Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
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|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| R |
R_synthesis
env
|
GeneralKinetics | R |
|
|
|
reaction rate (J): ((k1 * S) + k0)[mol.litre-1.s-1]
|
|
| R |
R_degradation
env
|
GeneralKinetics | R |
|
|
|
reaction rate (J): ((k2_prime * R * E) + (k2 * R))[mol.litre-1.s-1]
|
|
| EpE |
E_dephosphorylation
env
|
GeneralKinetics | EpE |
|
|
|
reaction rate (J): (k3 * Ep / (Km3 + Ep))[mol.litre-1.s-1]
|
|
| EEp |
E_phosphorylation
env
|
GeneralKinetics | EEp |
|
|
|
reaction rate (J): (k4 * R * E / (Km4 + E))[mol.litre-1.s-1]
|
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| env |
Compartment
(+) (-)
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| R | env | R(). |
|
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| S | env | S(). |
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| Ep | env | E(mod~P!-,). |
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| E | env | E(mod~U!-,). |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|---|---|
| E | Text Annotations | E(mod~U~P,) |
|
|
|
|
| R | Text Annotations | R() |
|
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| S | Text Annotations | S() |
|
|
|
| Name |
Type
Count
|
BioNetGen Definition |
|---|---|---|
| O0_E_tot |
Molecules Multimolecular |
E(mod!?,). |
|
|
|
|
| O0_R_tot |
Molecules Multimolecular |
R(). |
|
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|
|
| O0_S_tot |
Molecules Multimolecular |
S(). |
|
|
|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Deterministic | Deterministic (ODE) Compartmental |
Application - Deterministic
| Species | Initial Condition | Diffusion Constant | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| R | 0.0 [mol] | 0.0
[m2/s] | S |
0.0
[mol]
|
0.0
[m2/s] | Ep |
(Et - E)
[mol]
|
0.0
[m2/s] | E |
(Et * ((2.0 * k3 * J4) / (((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3) + pow((pow((((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3)),2.0) - (4.0 * ((k4 * R) - k3) * k3 * J4)),(1.0 / 2.0)))))
[mol]
|
0.0
[m2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| R_synthesis | included |
| R_degradation | included |
| E_dephosphorylation | included |
| E_phosphorylation | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 1.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
| Name | Variable | Assignment Function Expression |
|---|---|---|
| assignmentRule0 | Km3 | (J3 * Et) |
| assignmentRule1 | Km4 | (J4 * Et) |
| assignmentRule2 | E | (Et * ((2.0 * k3 * J4) / (((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3) + pow((pow((((k4 * R) - k3) + (J3 * (k4 * R)) + (J4 * k3)),2.0) - (4.0 * ((k4 * R) - k3) * k3 * J4)),(1.0 / 2.0))))) |
| assignmentRule3 | Ep | (Et - E) |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | env |
Global Parameters
| Name | Expression |
|---|---|
| k0 | 0.0[mol.s-1.l-1] |
|
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| k1 | 0.05[s-1] |
|
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| k2 | 0.1[s-1] |
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| k2_prime | 0.5[M-1.s-1] |
|
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| k3 | 0.2[mol.s-1.l-1] |
|
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| J3 | 0.05[1] |
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| k4 | 1.0[s-1] |
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| J4 | 0.05[1] |
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| Et | 1.0[M] |
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| Km3 | (J3 * Et)[M] |
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| Km4 | (J4 * Et)[M] |
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