Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Rac_inactRac_act r1 cytosol GeneralKinetics
Rho_inactRho_act r2 cytosol GeneralKinetics

r1 Universal ID's

r1 Text Annotations

r2 Universal ID's

r2 Text Annotations

Expressions for r1

reaction rate

J

((((b_Rac + gamma_Rho) * (1.0 / (1.0 + (Rho_act ^ n1)))) * (Rac_inact / Rac_tot)) - (I_Rac * Rac_act)) [uM.s-1]

global

gamma_Rho

1.0 [uM.s-1]

global

Rac_tot

7.5 [uM]

local

n1

4.0 [1]

local

b_Rac

(((0.7 + (0.125 * x)) * (t <= 10.0)) + (4.0 * (t > 10.0))) [uM.s-1]

local

I_Rac

1.0 [s-1]

Expressions for r2

reaction rate

J

((((b_Rho + gamma_Rho) * (1.0 / (1.0 + (Rac_act ^ n2)))) * (Rho_inact / Rho_tot)) - (I_Rho * Rho_act)) [uM.s-1]

global

Rho_tot

3.1 [uM]

global

gamma_Rho

1.0 [uM.s-1]

local

I_Rho

1.0 [s-1]

local

n2

4.0 [1]

local

b_Rho

4.0 [uM.s-1]

Structures

Name
Type
Electrical
plasma membrane Membrane (+)   (-)
extracellular space Compartment (+)   (-)
cytosol Compartment (+)   (-)

plasma membrane Universal ID's

plasma membrane Text Annotations

extracellular space Universal ID's

extracellular space Text Annotations

cytosol Universal ID's

cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Rac_inact cytosol cytosol
Rac_act cytosol cytosol
Rho_inact cytosol cytosol
Rho_act cytosol cytosol

Rac_inact Universal ID's

Rac_inact Text Annotations

Rac_act Universal ID's

Rac_act Text Annotations

Rho_inact Universal ID's

Rho_inact Text Annotations

Rho_act Universal ID's

Rho_act Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
real cell Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D) cloned from 'real cell' owned by user aureliecarlier (copied from real cell) (copied from Application0)

real cell Universal ID's

real cell Text Annotations

Specifications (Species) - real cell go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Rac_inact 4.5 [uM] 10.0 [um2/s] cytosol
Rac_act 3.0 [uM] 0.01 [um2/s] cytosol
Rho_inact 1.85 [uM] 10.0 [um2/s] cytosol
Rho_act 1.25 [uM] 0.01 [um2/s] cytosol

Specifications (Reaction) - real cell go to Simulations

Name
Enabled?
r1 included
r2 included

Simulations - real cell go to Specifications

Name
End Time
Output Options
Simulation1 50.0

OutputTimeStep 1.0
Simulation2 1000.0

OutputTimeStep 1.0

real cell Universal ID's

real cell Text Annotations

real cell Universal ID's

real cell Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20171120_183216

(Origin: 0.0, 0.0, 0.0; Extent: 50.0, 20.0, 9.0E-7 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Image Cell 640.0005147077745 [um2] cytosol
Volume Image EC 34.62053169313122 [um2] extracellular space
Surface Cell_EC_membrane Cell | EC 19.36700981687842 [um] plasma membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
Rho_tot 3.1[uM]
gamma_Rho 1.0[uM.s-1]
Rac_tot 7.5[uM]

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 real cell.bngl
SBML real cell.sbml
Matlab real cell.m
NFSim XML real cell.xml