org.simBio.bio.matsuoka_et_al_2003.current.carrier
Class ICaPump

java.lang.Object
  org.simBio.core.Component
      org.simBio.core.Parameter
          org.simBio.core.Composite
              org.simBio.core.Reactor
                  org.simBio.bio.matsuoka_et_al_2003.current.MembraneTransporter
                      org.simBio.bio.matsuoka_et_al_2003.current.carrier.Carrier
                          org.simBio.bio.matsuoka_et_al_2003.current.carrier.ICaPump

All Implemented Interfaces:

Node

Direct Known Subclasses:

ICaPump

public class ICaPump
extends Carrier

Ca pump on network SR. Modified on 2004/7/24 to calculate ATP consumption

Version:

$Revision: 1.1 $

Author:

Nobuaki Sarai, modified by B.J Kim

See Also:

Equation (26) -(37) of Table 7 in Matsuoka et al, 2003,
XML example,
explanation (Japanese, WORD doc)

Field Summary

Node	ATP intracellular ATP concentration (mM)
Node	ATPconsumingRate consuming rate of ATP; (mM/min)
Node	ATPconsumption ATP consumed at the time t (mM)
Node	Cai Ca2+ concentration in cytoplasm (mM)
Node	Cao Ca2+ concentration in SR (mM, uptake site compartment)
protected double	dATP variation of ATP concentration (mM/ms)
Node	F Faradey constant
double	KmATP mM, dissociation const for ATP binding within cytoplasm
double	KmCaCp mM, dissociation const for Ca binding within cytoplasm
double	KmCaSR mM, dissociation const for Ca binding within SR
double	t0 a starting time point for calculation of ATPconsumingRate
Node	Vi cell volume accessible for ion diffusion

Fields inherited from class org.simBio.bio.matsuoka_et_al_2003.current.carrier.Carrier

amplitude, Cm, E1A, E1B, E2A, E2B, gate, k1, k2, k3, k4, stoichiometryCa, stoichiometryK, stoichiometryNa

Fields inherited from class org.simBio.bio.matsuoka_et_al_2003.current.MembraneTransporter

cCa, CCa, cK, CK, cNa, CNa, current, currentCa, currentK, currentNa, total

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ICaPump()

Method Summary

protected void	calculate(double t) calculate total charge movement using reduced 2 state model 2 state gateを用いて電流を計算する
void	prepare() construct null current

Methods inherited from class org.simBio.core.Composite

accept, getLink, getNode, getNodesIterator, getNodesSize

Methods inherited from class org.simBio.core.Parameter

addValue, getValue, getValueString, setInitializer, setValue, setValueString, setValueToField

Methods inherited from class org.simBio.core.Component

addDydt, end, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented, quit, setLinks

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.simBio.core.Node

addDydt, addValue, getValue, setValue

Field Detail

Cai

public Node Cai

Ca2+ concentration in cytoplasm (mM)

Cao

public Node Cao

Ca2+ concentration in SR (mM, uptake site compartment)

ATP

public Node ATP

intracellular ATP concentration (mM)

Vi

public Node Vi

cell volume accessible for ion diffusion

F

public Node F

Faradey constant

ATPconsumption

public Node ATPconsumption

ATP consumed at the time t (mM)

ATPconsumingRate

public Node ATPconsumingRate

consuming rate of ATP; (mM/min)

t0

public double t0

a starting time point for calculation of ATPconsumingRate

dATP

protected double dATP

variation of ATP concentration (mM/ms)

KmCaSR

public double KmCaSR

mM, dissociation const for Ca binding within SR

KmCaCp

public double KmCaCp

mM, dissociation const for Ca binding within cytoplasm

KmATP

public double KmATP

mM, dissociation const for ATP binding within cytoplasm

Constructor Detail

ICaPump

public ICaPump()

Method Detail

calculate

protected void calculate(double t)

Description copied from class: Carrier

calculate total charge movement using reduced 2 state model
2 state gateを用いて電流を計算する

Overrides:

calculate in class Carrier

Parameters:

t - time

prepare

public void prepare()

Description copied from class: MembraneTransporter

construct null current

Overrides:

prepare in class MembraneTransporter

See Also:

Component.prepare()