Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
B2R_p+arrestinarrestin_bound_receptor | arrestin binding | cyto_mem | MassAction | |
Ligand+GRK+B2RB2R_p | receptor ligand binding | cyto_mem | MassAction |
arrestin binding Universal ID's
arrestin binding Text Annotations
receptor ligand binding Universal ID's
receptor ligand binding Text Annotations
Expressions for arrestin binding
reaction rate
J
(((Kf * B2R_p) * arrestin) - (Kr * arrestin_bound_receptor)) [molecules.um-2.s-1]
global
n
350.0 [molecules.um-2.uM-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
0.45 [s-1.uM-1]
reverse rate constant
Kr
1.0 [s-1]
Expressions for receptor ligand binding
reaction rate
J
((((Kf * Ligand) * GRK) * B2R) - (Kr * B2R_p)) [molecules.um-2.s-1]
global
n
350.0 [molecules.um-2.uM-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
forward rate constant
Kf
20.0 [s-1.uM-2]
reverse rate constant
Kr
0.06666666666666667 [s-1]
Structures
Name | Type | Electrical |
---|---|---|
cyto_mem | Membrane | cyto(+) extra(-) |
extra | Compartment | (+) (-) |
cyto | Compartment | (+) (-) |
cyto_mem Universal ID's
cyto_mem Text Annotations
extra Universal ID's
extra Text Annotations
cyto Universal ID's
cyto Text Annotations
Species
Name | Structure | BioNetGen Definition | Depiction |
---|---|---|---|
B2R | cyto_mem | ||
GRK | cyto | ||
B2R_p | cyto_mem | ||
Ligand | extra | ||
arrestin | cyto | ||
arrestin_bound_receptor | cyto_mem |
B2R Universal ID's
B2R Text Annotations
GRK Universal ID's
GRK Text Annotations
B2R_p Universal ID's
B2R_p Text Annotations
Ligand Universal ID's
Ligand Text Annotations
arrestin Universal ID's
arrestin Text Annotations
arrestin_bound_receptor Universal ID's
arrestin_bound_receptor Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
ellipse_099_nucleus5_1 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
spatially varying receptor |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
circle |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from Copy of ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus5_1) (copied from ellipse_099_nucleus3_1) (copied from ellipse_099_nucleus1_1) (copied from ellipse_0999 receptor activation only) (copied from ellipse_0999) (copied from compartmental) |
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
circle Universal ID's
circle Text Annotations
Specifications (Species) - ellipse_099_nucleus5_1 go to Simulations
Specifications (Reaction) - ellipse_099_nucleus5_1 go to Simulations
Simulations - ellipse_099_nucleus5_1 go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation4 | 60.0 |
OutputTimeStep 1.0 |
Copy of Simulation4 | 60.0 |
OutputTimeStep 1.0 |
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
ellipse_099_nucleus5_1 Universal ID's
ellipse_099_nucleus5_1 Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry ellipse sep 08 0999 with cyt-n 6:1
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | Cell | 74.97675 [um2] | cyto | |
Volume | Analytical | ECM | 42.52324999999999 [um2] | extra | |
Surface | Cell_ECM_membrane | Cell | ECM | 93.46482136095845 [um] | cyto_mem |
Events
Name | Variable | Rate Expression |
---|
Specifications (Species) - spatially varying receptor go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
Ligand | 1.0 [uM] | 1.0 [um2/s] | extra |
GRK | 0.2 [uM] | 0.1 [um2/s] | cyto |
arrestin | 1.0 [uM] | 1.0 [um2/s] | cyto |
B2R | (100.0 * (1.0 + (0.018 * abs(x)))) [uM] | 0.2 [um2/s] | cyto_mem |
B2R_p | 0.0 [uM] | 0.2 [um2/s] | cyto_mem |
arrestin_bound_receptor | 0.0 [uM] | 0.002 [um2/s] | cyto_mem |
Specifications (Reaction) - spatially varying receptor go to Simulations
Simulations - spatially varying receptor go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation0 | 60.0 |
OutputTimeStep 1.0 |
Copy of Simulation0 | 60.0 |
OutputTimeStep 1.0 |
spatially varying receptor Universal ID's
spatially varying receptor Text Annotations
spatially varying receptor Universal ID's
spatially varying receptor Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry ellipse sep 08 0999 with cyt-n 6:1
(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | Cell | 74.9298128342246 [um2] | cyto | |
Volume | Analytical | ECM | 42.5701871657754 [um2] | extra | |
Surface | Cell_ECM_membrane | Cell | ECM | 93.03794179617861 [um] | cyto_mem |
Events
Name | Variable | Rate Expression |
---|
Specifications (Species) - circle go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
Ligand | 1.0 [uM] | 1.0 [um2/s] | extra |
GRK | 0.2 [uM] | 0.1 [um2/s] | cyto |
arrestin | 1.0 [uM] | 1.0 [um2/s] | cyto |
B2R | (100.0 * (1.0 + (0.018 * abs(x)))) [uM] | 0.2 [um2/s] | cyto_mem |
B2R_p | 0.0 [uM] | 0.2 [um2/s] | cyto_mem |
arrestin_bound_receptor | 0.0 [uM] | 0.002 [um2/s] | cyto_mem |
Specifications (Reaction) - circle go to Simulations
Simulations - circle go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation1 | 60.0 |
OutputTimeStep 1.0 |
circle Universal ID's
circle Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry Geometry3
(Origin: -10.0, -10.0, 0.0; Extent: 20.0, 20.0, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | subdomain1 | 169.16 [um2] | cyto | |
Volume | Analytical | subdomain0 | 230.84 [um2] | extra | |
Surface | subdomain0_subdomain1_membrane | subdomain0 | subdomain1 | 46.24554814672766 [um] | cyto_mem |
Events
Name | Variable | Rate 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 | ellipse_099_nucleus5_1.bngl , spatially varying receptor.bngl , circle.bngl |
SBML | ellipse_099_nucleus5_1.sbml , spatially varying receptor.sbml , circle.sbml |
Matlab | ellipse_099_nucleus5_1.m , spatially varying receptor.m , circle.m |
NFSim XML | ellipse_099_nucleus5_1.xml , spatially varying receptor.xml , circle.xml |