org.simBio.bio.kuzumoto_et_al_2007.molecule
Class PLB

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.PLB

All Implemented Interfaces:

Node

public class PLB
extends Reactor

Phospholamban module.

   multi newton raphson function(F)
   F27: Inhib1ptot-PP1_Inhib1p-Inhib1p=0        
   F28: PP1tot-PP1_Inhib1p-PP1=0
   F29: PP1*Inhib1p/K_Inhib1-PP1_Inhib1p=0    
   
   PLB=PLBItot-PLBp
   PLBphos=PLBp/PLBItot
   d(PLB)/dt=kPP1_PLB*PP1*PLBp/(KmPP1_PLB+PLBp)-(kPKA_PLB*PKA*PLB/(KmPKA_PLB+PLB)
   Inhib1=Inhib1tot-Inhib1ptot
   d(Inhib1ptot)/dt=kPKA_Inhib1*PKA*Inhib1/(KmPKA_Inhib1+Inhib1)-VmaxPP2A_Inhib1*Inhib1ptot/(KmPP2A_Inhib1+Inhib1ptot)
 

Version:

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

Author:

Masanori Kuzumoto

See Also:

Kuzumoto et al, 2007.

Field Summary

Node	ADP ADP concentration (mM)
Node	ATP ATP concentration (mM)
Node	Inhib1 inhibitor-1 concentration (mM)
Node	Inhib1p phosphorylated inhibitor-1 concentration (mM)
Node	Inhib1ptot phosphorylated inhibitor-1 total (Inhib1p + PP1_Inhib) concentration (mM)
double	Inhib1tot total inhibitor-1 concentration (mM)
double	KInhib1
double	KmPKA_Inhib1 Km
double	KmPKA_PLB Km
double	KmPP1_PLB Km
double	KmPP2A_Inhib1 Km
double	kPKA_Inhib1 rate constant
double	kPKA_PLB rate constant
double	kPP1_PLB rate constant
Node	PKA PKA catalytic domain I concentration (mM)
Node	PLB PLB concentration (mM)
double	PLBItot PLB total concentration (mM)
Node	PLBp phosphorylated PLB concentration (mM)
Node	PLBphos percent of PLB phosphorylation
Node	PP1 protein phosphatase-1 concentration (mM)
Node	PP1_Inhib1p protein phosphatase-1 and phosphorylated inhibitor-1 complex concentration (mM)
double	PP1tot total protein phosphatase 1 (mM)
double	VmaxPP2A_Inhib1 rate constant

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

PLB()

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

PLBItot

public double PLBItot

PLB total concentration (mM)

PLBp

public Node PLBp

phosphorylated PLB concentration (mM)

PLB

public Node PLB

PLB concentration (mM)

PLBphos

public Node PLBphos

percent of PLB phosphorylation

Inhib1tot

public double Inhib1tot

total inhibitor-1 concentration (mM)

Inhib1

public Node Inhib1

inhibitor-1 concentration (mM)

Inhib1p

public Node Inhib1p

phosphorylated inhibitor-1 concentration (mM)

Inhib1ptot

public Node Inhib1ptot

phosphorylated inhibitor-1 total (Inhib1p + PP1_Inhib) concentration (mM)

PP1tot

public double PP1tot

total protein phosphatase 1 (mM)

PP1

public Node PP1

protein phosphatase-1 concentration (mM)

PP1_Inhib1p

public Node PP1_Inhib1p

protein phosphatase-1 and phosphorylated inhibitor-1 complex concentration (mM)

PKA

public Node PKA

PKA catalytic domain I concentration (mM)

ATP

public Node ATP

ATP concentration (mM)

ADP

public Node ADP

ADP concentration (mM)

kPKA_PLB

public double kPKA_PLB

rate constant

kPKA_Inhib1

public double kPKA_Inhib1

rate constant

kPP1_PLB

public double kPP1_PLB

rate constant

VmaxPP2A_Inhib1

public double VmaxPP2A_Inhib1

rate constant

KmPKA_PLB

public double KmPKA_PLB

Km

KmPKA_Inhib1

public double KmPKA_Inhib1

Km

KmPP1_PLB

public double KmPP1_PLB

Km

KmPP2A_Inhib1

public double KmPP2A_Inhib1

Km

KInhib1

public double KInhib1

Constructor Detail

PLB

public PLB()

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)