Dashboard
Name - Scott_Fraley_Rangamani_YAP_TAZ_model_2021 (2D and 3D simulations)
BioModel ID - 200301029
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)[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 ^ n1))[1] user defined (p): 9.0E-6[tbd] user defined (n1): 2.6[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)
|
---|---|
ECM |
Compartment
(+) (-)
|
|
|
Cyto |
Compartment
(+) (-)
|
|
|
Nuc |
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 figure 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 figure 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) |
R10 2D figure 4 | Deterministic (ODE) Spatial (3D) | Bottom -- 2D stimulus presentation simulation for 3 values of E for geometry with radius 10 with stimulus from the bottom |
SA 415 2xD figure 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 figure 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) |
R13 2D figure 4 | Deterministic (ODE) Spatial (3D) | cloned from 'Small z R13 Bottom' owned by user kscott cloned from 'Small z R13 Bottom' owned by user kscott2 cloned from 'Small z R13 Bottom' owned by user kscott (copied from Small z R13) (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) |
SA 314 3D figure 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'New SA 314' owned by user kscott cloned from 'New SA 314' owned by user kscott2 cloned from 'New SA 314' owned by user kscott (copied from Small z R13 Bottom) (copied from Small z R13) (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) |
SA 415 3D figure 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'New SA 415' owned by user kscott cloned from 'New SA 415' owned by user kscott2 cloned from 'New SA 415' owned by user kscott (copied from Small z R15 Bottom) (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) |
SA 490 3D figure 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'New SA 490' owned by user kscott cloned from 'New SA 490' owned by user kscott2 cloned from 'New SA 490' owned by user kscott (copied from New SA 415) (copied from Small z R15 Bottom) (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) |
SA 250 3D figure 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'New SA 250' owned by user kscott (copied from New SA 314) cloned from 'New SA 314' owned by user kscott2 cloned from 'New SA 314' owned by user kscott (copied from Small z R13 Bottom) (copied from Small z R13) (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) |
SA 200 3D figure 5,6 | Deterministic (ODE) Spatial (3D) | cloned from 'New SA 200' owned by user kscott (copied from New SA 250) (copied from New SA 314) cloned from 'New SA 314' owned by user kscott2 cloned from 'New SA 314' owned by user kscott (copied from Small z R13 Bottom) (copied from Small z R13) (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) |
SA 200 2xD figure 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) |
R15 LD 0.5 Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R15 Bottom tall' 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) |
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) |
R15LD 1.5Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R15 Bottom Wide V2' owned by user kscott (copied from R15 Bottom Nucleus Wide) (copied from R15 Bottom Nucleus) (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) |
R13 LD 1.5 Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R13 Bottom wide' owned by user kscott (copied from Small z R13 Bottom) cloned from 'Small z R13 Bottom' owned by user kscott2 cloned from 'Small z R13 Bottom' owned by user kscott (copied from Small z R13) (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) |
R13 LD 0.5 Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R13 Bottom Tall' owned by user kscott (copied from R13 Bottom wide) (copied from Small z R13 Bottom) cloned from 'Small z R13 Bottom' owned by user kscott2 cloned from 'Small z R13 Bottom' owned by user kscott (copied from Small z R13) (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) |
R16 LD 1.5Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R16 Bottom wide' owned by user kscott (copied from Small z R16 Bottom) (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) |
R16 LD 0.5 Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R16 Bottom tall' owned by user kscott (copied from R 16 Bottom wide) (copied from Small z R16 Bottom) (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) |
R10 Bottom wide Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R10 Bottom wide' owned by user kscott (copied from Small z R10 Bottom) cloned from 'Small z R10 Bottom' owned by user kscott2 cloned from 'Small z R10 Bottom' owned by user kscott (copied from Small z R10) (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) |
R10 LD 0.5 Figure 7 | Deterministic (ODE) Spatial (3D) | cloned from 'R10 Bottom tall' owned by user kscott (copied from R10 Bottom wide) (copied from Small z R10 Bottom) cloned from 'Small z R10 Bottom' owned by user kscott2 cloned from 'Small z R10 Bottom' owned by user kscott (copied from Small z R10) (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) |
R15 3D Figure 3, 4, and S7 | Deterministic (ODE) Spatial (3D) | cloned from 'R15 All' 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) |
R13 3D figure 4 | Deterministic (ODE) Spatial (3D) | cloned from 'R13 All' owned by user kscott (copied from Small z R13 Bottom) cloned from 'Small z R13 Bottom' owned by user kscott2 cloned from 'Small z R13 Bottom' owned by user kscott (copied from Small z R13) (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) |
R10 3D figure 4 | Deterministic (ODE) Spatial (3D) | cloned from 'R10 All' owned by user kscott (copied from Small z R10 Bottom) cloned from 'Small z R10 Bottom' owned by user kscott2 cloned from 'Small z R10 Bottom' owned by user kscott (copied from Small z R10) (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) |
R15 2D Fig 3, 4, and S7 | Deterministic (ODE) Spatial (3D) | (copied from Small z R15 Bottom FAK only) (copied from Small z R15 Bottom) cloned from 'Small z R15 Bottom' owned by user kscott 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) |
R16 LD 1Figure 7 | Deterministic (ODE) Spatial (3D) | (copied from R16 All) cloned from 'R16 All' owned by user kscott (copied from Small z R16 Bottom) (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) |
R-25 FAK diffusion variation 3D substrate stiffness Figure S7 | Deterministic (ODE) Spatial (3D) | (copied from SA 490 2xD figure 5,6) 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) |
R-25 FAK diffusion variation 2D substrate stiffness Fig S7 | Deterministic (ODE) Spatial (3D) | (copied from SA 490 2xD figure 5,6) 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) |
Application - SA 314 2xD figure 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 figure 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 - R10 2D figure 4
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 10 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.54344152011903 [um3] | Nuc | |
Volume | Analytical | cyto | 485.1320011716396 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 557.5525573082413 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 240.86870670542456 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.5507189516813 [um2] | NM |
Application - SA 415 2xD figure 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 figure 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 - R13 2D figure 4
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 13 Bot 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.58193494342953 [um3] | Nuc | |
Volume | Analytical | cyto | 480.10609925215147 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2092.0619658044193 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 320.54212819295253 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.478398304411165 [um2] | NM |
Application - SA 314 3D figure 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 |
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 |
---|---|---|
New SA 314 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.50818208513627 [um3] | Nuc | |
Volume | Analytical | cyto | 479.23301560784523 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1272.7588023070186 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 317.14948828594544 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.47910918771644 [um2] | NM |
Application - SA 415 3D figure 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 |
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 |
---|---|---|
New SA 415 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.5539381794935 [um3] | Nuc | |
Volume | Analytical | cyto | 479.7286658763266 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1627.7173959441798 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 412.4012633878866 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.46266334324532 [um2] | NM |
Application - SA 490 3D figure 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 |
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 |
---|---|---|
New SA 490 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.61954640302723 [um3] | Nuc | |
Volume | Analytical | cyto | 482.0296070920011 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1877.3508465049717 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 491.56304357194983 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.485578491222846 [um2] | NM |
Application - SA 250 3D figure 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 |
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 |
---|---|---|
New SA 250All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.57950089179491 [um3] | Nuc | |
Volume | Analytical | cyto | 480.43843423185876 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1021.9820648763465 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 248.23197450883632 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.66900242176558 [um2] | NM |
Application - SA 200 3D figure 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 |
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 |
---|---|---|
New SA 200 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.61799558518004 [um3] | Nuc | |
Volume | Analytical | cyto | 479.71012218045104 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 677.9218822343687 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 204.89423260560167 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.762002479997065 [um2] | NM |
Application - SA 200 2xD figure 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 - R15 LD 0.5 Figure 7
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 |
---|---|---|
Copy of Simulation88 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.19508659432897 [um3] | Nuc | |
Volume | Analytical | cyto | 483.35941544845053 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1704.7954979572205 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 393.6447697149652 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 51.83674295389707 [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 |
Parameter scan over cytosolic stiffness varying exponent | 4000.0 [s] |
OutputTimeStep 100.0 |
Parameter scan over cytosolic stiffness varying p | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | PM |
Application - R15LD 1.5Figure 7
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 |
---|---|---|
Simulation113 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 69.01063409868866 [um3] | Nuc | |
Volume | Analytical | cyto | 484.54386794409083 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1704.7954979572205 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 393.6447697149652 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 66.57578488722925 [um2] | NM |
Application - R13 LD 1.5 Figure 7
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 |
---|---|---|
Simulation114 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 68.95784440036894 [um3] | Nuc | |
Volume | Analytical | cyto | 481.7301897952121 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2092.0619658044193 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 320.54212819295253 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 66.55961505369686 [um2] | NM |
Application - R13 LD 0.5 Figure 7
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 |
---|---|---|
Simulation117 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.18724627286636 [um3] | Nuc | |
Volume | Analytical | cyto | 480.50078792271466 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2092.0619658044193 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 320.54212819295253 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 51.81718584619576 [um2] | NM |
Application - R16 LD 1.5Figure 7
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 >= - 0.008)
[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 |
---|---|---|
Simulation126 | 4000.0 [s] |
OutputTimeStep 100.0 |
Copy of Simulation126 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.09154705430733 [um3] | Nuc | |
Volume | Analytical | cyto | 487.7531709350866 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1618.1552820106067 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 435.24832146338537 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 68.27619662872442 [um2] | NM |
Application - R16 LD 0.5 Figure 7
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 >= - 0.008)
[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 |
---|---|---|
Simulation131 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.95341905764276 [um3] | Nuc | |
Volume | Analytical | cyto | 486.8912989317511 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1618.1552820106067 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 435.24832146338537 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 52.62011993122839 [um2] | NM |
Application - R10 Bottom wide Figure 7
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 |
---|---|---|
Simulation135 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 69.03094628957189 [um3] | Nuc | |
Volume | Analytical | cyto | 486.6444964021867 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 557.5525573082413 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 240.86870670542456 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 66.73660643736142 [um2] | NM |
Application - R10 LD 0.5 Figure 7
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 |
---|---|---|
Simulation138 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.20639366182374 [um3] | Nuc | |
Volume | Analytical | cyto | 485.46904902993487 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 557.5525573082413 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 240.86870670542456 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 51.90093094888727 [um2] | NM |
Application - R15 3D Figure 3, 4, and S7
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 |
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 |
---|---|---|
R 15 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
R 15 All 0.1,5.7,70E6 with different FAK diffusion | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.56972537790662 [um3] | Nuc | |
Volume | Analytical | cyto | 482.98477666487287 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1704.7954979572205 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 393.6447697149652 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.487600995005 [um2] | NM |
Application - R13 3D figure 4
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 |
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 |
---|---|---|
R 13 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.58193494342953 [um3] | Nuc | |
Volume | Analytical | cyto | 480.10609925215147 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 2092.0619658044193 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 320.54212819295253 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.478398304411165 [um2] | NM |
Application - R10 3D figure 4
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 |
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 |
---|---|---|
R 10 All 0.1,5.7,70E6 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.54344152011903 [um3] | Nuc | |
Volume | Analytical | cyto | 485.1320011716396 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 557.5525573082413 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 240.86870670542456 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.5507189516813 [um2] | NM |
Application - R15 2D Fig 3, 4, and S7
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 |
---|---|---|
R15 2D 0.1, 5.7, 7e6 | 4000.0 [s] |
OutputTimeStep 100.0 |
R15 2D 7e6 with different FAK diffusion | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.56972537790662 [um3] | Nuc | |
Volume | Analytical | cyto | 482.98477666487287 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1704.7954979572205 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 393.6447697149652 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.487600995005 [um2] | NM |
Application - R16 LD 1Figure 7
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 |
---|---|---|
Simulation22 | 4000.0 [s] |
OutputTimeStep 100.0 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Volume | Analytical | nuc | 70.6209511025692 [um3] | Nuc | |
Volume | Analytical | cyto | 487.2237668868247 [um3] | Cyto | |
Volume | Analytical | subdomain0 | 1618.1552820106067 [um3] | ECM | |
Surface | cyto_subdomain0_membrane | cyto | subdomain0 | 435.24832146338537 [um2] | PM | |
Surface | cyto_nuc_membrane | cyto | nuc | 58.486882421500134 [um2] | NM |
Application - R-25 FAK diffusion variation 3D substrate stiffness Figure S7
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 |
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 |
---|---|---|
R 25 3D 70E6 FAK diffusion 0.1 | 4000.0 [s] |
OutputTimeStep 100.0 |
R 25 3D 70E6 FAK diffusion 1 | 4000.0 [s] |
OutputTimeStep 100.0 |
R 25 3D 70E6 FAK diffusion 10 | 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 - R-25 FAK diffusion variation 2D substrate stiffness Fig S7
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 2D varying FAK diffusion 0.1 | 4000.0 [s] |
OutputTimeStep 100.0 |
R 25 2D varying FAK diffusion 1 | 4000.0 [s] |
OutputTimeStep 100.0 |
R 25 2D varying FAK diffusion 10 | 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 |
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[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] |
|
|