org.simBio.bio.matsuoka_et_al_2003.complex
Class ATPsynthesis

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_2003.complex.ATPsynthesis
All Implemented Interfaces:
Node

public class ATPsynthesis
extends Reactor

The lumped model of ATP synthesis.

  [ADP] = totalAdenosine - [ATP]
  d[ATP] / dt = maxProducingRate * [ADP]
 

Version:
$Id: ATPsynthesis.java,v 1.2 2006/06/17 05:36:51 nsarai Exp $
Author:
Nobuaki Sarai
See Also:
Equation (11) and (12) of Table 3 in Matsuoka et al, 2003
XML example
explanation (Japanese)
explanation (Japanese, WORD doc)

Field Summary
 Node ATP
          ATP concentration ([ATP]).
 double maxProducingRate
          max rate of ATP production (/msec).
 double totalAdenosine
          total adenosine concentration (= [ATP] + [ADP]) (mM).
 
Fields inherited from class org.simBio.core.Parameter
value
 
Constructor Summary
ATPsynthesis()
           
 
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

ATP

public Node ATP
ATP concentration ([ATP]). usually linked to the intracellular [ATP] (mM).


maxProducingRate

public double maxProducingRate
max rate of ATP production (/msec).


totalAdenosine

public double totalAdenosine
total adenosine concentration (= [ATP] + [ADP]) (mM).

Constructor Detail

ATPsynthesis

public ATPsynthesis()
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)
See Also:
Reactor.calculate(double)


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