Dashboard

Name - Scott_Fraley_Rangamani_YAP_TAZ_model_2021(Rho and FAK confined simulations (true 2D)

BioModel ID - 200301683

Reaction Diagram

reactionDiagram

Physiology

Universal ID's Text Annotations

Applications

Applications See in Dashboard
Name Math Type Annotation
SA 314 2xD Fig 5,6 Deterministic (ODE) Spatial (3D) cloned from 'Small z R20 Bottom' owned by user kscott cloned from 'Small z R20 Bottom' owned by user kscott2 cloned from 'Small z R20 Bottom' owned by user kscott (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)
SA 490 2xD Fig 5,6 Deterministic (ODE) Spatial (3D) cloned from 'Small z R25 Bottom' owned by user kscott cloned from 'Small z R25 Bottom' owned by user kscott2 cloned from 'Small z R25 Bottom' owned by user kscott (copied from Small z R25) (copied from V200 All R25) (copied from V200 Bottom R25) (copied from V200-stiffness from the bottom increase SA) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)
SA 415 2xD Fig 5,6 Deterministic (ODE) Spatial (3D) cloned from 'Small z R23 Bottom' owned by user kscott cloned from 'Small z R23 Bottom' owned by user kscott2 cloned from 'Small z R23 Bottom' owned by user kscott (copied from Small z R23) (copied from Small z R25) (copied from V200 All R25) (copied from V200 Bottom R25) (copied from V200-stiffness from the bottom increase SA) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)
SA 250 2xD Fig 5,6 Deterministic (ODE) Spatial (3D) cloned from 'Small z R18 Bottom' owned by user kscott cloned from 'Small z R18 Bottom' owned by user kscott2 cloned from 'Small z R18 Bottom' owned by user kscott (copied from Small z R18) (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)
SA 200 2xD Fig 5,6 Deterministic (ODE) Spatial (3D) cloned from 'Small z R16 Bottom' owned by user kscott (copied from Small z R18 Bottom) cloned from 'Small z R18 Bottom' owned by user kscott2 cloned from 'Small z R18 Bottom' owned by user kscott (copied from Small z R18) (copied from Small z R20) (copied from V200-stiffness from the bottom R20) (copied from V200-stiffness from the bottom) (copied from V200) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)
Compartmental model Deterministic (ODE) Compartmental cloned from 'Compartmental model' owned by user kscott (copied from Small z R15 Bottom) cloned from 'Small z R15 Bottom' owned by user kscott2 cloned from 'Small z R15 Bottom' owned by user kscott (copied from Small z R15) (copied from V200 All R15) (copied from Idealized geometry-Stiffness From Bottom) (copied from Idealized geometry) (copied from Adjusted Triangle) (copied from Scaled geometry) (copied from Scaled geometry) (copied from V2: Axisymmetric: Stiffness All Over 1) (copied from Axisymmetric: Stiffness All Over ) (copied from Cell shape) cloned from 'Cell shape' owned by user khaffey (copied from Copy of Application0) (copied from Application0)

Application - SA 314 2xD Fig 5,6

Specifications(Species) - SA 314 2xD Fig 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 Fig 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 Fig 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 Fig 5,6

Specifications(Species) - SA 490 2xD Fig 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 Fig 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 Fig 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 - SA 415 2xD Fig 5,6

Specifications(Species) - SA 415 2xD Fig 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 Fig 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 Fig 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 Fig 5,6

Specifications(Species) - SA 250 2xD Fig 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 Fig 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 Fig 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 - SA 200 2xD Fig 5,6

Specifications(Species) - SA 200 2xD Fig 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 Fig 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 Fig 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 - 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

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

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 * Positionboolean)[s-1]
gamma 77.56[uM-5]
kdp 0.625[s-1]
krp 0.648[uM-1.s-1]
alpha 50.0[uM-1]
epsilon 36.0[uM-1]
kdep 3.5[s-1]
kdl 2.0[s-1]
kdmdia 0.005[s-1]
kdmy 0.067[s-1]
kdrock 0.8[s-1]
kfc1 4.0[uM-1.s-1]
k11 16.0[uM-1]
kmp 0.002[uM-1.s-1]
kra 0.4[s-1]
tau 55.49[uM-1]
kly 120.0[uM-1.s-1]
kmr 0.03[s-1]
kturnover 0.04[s-1]
ROCKB 0.3[uM]
mDiaB 0.165[uM]
klr 0.07[s-1]
kCN 0.56[s-1]
kCY 7.6E-4[uM-2.s-1]
kNC 0.14[s-1]
kll 16.0[uM-1]
unitconversionfactor 602.2[molecules.um-3.uM-1]
kf 0.015[s-1]
SAV 1.8[um]
kfNPC 2.8E-7[um2.s-1.uM-2.molecules-1]
krNPC 8.7[s-1]
Clamin 100.0[kPa]