org.simBio.bio.matsuoka_et_al_2004.function
Class ConcentrationPi

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.MassConservation2
                      extended by org.simBio.bio.matsuoka_et_al_2004.function.ConcentrationPi
All Implemented Interfaces:
Node

public class ConcentrationPi
extends MassConservation2

calculation of iorganic phosphate concentration (conformed to mass conservation law)

  Pitotal = 3*[ATP]cell + 2*[ADP]cell + [AMP] + [PhosphoCreatine] + [Pi]cell + (3*[ATP]mito + 2*[ADP]mito + [Pi]mito) / Rcm
  [Pi]cell = Pitotal - (3*[ATP]cell + 2*[ADP]cell + [AMP] + [PhosphoCreatine] + (3*[ATP]mito + 2*[ADP]mito + [Pi]mito) / Rcm)
 

Since:
rc20
Version:
$Log: ConcentrationPi.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)
ConcentrationPi XML example explanation (Japanese, WORD doc)

Field Summary
 Node ADPtcell
          total ADP concentration in cytosol
 Node ADPtmit
          total ADP concentration in mitochondria
 Node AMP
          AMP concentration in cytosol
 Node ATPtcell
          total ATP concentration in cytosol
 Node ATPtmit
          total ATP concentration in mitochondria
 Node PCr
          phosphocreatine concentration in cytosol
 Node Pimit
          iorganic phosphate concentration in mitochondria
 double PiTotal
          total iorganic phosphate concentration in whole cell
 Node Rcm
          volume ratio between cytosol and mitochondrial matrix
 
Fields inherited from class org.simBio.bio.matsuoka_et_al_2004.function.MassConservation2
other1, other2, total
 
Fields inherited from class org.simBio.core.Parameter
value
 
Constructor Summary
ConcentrationPi()
           
 
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

ATPtcell

public Node ATPtcell
total ATP concentration in cytosol


ADPtcell

public Node ADPtcell
total ADP concentration in cytosol


AMP

public Node AMP
AMP concentration in cytosol


PCr

public Node PCr
phosphocreatine concentration in cytosol


ATPtmit

public Node ATPtmit
total ATP concentration in mitochondria


ADPtmit

public Node ADPtmit
total ADP concentration in mitochondria


Pimit

public Node Pimit
iorganic phosphate concentration in mitochondria


Rcm

public Node Rcm
volume ratio between cytosol and mitochondrial matrix


PiTotal

public double PiTotal
total iorganic phosphate concentration in whole cell

Constructor Detail

ConcentrationPi

public ConcentrationPi()
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。

Overrides:
calculate in class MassConservation2
Parameters:
t - elapsed time (ms)


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