Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| s4ms4m+Ca |
Ca_influx
m0
|
MassAction | s4ms4m+Ca |
|
|
|
reaction rate (J): ((Kf * s4m) - ((Kr * s4m) * Ca))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 200.0[s-1] reverse rate constant (Kr): 0.0[s-1.uM-1] |
|
| PDEa+cAMPPDEa |
cAMPdeg
c0
|
MassAction | PDEa+cAMPPDEa |
|
|
|
reaction rate (J): (((Kf * PDEa) * cAMP) - (Kr * PDEa))[uM.s-1]
forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1] |
|
| cAMP |
inddeg
c0
|
MassAction | cAMP |
|
|
|
reaction rate (J): (Kf * cAMP)[uM.s-1]
forward rate constant (Kf): 50.0[s-1] reverse rate constant (Kr): 0.0[uM.s-1] |
|
| AC+CaACa |
AC act
m0
|
MassAction | AC+CaACa |
|
|
|
reaction rate (J): (((Kf * AC) * Ca) - (Kr * ACa))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 100.0[s-1] |
|
| Ca+PDEPDEa |
PDEact
c0
|
MassAction | Ca+PDEPDEa |
|
|
|
reaction rate (J): (((Kf * Ca) * PDE) - (Kr * PDEa))[uM.s-1]
forward rate constant (Kf): 10.0[s-1.uM-1] reverse rate constant (Kr): 100.0[s-1] |
|
| PDE+cAMPPDE |
basedeg
c0
|
MassAction | PDE+cAMPPDE |
|
|
|
reaction rate (J): (((Kf * PDE) * cAMP) - (Kr * PDE))[uM.s-1]
forward rate constant (Kf): 10.0[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1] |
|
| ACAC+cAMP |
baseAC
m0
|
MassAction | ACAC+cAMP |
|
|
|
reaction rate (J): ((Kf * AC) - ((Kr * AC) * cAMP))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 10.0[s-1] reverse rate constant (Kr): 0.0[s-1.uM-1] |
|
| ACacAMP+ACa |
ACactive
m0
|
MassAction | ACacAMP+ACa |
|
|
|
reaction rate (J): ((Kf * ACa) - ((Kr * cAMP) * ACa))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 200.0[s-1] reverse rate constant (Kr): 0.0[s-1.uM-1] |
|
| Ca |
removeCa
m0
|
MassAction | Ca |
|
|
|
reaction rate (J): (Kf * Ca)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1000.0[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1] |
|
| cAMP |
cAMPind
m0
|
GeneralKinetics | cAMP |
|
|
|
reaction rate (J): 20.0[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] |
|
| s0ms0m |
r0m
m1
|
MassAction | s0ms0m |
|
|
|
reaction rate (J): ((Kf * s0m) - (Kr * pow(s0m,2.0)))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.0[s-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1] |
|
| s0m+s4ms4m |
r1m
m1
|
MassAction | s0m+s4ms4m |
|
|
|
reaction rate (J): (((Kf * s0m) * s4m) - (Kr * pow(s4m,2.0)))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 1.0[um2.s-1.molecules-1] reverse rate constant (Kr): 0.0[um2.s-1.molecules-1] |
|
| s4m |
r2m
m1
|
MassAction | s4m |
|
|
|
reaction rate (J): (Kf * s4m)[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): 5.0[s-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1] |
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| c2 |
Compartment
(+) (-)
|
|
|
|
| c0 |
Compartment
(+) (-)
|
|
|
|
| c1 |
Compartment
(+) (-)
|
|
|
|
| c3 |
Compartment
(+) (-)
|
|
|
|
| m0 |
Membrane
N/A
|
|
|
|
| m1 |
Membrane
N/A
|
|
|
|
| m2 |
Membrane
N/A
|
|
|
|
| m3 |
Membrane
N/A
|
|
|
|
| centermem |
Membrane
N/A
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| Ca | c0 | |
|
|
|
|
| AC | m0 | |
|
|
|
|
| cAMP | c0 | |
|
|
|
|
| PDE | c0 | |
|
|
|
|
| ACa | m0 | |
|
|
|
|
| PDEa | c0 | |
|
|
|
|
| s0m | m1 | |
|
|
|
|
| s4m | m1 | |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Copy of Application0 1 | Stochastic (SSA) Compartmental | (copied from Application0) |
Application - Copy of Application0 1
| Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ca | 10.0 [molecules] | 0.0
[um2/s] | cAMP |
0.0
[molecules]
|
0.0
[um2/s] | PDE |
45.0
[molecules]
|
0.0
[um2/s] | PDEa |
5.0
[molecules]
|
0.0
[um2/s] | AC |
0.0
[molecules]
|
0.0
[um2/s] | ACa |
0.0
[molecules]
|
0.0
[um2/s] | s0m |
0.0
[molecules]
|
0.0
[um2/s] | s4m |
0.0
[molecules]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| Ca_influx | included |
| cAMPdeg | included |
| inddeg | included |
| AC act | included |
| PDEact | included |
| basedeg | included |
| baseAC | included |
| ACactive | included |
| removeCa | included |
| cAMPind | included |
| r0m | included |
| r1m | included |
| r2m | included |
| Name | End Time | Output Options |
|---|---|---|
| done 1 2 1 | 99.9 [s] |
OutputTimeStep 0.1 |
| double done 1 2 1 | 99.9 [s] |
OutputTimeStep 0.1 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | centermem |
Global Parameters
| Name | Expression |
|---|---|
| g0 | (((2.0 * ((2.0 * floor((t / 4.0))) - floor((2.0 * t / 4.0)))) + 2.0) / 2.0)[molecules.um-2] |
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