org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain
Class ATPsynthase

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.molecule.RespiratoryChain.ATPsynthase
All Implemented Interfaces:
Node

public class ATPsynthase
extends Reactor

Mitochondrial F1/F0 ATP Synthase.

 vSN = kSN * (gamma - 1) / (gamma + 1)
 gamma = 10^(dGSN / Zett)
 dGSN = nA * dP - dGp
 dGp = dGp0 / F + Zett * log(1000*[ATP]total_mito/[ADP]total_mito/[Pi]mito)
                (concentrations expressed in mM)
 

Version:
$Id: ATPsynthase.java,v 1.2 2007/11/22 06:48:21 nsarai Exp $
Author:
SAITO Ryuta
See Also:
Matsuoka et al. (2004), Korzeniewski & Zoladz (2001), Korzeniewski & Zoladz (2003), XML example, explanation (Japanese, WORD doc)

Field Summary
 Node ADPtmito
          total ADP concentration in mitochondrial matrix
 double Amp
          amplifying factor described in Kuzumoto et al, 2007.
 Node ATPtmito
          total ATP concentration in mitochondrial matrix
 double dGp0
          standard free-energy change of ATP synthase
 Node dP
          proton driving force on mitochondrial inner membrane
 double F
          Faraday constant
 Node Hcell
          proton concentration in cytosol
 Node Hmito
          proton concentration in mitochondrial matrix
 double kSN
          rata constant of ATP synthase
 double nA
          phenomenological H+/ATP stoichiometry of ATP synthase
 Node Pitmito
          inorganic phosphate concentration in mitochondrial matrix
 Node rbuffermito
          buffering capacity for proton in mitochondrial matrix
 Node Rcm
          ratio of cytosol volume and mitochondria volume
 double Zvalue
          Z = 2.303 * R * T / F
 
Fields inherited from class org.simBio.core.Parameter
value
 
Constructor Summary
ATPsynthase()
           
 
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

dP

public Node dP
proton driving force on mitochondrial inner membrane


Hcell

public Node Hcell
proton concentration in cytosol


Hmito

public Node Hmito
proton concentration in mitochondrial matrix


ATPtmito

public Node ATPtmito
total ATP concentration in mitochondrial matrix


ADPtmito

public Node ADPtmito
total ADP concentration in mitochondrial matrix


Pitmito

public Node Pitmito
inorganic phosphate concentration in mitochondrial matrix


Rcm

public Node Rcm
ratio of cytosol volume and mitochondria volume


rbuffermito

public Node rbuffermito
buffering capacity for proton in mitochondrial matrix


Zvalue

public double Zvalue
Z = 2.303 * R * T / F


dGp0

public double dGp0
standard free-energy change of ATP synthase


kSN

public double kSN
rata constant of ATP synthase


nA

public double nA
phenomenological H+/ATP stoichiometry of ATP synthase


F

public double F
Faraday constant


Amp

public double Amp
amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

ATPsynthase

public ATPsynthase()
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)


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