Kaskade::MembraneModelBase< Derived, n > Struct Template Reference

Convenience base class for membrane models providing numerical differentiation. More...

#include <membraneModels.hh>

Detailed Description

template<class Derived, int n>
struct Kaskade::MembraneModelBase< Derived, n >

Convenience base class for membrane models providing numerical differentiation.

Definition at line 56 of file membraneModels.hh.

Public Types
typedef Dune::FieldVector< double, nGating >	Gating
	Vector type holding gating variables. More...
typedef Dune::FieldMatrix< double, nGating, nGating >	GatingJacobian
	Matrix type for the Jacobian of the gating dynamics. More...

Public Member Functions
	MembraneModelBase ()
	Default constructor. More...
	MembraneModelBase (std::string const &name)
	Constructor specifying the model data. More...
std::string const &	name () const
	Human-readable name of the membrane model. More...
std::pair< double, Gating > const &	restState () const
	Value of the resting state fixed point. More...
double	current_du (double u, Gating const &v, double h=1e-5) const
	The transmembrane ion current derivative w.r.t. the transmembrane voltage. More...
Gating	current_dv (double u, Gating const &v) const
	The transmembrane ion current derivative w.r.t. the gating variables. More...
Gating	gatingRhs_du (double u, Gating const &v) const
	The derivative of the right hand side for the evolution of gating variables w.r.t. the transmembrane voltage. More...
GatingJacobian	gatingRhs_dv (double u, Gating const &v) const
	The derivative of the right hand side for the evolution of gating variables w.r.t. the gating variables. More...

Static Public Attributes
static int const	nGating = n
	Number of gating variables. More...

Protected Member Functions
void	setRestState (double uFix, Gating const &vFix)
	Accepts an (approximate) resting state. More...

Member Typedef Documentation

Gating

template<class Derived , int n>

typedef Dune::FieldVector<double,nGating> Kaskade::MembraneModelBase< Derived, n >::Gating

Vector type holding gating variables.

Definition at line 66 of file membraneModels.hh.

GatingJacobian

template<class Derived , int n>

typedef Dune::FieldMatrix<double,nGating,nGating> Kaskade::MembraneModelBase< Derived, n >::GatingJacobian

Matrix type for the Jacobian of the gating dynamics.

Definition at line 71 of file membraneModels.hh.

Constructor & Destructor Documentation

MembraneModelBase() [1/2]

template<class Derived , int n>

Kaskade::MembraneModelBase< Derived, n >::MembraneModelBase ( )

inline

Default constructor.

Name and resting state are default initialized, i.e. set to "" and 0.0, respectively.

Definition at line 78 of file membraneModels.hh.

MembraneModelBase() [2/2]

template<class Derived , int n>

Kaskade::MembraneModelBase< Derived, n >::MembraneModelBase ( std::string const &  name )

inline

Constructor specifying the model data.

Parameters

name	the human-readable model name
uFix	the resting state of the transmembrane voltage
vFix	the resting state of the gating variables

Definition at line 86 of file membraneModels.hh.

Member Function Documentation

current_du()

template<class Derived , int n>

double Kaskade::MembraneModelBase< Derived, n >::current_du ( double  u, Gating const &  v, double  h = 1e-5  ) const

inline

The transmembrane ion current derivative w.r.t. the transmembrane voltage.

This is a default implementation based on numerical differentiation. Overload this if a better implementation is available.

Parameters

u	transmembrane voltage [V]
v	gating variables
h	step size for numerical differentiation

Definition at line 109 of file membraneModels.hh.

Referenced by Kaskade::MembraneModelBase< Derived, n >::setRestState().

current_dv()

template<class Derived , int n>

Gating Kaskade::MembraneModelBase< Derived, n >::current_dv ( double  u, Gating const &  v  ) const

inline

The transmembrane ion current derivative w.r.t. the gating variables.

This convenience method performs numerical differentiation and should be overwritten in derived classes by a better implementation.

Parameters

u	transmembrane voltage
v	gating variables

Definition at line 126 of file membraneModels.hh.

gatingRhs_du()

template<class Derived , int n>

Gating Kaskade::MembraneModelBase< Derived, n >::gatingRhs_du ( double  u, Gating const &  v  ) const

inline

The derivative of the right hand side for the evolution of gating variables w.r.t. the transmembrane voltage.

This default implementation uses numerical differentiation for computing the derivative.

Parameters

u	transmembrane voltage
v	gating variables

Definition at line 146 of file membraneModels.hh.

gatingRhs_dv()

template<class Derived , int n>

GatingJacobian Kaskade::MembraneModelBase< Derived, n >::gatingRhs_dv ( double  u, Gating const &  v  ) const

inline

The derivative of the right hand side for the evolution of gating variables w.r.t. the gating variables.

Parameters

u	transmembrane voltage
v	gating variables

Definition at line 158 of file membraneModels.hh.

Referenced by Kaskade::MembraneModelBase< Derived, n >::setRestState().

name()

template<class Derived , int n>

std::string const & Kaskade::MembraneModelBase< Derived, n >::name ( ) const

inline

Human-readable name of the membrane model.

Definition at line 93 of file membraneModels.hh.

restState()

template<class Derived , int n>

std::pair< double, Gating > const & Kaskade::MembraneModelBase< Derived, n >::restState ( ) const

inline

Value of the resting state fixed point.

Definition at line 98 of file membraneModels.hh.

setRestState()

template<class Derived , int n>

void Kaskade::MembraneModelBase< Derived, n >::setRestState ( double  uFix, Gating const &  vFix  )

inlineprotected

Accepts an (approximate) resting state.

Parameters

uFix	approximate resting state of the transmembrane voltage
vFix	approximate resting state of the gating variables

The method shall be used by derived classes to provide an approximate value of the resting state (which needs to be a stable fixed point). A few iterations of Newton's method are performed in order to obtain an accurate value.

Definition at line 181 of file membraneModels.hh.

Member Data Documentation

nGating

template<class Derived , int n>

int const Kaskade::MembraneModelBase< Derived, n >::nGating = n

static

Number of gating variables.

Definition at line 61 of file membraneModels.hh.

Referenced by Kaskade::MembraneModelBase< Derived, n >::current_dv(), Kaskade::MembraneModelBase< Derived, n >::gatingRhs_dv(), and Kaskade::MembraneModelBase< Derived, n >::setRestState().

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The documentation for this struct was generated from the following file:

• membraneModels.hh