org.simBio.bio.matsuoka_et_al_2003.complex
Class ATPsynthesis

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_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)