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

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.ComplexI

All Implemented Interfaces:

Node

public class ComplexI
extends Reactor

NADH-Ubiquinone oxidoreductase (complex I).

 vC1 = kC1 * dG_C1
 dG_C1 = EmU - EmN - dP * 4 / 2       : Thermodynamic span of complex I
 where;
        EmN =  EmN0 + Z/2*log([NAD+]/[NADH]): calculated in RedoxPotential.java
        EmU =  EmU0 + Z/2*log([UQ]/[UQH2])      : calculated in RedoxPotential.java
 

Version:

$Id: ComplexI.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 on mitochondrial inner membrane
Node	EmN redox potential for NADH
Node	EmU redox potential for ubiquinone
double	kC1 rate constant of complex I

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ComplexI()

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

EmN

public Node EmN

redox potential for NADH

EmU

public Node EmU

redox potential for ubiquinone

dP

public Node dP

proton driving force on mitochondrial inner membrane

kC1

public double kC1

rate constant of complex I

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

ComplexI

public ComplexI()

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)