameters

present - true if we want the fake ICC stimulus, false otherwise

Definition at line 129 of file CorriasBuistSMCModified.cpp.

References mFakeIccStimulusPresent.

void CorriasBuistSMCModified::VerifyStateVariables ( )

virtual

Now empty

Reimplemented from AbstractParameterisedSystem< std::vector< double > >.

Definition at line 121 of file CorriasBuistSMCModified.cpp.

Member Data Documentation

double CorriasBuistSMCModified::ACh

private

acetylcholine conc (mM)

Definition at line 100 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::Asurf

private

surface area (mm^2)

Definition at line 91 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::Asurf_in_cm_square

private

Surface area in cm^2

Definition at line 90 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

double CorriasBuistSMCModified::Ca_o

private

mM

Definition at line 131 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::CaiRest

private

baseline Ca conc (mM)

Definition at line 101 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), and EvaluateYDerivatives().

double CorriasBuistSMCModified::Cm

private

membrane capacitance, pF

Definition at line 88 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

double CorriasBuistSMCModified::EK

private

Nernst potential for K (mV)

Definition at line 127 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::ENa

private

Nernst potential for Na (mV)

Definition at line 128 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::EnsCC

private

Nernst potential for nsCC (mV)

Definition at line 129 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::F

private

nC/nmol

Definition at line 138 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::FoRT

private

1/mV

Definition at line 139 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

double CorriasBuistSMCModified::gBK_max

private

max conductance of IBK)

Definition at line 106 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

double CorriasBuistSMCModified::gCaL_max

private

max conductance of ICaL

Definition at line 105 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gcouple

private

coupling conductance bewteen fake ICC and SMC

Definition at line 112 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), and EvaluateYDerivatives().

double CorriasBuistSMCModified::gKA_max

private

max conductance of IKA

Definition at line 108 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gKb_max

private

max conductance of IKb

Definition at line 107 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gKr_max

private

max conductance of IKr

Definition at line 109 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gLVA_max

private

max conductance of ILVA

Definition at line 104 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gNa_max

private

max conductance of INa

Definition at line 110 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::gnsCC_max

private

max conductance of InsCC

Definition at line 111 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::hCa

private

conc for half inactivation of fCa

Definition at line 94 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), and EvaluateYDerivatives().

double CorriasBuistSMCModified::JCaExt_max

private

max flux of CaSR (mM/ms)

Definition at line 113 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), and GetIIonic().

double CorriasBuistSMCModified::K_o

private

mM

Definition at line 132 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

double CorriasBuistSMCModified::Ki

private

intra K conc (mM)

Definition at line 98 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified().

bool CorriasBuistSMCModified::mFakeIccStimulusPresent

private

True if the fake built-in ICC stimulus is present

Definition at line 86 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), GetFakeIccStimulusPresent(), and SetFakeIccStimulusPresent().

double CorriasBuistSMCModified::mScaleFactorCarbonMonoxide

private

Scale factor for CO-affected currents Note that this the number that multiply the currents, hence it is not [CO], but a function of [CO] (for example, 2.8*[CO] - 0.1)

Definition at line 81 of file CorriasBuistSMCModified.hpp.

Referenced by CorriasBuistSMCModified(), EvaluateYDerivatives(), GetCarbonMonoxideScaleFactor(), GetIIonic(), and SetCarbonMonoxideScaleFactor().