Dashboard

Name - Scott_Fraley_Rangamani_YAP_TAZ_model_2021 (2D and 3D simulations)

BioModel ID - 200301029

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
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

Specifications(Species) - SA 314 2xD figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 314 2xD figure 5,6 See in Dashboard
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
Simulations - SA 314 2xD figure 5,6 See in Dashboard
Name End Time Output Options
R 20 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1221349153 See in Dashboard
(Origin: 0.0, 0.0, -6.5; Extent: 20.0, 20.0, 6.7[um])
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

Specifications(Species) - SA 490 2xD figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 490 2xD figure 5,6 See in Dashboard
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
Simulations - SA 490 2xD figure 5,6 See in Dashboard
Name End Time Output Options
R 25 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry53651429 See in Dashboard
(Origin: 0.0, 0.0, -5.8; Extent: 26.0, 26.0, 6.0[um])
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

Specifications(Species) - R10 2D figure 4 See in Dashboard
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]
Specifications(Reaction) - R10 2D figure 4 See in Dashboard
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
Simulations - R10 2D figure 4 See in Dashboard
Name End Time Output Options
R 10 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry932813449 See in Dashboard
(Origin: 0.0, 0.0, -10.5; Extent: 10.2, 10.2, 10.7[um])
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

Specifications(Species) - SA 415 2xD figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 415 2xD figure 5,6 See in Dashboard
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
Simulations - SA 415 2xD figure 5,6 See in Dashboard
Name End Time Output Options
R 23 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry914749205 See in Dashboard
(Origin: 0.0, 0.0, -6.3; Extent: 23.0, 23.0, 6.5[um])
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

Specifications(Species) - SA 250 2xD figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 250 2xD figure 5,6 See in Dashboard
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
Simulations - SA 250 2xD figure 5,6 See in Dashboard
Name End Time Output Options
R 18 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry156779672 See in Dashboard
(Origin: 0.0, 0.0, -7.3; Extent: 18.0, 18.0, 7.5[um])
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

Specifications(Species) - R13 2D figure 4 See in Dashboard
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]
Specifications(Reaction) - R13 2D figure 4 See in Dashboard
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
Simulations - R13 2D figure 4 See in Dashboard
Name End Time Output Options
R 13 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry985620913 See in Dashboard
(Origin: 0.0, 0.0, -10.8; Extent: 15.5, 15.5, 11.0[um])
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

Specifications(Species) - SA 314 3D figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 314 3D figure 5,6 See in Dashboard
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
Simulations - SA 314 3D figure 5,6 See in Dashboard
Name End Time Output Options
New SA 314 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1014102724 See in Dashboard
(Origin: 0.0, 0.0, -9.8; Extent: 13.5, 13.5, 10.0[um])
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

Specifications(Species) - SA 415 3D figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 415 3D figure 5,6 See in Dashboard
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
Simulations - SA 415 3D figure 5,6 See in Dashboard
Name End Time Output Options
New SA 415 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry16904482 See in Dashboard
(Origin: 0.0, 0.0, -7.8; Extent: 16.5, 16.5, 8.0[um])
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

Specifications(Species) - SA 490 3D figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 490 3D figure 5,6 See in Dashboard
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
Simulations - SA 490 3D figure 5,6 See in Dashboard
Name End Time Output Options
New SA 490 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1758802084 See in Dashboard
(Origin: 0.0, 0.0, -7.3; Extent: 18.0, 18.0, 7.5[um])
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

Specifications(Species) - SA 250 3D figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 250 3D figure 5,6 See in Dashboard
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
Simulations - SA 250 3D figure 5,6 See in Dashboard
Name End Time Output Options
New SA 250All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry699305470 See in Dashboard
(Origin: 0.0, 0.0, -12.8; Extent: 11.0, 11.0, 13.0[um])
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

Specifications(Species) - SA 200 3D figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 200 3D figure 5,6 See in Dashboard
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
Simulations - SA 200 3D figure 5,6 See in Dashboard
Name End Time Output Options
New SA 200 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1864068944 See in Dashboard
(Origin: 0.0, 0.0, -16.8; Extent: 8.5, 8.5, 17.0[um])
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

Specifications(Species) - SA 200 2xD figure 5,6 See in Dashboard
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]
Specifications(Reaction) - SA 200 2xD figure 5,6 See in Dashboard
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
Simulations - SA 200 2xD figure 5,6 See in Dashboard
Name End Time Output Options
R 16 Bot 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1502075650 See in Dashboard
(Origin: 0.0, 0.0, -8.3; Extent: 16.0, 16.0, 8.5[um])
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

Specifications(Species) - R15 LD 0.5 Figure 7 See in Dashboard
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]
Specifications(Reaction) - R15 LD 0.5 Figure 7 See in Dashboard
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
Simulations - R15 LD 0.5 Figure 7 See in Dashboard
Name End Time Output Options
Copy of Simulation88 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1802559637 See in Dashboard
(Origin: 0.0, 0.0, -9.2; Extent: 15.5, 15.5, 9.4[um])
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

Specifications(Species) - Compartmental model See in Dashboard
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]
Specifications(Reaction) - Compartmental model See in Dashboard
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
Simulations - Compartmental model See in Dashboard
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

Geometry nonspatial898778521 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment PM

Application - R15LD 1.5Figure 7

Specifications(Species) - R15LD 1.5Figure 7 See in Dashboard
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]
Specifications(Reaction) - R15LD 1.5Figure 7 See in Dashboard
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
Simulations - R15LD 1.5Figure 7 See in Dashboard
Name End Time Output Options
Simulation113 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1657634976 See in Dashboard
(Origin: 0.0, 0.0, -9.2; Extent: 15.5, 15.5, 9.4[um])
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

Specifications(Species) - R13 LD 1.5 Figure 7 See in Dashboard
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]
Specifications(Reaction) - R13 LD 1.5 Figure 7 See in Dashboard
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
Simulations - R13 LD 1.5 Figure 7 See in Dashboard
Name End Time Output Options
Simulation114 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry718258602 See in Dashboard
(Origin: 0.0, 0.0, -10.8; Extent: 15.5, 15.5, 11.0[um])
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

Specifications(Species) - R13 LD 0.5 Figure 7 See in Dashboard
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]
Specifications(Reaction) - R13 LD 0.5 Figure 7 See in Dashboard
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
Simulations - R13 LD 0.5 Figure 7 See in Dashboard
Name End Time Output Options
Simulation117 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry2134989892 See in Dashboard
(Origin: 0.0, 0.0, -10.8; Extent: 15.5, 15.5, 11.0[um])
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

Specifications(Species) - R16 LD 1.5Figure 7 See in Dashboard
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]
Specifications(Reaction) - R16 LD 1.5Figure 7 See in Dashboard
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
Simulations - R16 LD 1.5Figure 7 See in Dashboard
Name End Time Output Options
Simulation126 4000.0 [s]

OutputTimeStep 100.0

Copy of Simulation126 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry2124162823 See in Dashboard
(Origin: 0.0, 0.0, -8.3; Extent: 16.0, 16.0, 8.5[um])
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

Specifications(Species) - R16 LD 0.5 Figure 7 See in Dashboard
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]
Specifications(Reaction) - R16 LD 0.5 Figure 7 See in Dashboard
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
Simulations - R16 LD 0.5 Figure 7 See in Dashboard
Name End Time Output Options
Simulation131 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry383313442 See in Dashboard
(Origin: 0.0, 0.0, -8.3; Extent: 16.0, 16.0, 8.5[um])
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

Specifications(Species) - R10 Bottom wide Figure 7 See in Dashboard
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]
Specifications(Reaction) - R10 Bottom wide Figure 7 See in Dashboard
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
Simulations - R10 Bottom wide Figure 7 See in Dashboard
Name End Time Output Options
Simulation135 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry772610680 See in Dashboard
(Origin: 0.0, 0.0, -10.5; Extent: 10.2, 10.2, 10.7[um])
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

Specifications(Species) - R10 LD 0.5 Figure 7 See in Dashboard
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]
Specifications(Reaction) - R10 LD 0.5 Figure 7 See in Dashboard
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
Simulations - R10 LD 0.5 Figure 7 See in Dashboard
Name End Time Output Options
Simulation138 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1111278234 See in Dashboard
(Origin: 0.0, 0.0, -10.5; Extent: 10.2, 10.2, 10.7[um])
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

Specifications(Species) - R15 3D Figure 3, 4, and S7 See in Dashboard
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]
Specifications(Reaction) - R15 3D Figure 3, 4, and S7 See in Dashboard
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
Simulations - R15 3D Figure 3, 4, and S7 See in Dashboard
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

Geometry Geometry2011185638 See in Dashboard
(Origin: 0.0, 0.0, -9.2; Extent: 15.5, 15.5, 9.4[um])
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

Specifications(Species) - R13 3D figure 4 See in Dashboard
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]
Specifications(Reaction) - R13 3D figure 4 See in Dashboard
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
Simulations - R13 3D figure 4 See in Dashboard
Name End Time Output Options
R 13 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry1941832331 See in Dashboard
(Origin: 0.0, 0.0, -10.8; Extent: 15.5, 15.5, 11.0[um])
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

Specifications(Species) - R10 3D figure 4 See in Dashboard
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]
Specifications(Reaction) - R10 3D figure 4 See in Dashboard
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
Simulations - R10 3D figure 4 See in Dashboard
Name End Time Output Options
R 10 All 0.1,5.7,70E6 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry341658218 See in Dashboard
(Origin: 0.0, 0.0, -10.5; Extent: 10.2, 10.2, 10.7[um])
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

Specifications(Species) - R15 2D Fig 3, 4, and S7 See in Dashboard
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]
Specifications(Reaction) - R15 2D Fig 3, 4, and S7 See in Dashboard
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
Simulations - R15 2D Fig 3, 4, and S7 See in Dashboard
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

Geometry Geometry2016532892 See in Dashboard
(Origin: 0.0, 0.0, -9.2; Extent: 15.5, 15.5, 9.4[um])
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

Specifications(Species) - R16 LD 1Figure 7 See in Dashboard
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]
Specifications(Reaction) - R16 LD 1Figure 7 See in Dashboard
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
Simulations - R16 LD 1Figure 7 See in Dashboard
Name End Time Output Options
Simulation22 4000.0 [s]

OutputTimeStep 100.0

Geometry Geometry631983955 See in Dashboard
(Origin: 0.0, 0.0, -8.3; Extent: 16.0, 16.0, 8.5[um])
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

Specifications(Species) - R-25 FAK diffusion variation 3D substrate stiffness Figure S7 See in Dashboard
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]
Specifications(Reaction) - R-25 FAK diffusion variation 3D substrate stiffness Figure S7 See in Dashboard
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
Simulations - R-25 FAK diffusion variation 3D substrate stiffness Figure S7 See in Dashboard
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

Geometry Geometry53651429 See in Dashboard
(Origin: 0.0, 0.0, -5.8; Extent: 26.0, 26.0, 6.0[um])
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

Specifications(Species) - R-25 FAK diffusion variation 2D substrate stiffness Fig S7 See in Dashboard
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]
Specifications(Reaction) - R-25 FAK diffusion variation 2D substrate stiffness Fig S7 See in Dashboard
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
Simulations - R-25 FAK diffusion variation 2D substrate stiffness Fig S7 See in Dashboard
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

Geometry Geometry53651429 See in Dashboard
(Origin: 0.0, 0.0, -5.8; Extent: 26.0, 26.0, 6.0[um])
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

Global Parameters See in Dashboard
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]