Bueno-Orovio ionic model. More...

#include <ionic_bueno_orovio.h>

Inheritance diagram for BuenoOrovio:

Classes
class	Parameters
	Model parameters class. More...

Public Member Functions
	BuenoOrovio ()
	Constructor.

virtual std::unique_ptr< IonicModelParameters >	get_parameters () const override
	Construct an instance of model parameters.

virtual void	read_parameters (const IonicModelParameters &params) override
	Read model parameters from a parameter object.

virtual void	distribute_parameters (const CmMod &cm_mod, const cmType &cm) override
	Distribute model parameters to all parallel processes.

virtual unsigned int	get_calcium_index () const override
	Get the calcium proxy index.

Public Member Functions inherited from IonicModel
	IonicModel (const InitialStates &initial_X_, const InitialStates &initial_Xg_, const double Vrest_)
	Constructor.

	IonicModel (const InitialStates &initial_X_, const InitialStates &initial_Xg_, const double Vrest_, const double Vscale_, const double Tscale_, const double Voffset_)
	Constructor with scaling factors.

virtual	~IonicModel ()=default
	Virtual destructor.

void	init (Vector< double > &X, Vector< double > &Xg) const
	Setup model initial conditions.

void	integ (const odeType &ode_solver_params, const int zone_id, const double t, const double dt, const double Istim, const double Ksac, Vector< double > &X, Vector< double > &Xg) const
	Integrate over one time step.

unsigned int	nX () const
	Get the number of state variables.

unsigned int	nG () const
	Get the number of gating variables.

virtual std::vector< std::pair< std::string, int > >	get_output_variables () const
	Get a list of state variables to export to VTU.

std::vector< outputType >	get_registered_outputs () const
	Get output variable information for output registration.

Static Public Attributes
static const std::string	label = "BO"
	Model label.

static const InitialStates	initial_X
	State variables.

static const InitialStates	initial_Xg = {}
	Gating variables.

static constexpr unsigned int	calcium_index = 3

Protected Member Functions
virtual void	update_g (const unsigned int zone_id, const double dt, const Vector< double > &X, Vector< double > &Xg) const override

virtual Vector< double >	getf (const unsigned int zone_id, const Vector< double > &X, const Vector< double > &Xg, const double I_stim, const double I_sac) const override
	Model right-hand side.

virtual Array< double >	getj (const unsigned int zone_id, const Vector< double > &X, const Vector< double > &Xg, const double Ksac) const override
	Model jacobian.

double	step (const double r) const
	Step function.

double	delta (const double r) const
	Delta function.

Protected Member Functions inherited from IonicModel
void	integ_fe (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac) const
	Integrate the model with the forward Euler method.

void	integ_rk (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac) const
	Integrate the model with the fourth-order explicit Runge-Kutta method.

void	integ_cn2 (const unsigned int zone_id, Vector< double > &X, Vector< double > &Xg, const double Ts, const double Ti, const double Istim, const double Ksac, const unsigned int max_iter, const double rtol, const double atol) const
	Integrate the model with the Crank-Nicolson method.

Model parameters
using	ModelParam = Vector< double >

ModelParam	u_o = {0.0, 0.0, 0.0}
	[1].

ModelParam	u_u = {1.550, 1.56, 1.61}
	[1].

ModelParam	theta_v = {0.30, 0.3, 0.3}
	[1].

ModelParam	theta_w = {0.130, 0.13, 0.13}
	[1].

ModelParam	thetam_v = {6.E-3, 0.2, 0.1}
	[1].

ModelParam	theta_o = {6.E-3, 6.E-3, 5.E-3}
	[1].

ModelParam	taum_v1 = {60.0, 75., 80.}
	[1/s].

ModelParam	taum_v2 = {1.15E3, 10., 1.4506}
	[1/s].

ModelParam	taup_v = {1.45060, 1.4506, 1.4506}
	[1/s].

ModelParam	taum_w1 = {60.0, 6., 70.}
	[1/s].

ModelParam	taum_w2 = {15.0, 140., 8.}
	[1/s].

ModelParam	km_w = {65.0, 200., 200.}
	[1].

ModelParam	um_w = {3.E-2, 1.6E-2, 1.6E-2}
	[1].

ModelParam	taup_w = {200.0, 280., 280.}
	[1/s].

ModelParam	tau_fi = {0.110, 0.1, 0.078}
	[1/s].

ModelParam	tau_o1 = {400.0, 470., 410.}
	[1/s].

ModelParam	tau_o2 = {6.0, 6., 7.}
	[1/s].

ModelParam	tau_so1 = {30.01810, 40., 91.}
	[1/s].

ModelParam	tau_so2 = {0.99570, 1.2, 0.8}
	[1/s].

ModelParam	k_so = {2.04580, 2., 2.1}
	[1].

ModelParam	u_so = {0.650, 0.65, 0.6}
	[1].

ModelParam	tau_s1 = {2.73420, 2.7342, 2.7342}
	[1/s].

ModelParam	tau_s2 = {16.0, 2., 2.}
	[1/s].

ModelParam	k_s = {2.09940, 2.0994, 2.0994}
	[1].

ModelParam	u_s = {0.90870, 0.9087, 0.9087}
	[1].

ModelParam	tau_si = {1.88750, 2.9013, 3.3849}
	[1/s].

ModelParam	tau_winf = {7.E-2, 2.73E-2, 1.E-2}
	[1/s].

ModelParam	ws_inf = {0.940, 0.78, 0.5}
	[1].

Additional Inherited Members
Public Types inherited from IonicModel
using	InitialStates = std::vector< std::pair< std::string, double > >

Protected Attributes inherited from IonicModel
InitialStates	initial_X
	Initial states.

InitialStates	initial_Xg
	Initial gating variables.

const double	Vrest

const double	Vscale
	Voltage scaling [mV].

const double	Tscale
	Time scaling [ms].

const double	Voffset
	Voltage offset parameter [mV].

Detailed Description

Bueno-Orovio ionic model.

Reference: Bueno-Orovio, Cherry, Fenton. Minimal model for human ventricular action potentials in tissue. Journal of Theoretical Biology (2008)

Member Typedef Documentation

◆ ModelParam

using BuenoOrovio::ModelParam = Vector<double>

protected

Alias for model parameters container. The three entries in each of these correspond to epicardium, endocardium and myocardium, respectively (see also table 1 in the reference paper).

Todo:

[TODO:DaveP] these guys should be maps map<int,double>.

[michelebucelli] Would it make sense to treat these in the same way as the epi/endo/myo zone are treated in the TTP model?

Constructor & Destructor Documentation

◆ BuenoOrovio()

BuenoOrovio::BuenoOrovio ( )

inline

Constructor.

Member Function Documentation

◆ delta()

double BuenoOrovio::delta ( const double r ) const

inlineprotected

Delta function.

◆ distribute_parameters()

void BuenoOrovio::distribute_parameters	(	const CmMod &	cm_mod,
		const cmType &	cm
	)

overridevirtual

Distribute model parameters to all parallel processes.

Reimplemented from IonicModel.

◆ get_calcium_index()

virtual unsigned int BuenoOrovio::get_calcium_index ( ) const

inlineoverridevirtual

Get the calcium proxy index.

Implements IonicModel.

◆ get_parameters()

virtual std::unique_ptr< IonicModelParameters > BuenoOrovio::get_parameters ( ) const

inlineoverridevirtual

Construct an instance of model parameters.

Reimplemented from IonicModel.

◆ getf()

Vector< double > BuenoOrovio::getf	(	const unsigned int	zone_id,
		const Vector< double > &	X,
		const Vector< double > &	Xg,
		const double	I_stim,
		const double	I_sac
	)		const

overrideprotectedvirtual

Model right-hand side.

Implements IonicModel.

◆ getj()

Array< double > BuenoOrovio::getj	(	const unsigned int	zone_id,
		const Vector< double > &	X,
		const Vector< double > &	Xg,
		const double	Ksac
	)		const

overrideprotectedvirtual

Model jacobian.

Reimplemented from IonicModel.

◆ read_parameters()

void BuenoOrovio::read_parameters ( const IonicModelParameters & params )

overridevirtual

Read model parameters from a parameter object.

Reimplemented from IonicModel.

◆ step()

double BuenoOrovio::step ( const double r ) const

inlineprotected

Step function.

◆ update_g()

virtual void BuenoOrovio::update_g	(	const unsigned int	zone_id,
		const double	dt,
		const Vector< double > &	X,
		Vector< double > &	Xg
	)		const

inlineoverrideprotectedvirtual

Update variable with analytical solution. This model has none, so this method does nothing.

Implements IonicModel.

Member Data Documentation

◆ calcium_index

constexpr unsigned int BuenoOrovio::calcium_index = 3

staticconstexpr

Index of the slow inward current gate (s), used as calcium proxy for electromechanical coupling.

◆ initial_X

const InitialStates BuenoOrovio::initial_X

inlinestatic

Initial value:

= {

{"u", -84.0}, {"v", 1.0}, {"w", 1.0}, {"s", 0.0}}

State variables.

◆ initial_Xg

const InitialStates BuenoOrovio::initial_Xg = {}

inlinestatic

Gating variables.

◆ k_s

ModelParam BuenoOrovio::k_s = {2.09940, 2.0994, 2.0994}

protected

[1].

◆ k_so

ModelParam BuenoOrovio::k_so = {2.04580, 2., 2.1}

protected

[1].

◆ km_w

ModelParam BuenoOrovio::km_w = {65.0, 200., 200.}

protected

[1].

◆ label

const std::string BuenoOrovio::label = "BO"

inlinestatic

Model label.

◆ tau_fi

ModelParam BuenoOrovio::tau_fi = {0.110, 0.1, 0.078}

protected

[1/s].

◆ tau_o1

ModelParam BuenoOrovio::tau_o1 = {400.0, 470., 410.}

protected

[1/s].

◆ tau_o2

ModelParam BuenoOrovio::tau_o2 = {6.0, 6., 7.}

protected

[1/s].

◆ tau_s1

ModelParam BuenoOrovio::tau_s1 = {2.73420, 2.7342, 2.7342}

protected

[1/s].

◆ tau_s2

ModelParam BuenoOrovio::tau_s2 = {16.0, 2., 2.}

protected

[1/s].

◆ tau_si

ModelParam BuenoOrovio::tau_si = {1.88750, 2.9013, 3.3849}

protected

[1/s].

◆ tau_so1

ModelParam BuenoOrovio::tau_so1 = {30.01810, 40., 91.}

protected

[1/s].

◆ tau_so2

ModelParam BuenoOrovio::tau_so2 = {0.99570, 1.2, 0.8}

protected

[1/s].

◆ tau_winf

ModelParam BuenoOrovio::tau_winf = {7.E-2, 2.73E-2, 1.E-2}

protected

[1/s].

◆ taum_v1

ModelParam BuenoOrovio::taum_v1 = {60.0, 75., 80.}

protected

[1/s].

◆ taum_v2

ModelParam BuenoOrovio::taum_v2 = {1.15E3, 10., 1.4506}

protected

[1/s].

◆ taum_w1

ModelParam BuenoOrovio::taum_w1 = {60.0, 6., 70.}

protected

[1/s].

◆ taum_w2

ModelParam BuenoOrovio::taum_w2 = {15.0, 140., 8.}

protected

[1/s].

◆ taup_v

ModelParam BuenoOrovio::taup_v = {1.45060, 1.4506, 1.4506}

protected

[1/s].

◆ taup_w

ModelParam BuenoOrovio::taup_w = {200.0, 280., 280.}

protected

[1/s].

◆ theta_o

ModelParam BuenoOrovio::theta_o = {6.E-3, 6.E-3, 5.E-3}

protected

[1].

◆ theta_v

ModelParam BuenoOrovio::theta_v = {0.30, 0.3, 0.3}

protected

[1].

◆ theta_w

ModelParam BuenoOrovio::theta_w = {0.130, 0.13, 0.13}

protected

[1].

◆ thetam_v

ModelParam BuenoOrovio::thetam_v = {6.E-3, 0.2, 0.1}

protected

[1].

◆ u_o

ModelParam BuenoOrovio::u_o = {0.0, 0.0, 0.0}

protected

[1].

◆ u_s

ModelParam BuenoOrovio::u_s = {0.90870, 0.9087, 0.9087}

protected

[1].

◆ u_so

ModelParam BuenoOrovio::u_so = {0.650, 0.65, 0.6}

protected

[1].

◆ u_u

ModelParam BuenoOrovio::u_u = {1.550, 1.56, 1.61}

protected

[1].

◆ um_w

ModelParam BuenoOrovio::um_w = {3.E-2, 1.6E-2, 1.6E-2}

protected

[1].

◆ ws_inf

ModelParam BuenoOrovio::ws_inf = {0.940, 0.78, 0.5}

protected

[1].

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

solver/ionic_bueno_orovio.h
solver/ionic_bueno_orovio.cpp

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Model parameters

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ModelParam

Constructor & Destructor Documentation

◆ BuenoOrovio()

Member Function Documentation

◆ delta()

◆ distribute_parameters()

◆ get_calcium_index()

◆ get_parameters()

◆ getf()

◆ getj()

◆ read_parameters()

◆ step()

◆ update_g()

Member Data Documentation

◆ calcium_index

◆ initial_X

◆ initial_Xg

◆ k_s

◆ k_so

◆ km_w

◆ label

◆ tau_fi

◆ tau_o1

◆ tau_o2

◆ tau_s1

◆ tau_s2

◆ tau_si

◆ tau_so1

◆ tau_so2

◆ tau_winf

◆ taum_v1

◆ taum_v2

◆ taum_w1

◆ taum_w2

◆ taup_v

◆ taup_w

◆ theta_o

◆ theta_v

◆ theta_w

◆ thetam_v

◆ u_o

◆ u_s

◆ u_so

◆ u_u

◆ um_w

◆ ws_inf