org.simBio.bio.matsuoka_et_al_2004.molecule
Class SubstrateDehydrogenation

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.SubstrateDehydrogenation

All Implemented Interfaces:

Node

public class SubstrateDehydrogenation
extends Reactor

NADH dehydrogenation.

 vDH = kDH /(1 + KmN/([NAD]/[NADH]))^PD
 

Version:

$Id: SubstrateDehydrogenation.java,v 1.3 2007/11/22 06:48:21 nsarai Exp $

Author:

SAITO Ryuta

See Also:

Korzeniewski & Zoladz 2001 Korzeniewski & Zoladz 2003

Field Summary

double	Amp amplifying factor described in Kuzumoto et al, 2007.
double	kDH rate constant of NADH dehydrogenation
double	KmN affinity of NAD/NADH for NADH dehydrogenation
Node	NAD NAD+ concentration
Node	NADH NADH concentration
double	PD power factor
Node	Rcm ratio of cytosol active volume and mitochondria volume

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

SubstrateDehydrogenation()

Method Summary

protected void

calculate(double arg0) 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

NAD

public Node NAD

NAD+ concentration

NADH

public Node NADH

NADH concentration

Rcm

public Node Rcm

ratio of cytosol active volume and mitochondria volume

kDH

public double kDH

rate constant of NADH dehydrogenation

KmN

public double KmN

affinity of NAD/NADH for NADH dehydrogenation

PD

public double PD

power factor

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

SubstrateDehydrogenation

public SubstrateDehydrogenation()

Method Detail

calculate

protected void calculate(double arg0)

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:

arg0 - elapsed time (ms)