Physiology

Reaction Diagram

reactionDiagram

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]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

env Universal ID's

env Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
R env R(). env
S env S(). env
Ep env E(mod~P!-,). env
E env E(mod~U!-,). env

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

Name
BioNetGen Definition
DEPICTION
R R()
S S()
E E(mod~P~U,)

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

Name
Enabled?
R_synthesis included
R_synthesis2 included
R_degradation included
E_phosphorylation included
E_dephosphorylation included

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