Physiology

Reaction Diagram

reactionDiagram

Cross-References

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Reactions

Reactions
Name
Structure
Kinetics
X R X_conversion_to_R env GeneralKinetics
X X_synthesis env GeneralKinetics
R R_degradation env GeneralKinetics
E Ep E_phosphorylation env GeneralKinetics
Ep E E_dephosphorylation env GeneralKinetics

Reaction Name: X_conversion_to_R

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Reaction Name: X_synthesis

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Reaction Name: R_degradation

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Reaction Name: E_phosphorylation

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Reaction Name: E_dephosphorylation

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Reaction Name: X_conversion_to_R

Expressions

reaction rate

((k0_prime + (k0 * Ep)) * X) [mol.litre-1.s-1]

Reaction Name: X_synthesis

Expressions

reaction rate

(k1 * S) [mol.litre-1.s-1]

Reaction Name: R_degradation

Expressions

reaction rate

(k2 * R) [mol.litre-1.s-1]

Reaction Name: E_phosphorylation

Expressions

reaction rate

(k3 * R * E / (Km3 + E)) [mol.litre-1.s-1]

Reaction Name: E_dephosphorylation

Expressions

reaction rate

(k4 * Ep / (Km4 + Ep)) [mol.litre-1.s-1]

Structures

Name
Type
Electrical
env Compartment (+)   (-)

Structure Name: env

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Species

Name
Structure
R env
X env
S env
Ep env
E env

Species Name: R

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Species Name: X

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Species Name: S

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Species Name: Ep

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Species Name: E

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Molecules

Name
Description
R R ()
X X ()
S S ()
E E ( mod ~P ~U )

Molucule Name: R

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Molucule Name: X

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Molucule Name: S

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Molucule Name: E

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Observables

Name
Domain
Molecular Type
Sequence Type
O0_R_tot Molecules R Multimolecular
O0_X_tot Molecules X Multimolecular
O0_S_tot Molecules S Multimolecular
O0_E_tot Molecules E Multimolecular

Observables Name: O0_R_tot

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Observables Name: O0_X_tot

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Observables Name: O0_S_tot

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Observables Name: O0_E_tot

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Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations

Application Name: Deterministic

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Annotations will come here

Universal ID's

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
R 0.0 0.0
X 0.0 0.0
S 0.0 0.0
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)))) * Et) 0.0
E (Et - Ep) 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
X_conversion_to_R included
X_synthesis included
R_degradation included
E_phosphorylation included
E_dephosphorylation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1.0 every

Simulation Name: Simulation0

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Global Parameters

Name
Expression
k0_prime 0.01[s-1]
k0 0.4[M-1.s-1]
k1 1.0[s-1]
k2 1.0[s-1]
k3 1.0[s-1]
J3 0.05[1]
k4 0.3[mol.s-1.l-1]
J4 0.05[1]
Et 1.0[M]
Km3 (J3 * Et)[M]
Km4 (J4 * Et)[M]

Global Parameter Name: k0_prime

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Global Parameter Name: k0

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Global Parameter Name: k1

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Global Parameter Name: k2

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Global Parameter Name: k3

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Global Parameter Name: J3

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Global Parameter Name: k4

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Global Parameter Name: J4

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Global Parameter Name: Et

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Global Parameter Name: Km3

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Global Parameter Name: Km4

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Downloads

Format
File
BNGL
Metlab
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Formatted XML
SEDML
Deterministic XML