org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
Class ProtonLeak

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_2004.molecule.Transporter.ProtonLeak

All Implemented Interfaces:

Node

public class ProtonLeak
extends Reactor

Proton leak from cytosol to intremitochondoria.

Version:

$Id: ProtonLeak.java,v 1.2 2007/11/22 06:48:21 nsarai Exp $

Author:

SAITO Ryuta

See Also:

Table 12 in Matsuoka et al, 2004 Table 2 in Korzeniewski & Zoladz 2001 Korzeniewski & Zoladz 2003
XML example explanation (Japanese, WORD doc)

Field Summary

double	Amp amplifying factor described in Kuzumoto et al, 2007.
Node	dP proton gradient of mitohocndrial inner membrane
Node	Hcell proton concentration in cytosol (mM)
Node	Hmito proton concentration in mitohocndria (mM)
Node	kLK1 rate constant of proton leak (mM/msec)
double	kLK2 rate constant of proton leak (/mV)
Node	rbuffermito buffering capacity for proton in mitochondrial matrix
Node	Rcm ratio of cytosol volume and mitochondria volume

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ProtonLeak()

Method Summary

protected void

calculate(double t) write equations here, and calculate dy over dt.

Methods inherited from class org.simBio.core.Composite

accept, getLink, getNode, getNodesIterator, getNodesSize

Methods inherited from class org.simBio.core.Parameter

addValue, getValue, getValueString, prepare, 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

dP

public Node dP

proton gradient of mitohocndrial inner membrane

Hmito

public Node Hmito

proton concentration in mitohocndria (mM)

Hcell

public Node Hcell

proton concentration in cytosol (mM)

Rcm

public Node Rcm

ratio of cytosol volume and mitochondria volume

rbuffermito

public Node rbuffermito

buffering capacity for proton in mitochondrial matrix

kLK1

public Node kLK1

rate constant of proton leak (mM/msec)

kLK2

public double kLK2

rate constant of proton leak (/mV)

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

ProtonLeak

public ProtonLeak()

Method Detail

calculate

protected void calculate(double t)

Description copied from class: Reactor

write equations here, and calculate dy over dt.
計算中に呼び出される。 計算式を記載する。dy/dtをここで計算する。

Specified by:

calculate in class Reactor

Parameters:

t - elapsed time (ms)