CaConc Class Reference

#include <CaConc.h>

Inheritance diagram for CaConc:

Collaboration diagram for CaConc:

Public Member Functions
	CaConc ()
void	vCurrent (const Eref &e, double I)
void	vCurrentFraction (const Eref &e, double I, double fraction)
void	vDecrease (const Eref &e, double I)
double	vGetB (const Eref &e) const
double	vGetCa (const Eref &e) const
double	vGetCaBasal (const Eref &e) const
double	vGetCeiling (const Eref &e) const
double	vGetFloor (const Eref &e) const
double	vGetTau (const Eref &e) const
void	vIncrease (const Eref &e, double I)
void	vProcess (const Eref &, ProcPtr info)
void	vReinit (const Eref &, ProcPtr info)
void	vSetB (const Eref &e, double val)
void	vSetCa (const Eref &e, double val)
void	vSetCaBasal (const Eref &e, double val)
void	vSetCeiling (const Eref &e, double val)
void	vSetFloor (const Eref &e, double val)
void	vSetTau (const Eref &e, double val)
Public Member Functions inherited from CaConcBase
	CaConcBase ()
void	current (const Eref &e, double I)
void	currentFraction (const Eref &e, double I, double fraction)
void	decrease (const Eref &e, double I)
double	getB (const Eref &e) const
double	getCa (const Eref &e) const
double	getCaBasal (const Eref &e) const
double	getCeiling (const Eref &e) const
double	getDiameter (const Eref &e) const
double	getFloor (const Eref &e) const
double	getLength (const Eref &e) const
double	getTau (const Eref &e) const
double	getThickness (const Eref &e) const
void	increase (const Eref &e, double I)
void	process (const Eref &, ProcPtr info)
void	reinit (const Eref &, ProcPtr info)
void	setB (const Eref &e, double val)
void	setCa (const Eref &e, double val)
void	setCaBasal (const Eref &e, double val)
void	setCeiling (const Eref &e, double val)
void	setDiameter (const Eref &e, double val)
void	setFloor (const Eref &e, double val)
void	setLength (const Eref &e, double val)
void	setTau (const Eref &e, double val)
void	setThickness (const Eref &e, double val)
void	updateDimensions (const Eref &e)
virtual void	vSetSolver (const Eref &e, Id hsolve)
	Used to set up the solver. Dummy for regular classes. More...

Static Public Member Functions
static const Cinfo *	initCinfo ()
Static Public Member Functions inherited from CaConcBase
static SrcFinfo1< double > *	concOut ()
static const Cinfo *	initCinfo ()
static void	zombify (Element *orig, const Cinfo *zClass, Id hsolve)

Private Attributes
double	activation_
double	B_
double	c_
double	Ca_
double	CaBasal_
double	ceiling_
double	floor_
double	tau_

Detailed Description

The CaConc object manages calcium dynamics in a single compartment without diffusion. It uses a simple exponential return of Ca to baseline, with influxes from ion channels. It solves the equation: dC/dt = B*Ik - C/tau where Ca = Ca_base + C.

From the GENESIS notes: In SI units, where concentration is moles/m^3 (milli-moles/liter) and current is in amperes, theory gives B = 5.2e-6/(shell volume). In practice, B is a parameter to be fitted or estimated from experiment, as buffering, non-uniform distribution of Ca, etc., will modify this value. If thick = 0, the readcell routine calculates B by dividing the "density" parameter in the cell parameter file by the volume of the compartment. Otherwise, it scales as a true shell, with the volume of a shell having thickness thick. A negative value of the "density" parameter may be used to indicate that it should be taken as an absolute value of B, without scaling.

Definition at line 36 of file CaConc.h.

Constructor & Destructor Documentation

CaConc::CaConc

(

)

Definition at line 45 of file CaConc.cpp.

    : CaConcBase(),
        Ca_( 0.0 ),
        CaBasal_( 0.0 ),
        tau_( 1.0 ),
        B_( 1.0 ),
        c_( 0.0 ),
        activation_( 0.0 ),
        ceiling_( 1.0e9 ),
        floor_( 0.0 )
{;}

Member Function Documentation

const Cinfo * CaConc::initCinfo ( )

static

Definition at line 16 of file CaConc.cpp.

References CaConcBase::initCinfo().

Referenced by HSolve::unzombify().

{
    static string doc[] =
    {
        "Name", "CaConc \n",
        "Author", "Upinder S. Bhalla, 2014, NCBS \n",
        "Description", "CaConc: Calcium concentration pool. Takes current from a \n"
                "channel and keeps track of calcium buildup and depletion by a \n"
                "single exponential process. \n",
    };

        static Dinfo< CaConc > dinfo;

    static Cinfo CaConcCinfo(
        "CaConc",
        CaConcBase::initCinfo(),
        0,
        0,
        &dinfo,
        doc,
        sizeof(doc)/sizeof(string)
    );

    return &CaConcCinfo;
}

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void CaConc::vCurrent ( const Eref &  e, double  I  )

virtual

Implements CaConcBase.

Definition at line 141 of file CaConc.cpp.

References activation_.

{
    activation_ += I;
}

void CaConc::vCurrentFraction ( const Eref &  e, double  I, double  fraction  )

virtual

Implements CaConcBase.

Definition at line 146 of file CaConc.cpp.

References activation_.

{
    activation_ += I * fraction;
}

void CaConc::vDecrease ( const Eref &  e, double  I  )

virtual

Implements CaConcBase.

Definition at line 156 of file CaConc.cpp.

References activation_.

{
    activation_ -= fabs( I );
}

double CaConc::vGetB ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 92 of file CaConc.cpp.

References B_.

{
    return B_;
}

double CaConc::vGetCa ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 65 of file CaConc.cpp.

References Ca_.

{
    return Ca_;
}

double CaConc::vGetCaBasal ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 74 of file CaConc.cpp.

References CaBasal_.

{
    return CaBasal_;
}

double CaConc::vGetCeiling ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 100 of file CaConc.cpp.

References ceiling_.

{
    return ceiling_;
}

double CaConc::vGetFloor ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 109 of file CaConc.cpp.

References floor_.

{
    return floor_;
}

double CaConc::vGetTau ( const Eref &  e ) const

virtual

Implements CaConcBase.

Definition at line 83 of file CaConc.cpp.

References tau_.

{
    return tau_;
}

void CaConc::vIncrease ( const Eref &  e, double  I  )

virtual

Implements CaConcBase.

Definition at line 151 of file CaConc.cpp.

References activation_.

{
    activation_ += fabs( I );
}

void CaConc::vProcess ( const Eref &  e, ProcPtr  info  )

virtual

Implements CaConcBase.

Definition at line 126 of file CaConc.cpp.

References activation_, B_, c_, Ca_, CaBasal_, ceiling_, CaConcBase::concOut(), ProcInfo::dt, floor_, and tau_.

{
    double x = exp( -p->dt / tau_ );
    Ca_ = CaBasal_ + c_ * x + ( B_ * activation_ * tau_ )  * (1.0 - x);
    if ( ceiling_ > 0.0 && Ca_ > ceiling_ ) {
        Ca_ = ceiling_;
    } else if ( Ca_ < floor_ ){
        Ca_ = floor_;
    }
    c_ = Ca_ - CaBasal_;
    concOut()->send( e, Ca_ );
    activation_ = 0;
}

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void CaConc::vReinit ( const Eref &  e, ProcPtr  info  )

virtual

Implements CaConcBase.

Definition at line 118 of file CaConc.cpp.

References activation_, c_, Ca_, CaBasal_, and CaConcBase::concOut().

{
    activation_ = 0.0;
    c_ = 0.0;
    Ca_ = CaBasal_;
    concOut()->send( e, Ca_ );
}

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void CaConc::vSetB ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 88 of file CaConc.cpp.

References B_.

{
    B_ = B;
}

void CaConc::vSetCa ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 61 of file CaConc.cpp.

References Ca_.

{
    Ca_ = Ca;
}

void CaConc::vSetCaBasal ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 70 of file CaConc.cpp.

References CaBasal_.

{
    CaBasal_ = CaBasal;
}

void CaConc::vSetCeiling ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 96 of file CaConc.cpp.

References ceiling_.

{
    ceiling_ = ceiling;
}

void CaConc::vSetFloor ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 105 of file CaConc.cpp.

References floor_.

{
    floor_ = floor;
}

void CaConc::vSetTau ( const Eref &  e, double  val  )

virtual

Implements CaConcBase.

Definition at line 79 of file CaConc.cpp.

References tau_.

{
    tau_ = tau;
}

Member Data Documentation

double CaConc::activation_

private

Definition at line 73 of file CaConc.h.

Referenced by vCurrent(), vCurrentFraction(), vDecrease(), vIncrease(), vProcess(), and vReinit().

double CaConc::B_

private

Definition at line 71 of file CaConc.h.

Referenced by vGetB(), vProcess(), and vSetB().

double CaConc::c_

private

Definition at line 72 of file CaConc.h.

Referenced by vProcess(), and vReinit().

double CaConc::Ca_

private

Definition at line 68 of file CaConc.h.

Referenced by vGetCa(), vProcess(), vReinit(), and vSetCa().

double CaConc::CaBasal_

private

Definition at line 69 of file CaConc.h.

Referenced by vGetCaBasal(), vProcess(), vReinit(), and vSetCaBasal().

double CaConc::ceiling_

private

Definition at line 74 of file CaConc.h.

Referenced by vGetCeiling(), vProcess(), and vSetCeiling().

double CaConc::floor_

private

Definition at line 75 of file CaConc.h.

Referenced by vGetFloor(), vProcess(), and vSetFloor().

double CaConc::tau_

private

Definition at line 70 of file CaConc.h.

Referenced by vGetTau(), vProcess(), and vSetTau().

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

• moose-core/biophysics/CaConc.h
• moose-core/biophysics/CaConc.cpp