org.simBio.bio.matsuoka_et_al_2004.function
Class ConcentrationCyta2

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.ConcentrationCyta2

All Implemented Interfaces:

Node

public class ConcentrationCyta2
extends Reactor

Calculation of the concentration of Cytochrome a2+

  [Cyt a2+] = [Cyt a]total/(1 + A_3/2)
 where;
  A_3/2 = 10^((Ema - Ema0)/Z) :ratio of oxidized cytochrome a3 to reduced cytochrome a3
 

Since:

rc20

Version:

$Log: ConcentrationCyta2.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)
ConcentrationCyta XML example explanation (Japanese, WORD doc)

Field Summary

Node	Ema redox potential of cytochrome a
double	Ema0 standard free-energy change
double	total total concentration of cytochrome a
Node	Zvalue Z = 2.303 * R * T / F

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

ConcentrationCyta2()

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

Ema

public Node Ema

redox potential of cytochrome a

Ema0

public double Ema0

standard free-energy change

total

public double total

total concentration of cytochrome a

Zvalue

public Node Zvalue

Z = 2.303 * R * T / F

Constructor Detail

ConcentrationCyta2

public ConcentrationCyta2()

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)