Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
R | R_synthesis | env | GeneralKinetics | |
R | R_synthesis2 | env | GeneralKinetics | |
R | R_degradation | env | GeneralKinetics | |
EEp | E_phosphorylation | env | GeneralKinetics | |
EpE | E_dephosphorylation | env | GeneralKinetics |
R_synthesis Universal ID's
R_synthesis Text Annotations
R_synthesis2 Universal ID's
R_synthesis2 Text Annotations
R_degradation Universal ID's
R_degradation Text Annotations
E_phosphorylation Universal ID's
E_phosphorylation Text Annotations
E_dephosphorylation Universal ID's
E_dephosphorylation Text Annotations
Expressions for R_synthesis
reaction rate
J
(k0 * Ep) [mol.litre-1.s-1]
global
k0
0.4 [s-1]
Expressions for R_synthesis2
reaction rate
J
(k1 * S) [mol.litre-1.s-1]
global
k1
0.01 [s-1]
Expressions for R_degradation
reaction rate
J
(k2 * R) [mol.litre-1.s-1]
global
k2
1.0 [s-1]
Expressions for E_phosphorylation
reaction rate
J
(k3 * R * E / (J3 + E)) [mol.litre-1.s-1]
global
k3
1.0 [s-1]
global
J3
0.05 [M]
Expressions for E_dephosphorylation
reaction rate
J
(k4 * Ep / (J4 + Ep)) [mol.litre-1.s-1]
global
k4
0.2 [mol.s-1.l-1]
global
J4
0.05 [M]
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
R | env | R(). | |
S | env | S(). | |
Ep | env | E(mod~P!-,). | |
E | env | E(mod~U!-,). |
R Universal ID's
R Text Annotations
S Universal ID's
S Text Annotations
Ep Universal ID's
Ep Text Annotations
E Universal ID's
E Text Annotations
Molecules
R Universal ID's
R Text Annotations
S Universal ID's
S Text Annotations
E Universal ID's
E Text Annotations
Observables
Name | Structure | Count | BNGL Definition | Sequence Type | DEPICTION |
---|---|---|---|---|---|
O0_R_tot | env | Molecules | R(). | Multimolecular | |
O0_S_tot | env | Molecules | S(). | Multimolecular | |
O0_E_tot | env | Molecules | E(mod!?,). | Multimolecular |
O0_R_tot Universal ID's
O0_R_tot Text Annotations
O0_S_tot Universal ID's
O0_S_tot Text Annotations
O0_E_tot Universal ID's
O0_E_tot Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
Deterministic |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental |
Deterministic Universal ID's
Deterministic Text Annotations
Specifications (Species) - Deterministic go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
R | 0.0 [mol] | 0.0 [m2/s] | env |
S | 0.0 [mol] | 0.0 [m2/s] | env |
Ep | ((2.0 * (k3 * R) * J4) / ((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R)) + pow((pow(((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R))),2.0) - (4.0 * (k4 - (k3 * R)) * (k3 * R) * J4)),(1.0 / 2.0)))) [mol] | 0.0 [m2/s] | env |
E | (Et - Ep) [mol] | 0.0 [m2/s] | env |
Specifications (Reaction) - Deterministic go to Simulations
Simulations - Deterministic go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation0 | 1.0 |
KeepEvery 1 KeepAtMost 1000 |
Deterministic Universal ID's
Deterministic Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|---|---|
assignmentRule0 | E | (Et - Ep) |
assignmentRule1 | Ep | ((2.0 * (k3 * R) * J4) / ((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R)) + pow((pow(((k4 - (k3 * R)) + (J3 * k4) + (J4 * (k3 * R))),2.0) - (4.0 * (k4 - (k3 * R)) * (k3 * R) * J4)),(1.0 / 2.0)))) |
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Compartmental481736209
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | env |
Events
Name | Variable | Rate Expression |
---|
Global Parameters
Name | Expression |
---|---|
k0 | 0.4[s-1] |
k1 | 0.01[s-1] |
k2 | 1.0[s-1] |
k3 | 1.0[s-1] |
J3 | 0.05[M] |
k4 | 0.2[mol.s-1.l-1] |
J4 | 0.05[M] |
Et | 1.0[M] |
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Universal ID's
Text Annotations
Downloads
Model Format | Model Downloads |
---|---|
Virtual Cell Markup Language | VCML File |
PDF Report | Report |
COMBINE Archive | OMEX File |
SEDML | SEDML File |
File Format | Application Downloads |
BNGL | Deterministic.bngl |
SBML | Deterministic.sbml |
Matlab | Deterministic.m |
NFSim XML | Deterministic.xml |