Dashboard

Name - Rangamani Cell 2013 B2R signaling

BioModel ID - 84235320

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
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

Specifications(Species) - ellipse_099_nucleus5_1 See in Dashboard
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]
Specifications(Reaction) - ellipse_099_nucleus5_1 See in Dashboard
Name Reaction Mapping
arrestin binding included
receptor ligand binding included
Simulations - ellipse_099_nucleus5_1 See in Dashboard
Name End Time Output Options
Simulation4 60.0 [s]

OutputTimeStep 1.0

Copy of Simulation4 60.0 [s]

OutputTimeStep 1.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 See in Dashboard
(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

Application - spatially varying receptor

Specifications(Species) - spatially varying receptor See in Dashboard
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]
Specifications(Reaction) - spatially varying receptor See in Dashboard
Name Reaction Mapping
arrestin binding included
receptor ligand binding included
Simulations - spatially varying receptor See in Dashboard
Name End Time Output Options
Simulation0 60.0 [s]

OutputTimeStep 1.0

Copy of Simulation0 60.0 [s]

OutputTimeStep 1.0

Geometry ellipse sep 08 0999 with cyt-n 6:1 See in Dashboard
(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

Application - circle

Specifications(Species) - circle See in Dashboard
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]
Specifications(Reaction) - circle See in Dashboard
Name Reaction Mapping
arrestin binding included
receptor ligand binding included
Simulations - circle See in Dashboard
Name End Time Output Options
Simulation1 60.0 [s]

OutputTimeStep 1.0

Geometry Geometry3 See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
Name Expression
n 350.0[molecules.um-2.uM-1]