org.simBio.bio.matsuoka_et_al_2004.molecule.enzyme
Class AK

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.enzyme.AK

All Implemented Interfaces:

Node

public class AK
extends Reactor

Adenylate Kinase (AK) System

  vAK = kf*[ADP]free_cell*[ADP]mg_cell - kb*[ATP]mg_cell*[AMP]cell
 

Since:

rc20

Version:

$Id: AK.java,v 1.2 2006/05/30 07:28:50 nsarai Exp $

Author:

SAITO Ryuta

See Also:

Korzeniewski & Zoladz 2001 Korzeniewski & Zoladz 2003 Thuma et al. 1972
XML example explanation (Japanese, WORD doc)

Field Summary

Node	ADPfree free ADP concentration in cytosol
Node	ADPmg Mg binding ADP concentration in cytosol
Node	ADPtotal total ADP concentration in cytosol
Node	AMP AMP concentration in cytosol
Node	ATPmg Mg binding ATP concentration in cytosol
Node	ATPtotal total ATP concentration in cytosol
double	kbAK rate constant of backward reaction of adenylate kinase, (Default value: 0.683333)
double	kfAK rate constant of forward reaction of adenylate kinase, (Default value: 0.783333)

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

AK()

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

ATPtotal

public Node ATPtotal

total ATP concentration in cytosol

ATPmg

public Node ATPmg

Mg binding ATP concentration in cytosol

ADPtotal

public Node ADPtotal

total ADP concentration in cytosol

ADPmg

public Node ADPmg

Mg binding ADP concentration in cytosol

ADPfree

public Node ADPfree

free ADP concentration in cytosol

AMP

public Node AMP

AMP concentration in cytosol

kfAK

public double kfAK

rate constant of forward reaction of adenylate kinase, (Default value: 0.783333)

kbAK

public double kbAK

rate constant of backward reaction of adenylate kinase, (Default value: 0.683333)

Constructor Detail

AK

public AK()

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)