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

java.lang.Object
  extended by org.simBio.core.Component
      extended by org.simBio.core.Parameter
          extended by org.simBio.core.Composite
              extended by org.simBio.core.Reactor
                  extended by 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)


Copyright © 2002-2008 Cell/Biodinamics simulation project. All Rights Reserved.