Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
Reactions | Name | Structure | Kinetics | Depiction |
---|---|---|---|---|
PDGFR_cyto_mem+PDGF_extraPDGF_PDGFR | PDGF_binds_PDGFR | cyto_mem | MassAction | |
PDGF_PDGFR_Srccyto_memSrc_active_cyto | Src activation | cyto_mem | HMMIrreversible | |
Src_active_cytoSrc_cyto | Src dephosphorylation in cyto | cyto | HMMIrreversible | |
csk_cyto_inactiveCsk_cyto_active | r0 | cyto | MassAction | |
PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem | Src association with receptor | cyto_mem | MassAction |
PDGF_binds_PDGFR Universal ID's
PDGF_binds_PDGFR Text Annotations
Src activation Universal ID's
Src activation Text Annotations
Src dephosphorylation in cyto Universal ID's
Src dephosphorylation in cyto Text Annotations
r0 Universal ID's
r0 Text Annotations
Src association with receptor Universal ID's
Src association with receptor Text Annotations
Expressions for PDGF_binds_PDGFR
reaction rate
J
(((Kf * PDGFR_cyto_mem) * PDGF_extra) - (Kr * PDGF_PDGFR)) [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
1.0 [s-1.uM-1]
reverse rate constant
Kr
0.01 [s-1]
Expressions for Src activation
reaction rate
J
((Vmax * PDGF_PDGFR_Srccyto_mem) / (Km + PDGF_PDGFR_Srccyto_mem)) [molecules.um-2.s-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
Km (1/2 max)
Km
0.1 [molecules.um-2]
max reaction rate
Vmax
(kcat * PTP) [molecules.um-2.s-1]
local
kcat
(0.01 * n) [molecules.um-2.uM-1.s-1]
global
n
900.0 [molecules.um-2.uM-1]
Expressions for Src dephosphorylation in cyto
reaction rate
J
((Vmax * Src_active_cyto) / (Km + Src_active_cyto)) [uM.s-1]
Km (1/2 max)
Km
1.5 [uM]
max reaction rate
Vmax
(0.3 * Csk_cyto_active) [uM.s-1]
Expressions for r0
reaction rate
J
((Kf * csk_cyto_inactive) - (Kr * Csk_cyto_active)) [uM.s-1]
global
n
900.0 [molecules.um-2.uM-1]
forward rate constant
Kf
0.001 [s-1]
reverse rate constant
Kr
0.0 [s-1]
Expressions for Src association with receptor
reaction rate
J
(((Kf * PDGF_PDGFR) * Src_cyto) - (Kr * PDGF_PDGFR_Srccyto_mem)) [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
1.0 [s-1.uM-1]
reverse rate constant
Kr
0.1 [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 |
---|---|---|---|
PDGFR_cyto_mem | cyto_mem | ||
PDGF_extra | extra | ||
PTP | cyto | ||
Csk_cyto_active | cyto | ||
PDGF_PDGFR_Srccyto_mem | cyto_mem | ||
Src_active_cyto | cyto | ||
csk_cyto_inactive | cyto | ||
Src_cyto | cyto | ||
PDGF_PDGFR | cyto_mem |
PDGFR_cyto_mem Universal ID's
PDGFR_cyto_mem Text Annotations
PDGF_extra Universal ID's
PDGF_extra Text Annotations
PTP Universal ID's
PTP Text Annotations
Csk_cyto_active Universal ID's
Csk_cyto_active Text Annotations
PDGF_PDGFR_Srccyto_mem Universal ID's
PDGF_PDGFR_Srccyto_mem Text Annotations
Src_active_cyto Universal ID's
Src_active_cyto Text Annotations
csk_cyto_inactive Universal ID's
csk_cyto_inactive Text Annotations
Src_cyto Universal ID's
Src_cyto Text Annotations
PDGF_PDGFR Universal ID's
PDGF_PDGFR Text Annotations
Applications
Name | Properties | Math Type | Annotation |
---|---|---|---|
compartmental |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
ellipse 0999 |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
circle |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (2D) | (copied from ellipse 0999) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
compartmental Universal ID's
compartmental Text Annotations
ellipse 0999 Universal ID's
ellipse 0999 Text Annotations
circle Universal ID's
circle Text Annotations
Specifications (Species) - compartmental go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
PDGF_extra | 1.0 [uM] | 0.0 [um2/s] | extra |
PTP | 0.1 [uM] | 0.0 [um2/s] | cyto |
Csk_cyto_active | 0.0 [uM] | 0.0 [um2/s] | cyto |
Src_active_cyto | 0.0 [uM] | 0.0 [um2/s] | cyto |
csk_cyto_inactive | 0.1 [uM] | 0.0 [um2/s] | cyto |
Src_cyto | 1.0 [uM] | 0.0 [um2/s] | cyto |
PDGFR_cyto_mem | 250.0 [uM] | 0.0 [um2/s] | cyto_mem |
PDGF_PDGFR_Srccyto_mem | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
PDGF_PDGFR | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - compartmental go to Simulations
Simulations - compartmental go to Specifications
Name | End Time | Output Options |
---|---|---|
compartmental | 2700.0 |
OutputTimeStep 10.0 |
compartmental Universal ID's
compartmental Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry non-spatial969899354
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | cyto_mem |
Events
Name | Variable | Rate Expression |
---|
Specifications (Species) - ellipse 0999 go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
PDGF_extra | 1.0 [uM] | 10.0 [um2/s] | extra |
PTP | 0.1 [uM] | 10.0 [um2/s] | cyto |
Csk_cyto_active | 0.0 [uM] | 10.0 [um2/s] | cyto |
Src_active_cyto | 0.0 [uM] | 1.0 [um2/s] | cyto |
csk_cyto_inactive | 0.1 [uM] | 10.0 [um2/s] | cyto |
Src_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
PDGFR_cyto_mem | 250.0 [uM] | 0.041 [um2/s] | cyto_mem |
PDGF_PDGFR_Srccyto_mem | 0.0 [uM] | 0.041 [um2/s] | cyto_mem |
PDGF_PDGFR | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - ellipse 0999 go to Simulations
Simulations - ellipse 0999 go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation0 | 1800.0 |
OutputTimeStep 10.0 |
ellipse 0999 Universal ID's
ellipse 0999 Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry ellipse sep 08 0999
(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) - circle go to Simulations
Species | Initial Condition | Diffusion Constant | Structure |
---|---|---|---|
PDGF_extra | 1.0 [uM] | 10.0 [um2/s] | extra |
PTP | 0.1 [uM] | 10.0 [um2/s] | cyto |
Csk_cyto_active | 0.0 [uM] | 10.0 [um2/s] | cyto |
Src_active_cyto | 0.0 [uM] | 1.0 [um2/s] | cyto |
csk_cyto_inactive | 0.1 [uM] | 10.0 [um2/s] | cyto |
Src_cyto | 1.0 [uM] | 10.0 [um2/s] | cyto |
PDGFR_cyto_mem | 250.0 [uM] | 0.041 [um2/s] | cyto_mem |
PDGF_PDGFR_Srccyto_mem | 0.0 [uM] | 0.041 [um2/s] | cyto_mem |
PDGF_PDGFR | 0.0 [uM] | 0.0 [um2/s] | cyto_mem |
Specifications (Reaction) - circle go to Simulations
Simulations - circle go to Specifications
Name | End Time | Output Options |
---|---|---|
Simulation1 | 1800.0 |
OutputTimeStep 10.0 |
Copy of Simulation1 | 300.0 |
OutputTimeStep 10.0 |
circle Universal ID's
circle Text Annotations
circle Universal ID's
circle Text Annotations
Assignments
Name | Variable | Assignment Function Expression |
---|
Events
Name | Trigger Type | Variable Assignment |
---|
Geometry circle sep 08
(Origin: -5.0, -5.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | Cell | 78.39 [um2] | cyto | |
Volume | Analytical | ECM | 5.4125000000000005 [um2] | extra | |
Surface | Cell_ECM_membrane | Cell | ECM | 7.704697811481667 [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 | compartmental.bngl , ellipse 0999.bngl , circle.bngl |
SBML | compartmental.sbml , ellipse 0999.sbml , circle.sbml |
Matlab | compartmental.m , ellipse 0999.m , circle.m |
NFSim XML | compartmental.xml , ellipse 0999.xml , circle.xml |