org.simBio.bio.matsuoka_et_al_2004.molecule
Class SubstrateDehydrogenation

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.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)


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