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

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.OxidativePhosphorylation

All Implemented Interfaces:

Node

public class OxidativePhosphorylation
extends Reactor

Differential equation for reactions of oxidattive phosphorylation.

Since:

rc20

Version:

$Log: OxidativePhosphorylation.java,v $ Revision 1.1 2005/11/01 06:32:39 mikaelwing First version of simBio hosted on sourceforge, version 0.3 Revision 1.1 2005/09/12 04:57:19 sarai rearrenge folder structure as a Maven style Revision 1.2 2005/08/04 08:43:04 sarai revise Javadoc to suppress Warnings
2005/05/13 14:30:41 Complex I, III and IV were gradually stopped if these velocities are negative. Because respiratory chain is one-way reaction.
2005/02/01 08:53:47 Some comments were updated to make Javadoc.
2004/12/20 10:53:15 Type of the Oxygen is checked instead of using flag
2004/12/20 09:31:02 Defined oxygen concentration as "Node" parameter.
2004/12/17 05:43:03 update
2004/09/16 10:32:07 Created

Author:

SAITO Ryuta

See Also:

Matsuoka et al. (2004) Korzeniewski & Zoladz (2001) Korzeniewski & Zoladz (2003)
Oxidative Phosphorylation XML example explanation (Japanese, WORD doc)

Field Summary

Node	Cytc2 cytochrome c2+ (reduced) concentration
Node	Hmito proton concentration in mitochondrial matrix
double	myu u value
Node	NADH mitochondrial NADH concentration
Node	Oxygen oxygen concentration
Node	rbuffermito buffering capacity for proton in mitochondrial matrix
Node	Rcm ratio of cytosol volume and mitochondria volume
Node	UQH2 ubiquinol (UQH2) concentration
Node	vC1 rate of complex I
Node	vC3 rate of complex III
Node	vC4 rate of complex IV

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

OxidativePhosphorylation()

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

vC1

public Node vC1

rate of complex I

vC3

public Node vC3

rate of complex III

vC4

public Node vC4

rate of complex IV

NADH

public Node NADH

mitochondrial NADH concentration

Hmito

public Node Hmito

proton concentration in mitochondrial matrix

UQH2

public Node UQH2

ubiquinol (UQH2) concentration

Cytc2

public Node Cytc2

cytochrome c2+ (reduced) concentration

Oxygen

public Node Oxygen

oxygen concentration

Rcm

public Node Rcm

ratio of cytosol volume and mitochondria volume

rbuffermito

public Node rbuffermito

buffering capacity for proton in mitochondrial matrix

myu

public double myu

u value

Constructor Detail

OxidativePhosphorylation

public OxidativePhosphorylation()

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)