Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| X |
X_degradation
c0
|
MassAction | X |
|
|
|
reaction rate (J): (Kf * X)[uM.s-1]
forward rate constant (Kf): k4[s-1] reverse rate constant (Kr): 0.0[uM.s-1] user defined (k4): 1.0[s-1] |
|
| X |
X_synthesis
c0
|
GeneralKinetics | X |
|
|
|
reaction rate (J): (k3 * S)[uM.s-1]
user defined (k3): 1.0[s-1] |
|
| R |
R_synthesis
c0
|
GeneralKinetics | R |
|
|
|
reaction rate (J): (k1 * S)[uM.s-1]
user defined (k1): 2.0[s-1] |
|
| R |
R_degradation
c0
|
GeneralKinetics | R |
|
|
|
reaction rate (J): (k2 * X * R)[uM.s-1]
user defined (k2): 2.0[s-1.uM-1] |
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| c0 |
Compartment
(+) (-)
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| S | c0 | S(). |
|
|
|
|
| R | c0 | R(). |
|
|
|
|
| X | c0 | X(). |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|---|---|
| S | Text Annotations | S() |
|
|
|
|
| R | Text Annotations | R() |
|
|
|
|
| X | Text Annotations | X() |
|
|
|
| Name |
Type
Count
|
BioNetGen Definition |
|---|---|---|
| O0_S_tot |
Molecules Multimolecular |
S(). |
|
|
|
|
| O0_R_tot |
Molecules Multimolecular |
R(). |
|
|
|
|
| O0_X_tot |
Molecules Multimolecular |
X(). |
|
|
|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| PerfectlyAdapted | Deterministic (ODE) Compartmental |
Application - PerfectlyAdapted
| Species | Initial Condition | Diffusion Constant | ||||||
|---|---|---|---|---|---|---|---|---|
| S | 1.0 [uM] | 0.0
[um2/s] | R |
0.0
[uM]
|
0.0
[um2/s] | X |
0.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| X_degradation | included |
| X_synthesis | included |
| R_synthesis | included |
| R_degradation | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 20.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| event0 | at times: [4.0,8.0,12.0,16.0] | S --> (S + 0.2) |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | c0 |
Global Parameters
| Name | Expression |
|---|