org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter
Class PhosphateCarrier

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.molecule.Transporter.PhosphateCarrier

All Implemented Interfaces:

Node

public class PhosphateCarrier
extends Reactor

Phosphate Transporter.

Version:

$Id: PhosphateCarrier.java,v 1.2 2007/11/22 06:48:21 nsarai Exp $

Author:

SAITO Ryuta

See Also:

Table 12 in Matsuoka et al, 2004 Table 2 in Korzeniewski & Zoladz 2001 Korzeniewski & Zoladz 2003
XML example explanation (Japanese, WORD doc)

Field Summary

double	Amp amplifying factor described in Kuzumoto et al, 2007.
Node	Hcell proton concentration in cytosol (mM)
Node	Hmito proton concentration in mitochondrial matrix (mM)
double	kPI rate constant of inorganic phosphate carrier (/mM/msec)
double	myu u value (=0.861)
Node	pHcell pH in cytosol
Node	pHmito pH in mitochondrial matrix
Node	Pitcell inorganic phosphate concentration in cytosol (mM)
Node	Pitmito inorganic phosphate concentration in mitochondrial matrix (mM)
double	pKa acid dissociation constant
Node	rbuffermito buffering capacity for proton in mitochondrial matrix
Node	Rcm ratio of cytosol volume and mitochondria volume

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

PhosphateCarrier()

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

Pitcell

public Node Pitcell

inorganic phosphate concentration in cytosol (mM)

Hcell

public Node Hcell

proton concentration in cytosol (mM)

pHcell

public Node pHcell

pH in cytosol

Pitmito

public Node Pitmito

inorganic phosphate concentration in mitochondrial matrix (mM)

Hmito

public Node Hmito

proton concentration in mitochondrial matrix (mM)

pHmito

public Node pHmito

pH 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

kPI

public double kPI

rate constant of inorganic phosphate carrier (/mM/msec)

pKa

public double pKa

acid dissociation constant

myu

public double myu

u value (=0.861)

Amp

public double Amp

amplifying factor described in Kuzumoto et al, 2007.

Constructor Detail

PhosphateCarrier

public PhosphateCarrier()

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)