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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
public class BetaAR_Gs
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
Field Summary | |
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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 |
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value |
Constructor Summary | |
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BetaAR_Gs()
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Method Summary | |
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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 |
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accept, getLink, getNode, getNodesIterator, getNodesSize |
Methods inherited from class org.simBio.core.Parameter |
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addValue, getValue, getValueString, setInitializer, setValue, setValueString, setValueToField |
Methods inherited from class org.simBio.core.Component |
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addDydt, end, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented, quit, setLinks |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.simBio.core.Node |
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addDydt, addValue, getValue, setValue |
Field Detail |
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public Node L
public Node LR
public Node LRG
public Node RG
public Node beta1_AR
public Node beta1_ARact
public Node beta1_AR_S464
public Node beta1_AR_S301
public Node Gstot
public Node Gs
public Node Gs_beta_gamma
public Node PKA
public double beta1_ARtot
public double k_betaARK_plus
public double k_betaARK_minus
public double k_PKA_plus
public double k_PKA_minus
public Node Gs_alpha_GTPtot
public Node Gs_alpha_GDP
public Node d_Gs_alpha_GTPtot
public double k_gact
public double k_hyd
public double k_reassoc
public Node Iso
public double KL
public double KR
public double KC
Constructor Detail |
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public BetaAR_Gs()
Method Detail |
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protected void prepare()
Parameter
prepare
in class Parameter
Component.prepare()
protected void calculate(double t)
Reactor
calculate
in class Reactor
t
- elapsed time (ms)
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