org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
Class ComplexIII

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.RespiratoryChain.ComplexIII

All Implemented Interfaces:

Node

public class ComplexIII
extends Reactor

Cytochrome bc1 Complex (complex III).

 vC3 = kC3 * dG_C3
 dG_C3 = Emc - EmU - dP*(4 - 2*u)/2     : Thermodynamic span of complex III
 where;
        EmU = EmU0 + Z/2*log([UQ]/[UQH2])       : calculated in RedoxPotential.java
        Emc = Emc0 + Z*log([c3+]/[c2+])         : calculated in RedoxPotential.java
 

Version:

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

Author:

SAITO Ryuta

See Also:

Matsuoka et al. (2004) 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 driving force of mitochondrial inner membrane
Node	Emc redox potential for cytochrome c
Node	EmU redox potential for ubiquinone
double	kC3 rate constant of complex III
double	myu u value

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ComplexIII()

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

EmU

public Node EmU

redox potential for ubiquinone

Emc

public Node Emc

redox potential for cytochrome c

myu

public double myu

u value

dP

public Node dP

proton driving force of mitochondrial inner membrane

kC3

public double kC3

rate constant of complex III

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

ComplexIII

public ComplexIII()

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)