Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
PDGFR_cyto_mem+PDGF_extraPDGF_PDGFR |
PDGF_binds_PDGFR
cyto_mem
|
MassAction | PDGFR_cyto_mem+PDGF_extraPDGF_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] |
|
PDGF_PDGFR_Srccyto_memSrc_active_cyto |
Src activation
cyto_mem
|
HMMIrreversible | PDGF_PDGFR_Srccyto_memSrc_active_cyto |
|
|
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] user defined (kcat): (0.01 * n)[molecules.um-2.uM-1.s-1] |
|
Src_active_cytoSrc_cyto |
Src dephosphorylation in cyto
cyto
|
HMMIrreversible | Src_active_cytoSrc_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] |
|
csk_cyto_inactiveCsk_cyto_active |
r0
cyto
|
MassAction | csk_cyto_inactiveCsk_cyto_active |
|
|
reaction rate (J): ((Kf * csk_cyto_inactive) - (Kr * Csk_cyto_active))[uM.s-1]
forward rate constant (Kf): 0.001[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem |
Src association with receptor
cyto_mem
|
MassAction | PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem |
|
|
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] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
extra |
Compartment
(+) (-)
|
|
|
cyto |
Compartment
(+) (-)
|
|
|
cyto_mem |
Membrane
N/A
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
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 | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
compartmental | Deterministic (ODE) Compartmental | cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
ellipse 0999 | Deterministic (ODE) Spatial (2D) | (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
circle | Deterministic (ODE) Spatial (2D) | (copied from ellipse 0999) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1 |
Application - compartmental
Species | Initial Condition | Diffusion Constant | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDGF_extra | 1.0 [uM] | 0.0
[um2/s] PTP |
0.1
[uM]
|
0.0
[um2/s] | Csk_cyto_active |
0.0
[uM]
|
0.0
[um2/s] | Src_active_cyto |
0.0
[uM]
|
0.0
[um2/s] | csk_cyto_inactive |
0.1
[uM]
|
0.0
[um2/s] | Src_cyto |
1.0
[uM]
|
0.0
[um2/s] | PDGFR_cyto_mem |
250.0
[uM]
|
0.0
[um2/s] | PDGF_PDGFR_Srccyto_mem |
0.0
[uM]
|
0.0
[um2/s] | PDGF_PDGFR |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
PDGF_binds_PDGFR | included |
Src activation | included |
Src dephosphorylation in cyto | included |
r0 | included |
Src association with receptor | included |
Name | End Time | Output Options |
---|---|---|
compartmental | 2700.0 [s] |
OutputTimeStep 10.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | cyto_mem |
Application - ellipse 0999
Species | Initial Condition | Diffusion Constant | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDGF_extra | 1.0 [uM] | 10.0
[um2/s] PTP |
0.1
[uM]
|
10.0
[um2/s] | Csk_cyto_active |
0.0
[uM]
|
10.0
[um2/s] | Src_active_cyto |
0.0
[uM]
|
1.0
[um2/s] | csk_cyto_inactive |
0.1
[uM]
|
10.0
[um2/s] | Src_cyto |
1.0
[uM]
|
10.0
[um2/s] | PDGFR_cyto_mem |
250.0
[uM]
|
0.041
[um2/s] | PDGF_PDGFR_Srccyto_mem |
0.0
[uM]
|
0.041
[um2/s] | PDGF_PDGFR |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
PDGF_binds_PDGFR | included |
Src activation | included |
Src dephosphorylation in cyto | included |
r0 | included |
Src association with receptor | included |
Name | End Time | Output Options |
---|---|---|
Simulation0 | 1800.0 [s] |
OutputTimeStep 10.0 |
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 - circle
Species | Initial Condition | Diffusion Constant | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDGF_extra | 1.0 [uM] | 10.0
[um2/s] PTP |
0.1
[uM]
|
10.0
[um2/s] | Csk_cyto_active |
0.0
[uM]
|
10.0
[um2/s] | Src_active_cyto |
0.0
[uM]
|
1.0
[um2/s] | csk_cyto_inactive |
0.1
[uM]
|
10.0
[um2/s] | Src_cyto |
1.0
[uM]
|
10.0
[um2/s] | PDGFR_cyto_mem |
250.0
[uM]
|
0.041
[um2/s] | PDGF_PDGFR_Srccyto_mem |
0.0
[uM]
|
0.041
[um2/s] | PDGF_PDGFR |
0.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
PDGF_binds_PDGFR | included |
Src activation | included |
Src dephosphorylation in cyto | included |
r0 | included |
Src association with receptor | included |
Name | End Time | Output Options |
---|---|---|
Simulation1 | 1800.0 [s] |
OutputTimeStep 10.0 |
Copy of Simulation1 | 300.0 [s] |
OutputTimeStep 10.0 |
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 |
Global Parameters
Name | Expression |
---|---|
n | 900.0[molecules.um-2.uM-1] |
|
|