Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
fXb+fXbfX2 dimerisation Membrane0 MassAction
fXb+fX2fX3 trimerisation Membrane0 MassAction
s+fXfXb Binding Membrane0 MassAction

dimerisation Universal ID's

dimerisation Text Annotations

trimerisation Universal ID's

trimerisation Text Annotations

Binding Universal ID's

Binding Text Annotations

Expressions for dimerisation

reaction rate

J

(((Kf * fXb) * fXb) - (Kr * fX2)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

0.27 [um2.s-1.molecules-1]

reverse rate constant

Kr

100.0 [s-1]

Expressions for trimerisation

reaction rate

J

(((Kf * fXb) * fX2) - (Kr * fX3)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

3.66E-4 [um2.s-1.molecules-1]

reverse rate constant

Kr

1.0E-4 [s-1]

Expressions for Binding

reaction rate

J

(((Kf * s) * fX) - (Kr * fXb)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

1.0 [s-1.uM-1]

reverse rate constant

Kr

0.14 [s-1]

Structures

Name
Type
Electrical
Membrane0 Membrane c1(+)   c0(-)
c1 Compartment (+)   (-)
c0 Compartment (+)   (-)

Membrane0 Universal ID's

Membrane0 Text Annotations

c1 Universal ID's

c1 Text Annotations

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
s Membrane0 Membrane0
fXb Membrane0 Membrane0
fX c0 c0
fX2 Membrane0 Membrane0
fX3 Membrane0 Membrane0

s Universal ID's

s Text Annotations

fXb Universal ID's

fXb Text Annotations

fX Universal ID's

fX Text Annotations

fX2 Universal ID's

fX2 Text Annotations

fX3 Universal ID's

fX3 Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application1 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D)

Application1 Universal ID's

Application1 Text Annotations

Specifications (Species) - Application1 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
fX 0.015 [uM] 100.0 [um2/s] c0
s 198.0 [uM] 0.0 [um2/s] Membrane0
fXb 0.0 [uM] 0.0 [um2/s] Membrane0
fX2 0.0 [uM] 0.0 [um2/s] Membrane0
fX3 0.0 [uM] 0.0 [um2/s] Membrane0

Specifications (Reaction) - Application1 go to Simulations

Name
Enabled?
dimerisation included
trimerisation included
Binding included

Simulations - Application1 go to Specifications

Name
End Time
Output Options
Simulation1 500.0

OutputTimeStep 3.0

Application1 Universal ID's

Application1 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry5

(Origin: -5.0, -10.0, 0.0; Extent: 10.0, 100.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain1 4.7 [um2] c1
Volume Analytical subdomain0 929.5000000000001 [um2] c0
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 8.207720179183681 [um] Membrane0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

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 Application1.bngl
SBML Application1.sbml
Matlab Application1.m
NFSim XML Application1.xml