org.simBio.bio.matsuoka_et_al_2004.function
Class MetalFreeConcentration

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.MetalFreeConcentration

All Implemented Interfaces:

Node

public class MetalFreeConcentration
extends Reactor

free concentration of metal affinity molecule

  [A]free = [A]total / (1 + [metal]free / kD)
 

Since:

rc20

Version:

$Log: MetalFreeConcentration.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 04:57:23 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)
MetalFreeConcentration XML example explanation (Japanese, WORD doc)

Field Summary

double	kD metal affinity parameter
Node	metal metal ion concentration
Node	total total concentration

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

MetalFreeConcentration()

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

total

public Node total

total concentration

metal

public Node metal

metal ion concentration

kD

public double kD

metal affinity parameter

Constructor Detail

MetalFreeConcentration

public MetalFreeConcentration()

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)