#include <CorriasBuistICCModified.hpp>

Inheritance diagram for CorriasBuistICCModified:

Collaboration diagram for CorriasBuistICCModified:

Public Member Functions
	CorriasBuistICCModified (boost::shared_ptr< AbstractIvpOdeSolver > pSolver, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
	~CorriasBuistICCModified ()
void	VerifyStateVariables ()
double	GetIIonic (const std::vector< double > *pStateVariables=NULL)
void	EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY)
void	SetFractionOfVDDRInPU (double fraction)
void	SetIP3Concentration (double concentration)
void	SetSercaPumpScaleFactor (double scaleFactor)
void	SetCarbonMonoxideScaleFactor (double scaleFactor)
double	GetCarbonMonoxideScaleFactor ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mFractionOfVDDRInPU
double	mIP3Concentration
double	mScaleFactorSerca
double	mScaleFactorCarbonMonoxide
double	Ca_o
double	Cl_o
double	K_o
double	Na_o
double	R
double	T
double	F
double	FoRT
double	RToF
double	Cm
double	Asurf_in_cm_square
double	Asurf
double	Cl_i
double	K_i
double	Na_i
double	P_cyto
double	Vol
double	fc
double	fe
double	fm
double	Q10Ca
double	Q10K
double	Q10Na
double	T_exp
double	G_max_BK
double	G_max_CaCl
double	G_max_ERG
double	G_max_Ltype
double	G_max_NSCC
double	G_max_Na
double	G_max_VDDR
double	G_max_bk
double	G_max_kv11
double	J_max_PMCA
double	J_max_PMCA_PU
double	J_ERleak
double	J_max_leak
double	Jmax_IP3
double	Jmax_NaCa
double	Jmax_serca
double	Jmax_uni
double	NaPerm_o_Kperm
double	L
double	P_ER
double	P_PU
double	P_mito
double	b
double	na
double	K_Ca
double	K_Na
double	K_act
double	K_trans
double	k_serca
double	conc
double	d_ACT
double	d_IP3
double	d_INH
double	tau_d_CaCl
double	tau_d_NSCC
double	tauh
double	deltaPsi_B
double	deltaPsi_star
double	deltaPsi
double	V_cyto
double	V_ER
double	V_MITO
double	V_PU
double	T_correction_Ca
double	T_correction_K
double	T_correction_Na
double	T_correction_BK
double	E_Na
double	E_K
double	E_Cl
double	E_NSCC
double	tau_d_ERG
double	tau_d_Ltype
double	tau_d_Na
double	tau_d_VDDR
double	tau_d_kv11
double	tau_f_Ltype
double	tau_f_Na
double	tau_f_VDDR
double	tau_f_ca_Ltype
double	tau_f_kv11
double	e2FoRTdPsiMdPsiS
double	ebFoRTdPsiMdPsiS
Friends
class	boost::serialization::access

Detailed Description

This class is a modified version of the model of a gastric Interstitial Cell of Cajal.

Reference publication is:

Corrias A, Buist ML. "Quantitative cellular description of gastric slow wave activity." Am J Physiol Gastrointest Liver Physiol. 2008 Apr;294(4):G989-95. Epub 2008 Feb 14.

Modifications include:

simplified mitochondria dynamics (assumed mitochondrial potential is almost constant
ability to set K+ channels-affecting CO concentrations
ability to deflect a fraction of VDDR channels into the pacemaker unit.

Definition at line 59 of file CorriasBuistICCModified.hpp.

Constructor & Destructor Documentation

CorriasBuistICCModified::CorriasBuistICCModified	(	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 44 of file CorriasBuistICCModified.cpp.

References Asurf, Asurf_in_cm_square, b, Ca_o, Cl_i, Cl_o, Cm, conc, d_ACT, d_INH, d_IP3, deltaPsi, deltaPsi_B, deltaPsi_star, e2FoRTdPsiMdPsiS, E_Cl, E_K, E_Na, E_NSCC, ebFoRTdPsiMdPsiS, F, fc, fe, fm, FoRT, G_max_bk, G_max_BK, G_max_CaCl, G_max_ERG, G_max_kv11, G_max_Ltype, G_max_Na, G_max_NSCC, G_max_VDDR, HeartConfig::GetCapacitance(), AbstractCardiacCell::Init(), HeartConfig::Instance(), J_ERleak, J_max_leak, J_max_PMCA, J_max_PMCA_PU, Jmax_IP3, Jmax_NaCa, Jmax_serca, Jmax_uni, K_act, K_Ca, K_i, K_Na, K_o, k_serca, K_trans, L, mFractionOfVDDRInPU, mIP3Concentration, AbstractUntemplatedParameterisedSystem::mpSystemInfo, mScaleFactorCarbonMonoxide, mScaleFactorSerca, na, Na_i, Na_o, NaPerm_o_Kperm, P_cyto, P_ER, P_mito, P_PU, Q10Ca, Q10K, Q10Na, R, RToF, T, T_correction_BK, T_correction_Ca, T_correction_K, T_correction_Na, T_exp, tau_d_CaCl, tau_d_ERG, tau_d_kv11, tau_d_Ltype, tau_d_Na, tau_d_NSCC, tau_d_VDDR, tau_f_ca_Ltype, tau_f_kv11, tau_f_Ltype, tau_f_Na, tau_f_VDDR, tauh, V_cyto, V_ER, V_MITO, V_PU, and Vol.

CorriasBuistICCModified::~CorriasBuistICCModified ( )

Destructor

Definition at line 184 of file CorriasBuistICCModified.cpp.

Member Function Documentation

void CorriasBuistICCModified::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 272 of file CorriasBuistICCModified.cpp.

References Asurf, Ca_o, conc, d_ACT, d_INH, d_IP3, deltaPsi, deltaPsi_star, e2FoRTdPsiMdPsiS, E_Cl, E_K, E_Na, E_NSCC, ebFoRTdPsiMdPsiS, F, fc, fe, fm, FoRT, G_max_bk, G_max_BK, G_max_CaCl, G_max_ERG, G_max_kv11, G_max_Ltype, G_max_Na, G_max_NSCC, G_max_VDDR, AbstractCardiacCellInterface::GetStimulus(), J_ERleak, J_max_leak, J_max_PMCA, J_max_PMCA_PU, Jmax_IP3, Jmax_NaCa, Jmax_serca, Jmax_uni, K_act, K_Ca, K_Na, k_serca, K_trans, L, mFractionOfVDDRInPU, mIP3Concentration, mScaleFactorCarbonMonoxide, mScaleFactorSerca, AbstractCardiacCellInterface::mSetVoltageDerivativeToZero, na, Na_i, RToF, T_correction_BK, tau_d_CaCl, tau_d_ERG, tau_d_kv11, tau_d_Ltype, tau_d_Na, tau_d_NSCC, tau_d_VDDR, tau_f_ca_Ltype, tau_f_kv11, tau_f_Ltype, tau_f_Na, tau_f_VDDR, tauh, V_cyto, V_ER, V_MITO, and V_PU.

double CorriasBuistICCModified::GetCarbonMonoxideScaleFactor ( )

Returns the Carbon Monoxide scale factor

Definition at line 211 of file CorriasBuistICCModified.cpp.

References mScaleFactorCarbonMonoxide.

double CorriasBuistICCModified::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 216 of file CorriasBuistICCModified.cpp.

References Asurf, Ca_o, E_Cl, E_K, E_Na, E_NSCC, F, G_max_bk, G_max_BK, G_max_CaCl, G_max_ERG, G_max_kv11, G_max_Ltype, G_max_Na, G_max_NSCC, G_max_VDDR, J_max_PMCA, mScaleFactorCarbonMonoxide, AbstractParameterisedSystem< std::vector< double > >::rGetStateVariables(), RToF, T_correction_BK, and V_cyto.

template<class Archive >

void CorriasBuistICCModified::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 CorriasBuistICCModified.hpp.

References mFractionOfVDDRInPU, mIP3Concentration, mScaleFactorCarbonMonoxide, and mScaleFactorSerca.

void CorriasBuistICCModified::SetCarbonMonoxideScaleFactor ( double scaleFactor )

Set the carbon monoxide scale factor. This will multiply the following currents: I_kv11, I_ERG, Ibk

Parameters:

scaleFactor the scale factor that multiply the currents.

Definition at line 206 of file CorriasBuistICCModified.cpp.

References mScaleFactorCarbonMonoxide.

void CorriasBuistICCModified::SetFractionOfVDDRInPU ( double fraction )

Sets the fraction of VDDR channels in the Pacemaker unit

Parameters:

fraction the fraction of VDDr channels in the PU

Definition at line 196 of file CorriasBuistICCModified.cpp.

References mFractionOfVDDRInPU.

void CorriasBuistICCModified::SetIP3Concentration ( double concentration )

Set the value of IP3 concentration in the cell

Parameters:

concentration the concentration of IP3

Definition at line 201 of file CorriasBuistICCModified.cpp.

References mIP3Concentration.

void CorriasBuistICCModified::SetSercaPumpScaleFactor ( double scaleFactor )

Set a multiplying factor for the influx of Ca2+ into the Er via the SERCA pump (set to zero will block the SW generation)

Parameters:

scaleFactor the scale factor (=0 --> no Ca2+ uptake into the ER and, consequently, no SW)

Definition at line 191 of file CorriasBuistICCModified.cpp.

References mScaleFactorSerca.

void CorriasBuistICCModified::VerifyStateVariables ( ) [virtual]

Now empty

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

Definition at line 188 of file CorriasBuistICCModified.cpp.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractCardiacCell.

Definition at line 61 of file CorriasBuistICCModified.hpp.

Member Data Documentation

double CorriasBuistICCModified::Asurf [private]

mm2

Definition at line 102 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::Asurf_in_cm_square [private]

cm2

Definition at line 101 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::b [private]

dim

Definition at line 141 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::Ca_o [private]

mM

Definition at line 88 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::Cl_i [private]

mM

Definition at line 103 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::Cl_o [private]

mM

Definition at line 89 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::Cm [private]

pF

Definition at line 100 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::conc [private]

mM

Definition at line 149 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::d_ACT [private]

mM

Definition at line 150 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::d_INH [private]

mM

Definition at line 152 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::d_IP3 [private]

mM

Definition at line 151 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::deltaPsi [private]

mV

Definition at line 160 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::deltaPsi_B [private]

mV

Definition at line 158 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::deltaPsi_star [private]

mV

Definition at line 159 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::e2FoRTdPsiMdPsiS [private]

speed-up constant

Definition at line 199 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::E_Cl [private]

mV

Definition at line 181 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::E_K [private]

mV

Definition at line 180 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::E_Na [private]

mV

Definition at line 179 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::E_NSCC [private]

mV

Definition at line 182 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::ebFoRTdPsiMdPsiS [private]

speed-up constant

Definition at line 200 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::F [private]

nC/nmol

Definition at line 96 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::fc [private]

dim

Definition at line 108 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::fe [private]

dim

Definition at line 109 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::fm [private]

dim

Definition at line 110 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::FoRT [private]

1/mV

Definition at line 97 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::G_max_bk [private]

nS

Definition at line 123 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_BK [private]

nS

Definition at line 116 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_CaCl [private]

nS

Definition at line 117 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_ERG [private]

nS

Definition at line 118 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_kv11 [private]

nS

Definition at line 124 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_Ltype [private]

nS

Definition at line 119 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_Na [private]

nS

Definition at line 121 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_NSCC [private]

nS

Definition at line 120 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::G_max_VDDR [private]

nS

Definition at line 122 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::J_ERleak [private]

1/ms (1/s) * 1/1000 (ms/s) = 1/ms

Definition at line 129 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::J_max_leak [private]

1/ms (1/s) * 1/1000 (ms/s) = 1/ms

Definition at line 130 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::J_max_PMCA [private]

mM/ms (mM/s) * 1/1000 (s/ms) = mM/ms

Definition at line 127 of file CorriasBuistICCModified.hpp.

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

double CorriasBuistICCModified::J_max_PMCA_PU [private]

mM/ms (mM/s) * 1/1000 (s/ms) = mM/ms

Definition at line 128 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::Jmax_IP3 [private]

1/ms (1/s) * 1/1000 (ms/s) = 1/ms

Definition at line 131 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::Jmax_NaCa [private]

mM/ms (mM/s) * 1/1000 (s/ms) = mM/ms

Definition at line 132 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::Jmax_serca [private]

mM/ms (mM/s) * 1/1000 (s/ms) = mM/ms

Definition at line 133 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::Jmax_uni [private]

1/ms (1/s) * 1/1000 (ms/s) = 1/ms

Definition at line 134 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::K_act [private]

mM

Definition at line 146 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::K_Ca [private]

mM

Definition at line 144 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::K_i [private]

mM

Definition at line 104 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::K_Na [private]

mM

Definition at line 145 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::K_o [private]

mM

Definition at line 90 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified().

double CorriasBuistICCModified::k_serca [private]

mM

Definition at line 148 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::K_trans [private]

mM

Definition at line 147 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::L [private]

dim

Definition at line 137 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), and EvaluateYDerivatives().

double CorriasBuistICCModified::mFractionOfVDDRInPU [private]

fraction of VDDR channel in the PU, initialised to zero

Definition at line 75 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), EvaluateYDerivatives(), serialize(), and SetFractionOfVDDRInPU().

double CorriasBuistICCModified::mIP3Concentration [private]

the IP3 concentration, defaults to 0.0006 mM

Definition at line 77 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), EvaluateYDerivatives(), serialize(), and SetIP3Concentration().

double CorriasBuistICCModified::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 85 of file CorriasBuistICCModified.hpp.

Referenced by CorriasBuistICCModified(), EvaluateYDerivatives(), GetCarbonMonoxideScaleFactor(), GetIIonic(), serialize(), and SetCarbonMonoxideScaleFactor().