org.simBio.bio.kuzumoto_et_al_2007.molecule
Class PKA

java.lang.Object
  org.simBio.core.Component
      org.simBio.core.Parameter
          org.simBio.core.Composite
              org.simBio.core.Reactor
                  org.simBio.bio.kuzumoto_et_al_2007.molecule.PKA

All Implemented Interfaces:

Node

public class PKA
extends Reactor

PKA module.

   Broyden method function(F)
   F0: cAMP=cAMPtot-(ARCI+2.0*A2RCI+2.0*A2RI)
   F1: PKA=2.0*PKAItot-(RCI+ARCI+A2RCI+PKACI_PKI)
 

Version:

$Id: PKA.java,v 1.1 2007/12/15 07:21:54 nsarai Exp $

Author:

M. Kuzumoto

See Also:

Kuzumoto et al, 2007.

Field Summary

Node	A2RCI A2RCI concentration (mM)
Node	A2RI A2RI concentration (mM)
Node	ARCI ARCI concentration (mM)
Node	cAMP cAMP concentration (mM)
Node	cAMPtot total cAMP concentration (mM)
MathMultivariableFunction	f13 Broyden function
MathMultivariableFunction	f14
double	KA
double	KB
double	KD
double	KPKI
Node	PKA PKA concentration (mM)
Node	PKACI_PKI PKA and PKI complex concentration (mM)
double	PKAtot
Node	PKI protein kinase inhibitor (mM)
double	PKItot
Node	RCI RCI concentration (mM)

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

PKA()

Method Summary

protected void	calculate(double t) write equations here, and calculate dy over dt.
protected void	prepare() 親が自分と同じ名前のpublic doubleを持っていれば、自分の値を設定する。

Methods inherited from class org.simBio.core.Composite

accept, getLink, getNode, getNodesIterator, getNodesSize

Methods inherited from class org.simBio.core.Parameter

addValue, getValue, getValueString, 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

cAMPtot

public Node cAMPtot

total cAMP concentration (mM)

cAMP

public Node cAMP

cAMP concentration (mM)

PKA

public Node PKA

PKA concentration (mM)

ARCI

public Node ARCI

ARCI concentration (mM)

A2RCI

public Node A2RCI

A2RCI concentration (mM)

A2RI

public Node A2RI

A2RI concentration (mM)

RCI

public Node RCI

RCI concentration (mM)

PKACI_PKI

public Node PKACI_PKI

PKA and PKI complex concentration (mM)

PKI

public Node PKI

protein kinase inhibitor (mM)

PKAtot

public double PKAtot

KPKI

public double KPKI

PKItot

public double PKItot

KA

public double KA

KB

public double KB

KD

public double KD

f13

public MathMultivariableFunction f13

Broyden function

f14

public MathMultivariableFunction f14

Constructor Detail

PKA

public PKA()

Method Detail

prepare

protected void prepare()

Description copied from class: Parameter

親が自分と同じ名前のpublic doubleを持っていれば、自分の値を設定する。

Overrides:

prepare in class Parameter

See Also:

Component.prepare()

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)