Dashboard
Name - Scott_Fraley_Rangamani_YAP_TAZ_model_2021(Rho and FAK confined simulations (true 2D)
BioModel ID - 200301683
Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
RhoAGTP_MEMRhoAGDP |
r3
PM
|
MassAction | RhoAGTP_MEMRhoAGDP |
|
|
reaction rate (J): ((Kf * RhoAGTP_MEM) - (Kr * RhoAGDP))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): kdp[s-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1] |
|
ROCKROCKA |
r4
PM
|
MassAction | ROCKROCKA |
|
|
reaction rate (J): ((Kf * ROCK) - (Kr * ROCKA))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (krp * RhoAGTP_MEM)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1] |
|
mDiamDiaA |
r5
PM
|
MassAction | mDiamDiaA |
|
|
reaction rate (J): ((Kf * mDia) - (Kr * mDiaA))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kmp * RhoAGTP_MEM)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1] |
|
ROCKAROCK |
r6
Cyto
|
MassAction | ROCKAROCK |
|
|
reaction rate (J): ((Kf * ROCKA) - (Kr * ROCK))[uM.s-1]
forward rate constant (Kf): kdrock[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
LIMKLIMKA |
r8
Cyto
|
MassAction | LIMKLIMKA |
|
|
reaction rate (J): ((Kf * LIMK) - (Kr * LIMKA))[uM.s-1]
forward rate constant (Kf): (klr * (1.0 + (0.5 * tau * (1.0 + tanh((20.0 * (ROCKA - ROCKB)))) * ROCKA)))[s-1] reverse rate constant (Kr): kdl[s-1] |
|
MyoMyoA |
r9
Cyto
|
MassAction | MyoMyoA |
|
|
reaction rate (J): ((Kf * Myo) - (Kr * MyoA))[uM.s-1]
forward rate constant (Kf): (kmr * (1.0 + (0.5 * epsilon * (1.0 + tanh((20.0 * (ROCKA - ROCKB)))) * ROCKA)))[s-1] reverse rate constant (Kr): kdmy[s-1] |
|
CofilinPCofilinNP |
r10
Cyto
|
MassAction | CofilinPCofilinNP |
|
|
reaction rate (J): ((Kf * CofilinP) - (Kr * CofilinNP))[uM.s-1]
forward rate constant (Kf): kturnover[s-1] reverse rate constant (Kr): (kcatcof * LIMKA / (kmCof + CofilinNP))[s-1] user defined (kcatcof): 0.34[s-1.uM-1] user defined (kmCof): 4.0[uM] |
|
GactinFcyto |
r11
Cyto
|
MassAction | GactinFcyto |
|
|
reaction rate (J): ((Kf * Gactin) - (Kr * Fcyto))[uM.s-1]
forward rate constant (Kf): (kra * (1.0 + (0.5 * alpha * (1.0 + tanh((20.0 * (mDiaA - mDiaB)))) * mDiaA)))[s-1] reverse rate constant (Kr): (kdep + (kfc1 * CofilinNP))[s-1] |
|
mDiaAmDia |
r7
Cyto
|
MassAction | mDiaAmDia |
|
|
reaction rate (J): ((Kf * mDiaA) - (Kr * mDia))[uM.s-1]
forward rate constant (Kf): kdmdia[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
YAPTAZPYAPTAZN |
r13
Cyto
|
MassAction | YAPTAZPYAPTAZN |
|
|
reaction rate (J): ((Kf * YAPTAZP) - (Kr * YAPTAZN))[uM.s-1]
forward rate constant (Kf): (kCN + (kCY * MyoA * Fcyto))[s-1] reverse rate constant (Kr): kNC[s-1] |
|
FakFakp |
r12
PM
|
MassAction | FakFakp |
|
|
reaction rate (J): ((Kf * Fak) - (Kr * Fakp))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (ksf * Emol * unitconversionfactor * SAV * Positionboolean / (C + Emol))[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1] |
|
FakpFak |
r0
Cyto
|
MassAction | FakpFak |
|
|
reaction rate (J): ((Kf * Fakp) - (Kr * Fak))[uM.s-1]
forward rate constant (Kf): kdf[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
RhoAGDPRhoAGTP_MEM |
r1
PM
|
MassAction | RhoAGDPRhoAGTP_MEM |
|
|
reaction rate (J): ((Kf * RhoAGDP) - (Kr * RhoAGTP_MEM))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kfkp * (1.0 + (gamma * (Fakp ^ n2))) * unitconversionfactor * SAV * Positionboolean)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[s-1] user defined (n2): 5.0[1] |
|
FakFakp |
r2
Cyto
|
MassAction | FakFakp |
|
|
reaction rate (J): ((Kf * Fak) - (Kr * Fakp))[uM.s-1]
forward rate constant (Kf): kf[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
NPCNPCA |
r14
NM
|
MassAction | NPCNPCA |
|
|
reaction rate (J): ((Kf * NPC) - (Kr * NPCA))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kfNPC * MyoA * Fcyto * LaminA)[s-1] reverse rate constant (Kr): krNPC[s-1] |
|
LaminApLaminA |
r15
NM
|
MassAction | LaminApLaminA |
|
|
reaction rate (J): ((Kf * LaminAp) - (Kr * LaminA))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kflaminA * Ecytosol / (Clamin + Ecytosol))[s-1] reverse rate constant (Kr): 0.001[s-1] user defined (kflaminA): 0.46[s-1] user defined (Ecytosol): (p * (Fcyto ^ 2.6))[1] user defined (p): 9.0E-6[tbd] |
|
YAPTAZNYAPTAZnuc |
r16
NM
|
MassAction | YAPTAZNYAPTAZnuc |
|
|
reaction rate (J): ((Kf * YAPTAZN) - (Kr * YAPTAZnuc))[molecules.um-2.s-1]
inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): ((kin2 * NPCA) + kinSolo2)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): kout2[molecules.um-2.s-1.uM-1] user defined (kin2): 10.0[s-1.uM-1] user defined (kinSolo2): 1.0[molecules.um-2.s-1.uM-1] user defined (kout2): 1.0[molecules.um-2.s-1.uM-1] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
Cyto |
Compartment
(+) (-)
|
|
|
Nuc |
Compartment
(+) (-)
|
|
|
ECM |
Compartment
(+) (-)
|
|
|
NM |
Membrane
N/A
|
|
|
PM |
Membrane
N/A
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
RhoAGTP_MEM | PM | |
|
|
|
Fakp | Cyto | |
|
|
|
RhoAGDP | Cyto | |
|
|
|
Fak | Cyto | |
|
|
|
ROCKA | Cyto | |
|
|
|
ROCK | Cyto | |
|
|
|
mDia | Cyto | |
|
|
|
mDiaA | Cyto | |
|
|
|
Myo | Cyto | |
|
|
|
MyoA | Cyto | |
|
|
|
LIMK | Cyto | |
|
|
|
CofilinP | Cyto | |
|
|
|
LIMKA | Cyto | |
|
|
|
CofilinNP | Cyto | |
|
|
|
Fcyto | Cyto | |
|
|
|
Gactin | Cyto | |
|
|
|
YAPTAZP | Cyto | |
|
|
|
YAPTAZN | Cyto | |
|
|
|
YAPTAZnuc | Nuc | |
|
|
|
Positionboolean | PM | |
|
|
|
NPCA | NM | |
|
|
|
NPC | NM | |
|
|
|
LaminA | NM | |
|
|
|
LaminAp | NM | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
SA 314 2xD Fig 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R20 Bottom' owned by user kscott cloned from 'Small z R20 Bottom' owned by user kscott2 cloned from 'Small z R20 Bottom' owned by user kscott (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
SA 490 2xD Fig 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R25 Bottom' owned by user kscott cloned from 'Small z R25 Bottom' owned by user kscott2 cloned from 'Small z R25 Bottom' owned by user kscott (copied from Small z R25) (copied from V200 All R25) (copied from V200 Bottom R25) (copied from V200-stiffness from the bottom increase SA) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
SA 415 2xD Fig 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R23 Bottom' owned by user kscott cloned from 'Small z R23 Bottom' owned by user kscott2 cloned from 'Small z R23 Bottom' owned by user kscott (copied from Small z R23) (copied from Small z R25) (copied from V200 All R25) (copied from V200 Bottom R25) (copied from V200-stiffness from the bottom increase SA) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
SA 250 2xD Fig 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R18 Bottom' owned by user kscott cloned from 'Small z R18 Bottom' owned by user kscott2 cloned from 'Small z R18 Bottom' owned by user kscott (copied from Small z R18) (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
SA 200 2xD Fig 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R16 Bottom' owned by user kscott (copied from Small z R18 Bottom) cloned from 'Small z R18 Bottom' owned by user kscott2 cloned from 'Small z R18 Bottom' owned by user kscott (copied from Small z R18) (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
Compartmental model | Deterministic (ODE) Compartmental | cloned from 'Compartmental model' owned by user kscott (copied from Small z R15 Bottom) cloned from 'Small z R15 Bottom' owned by user kscott2 cloned from 'Small z R15 Bottom' owned by user kscott (copied from Small z R15) (copied from V200 All R15) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0) |
Application - SA 314 2xD Fig 5,6
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 10.0
[um2/s] RhoAGDP |
1.0
[uM]
|
10.0
[um2/s] | Fak |
0.7
[uM]
|
10.0
[um2/s] | ROCKA |
0.0
[uM]
|
75.0
[um2/s] | ROCK |
1.0
[uM]
|
75.0
[um2/s] | mDia |
0.8
[uM]
|
10.0
[um2/s] | mDiaA |
0.0
[uM]
|
10.0
[um2/s] | Myo |
3.5
[uM]
|
10.0
[um2/s] | MyoA |
1.5
[uM]
|
10.0
[um2/s] | LIMK |
1.9
[uM]
|
10.0
[um2/s] | CofilinP |
0.2
[uM]
|
10.0
[um2/s] | LIMKA |
0.1
[uM]
|
10.0
[um2/s] | CofilinNP |
1.8
[uM]
|
10.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.6
[um2/s] | Gactin |
482.4
[uM]
|
13.37
[um2/s] | YAPTAZP |
0.2
[uM]
|
19.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
19.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
19.0
[um2/s] | NPCA |
0.0
[uM]
|
0.001
[um2/s] | NPC |
6.5
[uM]
|
0.001
[um2/s] | LaminA |
0.0
[uM]
|
0.001
[um2/s] | LaminAp |
3500.0
[uM]
|
0.001
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.348
[um2/s] | Positionboolean |
(z >= - 0.001)
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
R 20 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.62352358303608 [um3] | Nuc | |
Volume | Analytical | cyto | 479.7517340467698 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2129.6247423701943 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 652.1738925334953 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.4720187315763 [um2] | NM |
Application - SA 490 2xD Fig 5,6
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 10.0
[um2/s] RhoAGDP |
1.0
[uM]
|
10.0
[um2/s] | Fak |
0.7
[uM]
|
10.0
[um2/s] | ROCKA |
0.0
[uM]
|
75.0
[um2/s] | ROCK |
1.0
[uM]
|
75.0
[um2/s] | mDia |
0.8
[uM]
|
10.0
[um2/s] | mDiaA |
0.0
[uM]
|
10.0
[um2/s] | Myo |
3.5
[uM]
|
10.0
[um2/s] | MyoA |
1.5
[uM]
|
10.0
[um2/s] | LIMK |
1.9
[uM]
|
10.0
[um2/s] | CofilinP |
0.2
[uM]
|
10.0
[um2/s] | LIMKA |
0.1
[uM]
|
10.0
[um2/s] | CofilinNP |
1.8
[uM]
|
10.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.6
[um2/s] | Gactin |
482.4
[uM]
|
13.37
[um2/s] | YAPTAZP |
0.2
[uM]
|
19.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
19.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
19.0
[um2/s] | NPCA |
0.0
[uM]
|
0.001
[um2/s] | NPC |
6.5
[uM]
|
0.001
[um2/s] | LaminA |
0.0
[uM]
|
0.001
[um2/s] | LaminAp |
3500.0
[uM]
|
0.001
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.348
[um2/s] | Positionboolean |
(z >= - 0.01)
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
R 25 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.63087045999002 [um3] | Nuc | |
Volume | Analytical | cyto | 481.59273558210197 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 3503.776393957908 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 990.4520121825556 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.40088897755887 [um2] | NM |
Application - SA 415 2xD Fig 5,6
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 10.0
[um2/s] RhoAGDP |
1.0
[uM]
|
10.0
[um2/s] | Fak |
0.7
[uM]
|
10.0
[um2/s] | ROCKA |
0.0
[uM]
|
75.0
[um2/s] | ROCK |
1.0
[uM]
|
75.0
[um2/s] | mDia |
0.8
[uM]
|
10.0
[um2/s] | mDiaA |
0.0
[uM]
|
10.0
[um2/s] | Myo |
3.5
[uM]
|
10.0
[um2/s] | MyoA |
1.5
[uM]
|
10.0
[um2/s] | LIMK |
1.9
[uM]
|
10.0
[um2/s] | CofilinP |
0.2
[uM]
|
10.0
[um2/s] | LIMKA |
0.1
[uM]
|
10.0
[um2/s] | CofilinNP |
1.8
[uM]
|
10.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.6
[um2/s] | Gactin |
482.4
[uM]
|
13.37
[um2/s] | YAPTAZP |
0.2
[uM]
|
19.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
19.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
19.0
[um2/s] | NPCA |
0.0
[uM]
|
0.001
[um2/s] | NPC |
6.5
[uM]
|
0.001
[um2/s] | LaminA |
0.0
[uM]
|
0.001
[um2/s] | LaminAp |
3500.0
[uM]
|
0.001
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.348
[um2/s] | Positionboolean |
(z >= - 0.1)
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
R 23 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.58292490826426 [um3] | Nuc | |
Volume | Analytical | cyto | 481.89401114926034 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2886.0230639424753 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 845.7864067309622 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.39311053387225 [um2] | NM |
Application - SA 250 2xD Fig 5,6
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 10.0
[um2/s] RhoAGDP |
1.0
[uM]
|
10.0
[um2/s] | Fak |
0.7
[uM]
|
10.0
[um2/s] | ROCKA |
0.0
[uM]
|
75.0
[um2/s] | ROCK |
1.0
[uM]
|
75.0
[um2/s] | mDia |
0.8
[uM]
|
10.0
[um2/s] | mDiaA |
0.0
[uM]
|
10.0
[um2/s] | Myo |
3.5
[uM]
|
10.0
[um2/s] | MyoA |
1.5
[uM]
|
10.0
[um2/s] | LIMK |
1.9
[uM]
|
10.0
[um2/s] | CofilinP |
0.2
[uM]
|
10.0
[um2/s] | LIMKA |
0.1
[uM]
|
10.0
[um2/s] | CofilinNP |
1.8
[uM]
|
10.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.6
[um2/s] | Gactin |
482.4
[uM]
|
13.37
[um2/s] | YAPTAZP |
0.2
[uM]
|
19.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
19.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
19.0
[um2/s] | NPCA |
0.0
[uM]
|
0.001
[um2/s] | NPC |
6.5
[uM]
|
0.001
[um2/s] | LaminA |
0.0
[uM]
|
0.001
[um2/s] | LaminAp |
3500.0
[uM]
|
0.001
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.348
[um2/s] | Positionboolean |
(z >= - 0.08)
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
R 18 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.61185688075281 [um3] | Nuc | |
Volume | Analytical | cyto | 480.857859789597 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1878.53028332965 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 536.9024388114472 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.494055780161 [um2] | NM |
Application - SA 200 2xD Fig 5,6
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 10.0
[um2/s] RhoAGDP |
1.0
[uM]
|
10.0
[um2/s] | Fak |
0.7
[uM]
|
10.0
[um2/s] | ROCKA |
0.0
[uM]
|
75.0
[um2/s] | ROCK |
1.0
[uM]
|
75.0
[um2/s] | mDia |
0.8
[uM]
|
10.0
[um2/s] | mDiaA |
0.0
[uM]
|
10.0
[um2/s] | Myo |
3.5
[uM]
|
10.0
[um2/s] | MyoA |
1.5
[uM]
|
10.0
[um2/s] | LIMK |
1.9
[uM]
|
10.0
[um2/s] | CofilinP |
0.2
[uM]
|
10.0
[um2/s] | LIMKA |
0.1
[uM]
|
10.0
[um2/s] | CofilinNP |
1.8
[uM]
|
10.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.6
[um2/s] | Gactin |
482.4
[uM]
|
13.37
[um2/s] | YAPTAZP |
0.2
[uM]
|
19.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
19.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
19.0
[um2/s] | NPCA |
0.0
[uM]
|
0.001
[um2/s] | NPC |
6.5
[uM]
|
0.001
[um2/s] | LaminA |
0.0
[uM]
|
0.001
[um2/s] | LaminAp |
3500.0
[uM]
|
0.001
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.0
[um2/s] | Positionboolean |
(z >= - 0.008)
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
R 16 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.63872668684698 [um3] | Nuc | |
Volume | Analytical | cyto | 480.4916296208738 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1624.8696436922792 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 434.48289037648874 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.553287688431425 [um2] | NM |
Application - Compartmental model
Species | Initial Condition | Diffusion Constant | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fakp | 0.3 [uM] | 0.0
[um2/s] RhoAGDP |
1.0
[uM]
|
0.0
[um2/s] | Fak |
0.7
[uM]
|
0.0
[um2/s] | ROCKA |
0.0
[uM]
|
0.0
[um2/s] | ROCK |
1.0
[uM]
|
0.0
[um2/s] | mDia |
0.8
[uM]
|
0.0
[um2/s] | mDiaA |
0.0
[uM]
|
0.0
[um2/s] | Myo |
3.5
[uM]
|
0.0
[um2/s] | MyoA |
1.5
[uM]
|
0.0
[um2/s] | LIMK |
1.9
[uM]
|
0.0
[um2/s] | CofilinP |
0.2
[uM]
|
0.0
[um2/s] | LIMKA |
0.1
[uM]
|
0.0
[um2/s] | CofilinNP |
1.8
[uM]
|
0.0
[um2/s] | Fcyto |
17.9
[uM]
|
0.0
[um2/s] | Gactin |
482.4
[uM]
|
0.0
[um2/s] | YAPTAZP |
0.2
[uM]
|
0.0
[um2/s] | YAPTAZN |
0.7
[uM]
|
0.0
[um2/s] | YAPTAZnuc |
0.7
[uM]
|
0.0
[um2/s] | NPCA |
0.0
[uM]
|
0.0
[um2/s] | NPC |
6.5
[uM]
|
0.0
[um2/s] | LaminA |
0.0
[uM]
|
0.0
[um2/s] | LaminAp |
3500.0
[uM]
|
0.0
[um2/s] | RhoAGTP_MEM |
33.6
[uM]
|
0.0
[um2/s] | Positionboolean |
1.0
[uM]
|
0.0
[um2/s]
|
|
Name | Reaction Mapping |
---|---|
r3 | included |
r4 | included |
r5 | included |
r6 | included |
r8 | included |
r9 | included |
r10 | included |
r11 | included |
r7 | included |
r13 | included |
r12 | included |
r0 | included |
r1 | included |
r2 | included |
r14 | included |
r15 | included |
r16 | included |
Name | End Time | Output Options |
---|---|---|
Parameter scan over stiffness | 2000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | PM |
Global Parameters
Name | Expression |
---|---|
ksf | 0.379[s-1] |
|
|
C | 3.25[kPa] |
|
|
Emol | 25.0[kPa] |
|
|
kdf | 0.035[s-1] |
|
|
kfkp | (0.0168 * Positionboolean)[s-1] |
|
|
gamma | 77.56[uM-5] |
|
|
kdp | 0.625[s-1] |
|
|
krp | 0.648[uM-1.s-1] |
|
|
alpha | 50.0[uM-1] |
|
|
epsilon | 36.0[uM-1] |
|
|
kdep | 3.5[s-1] |
|
|
kdl | 2.0[s-1] |
|
|
kdmdia | 0.005[s-1] |
|
|
kdmy | 0.067[s-1] |
|
|
kdrock | 0.8[s-1] |
|
|
kfc1 | 4.0[uM-1.s-1] |
|
|
k11 | 16.0[uM-1] |
|
|
kmp | 0.002[uM-1.s-1] |
|
|
kra | 0.4[s-1] |
|
|
tau | 55.49[uM-1] |
|
|
kly | 120.0[uM-1.s-1] |
|
|
kmr | 0.03[s-1] |
|
|
kturnover | 0.04[s-1] |
|
|
ROCKB | 0.3[uM] |
|
|
mDiaB | 0.165[uM] |
|
|
klr | 0.07[s-1] |
|
|
kCN | 0.56[s-1] |
|
|
kCY | 7.6E-4[uM-2.s-1] |
|
|
kNC | 0.14[s-1] |
|
|
kll | 16.0[uM-1] |
|
|
unitconversionfactor | 602.2[molecules.um-3.uM-1] |
|
|
kf | 0.015[s-1] |
|
|
SAV | 1.8[um] |
|
|
kfNPC | 2.8E-7[um2.s-1.uM-2.molecules-1] |
|
|
krNPC | 8.7[s-1] |
|
|
Clamin | 100.0[kPa] |
|
|