Reaction Diagram
Physiology
Universal ID's | Text Annotations |
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|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
B2R_p+arrestinarrestin_bound_receptor |
arrestin binding
cyto_mem
|
MassAction | B2R_p+arrestinarrestin_bound_receptor |
|
|
reaction rate (J): (((Kf * B2R_p) * arrestin) - (Kr * arrestin_bound_receptor))[molecules.um-2.s-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] |
|
Ligand+GRK+B2RB2R_p |
receptor ligand binding
cyto_mem
|
MassAction | Ligand+GRK+B2RB2R_p |
|
|
reaction rate (J): ((((Kf * Ligand) * GRK) * B2R) - (Kr * B2R_p))[molecules.um-2.s-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] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
extra |
Compartment
(+) (-)
|
|
|
cyto |
Compartment
(+) (-)
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|
|
cyto_mem |
Membrane
N/A
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|
|
Name | Structure | BioNetGen Definition |
---|---|---|
B2R | cyto_mem | |
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|
|
GRK | cyto | |
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|
|
B2R_p | cyto_mem | |
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|
|
Ligand | extra | |
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|
|
arrestin | cyto | |
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|
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arrestin_bound_receptor | cyto_mem | |
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Name | Text Annotations | BioNetGen Definition |
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Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
ellipse_099_nucleus5_1 | 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 | 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 | 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) |
Application - ellipse_099_nucleus5_1
Species | Initial Condition | Diffusion Constant | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ligand | 1.0 [uM] | 1.0
[um2/s] GRK |
0.2
[uM]
|
0.1
[um2/s] | arrestin |
1.0
[uM]
|
1.0
[um2/s] | B2R |
100.0
[uM]
|
0.2
[um2/s] | B2R_p |
0.0
[uM]
|
0.2
[um2/s] | arrestin_bound_receptor |
0.0
[uM]
|
0.002
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
arrestin binding | included |
receptor ligand binding | included |
Name | End Time | Output Options |
---|---|---|
Simulation4 | 60.0 [s] |
OutputTimeStep 1.0 |
Copy of Simulation4 | 60.0 [s] |
OutputTimeStep 1.0 |
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 |
Application - spatially varying receptor
Species | Initial Condition | Diffusion Constant | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ligand | 1.0 [uM] | 1.0
[um2/s] GRK |
0.2
[uM]
|
0.1
[um2/s] | arrestin |
1.0
[uM]
|
1.0
[um2/s] | B2R |
(100.0 * (1.0 + (0.018 * abs(x))))
[uM]
|
0.2
[um2/s] | B2R_p |
0.0
[uM]
|
0.2
[um2/s] | arrestin_bound_receptor |
0.0
[uM]
|
0.002
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
arrestin binding | included |
receptor ligand binding | included |
Name | End Time | Output Options |
---|---|---|
Simulation0 | 60.0 [s] |
OutputTimeStep 1.0 |
Copy of Simulation0 | 60.0 [s] |
OutputTimeStep 1.0 |
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 |
Application - circle
Species | Initial Condition | Diffusion Constant | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ligand | 1.0 [uM] | 1.0
[um2/s] GRK |
0.2
[uM]
|
0.1
[um2/s] | arrestin |
1.0
[uM]
|
1.0
[um2/s] | B2R |
(100.0 * (1.0 + (0.018 * abs(x))))
[uM]
|
0.2
[um2/s] | B2R_p |
0.0
[uM]
|
0.2
[um2/s] | arrestin_bound_receptor |
0.0
[uM]
|
0.002
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
arrestin binding | included |
receptor ligand binding | included |
Name | End Time | Output Options |
---|---|---|
Simulation1 | 60.0 [s] |
OutputTimeStep 1.0 |
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 |
Global Parameters
Name | Expression |
---|---|
n | 350.0[molecules.um-2.uM-1] |
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|