org.simBio.bio.kuzumoto_et_al_2007.molecule
Class BetaAR_Gs

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.BetaAR_Gs

All Implemented Interfaces:

Node

public class BetaAR_Gs
extends Reactor

betaAR and Gs signaling module.

  multi newton raphson function(F)
  F1:  Iso-LR-LRG-L=0
  F2:    Gstot-RG-LRG-Gs_beta_gamma-Gs=0
  F3:  beta1_ARact-LR-LRG-RG-beta1_AR=0
  F4:  L*beta1_AR/KL-LR=0
  F5:  L*beta1_AR*Gs/KL*KR-LR=0
  F6:  beta1_AR*Gs/KC-RG=0
  
  d(beta1_AR_S464)/dt=k_betaARK_plus*(LR+LRG)-k_betaARK_minus*beta1_AR_S464                 
  d(beta1_AR_S301)=k_PKA_plus*PKA*beta1_ARact-k_PKA_minus*beta1_AR_S301 
  beta1_ARact=beta1_ARtot-beta1_AR_S464-beta1_AR_S301
  
  d(Gs_alpha_GTPtot)/dt=k_gact*(RG+LRG)-k_hyd*Gs_alpha_GTPtot
  d(Gs_beta_gamma)/dt=k_gact*(RG+LRG)-k_reassoc*Gs_alpha_GDP*Gs_beta_gamma
  d(Gs_alpha_GDP)dt=k_hyd*Gs_alpha_GTPtot-k_reassoc*Gs_alpha_GDP*Gs_beta_gamma
 

Version:

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

Author:

M.Kuzumoto, Hiroyuki Nakai

See Also:

Kuzumoto et al, 2007.

Field Summary

Node	beta1_AR free receptor concentration
Node	beta1_AR_S301 site of 301 phosphorylated receptor concentration
Node	beta1_AR_S464 site of 464 phosphorylated receptor concentration
Node	beta1_ARact active receptor concentration
double	beta1_ARtot total beta1 receptor concentration
Node	d_Gs_alpha_GTPtot Multi newton raphson function
Node	Gs free gs_protein concentration
Node	Gs_alpha_GDP Multi newton raphson function
Node	Gs_alpha_GTPtot Multi newton raphson function
Node	Gs_beta_gamma gs_beta_gamma_protein concentration
Node	Gstot total gs_protein concentration
Node	Iso total ligand concentration
double	k_betaARK_minus rate constant
double	k_betaARK_plus rate constant
double	k_gact rate constant
double	k_hyd rate constant
double	k_PKA_minus rate constant
double	k_PKA_plus rate constant
double	k_reassoc rate constant
double	KC
double	KL
double	KR
Node	L free ligand concentration
Node	LR ligand-receptor complex concentration
Node	LRG ligand-receptor-gs_protein complex concentration
Node	PKA PKA catalitic domain I
Node	RG receptor-gs_protein complex concentration

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

BetaAR_Gs()

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

L

public Node L

free ligand concentration

LR

public Node LR

ligand-receptor complex concentration

LRG

public Node LRG

ligand-receptor-gs_protein complex concentration

RG

public Node RG

receptor-gs_protein complex concentration

beta1_AR

public Node beta1_AR

free receptor concentration

beta1_ARact

public Node beta1_ARact

active receptor concentration

beta1_AR_S464

public Node beta1_AR_S464

site of 464 phosphorylated receptor concentration

beta1_AR_S301

public Node beta1_AR_S301

site of 301 phosphorylated receptor concentration

Gstot

public Node Gstot

total gs_protein concentration

Gs

public Node Gs

free gs_protein concentration

Gs_beta_gamma

public Node Gs_beta_gamma

gs_beta_gamma_protein concentration

PKA

public Node PKA

PKA catalitic domain I

beta1_ARtot

public double beta1_ARtot

total beta1 receptor concentration

k_betaARK_plus

public double k_betaARK_plus

rate constant

k_betaARK_minus

public double k_betaARK_minus

rate constant

k_PKA_plus

public double k_PKA_plus

rate constant

k_PKA_minus

public double k_PKA_minus

rate constant

Gs_alpha_GTPtot

public Node Gs_alpha_GTPtot

Multi newton raphson function

Gs_alpha_GDP

public Node Gs_alpha_GDP

Multi newton raphson function

d_Gs_alpha_GTPtot

public Node d_Gs_alpha_GTPtot

Multi newton raphson function

k_gact

public double k_gact

rate constant

k_hyd

public double k_hyd

rate constant

k_reassoc

public double k_reassoc

rate constant

Iso

public Node Iso

total ligand concentration

KL

public double KL

KR

public double KR

KC

public double KC

Constructor Detail

BetaAR_Gs

public BetaAR_Gs()

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)