org.simBio.bio.matsuoka_et_al_2004.function
Class RedoxPotential

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.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)


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