Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| GDIuuco_Rac1cgTpGDIuuco+Rac1cgTp | R20 | Cytoplasm | GeneralKinetics | |
| Rac1cgDpRac1ggDp | R14 | Granules | GeneralKinetics | |
| Rac1mgDpRac1mgTp | R15 | Membrane | GeneralKinetics | |
| Rac1cgDpRac1mgDp | R11 | Membrane | GeneralKinetics | |
| Rac1mgTpRac1cgTp | R13 | Membrane | GeneralKinetics | |
| GDIpuco+Rac1cgDpGDIpuco_Rac1cgDp | R21 | Cytoplasm | GeneralKinetics | |
| Rac1ggDpRac1ggTp | R31 | Granules | GeneralKinetics | |
| GDIpuco+Rac1cgTpGDIpuco_Rac1cgTp | R35 | Cytoplasm | GeneralKinetics | |
| Rac1cgDpRac1cgTp | R17 | Cytoplasm | GeneralKinetics | |
| GDIuuco+Rac1cgDpGDIuuco_Rac1cgDp | R18 | Cytoplasm | GeneralKinetics | |
| PLDmaTrashm | R41 | Membrane | GeneralKinetics | |
| PLDgiPLDci | R1 | Granules | GeneralKinetics | |
| GDIuucoGDIuumo | R2 | Membrane | GeneralKinetics | |
| GDIuucoGDIuugo | R4 | Granules | GeneralKinetics | |
| GDIpucoGDIpugo | R5 | Granules | GeneralKinetics | |
| pakucpakpc | R6 | Cytoplasm | GeneralKinetics | |
| GDIuucoGDIpuco | R7 | Cytoplasm | GeneralKinetics | |
| NonGlucLcGlucLc | R9 | Cytoplasm | GeneralKinetics | |
| GDIpucoGDIpumo | R3 | Membrane | GeneralKinetics | |
| Rac1cgTpRac1ggTp | R30 | Granules | GeneralKinetics | |
| PLDmiTrashm | R36 | Membrane | GeneralKinetics | |
| PLDciPLDmi | R22 | Membrane | GeneralKinetics | |
| PLDmiPLDma | R37 | Membrane | GeneralKinetics |
R20 Universal ID's
R20 Text Annotations
R14 Universal ID's
R14 Text Annotations
R15 Universal ID's
R15 Text Annotations
R11 Universal ID's
R11 Text Annotations
R13 Universal ID's
R13 Text Annotations
R21 Universal ID's
R21 Text Annotations
R31 Universal ID's
R31 Text Annotations
R35 Universal ID's
R35 Text Annotations
R17 Universal ID's
R17 Text Annotations
R18 Universal ID's
R18 Text Annotations
R41 Universal ID's
R41 Text Annotations
R1 Universal ID's
R1 Text Annotations
R2 Universal ID's
R2 Text Annotations
R4 Universal ID's
R4 Text Annotations
R5 Universal ID's
R5 Text Annotations
R6 Universal ID's
R6 Text Annotations
R7 Universal ID's
R7 Text Annotations
R9 Universal ID's
R9 Text Annotations
R3 Universal ID's
R3 Text Annotations
R30 Universal ID's
R30 Text Annotations
R36 Universal ID's
R36 Text Annotations
R22 Universal ID's
R22 Text Annotations
R37 Universal ID's
R37 Text Annotations
Expressions for R20
reaction rate
J
((koffT_3d_R1 * GDIuuco_Rac1cgTp) - (konT_3d_R1 * GDIuuco * Rac1cgTp)) [uM.s-1]
global
koffT_3d_R1
koff1_3d_R1 [tbd]
global
konT_3d_R1
(koffT_3d_R1 / KDT_3d_R1) [tbd]
Expressions for R14
reaction rate
J
(sbmlRateFactor * ((rateParam17 * Rac1cgDp) - (rateParam18 * Rac1ggDp * Rac1ggDp_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam1
(fusRate * pmp0) [tbd]
global
rateParam17
(konGr_R1 * pmpGr) [tbd]
global
rateParam18
(koffGrD_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1ggDp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R15
reaction rate
J
(sbmlRateFactor * ((rateParam21 * Rac1mgDp * Rac1mgDp_ConcFactor) - (rateParam22 * Rac1mgTp * Rac1mgTp_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
global
rateParam21
(gef_R1 * pmp0) [tbd]
global
rateParam22
(gap_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1mgDp_ConcFactor
1.6611295681063123E-6 [1000]
local
Rac1mgTp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R11
reaction rate
J
(sbmlRateFactor * ((rateParam13 * Rac1cgDp) - (rateParam14 * Rac1mgDp * Rac1mgDp_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam1
(fusRate * pmp0) [tbd]
global
rateParam13
(konM_R1 * pmp) [tbd]
global
rateParam14
(koffMD_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1mgDp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R13
reaction rate
J
(sbmlRateFactor * ((rateParam16 * Rac1mgTp * Rac1mgTp_ConcFactor) - (rateParam15 * Rac1cgTp)) / KMOLE) [molecules.um-2.s-1]
global
rateParam1
(fusRate * pmp0) [tbd]
global
rateParam15
(konM_R1 * pmp) [tbd]
global
rateParam16
(koffMT_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1mgTp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R21
reaction rate
J
((rateParam27 * GDIpuco * Rac1cgDp) - (koffD_3d_R1 * GDIpuco_Rac1cgDp)) [uM.s-1]
global
koffD_3d_R1
koff1_3d_R1 [tbd]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
global
rateParam27
(psGdifactor_R1 * konD_3d_R1) [tbd]
Expressions for R31
reaction rate
J
(sbmlRateFactor * ((rateParam23 * Rac1ggDp * Rac1ggDp_ConcFactor) - (rateParam24 * Rac1ggTp * Rac1ggTp_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
global
rateParam23
(gef_Gr_R1 * pmp0) [tbd]
global
rateParam24
(gap_Gr_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1ggDp_ConcFactor
1.6611295681063123E-6 [1000]
local
Rac1ggTp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R35
reaction rate
J
((rateParam28 * GDIpuco * Rac1cgTp) - (koffT_3d_R1 * GDIpuco_Rac1cgTp)) [uM.s-1]
global
koffT_3d_R1
koff1_3d_R1 [tbd]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
global
rateParam28
(psGdifactor_R1 * konT_3d_R1) [tbd]
Expressions for R17
reaction rate
J
((gef_Cyt_R1 * Rac1cgDp) - (gap_Cyt_R1 * Rac1cgTp)) [uM.s-1]
global
gef_Cyt_R1
0.0 [tbd]
global
gap_Cyt_R1
(4.0 * gap_R1) [tbd]
Expressions for R18
reaction rate
J
((konD_3d_R1 * GDIuuco * Rac1cgDp) - (koffD_3d_R1 * GDIuuco_Rac1cgDp)) [uM.s-1]
global
koffD_3d_R1
koff1_3d_R1 [tbd]
global
konD_3d_R1
(koffD_3d_R1 / KDD_3d_R1) [tbd]
Expressions for R41
reaction rate
J
(sbmlRateFactor * rateParam3 * PLDma * PLDma_ConcFactor / KMOLE) [molecules.um-2.s-1]
global
rateParam3
(7.2 * fusRate * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
PLDma_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R1
reaction rate
J
(sbmlRateFactor * rateParam1 * PLDgi * PLDgi_ConcFactor / KMOLE) [molecules.um-2.s-1]
global
rateParam1
(fusRate * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
PLDgi_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R2
reaction rate
J
(sbmlRateFactor * ((rateParam5 * GDIuuco) - (rateParam4 * GDIuumo * GDIuumo_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam4
(koffM_G * pmp0) [tbd]
global
rateParam5
(konM_G * pmp) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
GDIuumo_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R4
reaction rate
J
(sbmlRateFactor * ((rateParam9 * GDIuuco) - (rateParam8 * GDIuugo * GDIuugo_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam8
(koffGr_G * pmp0) [tbd]
global
rateParam9
(konGr_G * pmp) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
GDIuugo_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R5
reaction rate
J
(sbmlRateFactor * ((rateParam9 * GDIpuco) - (rateParam8 * GDIpugo * GDIpugo_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam8
(koffGr_G * pmp0) [tbd]
global
rateParam9
(konGr_G * pmp) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
GDIpugo_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R6
reaction rate
J
((P_pak * pakuc) - (dP_pak * pakpc)) [uM.s-1]
global
dP_pak
0.1 [tbd]
global
P_pak
(alphaPak * gtpm_C2 / KD_pak_C2) [tbd]
Expressions for R7
reaction rate
J
((P_G_s * GDIuuco) - (dP_G_s * GDIpuco)) [uM.s-1]
global
P_G_s
(actPak * coefP_G_s) [tbd]
global
dP_G_s
(0.1 * coefP_G_s) [tbd]
Expressions for R9
reaction rate
J
((rateParam12 * NonGlucLc) - (koffGluc * GlucLc)) [uM.s-1]
global
koffGluc
0.001 [tbd]
global
rateParam1
(fusRate * pmp0) [tbd]
global
rateParam12
(konGluc * gluc0) [tbd]
Expressions for R3
reaction rate
J
(sbmlRateFactor * ((rateParam5 * GDIpuco) - (rateParam4 * GDIpumo * GDIpumo_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam4
(koffM_G * pmp0) [tbd]
global
rateParam5
(konM_G * pmp) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
GDIpumo_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R30
reaction rate
J
(sbmlRateFactor * ((rateParam19 * Rac1cgTp) - (rateParam20 * Rac1ggTp * Rac1ggTp_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
rateParam1
(fusRate * pmp0) [tbd]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
global
rateParam19
(konGr_R1 * pmpGr) [tbd]
global
rateParam20
(koffGrT_R1 * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
Rac1ggTp_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R36
reaction rate
J
(sbmlRateFactor * rateParam3 * PLDmi * PLDmi_ConcFactor / KMOLE) [molecules.um-2.s-1]
global
rateParam3
(7.2 * fusRate * pmp0) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
PLDmi_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R22
reaction rate
J
(sbmlRateFactor * rateParam2 * PLDci / KMOLE) [molecules.um-2.s-1]
global
rateParam2
(1.0E10 * fusRate * pmpGr) [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Expressions for R37
reaction rate
J
(sbmlRateFactor * ((actPLD * PLDmi * PLDmi_ConcFactor) - (inacPLD * PLDma * PLDma_ConcFactor)) / KMOLE) [molecules.um-2.s-1]
global
actPLD
0.1 [tbd]
global
inacPLD
0.1 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
0.0 [1]
local
PLDma_ConcFactor
1.6611295681063123E-6 [1000]
local
PLDmi_ConcFactor
1.6611295681063123E-6 [1000]
local
sbmlRateFactor
9.999999999999999E14 [1.0E-15]
Structures
| Name | Type | Electrical |
|---|---|---|
| Granules | Membrane | inGranules(+) Cytoplasm(-) |
| Membrane | Membrane | Cytoplasm(+) Extracellular(-) |
| Extracellular | Compartment | (+) (-) |
| Cytoplasm | Compartment | (+) (-) |
| inGranules | Compartment | (+) (-) |
Granules Universal ID's
Granules Text Annotations
Membrane Universal ID's
Membrane Text Annotations
Extracellular Universal ID's
Extracellular Text Annotations
Cytoplasm Universal ID's
Cytoplasm Text Annotations
inGranules Universal ID's
inGranules Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| GDIuuco_Rac1cgTp | Cytoplasm | ||
| GDIuumo_Rac1mgDp | Membrane | ||
| GDIuumo_Rac1mgTp | Membrane | ||
| Rac1mgDp | Membrane | ||
| Rac1mgTp | Membrane | ||
| pakuc | Cytoplasm | ||
| NonGlucLc | Cytoplasm | ||
| glucc | Cytoplasm | ||
| GlucLc | Cytoplasm | ||
| PLDgi | Granules | ||
| Trashm | Membrane | ||
| PLDci | Cytoplasm | ||
| GDIuumo | Membrane | ||
| GDIpumo | Membrane | ||
| GDIuugo | Granules | ||
| GDIpugo | Granules | ||
| pakpc | Cytoplasm | ||
| Rac1cgTp | Cytoplasm | ||
| Rac1ggDp | Granules | ||
| GDIpuco_Rac1cgDp | Cytoplasm | ||
| PLDmi | Membrane | ||
| Rac1ggTp | Granules | ||
| GDIpuco_Rac1cgTp | Cytoplasm | ||
| PLDma | Membrane | ||
| GDIuuco | Cytoplasm | ||
| GDIpuco | Cytoplasm | ||
| Rac1cgDp | Cytoplasm | ||
| GDIuuco_Rac1cgDp | Cytoplasm |
GDIuuco_Rac1cgTp Universal ID's
GDIuuco_Rac1cgTp Text Annotations
GDIuumo_Rac1mgDp Universal ID's
GDIuumo_Rac1mgDp Text Annotations
GDIuumo_Rac1mgTp Universal ID's
GDIuumo_Rac1mgTp Text Annotations
Rac1mgDp Universal ID's
Rac1mgDp Text Annotations
Rac1mgTp Universal ID's
Rac1mgTp Text Annotations
pakuc Universal ID's
pakuc Text Annotations
NonGlucLc Universal ID's
NonGlucLc Text Annotations
glucc Universal ID's
glucc Text Annotations
GlucLc Universal ID's
GlucLc Text Annotations
PLDgi Universal ID's
PLDgi Text Annotations
Trashm Universal ID's
Trashm Text Annotations
PLDci Universal ID's
PLDci Text Annotations
GDIuumo Universal ID's
GDIuumo Text Annotations
GDIpumo Universal ID's
GDIpumo Text Annotations
GDIuugo Universal ID's
GDIuugo Text Annotations
GDIpugo Universal ID's
GDIpugo Text Annotations
pakpc Universal ID's
pakpc Text Annotations
Rac1cgTp Universal ID's
Rac1cgTp Text Annotations
Rac1ggDp Universal ID's
Rac1ggDp Text Annotations
GDIpuco_Rac1cgDp Universal ID's
GDIpuco_Rac1cgDp Text Annotations
PLDmi Universal ID's
PLDmi Text Annotations
Rac1ggTp Universal ID's
Rac1ggTp Text Annotations
GDIpuco_Rac1cgTp Universal ID's
GDIpuco_Rac1cgTp Text Annotations
PLDma Universal ID's
PLDma Text Annotations
GDIuuco Universal ID's
GDIuuco Text Annotations
GDIpuco Universal ID's
GDIpuco Text Annotations
Rac1cgDp Universal ID's
Rac1cgDp Text Annotations
GDIuuco_Rac1cgDp Universal ID's
GDIuuco_Rac1cgDp Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| psGDIfactor_R1=0.1; find SS with no gluc |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from C:\Documents and Settings\cfalkenberg\.vcell\BioNetGen\vcell_bng_1222\vcell_bng_1222_Compartmental) |
| psGDIfactor_R1=0.1+change konM+coefonGR; transient studies |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from psGDIfactor_R1=0.1; transient studies) (copied from psGDIfactor_R1=0; transient studies) (copied from C:\Documents and Settings\cfalkenberg\.vcell\BioNetGen\vcell_bng_1222\vcell_bng_1222_Compartmental) |
psGDIfactor_R1=0.1; find SS with no gluc Universal ID's
psGDIfactor_R1=0.1; find SS with no gluc Text Annotations
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Universal ID's
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Text Annotations
Specifications (Species) - psGDIfactor_R1=0.1; find SS with no gluc go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| GDIuuco_Rac1cgTp | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| pakuc | 0.5 [uM] | 0.0 [um2/s] | Cytoplasm |
| NonGlucLc | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| glucc | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| GlucLc | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| PLDci | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| pakpc | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| Rac1cgTp | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco_Rac1cgDp | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco_Rac1cgTp | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIuuco | 0.07 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco | 0.06 [uM] | 0.0 [um2/s] | Cytoplasm |
| Rac1cgDp | 0.0427 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIuuco_Rac1cgDp | 0.11 [uM] | 0.0 [um2/s] | Cytoplasm |
| PLDgi | 2.7777777777777777 [uM] | 0.0 [um2/s] | Granules |
| GDIuugo | 0.0 [uM] | 0.0 [um2/s] | Granules |
| GDIpugo | 0.0 [uM] | 0.0 [um2/s] | Granules |
| Rac1ggDp | 0.0 [uM] | 0.0 [um2/s] | Granules |
| Rac1ggTp | 0.0 [uM] | 0.0 [um2/s] | Granules |
| GDIuumo_Rac1mgDp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| GDIuumo_Rac1mgTp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| Rac1mgDp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| Rac1mgTp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| Trashm | 601999.9999999999 [uM] | 0.0 [um2/s] | Membrane |
| GDIuumo | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| GDIpumo | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| PLDmi | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| PLDma | 0.0 [uM] | 0.0 [um2/s] | Membrane |
Specifications (Reaction) - psGDIfactor_R1=0.1; find SS with no gluc go to Simulations
| Name | Enabled? |
|---|---|
| R20 | included |
| R14 | included |
| R15 | included |
| R11 | included |
| R13 | included |
| R21 | included |
| R31 | included |
| R35 | included |
| R17 | included |
| R18 | included |
| R41 | included |
| R1 | included |
| R2 | included |
| R4 | included |
| R5 | included |
| R6 | included |
| R7 | included |
| R9 | included |
| R3 | included |
| R30 | included |
| R36 | included |
| R22 | included |
| R37 | included |
Simulations - psGDIfactor_R1=0.1; find SS with no gluc go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| find SS | 5000.0 |
KeepEvery 500 KeepAtMost 1000 |
psGDIfactor_R1=0.1; find SS with no gluc Universal ID's
psGDIfactor_R1=0.1; find SS with no gluc Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| event0 | on condition: (t > tgluc) | glucc --> 20000.0, actPak --> (0.116 + (0.116 * changePsGDI)), gef_R1 --> (gef0_R1 + (((gef0_R1 * coef_gef) - gef0_R1) * change_gef_only)) |
Geometry Compartmental1146174258
(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 | Membrane |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| GDIuuco_Rac1cgTp | 1.6563957705568633E-4 [uM] | 0.0 [um2/s] | Cytoplasm |
| pakuc | 0.11240310077519382 [uM] | 0.0 [um2/s] | Cytoplasm |
| NonGlucLc | 1.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| glucc | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| GlucLc | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| PLDci | 0.0 [uM] | 0.0 [um2/s] | Cytoplasm |
| pakpc | 0.38759689922480617 [uM] | 0.0 [um2/s] | Cytoplasm |
| Rac1cgTp | 3.622850570650371E-7 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco_Rac1cgDp | 0.011582451335819324 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco_Rac1cgTp | 1.9214186222063993E-5 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIuuco | 0.05943702212607566 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIpuco | 0.06894692985331065 [uM] | 0.0 [um2/s] | Cytoplasm |
| Rac1cgDp | 2.183880698389099E-4 [uM] | 0.0 [um2/s] | Cytoplasm |
| GDIuuco_Rac1cgDp | 0.09984874292151663 [uM] | 0.0 [um2/s] | Cytoplasm |
| PLDgi | 2.7777777777777777 [uM] | 0.0 [um2/s] | Granules |
| GDIuugo | 0.0 [uM] | 0.0 [um2/s] | Granules |
| GDIpugo | 0.0 [uM] | 0.0 [um2/s] | Granules |
| Rac1ggDp | 4.770672010383799 [uM] | 0.0 [um2/s] | Granules |
| Rac1ggTp | 0.0031608535148760723 [uM] | 0.0 [um2/s] | Granules |
| GDIuumo_Rac1mgDp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| GDIuumo_Rac1mgTp | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| Rac1mgDp | 4.554384740079095 [uM] | 0.0 [um2/s] | Membrane |
| Rac1mgTp | 2.9446676851097253 [uM] | 0.0 [um2/s] | Membrane |
| Trashm | 601999.9999999999 [uM] | 0.0 [um2/s] | Membrane |
| GDIuumo | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| GDIpumo | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| PLDmi | 0.0 [uM] | 0.0 [um2/s] | Membrane |
| PLDma | 0.0 [uM] | 0.0 [um2/s] | Membrane |
Specifications (Reaction) - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies go to Simulations
| Name | Enabled? |
|---|---|
| R20 | included |
| R14 | included |
| R15 | included |
| R11 | included |
| R13 | included |
| R21 | included |
| R31 | included |
| R35 | included |
| R17 | included |
| R18 | included |
| R41 | included |
| R1 | included |
| R2 | included |
| R4 | included |
| R5 | included |
| R6 | included |
| R7 | included |
| R9 | included |
| R3 | included |
| R30 | included |
| R36 | included |
| R22 | included |
| R37 | included |
Simulations - psGDIfactor_R1=0.1+change konM+coefonGR; transient studies go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| effect of ps-gdi only | 4000.0 |
KeepEvery 500 KeepAtMost 1000 |
| effect of increase konM over t; coef on Gr=0; coef pld0=1.5 | 4000.0 |
KeepEvery 500 KeepAtMost 1000 |
| effect of increase konM and konGr: coef on Gr=1.5; coef pld0=[1,1.5,2] | 4000.0 |
KeepEvery 500 KeepAtMost 1000 |
| effect of increase konM and konGr: coef on Gr=2; coef pld0=[1,1.5,2] | 4000.0 |
KeepEvery 500 KeepAtMost 1000 |
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Universal ID's
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Text Annotations
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Universal ID's
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Text Annotations
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Universal ID's
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Text Annotations
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Universal ID's
psGDIfactor_R1=0.1+change konM+coefonGR; transient studies Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|---|---|
| event0 | on condition: (t > tgluc) | glucc --> 20000.0, actPak --> (0.116 + (0.116 * changePsGDI)), gef_R1 --> (gef0_R1 + (((gef0_R1 * coef_gef) - gef0_R1) * change_gef_only)) |
Geometry Compartmental1146174258
(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 | Membrane |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| SfRAVolNIH3T3 | 0.524[tbd] |
| SfRAVol | 0.587[tbd] |
| toexport2 | 1.0E-12[tbd] |
| FR | 1.0[tbd] |
| fusRate | ((1.67E-5 * (t >= (600.0 + tgluc))) + (2.779166666666666E-7 * (t > (60.0 + tgluc)) * (t < (300.0 + tgluc)) * ( - (60.0 + tgluc) + t)) + ((t >= (300.0 + tgluc)) * (t < (600.0 + tgluc)) * (6.67E-5 - (1.6666666666666668E-7 * ( - (300.0 + tgluc) + t)))))[tbd] |
| coef_on_Gr | 1.0[tbd] |
| actPLD | 0.1[tbd] |
| inacPLD | 0.1[tbd] |
| actPak | 0.116[tbd] |
| coefP_G_s | 0.02[tbd] |
| changePsGDI | 0.0[tbd] |
| gluc0 | glucc[tbd] |
| KDM_G | 10.0[tbd] |
| koffM_G | 1.0[tbd] |
| KDMp_G | 0.1[tbd] |
| koffMp_G | 0.1[tbd] |
| KDGr_G | 10.0[tbd] |
| koffGr_G | 1.0[tbd] |
| KDGrp_G | 0.1[tbd] |
| koffGrp_G | 0.1[tbd] |
| kon_Pak_G | 1.0[tbd] |
| koff_Pak_G | 1.0[tbd] |
| alphaPak | 1.0[tbd] |
| KD_pak_C2 | 2.9[tbd] |
| KD_pak_R1 | 0.7[tbd] |
| koffPak_C2 | 1.0[tbd] |
| koffPak_R1 | 1.0[tbd] |
| gtpm_C2 | 1.0[tbd] |
| gtpm_R1 | 1.0[tbd] |
| dP_pak | 0.1[tbd] |
| P_R1 | 0.0[tbd] |
| dP_R1 | 0.0[tbd] |
| pld0 | (changekonM * PLDma / (0.1 + PLDma))[tbd] |
| koffMD_R1 | 0.1496[tbd] |
| koffMT_R1 | 0.011[tbd] |
| koffGrD_R1 | 0.1496[tbd] |
| koffGrT_R1 | 0.011[tbd] |
| gef_R1 | gef0_R1[tbd] |
| gef_Cyt_R1 | 0.0[tbd] |
| gef_Gr_R1 | 0.01[tbd] |
| KDD_2d_R1 | 1.0[tbd] |
| KDT_2d_R1 | 1.0[tbd] |
| koff1_2d_R1 | 0.0[tbd] |
| phospFactor2_R1 | 1.0[tbd] |
| koff1P_2d_R1 | 0.0[tbd] |
| geomFac25_R1 | 1.0[tbd] |
| koff1_25d_R1 | 0.0[tbd] |
| phospFactor25_R1 | 1.0[tbd] |
| koff1P_25d_R1 | 0.0[tbd] |
| alpha_R1 | 1.0[tbd] |
| koff1_3d_R1 | 0.044[tbd] |
| phospFactor3_R1 | 1.0[tbd] |
| koff1P_3d_R1 | 0.044[tbd] |
| koffMD_gG_R1 | 0.1496[tbd] |
| koffMT_gG_R1 | 0.1496[tbd] |
| konM_gG_R1 | 0.0[tbd] |
| konE_R1 | 0.1[tbd] |
| koffE_R1 | 0.1[tbd] |
| pGdifactor_R1 | 0.1[tbd] |
| psGdifactor_R1 | 0.1[tbd] |
| konGluc | 1.0E-7[tbd] |
| koffGluc | 0.001[tbd] |
| Vol2Sfc | (1.0 / SfRAVol)[tbd] |
| SfcGr | 4.230317273795534[tbd] |
| VolGr | 0.23501762632197415[tbd] |
| VolCyt2SfcGr | (1.0 / SfcGr)[tbd] |
| toexportM | 0.0019083969465648854[tbd] |
| toexport1 | (0.001 * Vol2Sfc)[tbd] |
| toexport1gr | (0.001 * VolCyt2SfcGr)[tbd] |
| pmp | (toexportM * toexport2)[tbd] |
| pmp0 | toexport2[tbd] |
| pmpGr | (toexportM * toexport2)[tbd] |
| P_G_s | (actPak * coefP_G_s)[tbd] |
| dP_G_s | (0.1 * coefP_G_s)[tbd] |
| konM_G | 0.0[tbd] |
| konMp_G | 0.0[tbd] |
| konGr_G | 0.0[tbd] |
| konGrp_G | 0.0[tbd] |
| konPak_C2 | (koffPak_C2 / KD_pak_C2)[tbd] |
| konPak_R1 | (koffPak_R1 / KD_pak_R1)[tbd] |
| P_pak | (alphaPak * gtpm_C2 / KD_pak_C2)[tbd] |
| konM_R1 | (2.84 * (1.0 + (coef_pld0 * pld0)))[tbd] |
| konGr_R1 | (2.84 * (1.0 + (coef_on_Gr * pld0)))[tbd] |
| gap_R1 | (1.5455950540958268 * gef0_R1)[tbd] |
| gap_Cyt_R1 | (4.0 * gap_R1)[tbd] |
| gap_Gr_R1 | gap_R1[tbd] |
| koffD_2d_R1 | koff1_2d_R1[tbd] |
| koffT_2d_R1 | koff1_2d_R1[tbd] |
| konD_2d_R1 | (koffD_2d_R1 / KDD_2d_R1)[tbd] |
| konT_2d_R1 | (koffT_2d_R1 / KDT_2d_R1)[tbd] |
| KDDP_2d_R1 | (KDD_2d_R1 / phospFactor2_R1)[tbd] |
| KDTP_2d_R1 | (KDD_2d_R1 / phospFactor2_R1)[tbd] |
| koffDP_2d_R1 | koff1P_2d_R1[tbd] |
| koffTP_2d_R1 | koff1P_2d_R1[tbd] |
| konDP_2d_R1 | (koffDP_2d_R1 / KDDP_2d_R1)[tbd] |
| konTP_2d_R1 | (koffTP_2d_R1 / KDTP_2d_R1)[tbd] |
| KDD_25d_R1 | (5.2E-4 / geomFac25_R1)[tbd] |
| KDT_25d_R1 | (5.2E-4 / geomFac25_R1)[tbd] |
| koffD_25d_R1 | koff1_25d_R1[tbd] |
| koffT_25d_R1 | koff1_25d_R1[tbd] |
| konD_25d_R1 | (koffD_25d_R1 / KDD_25d_R1)[tbd] |
| konT_25d_R1 | (koffT_25d_R1 / KDT_25d_R1)[tbd] |
| KDDP_25d_R1 | (KDD_25d_R1 / phospFactor25_R1)[tbd] |
| KDTP_25d_R1 | (KDD_25d_R1 / phospFactor25_R1)[tbd] |
| koffDP_25d_R1 | koff1P_25d_R1[tbd] |
| koffTP_25d_R1 | koff1P_25d_R1[tbd] |
| konDP_25d_R1 | (koffDP_25d_R1 / KDDP_25d_R1)[tbd] |
| konTP_25d_R1 | (koffTP_25d_R1 / KDTP_25d_R1)[tbd] |
| KDD_3d_R1 | (1.3E-4 * alpha_R1)[tbd] |
| KDT_3d_R1 | (1.3E-4 * alpha_R1)[tbd] |
| koffD_3d_R1 | koff1_3d_R1[tbd] |
| koffT_3d_R1 | koff1_3d_R1[tbd] |
| konD_3d_R1 | (koffD_3d_R1 / KDD_3d_R1)[tbd] |
| konT_3d_R1 | (koffT_3d_R1 / KDT_3d_R1)[tbd] |
| KDDP_3d_R1 | (KDD_3d_R1 / phospFactor3_R1)[tbd] |
| KDTP_3d_R1 | (KDD_3d_R1 / phospFactor3_R1)[tbd] |
| koffDP_3d_R1 | koff1P_3d_R1[tbd] |
| koffTP_3d_R1 | koff1P_3d_R1[tbd] |
| konDP_3d_R1 | (koffDP_3d_R1 / KDDP_3d_R1)[tbd] |
| konTP_3d_R1 | (koffTP_3d_R1 / KDTP_3d_R1)[tbd] |
| ppGdifactor_R1 | (pGdifactor_R1 * psGdifactor_R1)[tbd] |
| InitialConc1 | 0.0[tbd] |
| InitialConc2 | 0.0[tbd] |
| InitialConc3 | 0.0[tbd] |
| InitialConc4 | 0.0[tbd] |
| InitialConc5 | (pmpGr / pmp0)[tbd] |
| rateParam1 | (fusRate * pmp0)[tbd] |
| rateParam2 | (1.0E10 * fusRate * pmpGr)[tbd] |
| rateParam3 | (7.2 * fusRate * pmp0)[tbd] |
| rateParam4 | (koffM_G * pmp0)[tbd] |
| rateParam5 | (konM_G * pmp)[tbd] |
| rateParam6 | (koffMp_G * pmp0)[tbd] |
| rateParam7 | (konMp_G * pmp)[tbd] |
| rateParam8 | (koffGr_G * pmp0)[tbd] |
| rateParam9 | (konGr_G * pmp)[tbd] |
| rateParam10 | (koffGrp_G * pmp0)[tbd] |
| rateParam11 | (konGrp_G * pmp)[tbd] |
| rateParam12 | (konGluc * gluc0)[tbd] |
| rateParam13 | (konM_R1 * pmp)[tbd] |
| rateParam14 | (koffMD_R1 * pmp0)[tbd] |
| rateParam15 | (konM_R1 * pmp)[tbd] |
| rateParam16 | (koffMT_R1 * pmp0)[tbd] |
| rateParam17 | (konGr_R1 * pmpGr)[tbd] |
| rateParam18 | (koffGrD_R1 * pmp0)[tbd] |
| rateParam19 | (konGr_R1 * pmpGr)[tbd] |
| rateParam20 | (koffGrT_R1 * pmp0)[tbd] |
| rateParam21 | (gef_R1 * pmp0)[tbd] |
| rateParam22 | (gap_R1 * pmp0)[tbd] |
| rateParam23 | (gef_Gr_R1 * pmp0)[tbd] |
| rateParam24 | (gap_Gr_R1 * pmp0)[tbd] |
| rateParam25 | (pGdifactor_R1 * konD_3d_R1)[tbd] |
| rateParam26 | (pGdifactor_R1 * konT_3d_R1)[tbd] |
| rateParam27 | (psGdifactor_R1 * konD_3d_R1)[tbd] |
| rateParam28 | (psGdifactor_R1 * konT_3d_R1)[tbd] |
| Group_nonG | NonGlucLc[tbd] |
| Group_glucL | GlucLc[tbd] |
| VC_SpConcFactor_1000_0 | 1.6611295681063123E-6 [1000] |
| Group_Rac1 | (Rac1cgDp + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + (GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0) + Rac1cgTp + (Rac1ggDp * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgDp + (Rac1ggTp * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgTp)[tbd] |
| Group_GDI | (GDIuuco + GDIpuco + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + (GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0) + (GDIuugo * VC_SpConcFactor_1000_0) + (GDIpugo * VC_SpConcFactor_1000_0) + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd] |
| Group_pak | (pakuc + pakpc)[tbd] |
| Group_tot_Rac1_M | (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_tot_Rac1_G | (((Rac1ggDp * VC_SpConcFactor_1000_0) + (Rac1ggTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_tot_Rac1_C | (Rac1cgDp + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd] |
| Group_Rac1_Mfree | (((Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_Rac1_GDP_m | (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (Rac1mgDp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_Rac1_GTP_m | (((GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_Rac1_GDP_c | (Rac1cgDp + GDIuuco_Rac1cgDp + GDIpuco_Rac1cgDp)[tbd] |
| Group_Rac1_GTP_c | (GDIuuco_Rac1cgTp + Rac1cgTp + GDIpuco_Rac1cgTp)[tbd] |
| Group_Rac1_c_g | (GDIuuco_Rac1cgDp + GDIpuco_Rac1cgDp)[tbd] |
| Group_GDI_c | (GDIuuco + GDIpuco + GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd] |
| Group_GDI_m | (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0) + (GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_GDI_g | (((GDIuugo * VC_SpConcFactor_1000_0) + (GDIpugo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_GDI_mb_g | (((GDIuumo_Rac1mgDp * VC_SpConcFactor_1000_0) + (GDIuumo_Rac1mgTp * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_GDI_mf | (((GDIuumo * VC_SpConcFactor_1000_0) + (GDIpumo * VC_SpConcFactor_1000_0)) / VC_SpConcFactor_1000_0)[tbd] |
| Group_GDI_cb | (GDIuuco_Rac1cgDp + GDIuuco_Rac1cgTp + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd] |
| Group_GDI_cf | (GDIuuco + GDIpuco)[tbd] |
| Group_GDI_py_m | 0.0[tbd] |
| Group_GDI_py_c | 0.0[tbd] |
| Group_gdiSp_m | (GDIpumo * VC_SpConcFactor_1000_0 / VC_SpConcFactor_1000_0)[tbd] |
| Group_gdiSp_c | (GDIpuco + GDIpuco_Rac1cgDp + GDIpuco_Rac1cgTp)[tbd] |
| Group_pak_m | 0.0[tbd] |
| Group_pak_Ac_m | 0.0[tbd] |
| Group_pak_Ac_c | pakpc[tbd] |
| g0 | 0.0[tbd] |
| tgluc | 60.0[tbd] |
| gef0_R1 | 10.0[tbd] |
| changekonM | 0.0[tbd] |
| coef_pld0 | 2.0[tbd] |
| change_gef_only | 0.0[tbd] |
| coef_gef | 5.0[tbd] |
| KD4_sys | (koff_granule * koff_membrane * SfRAVolNIH3T3 / (1.0E-20 + (koff_membrane * konGr_R1 * SfcGr) + (koff_granule * konM_R1 * SfRAVol)))[tbd] |
| koff_granule | (((koffGrD_R1 * Rac1ggDp) + (koffGrT_R1 * Rac1ggTp)) / (1.0E-20 + Rac1ggDp + Rac1ggTp))[tbd] |
| koff_membrane | (((koffMD_R1 * Rac1mgDp) + (koffMT_R1 * Rac1mgTp)) / (1.0E-20 + Rac1mgDp + Rac1mgTp))[tbd] |
| KD4_sys_c | ((Rac1cgDp + Rac1cgTp) / (0.0016611295681063123 * (((Rac1mgDp + Rac1mgTp) * SfRAVol) + ((Rac1ggDp + Rac1ggTp) * SfcGr))))[tbd] |
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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 | psGDIfactor_R1=0.1; find SS with no gluc.bngl , psGDIfactor_R1=0.1+change konM+coefonGR; transient studies.bngl |
| SBML | psGDIfactor_R1=0.1; find SS with no gluc.sbml , psGDIfactor_R1=0.1+change konM+coefonGR; transient studies.sbml |
| Matlab | psGDIfactor_R1=0.1; find SS with no gluc.m , psGDIfactor_R1=0.1+change konM+coefonGR; transient studies.m |
| NFSim XML | psGDIfactor_R1=0.1; find SS with no gluc.xml , psGDIfactor_R1=0.1+change konM+coefonGR; transient studies.xml |