org.simBio.bio.matsuoka_et_al_2004.function
Class RedoxPotential

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.function.RedoxPotential

All Implemented Interfaces:

Node

public class RedoxPotential
extends Reactor

Calculation of the redox potential.

  Em = Em0 + Zscale*Z/2*log([A]/[B])
 

Since:

rc20

Version:

$Log: RedoxPotential.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 04:57:24 sarai rearrenge folder structure as a Maven style Revision 1.2 2005/08/04 08:43:04 sarai revise Javadoc to suppress Warnings
2005/02/01 08:51:20 Some comments were updated to make Javadoc.
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)
RedoxPotential XML example explanation (Japanese, WORD doc)

Field Summary

double	Em0 standard free-energy chage of reaction
Node	Product product and substrate concentrations of reaction
Node	Substrate product and substrate concentrations of reaction
double	Zscale scale factor of Z
double	Zvalue Z = 2.303 * R * T / F

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

RedoxPotential()

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

Product

public Node Product

product and substrate concentrations of reaction

Substrate

public Node Substrate

product and substrate concentrations of reaction

Em0

public double Em0

standard free-energy chage of reaction

Zvalue

public double Zvalue

Z = 2.303 * R * T / F

Zscale

public double Zscale

scale factor of Z

Constructor Detail

RedoxPotential

public RedoxPotential()

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)