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

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.ComplexIV

All Implemented Interfaces:

Node

public class ComplexIV
extends Reactor

Cytochrome c Oxidase (complex IV).

 vC4 = kC4 * [a2+] * [c2+] * 1/(1 + KmO/[Oxygen])
 

Version:

$Id: ComplexIV.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

Node	a2 cytochrome a2+ (reduced) concentration
double	Amp amplifying factor described in Kuzumoto et al, 2007.
Node	c2 cytochrome c2+ (reduced) concentration
Node	kC4 rate constant of complex IV
double	KmO oxygen affinity of complex IV
Node	O2 oxygen concentration

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ComplexIV()

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

a2

public Node a2

cytochrome a2+ (reduced) concentration

c2

public Node c2

cytochrome c2+ (reduced) concentration

O2

public Node O2

oxygen concentration

KmO

public double KmO

oxygen affinity of complex IV

kC4

public Node kC4

rate constant of complex IV

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

ComplexIV

public ComplexIV()

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)