Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RhoAGTP_MEMRhoAGDP r3 PM MassAction
ROCKROCKA r4 PM MassAction
mDiamDiaA r5 PM MassAction
ROCKAROCK r6 Cyto MassAction
LIMKLIMKA r8 Cyto MassAction
MyoMyoA r9 Cyto MassAction
CofilinPCofilinNP r10 Cyto MassAction
GactinFcyto r11 Cyto MassAction
mDiaAmDia r7 Cyto MassAction
YAPTAZPYAPTAZN r13 Cyto MassAction
FakFakp r12 PM MassAction
FakpFak r0 Cyto MassAction
RhoAGDPRhoAGTP_MEM r1 PM MassAction
FakFakp r2 Cyto MassAction
NPCNPCA r14 NM MassAction
LaminApLaminA r15 NM MassAction
YAPTAZNYAPTAZnuc r16 NM MassAction

r3 Universal ID's

r3 Text Annotations

r4 Universal ID's

r4 Text Annotations

r5 Universal ID's

r5 Text Annotations

r6 Universal ID's

r6 Text Annotations

r8 Universal ID's

r8 Text Annotations

r9 Universal ID's

r9 Text Annotations

r10 Universal ID's

r10 Text Annotations

r11 Universal ID's

r11 Text Annotations

r7 Universal ID's

r7 Text Annotations

r13 Universal ID's

r13 Text Annotations

r12 Universal ID's

r12 Text Annotations

r0 Universal ID's

r0 Text Annotations

r1 Universal ID's

r1 Text Annotations

r2 Universal ID's

r2 Text Annotations

r14 Universal ID's

r14 Text Annotations

r15 Universal ID's

r15 Text Annotations

r16 Universal ID's

r16 Text Annotations

Expressions for r3

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]

global

kdp

0.625 [s-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Expressions for r4

reaction rate

J

((Kf * ROCK) - (Kr * ROCKA)) [molecules.um-2.s-1]

global

C

3.25 [kPa]

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]

global

krp

0.648 [uM-1.s-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Expressions for r5

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]

global

kmp

0.002 [uM-1.s-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Expressions for r6

reaction rate

J

((Kf * ROCKA) - (Kr * ROCK)) [uM.s-1]

global

C

3.25 [kPa]

forward rate constant

Kf

kdrock [s-1]

global

kdrock

0.8 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for r8

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]

global

C

3.25 [kPa]

global

tau

55.49 [uM-1]

global

ROCKB

0.3 [uM]

global

klr

0.07 [s-1]

reverse rate constant

Kr

kdl [s-1]

global

kdl

2.0 [s-1]

Expressions for r9

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]

global

C

3.25 [kPa]

global

epsilon

36.0 [uM-1]

global

kmr

0.03 [s-1]

global

ROCKB

0.3 [uM]

reverse rate constant

Kr

kdmy [s-1]

global

kdmy

0.067 [s-1]

Expressions for r10

reaction rate

J

((Kf * CofilinP) - (Kr * CofilinNP)) [uM.s-1]

global

C

3.25 [kPa]

forward rate constant

Kf

kturnover [s-1]

global

kturnover

0.04 [s-1]

reverse rate constant

Kr

(kcatcof * LIMKA / (kmCof + CofilinNP)) [s-1]

global

C

3.25 [kPa]

local

kcatcof

0.34 [s-1.uM-1]

local

kmCof

4.0 [uM]

Expressions for r11

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]

global

alpha

50.0 [uM-1]

global

kra

0.4 [s-1]

global

mDiaB

0.165 [uM]

reverse rate constant

Kr

(kdep + (kfc1 * CofilinNP)) [s-1]

global

C

3.25 [kPa]

global

kdep

3.5 [s-1]

global

kfc1

4.0 [uM-1.s-1]

global

kf

0.015 [s-1]

Expressions for r7

reaction rate

J

((Kf * mDiaA) - (Kr * mDia)) [uM.s-1]

forward rate constant

Kf

kdmdia [s-1]

global

kdmdia

0.005 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for r13

reaction rate

J

((Kf * YAPTAZP) - (Kr * YAPTAZN)) [uM.s-1]

forward rate constant

Kf

(kCN + (kCY * MyoA * Fcyto)) [s-1]

global

C

3.25 [kPa]

global

kCN

0.56 [s-1]

global

kCY

7.6E-4 [uM-2.s-1]

reverse rate constant

Kr

kNC [s-1]

global

C

3.25 [kPa]

global

kNC

0.14 [s-1]

Expressions for r12

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]

global

ksf

0.379 [s-1]

global

C

3.25 [kPa]

global

Emol

25.0 [kPa]

global

unitconversionfactor

602.2 [molecules.um-3.uM-1]

global

SAV

1.8 [um]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Expressions for r0

reaction rate

J

((Kf * Fakp) - (Kr * Fak)) [uM.s-1]

forward rate constant

Kf

kdf [s-1]

global

kdf

0.035 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for r1

reaction rate

J

((Kf * RhoAGDP) - (Kr * RhoAGTP_MEM)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

forward rate constant

Kf

(kfkp * (1.0 + (gamma * (Fakp ^ n2))) * unitconversionfactor * SAV * Positionboolean) [molecules.um-2.s-1.uM-1]

global

kfkp

(0.0168 * Positionboolean) [s-1]

global

gamma

77.56 [uM-5]

global

unitconversionfactor

602.2 [molecules.um-3.uM-1]

global

kf

0.015 [s-1]

global

SAV

1.8 [um]

reverse rate constant

Kr

0.0 [s-1]

local

n2

5.0 [1]

Expressions for r2

reaction rate

J

((Kf * Fak) - (Kr * Fakp)) [uM.s-1]

forward rate constant

Kf

kf [s-1]

global

kf

0.015 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for r14

reaction rate

J

((Kf * NPC) - (Kr * NPCA)) [molecules.um-2.s-1]

global

C

3.25 [kPa]

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]

global

C

3.25 [kPa]

global

kf

0.015 [s-1]

global

kfNPC

2.8E-7 [um2.s-1.uM-2.molecules-1]

reverse rate constant

Kr

krNPC [s-1]

global

C

3.25 [kPa]

global

krNPC

8.7 [s-1]

Expressions for r15

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]

global

C

3.25 [kPa]

global

kf

0.015 [s-1]

global

Clamin

100.0 [kPa]

reverse rate constant

Kr

0.001 [s-1]

local

kflaminA

0.46 [s-1]

local

Ecytosol

(p * (Fcyto ^ 2.6)) [1]

local

p

9.0E-6 [tbd]

Expressions for r16

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]

global

C

3.25 [kPa]

reverse rate constant

Kr

kout2 [molecules.um-2.s-1.uM-1]

local

kin2

10.0 [s-1.uM-1]

local

kinSolo2

1.0 [molecules.um-2.s-1.uM-1]

local

kout2

1.0 [molecules.um-2.s-1.uM-1]

Structures

Name
Type
Electrical
NM Membrane (+)   (-)
PM Membrane (+)   (-)
Cyto Compartment (+)   (-)
Nuc Compartment (+)   (-)
ECM Compartment (+)   (-)

NM Universal ID's

NM Text Annotations

PM Universal ID's

PM Text Annotations

Cyto Universal ID's

Cyto Text Annotations

Nuc Universal ID's

Nuc Text Annotations

ECM Universal ID's

ECM Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
RhoAGTP_MEM PM PM
Fakp Cyto Cyto
RhoAGDP Cyto Cyto
Fak Cyto Cyto
ROCKA Cyto Cyto
ROCK Cyto Cyto
mDia Cyto Cyto
mDiaA Cyto Cyto
Myo Cyto Cyto
MyoA Cyto Cyto
LIMK Cyto Cyto
CofilinP Cyto Cyto
LIMKA Cyto Cyto
CofilinNP Cyto Cyto
Fcyto Cyto Cyto
Gactin Cyto Cyto
YAPTAZP Cyto Cyto
YAPTAZN Cyto Cyto
YAPTAZnuc Nuc Nuc
Positionboolean PM PM
NPCA NM NM
NPC NM NM
LaminA NM NM
LaminAp NM NM

RhoAGTP_MEM Universal ID's

RhoAGTP_MEM Text Annotations

Fakp Universal ID's

Fakp Text Annotations

RhoAGDP Universal ID's

RhoAGDP Text Annotations

Fak Universal ID's

Fak Text Annotations

ROCKA Universal ID's

ROCKA Text Annotations

ROCK Universal ID's

ROCK Text Annotations

mDia Universal ID's

mDia Text Annotations

mDiaA Universal ID's

mDiaA Text Annotations

Myo Universal ID's

Myo Text Annotations

MyoA Universal ID's

MyoA Text Annotations

LIMK Universal ID's

LIMK Text Annotations

CofilinP Universal ID's

CofilinP Text Annotations

LIMKA Universal ID's

LIMKA Text Annotations

CofilinNP Universal ID's

CofilinNP Text Annotations

Fcyto Universal ID's

Fcyto Text Annotations

Gactin Universal ID's

Gactin Text Annotations

YAPTAZP Universal ID's

YAPTAZP Text Annotations

YAPTAZN Universal ID's

YAPTAZN Text Annotations

YAPTAZnuc Universal ID's

YAPTAZnuc Text Annotations

Positionboolean Universal ID's

Positionboolean Text Annotations

NPCA Universal ID's

NPCA Text Annotations

NPC Universal ID's

NPC Text Annotations

LaminA Universal ID's

LaminA Text Annotations

LaminAp Universal ID's

LaminAp Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
SA 314 2xD Fig 5,6 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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)

SA 314 2xD Fig 5,6 Universal ID's

SA 314 2xD Fig 5,6 Text Annotations

SA 490 2xD Fig 5,6 Universal ID's

SA 490 2xD Fig 5,6 Text Annotations

SA 415 2xD Fig 5,6 Universal ID's

SA 415 2xD Fig 5,6 Text Annotations

SA 250 2xD Fig 5,6 Universal ID's

SA 250 2xD Fig 5,6 Text Annotations

SA 200 2xD Fig 5,6 Universal ID's

SA 200 2xD Fig 5,6 Text Annotations

Compartmental model Universal ID's

Compartmental model Text Annotations

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

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 10.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 10.0 [um2/s] Cyto
Fak 0.7 [uM] 10.0 [um2/s] Cyto
ROCKA 0.0 [uM] 75.0 [um2/s] Cyto
ROCK 1.0 [uM] 75.0 [um2/s] Cyto
mDia 0.8 [uM] 10.0 [um2/s] Cyto
mDiaA 0.0 [uM] 10.0 [um2/s] Cyto
Myo 3.5 [uM] 10.0 [um2/s] Cyto
MyoA 1.5 [uM] 10.0 [um2/s] Cyto
LIMK 1.9 [uM] 10.0 [um2/s] Cyto
CofilinP 0.2 [uM] 10.0 [um2/s] Cyto
LIMKA 0.1 [uM] 10.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 10.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.6 [um2/s] Cyto
Gactin 482.4 [uM] 13.37 [um2/s] Cyto
YAPTAZP 0.2 [uM] 19.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 19.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 19.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.001 [um2/s] NM
NPC 6.5 [uM] 0.001 [um2/s] NM
LaminA 0.0 [uM] 0.001 [um2/s] NM
LaminAp 3500.0 [uM] 0.001 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.348 [um2/s] PM
Positionboolean (z >= - 0.001) [uM] 0.0 [um2/s] PM

Specifications (Reaction) - SA 314 2xD Fig 5,6 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
R 20 Bot 0.1,5.7,70E6 4000.0

OutputTimeStep 100.0

SA 314 2xD Fig 5,6 Universal ID's

SA 314 2xD Fig 5,6 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1221349153

(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

Events

Name Variable Rate Expression

Specifications (Species) - SA 490 2xD Fig 5,6 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 10.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 10.0 [um2/s] Cyto
Fak 0.7 [uM] 10.0 [um2/s] Cyto
ROCKA 0.0 [uM] 75.0 [um2/s] Cyto
ROCK 1.0 [uM] 75.0 [um2/s] Cyto
mDia 0.8 [uM] 10.0 [um2/s] Cyto
mDiaA 0.0 [uM] 10.0 [um2/s] Cyto
Myo 3.5 [uM] 10.0 [um2/s] Cyto
MyoA 1.5 [uM] 10.0 [um2/s] Cyto
LIMK 1.9 [uM] 10.0 [um2/s] Cyto
CofilinP 0.2 [uM] 10.0 [um2/s] Cyto
LIMKA 0.1 [uM] 10.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 10.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.6 [um2/s] Cyto
Gactin 482.4 [uM] 13.37 [um2/s] Cyto
YAPTAZP 0.2 [uM] 19.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 19.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 19.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.001 [um2/s] NM
NPC 6.5 [uM] 0.001 [um2/s] NM
LaminA 0.0 [uM] 0.001 [um2/s] NM
LaminAp 3500.0 [uM] 0.001 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.348 [um2/s] PM
Positionboolean (z >= - 0.01) [uM] 0.0 [um2/s] PM

Specifications (Reaction) - SA 490 2xD Fig 5,6 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
R 25 Bot 0.1,5.7,70E6 4000.0

OutputTimeStep 100.0

SA 490 2xD Fig 5,6 Universal ID's

SA 490 2xD Fig 5,6 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry53651429

(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

Events

Name Variable Rate Expression

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

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 10.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 10.0 [um2/s] Cyto
Fak 0.7 [uM] 10.0 [um2/s] Cyto
ROCKA 0.0 [uM] 75.0 [um2/s] Cyto
ROCK 1.0 [uM] 75.0 [um2/s] Cyto
mDia 0.8 [uM] 10.0 [um2/s] Cyto
mDiaA 0.0 [uM] 10.0 [um2/s] Cyto
Myo 3.5 [uM] 10.0 [um2/s] Cyto
MyoA 1.5 [uM] 10.0 [um2/s] Cyto
LIMK 1.9 [uM] 10.0 [um2/s] Cyto
CofilinP 0.2 [uM] 10.0 [um2/s] Cyto
LIMKA 0.1 [uM] 10.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 10.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.6 [um2/s] Cyto
Gactin 482.4 [uM] 13.37 [um2/s] Cyto
YAPTAZP 0.2 [uM] 19.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 19.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 19.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.001 [um2/s] NM
NPC 6.5 [uM] 0.001 [um2/s] NM
LaminA 0.0 [uM] 0.001 [um2/s] NM
LaminAp 3500.0 [uM] 0.001 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.348 [um2/s] PM
Positionboolean (z >= - 0.1) [uM] 0.0 [um2/s] PM

Specifications (Reaction) - SA 415 2xD Fig 5,6 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
R 23 Bot 0.1,5.7,70E6 4000.0

OutputTimeStep 100.0

SA 415 2xD Fig 5,6 Universal ID's

SA 415 2xD Fig 5,6 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry914749205

(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

Events

Name Variable Rate Expression

Specifications (Species) - SA 250 2xD Fig 5,6 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 10.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 10.0 [um2/s] Cyto
Fak 0.7 [uM] 10.0 [um2/s] Cyto
ROCKA 0.0 [uM] 75.0 [um2/s] Cyto
ROCK 1.0 [uM] 75.0 [um2/s] Cyto
mDia 0.8 [uM] 10.0 [um2/s] Cyto
mDiaA 0.0 [uM] 10.0 [um2/s] Cyto
Myo 3.5 [uM] 10.0 [um2/s] Cyto
MyoA 1.5 [uM] 10.0 [um2/s] Cyto
LIMK 1.9 [uM] 10.0 [um2/s] Cyto
CofilinP 0.2 [uM] 10.0 [um2/s] Cyto
LIMKA 0.1 [uM] 10.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 10.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.6 [um2/s] Cyto
Gactin 482.4 [uM] 13.37 [um2/s] Cyto
YAPTAZP 0.2 [uM] 19.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 19.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 19.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.001 [um2/s] NM
NPC 6.5 [uM] 0.001 [um2/s] NM
LaminA 0.0 [uM] 0.001 [um2/s] NM
LaminAp 3500.0 [uM] 0.001 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.348 [um2/s] PM
Positionboolean (z >= - 0.08) [uM] 0.0 [um2/s] PM

Specifications (Reaction) - SA 250 2xD Fig 5,6 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
R 18 Bot 0.1,5.7,70E6 4000.0

OutputTimeStep 100.0

SA 250 2xD Fig 5,6 Universal ID's

SA 250 2xD Fig 5,6 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry156779672

(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

Events

Name Variable Rate Expression

Specifications (Species) - SA 200 2xD Fig 5,6 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 10.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 10.0 [um2/s] Cyto
Fak 0.7 [uM] 10.0 [um2/s] Cyto
ROCKA 0.0 [uM] 75.0 [um2/s] Cyto
ROCK 1.0 [uM] 75.0 [um2/s] Cyto
mDia 0.8 [uM] 10.0 [um2/s] Cyto
mDiaA 0.0 [uM] 10.0 [um2/s] Cyto
Myo 3.5 [uM] 10.0 [um2/s] Cyto
MyoA 1.5 [uM] 10.0 [um2/s] Cyto
LIMK 1.9 [uM] 10.0 [um2/s] Cyto
CofilinP 0.2 [uM] 10.0 [um2/s] Cyto
LIMKA 0.1 [uM] 10.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 10.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.6 [um2/s] Cyto
Gactin 482.4 [uM] 13.37 [um2/s] Cyto
YAPTAZP 0.2 [uM] 19.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 19.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 19.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.001 [um2/s] NM
NPC 6.5 [uM] 0.001 [um2/s] NM
LaminA 0.0 [uM] 0.001 [um2/s] NM
LaminAp 3500.0 [uM] 0.001 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.0 [um2/s] PM
Positionboolean (z >= - 0.008) [uM] 0.0 [um2/s] PM

Specifications (Reaction) - SA 200 2xD Fig 5,6 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
R 16 Bot 0.1,5.7,70E6 4000.0

OutputTimeStep 100.0

SA 200 2xD Fig 5,6 Universal ID's

SA 200 2xD Fig 5,6 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1502075650

(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

Events

Name Variable Rate Expression

Specifications (Species) - Compartmental model go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Fakp 0.3 [uM] 0.0 [um2/s] Cyto
RhoAGDP 1.0 [uM] 0.0 [um2/s] Cyto
Fak 0.7 [uM] 0.0 [um2/s] Cyto
ROCKA 0.0 [uM] 0.0 [um2/s] Cyto
ROCK 1.0 [uM] 0.0 [um2/s] Cyto
mDia 0.8 [uM] 0.0 [um2/s] Cyto
mDiaA 0.0 [uM] 0.0 [um2/s] Cyto
Myo 3.5 [uM] 0.0 [um2/s] Cyto
MyoA 1.5 [uM] 0.0 [um2/s] Cyto
LIMK 1.9 [uM] 0.0 [um2/s] Cyto
CofilinP 0.2 [uM] 0.0 [um2/s] Cyto
LIMKA 0.1 [uM] 0.0 [um2/s] Cyto
CofilinNP 1.8 [uM] 0.0 [um2/s] Cyto
Fcyto 17.9 [uM] 0.0 [um2/s] Cyto
Gactin 482.4 [uM] 0.0 [um2/s] Cyto
YAPTAZP 0.2 [uM] 0.0 [um2/s] Cyto
YAPTAZN 0.7 [uM] 0.0 [um2/s] Cyto
YAPTAZnuc 0.7 [uM] 0.0 [um2/s] Nuc
NPCA 0.0 [uM] 0.0 [um2/s] NM
NPC 6.5 [uM] 0.0 [um2/s] NM
LaminA 0.0 [uM] 0.0 [um2/s] NM
LaminAp 3500.0 [uM] 0.0 [um2/s] NM
RhoAGTP_MEM 33.6 [uM] 0.0 [um2/s] PM
Positionboolean 1.0 [uM] 0.0 [um2/s] PM

Specifications (Reaction) - Compartmental model go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Parameter scan over stiffness 2000.0

OutputTimeStep 100.0

Compartmental model Universal ID's

Compartmental model Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry nonspatial898778521

(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

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
ksf 0.379[s-1]
C 3.25[kPa]
Emol 25.0[kPa]
kdf 0.035[s-1]
kfkp (0.0168 * Positionboolean)[s-1]
gamma 77.56[uM-5]
kdp 0.625[s-1]
krp 0.648[uM-1.s-1]
alpha 50.0[uM-1]
epsilon 36.0[uM-1]
kdep 3.5[s-1]
kdl 2.0[s-1]
kdmdia 0.005[s-1]
kdmy 0.067[s-1]
kdrock 0.8[s-1]
kfc1 4.0[uM-1.s-1]
k11 16.0[uM-1]
kmp 0.002[uM-1.s-1]
kra 0.4[s-1]
tau 55.49[uM-1]
kly 120.0[uM-1.s-1]
kmr 0.03[s-1]
kturnover 0.04[s-1]
ROCKB 0.3[uM]
mDiaB 0.165[uM]
klr 0.07[s-1]
kCN 0.56[s-1]
kCY 7.6E-4[uM-2.s-1]
kNC 0.14[s-1]
kll 16.0[uM-1]
unitconversionfactor 602.2[molecules.um-3.uM-1]
kf 0.015[s-1]
SAV 1.8[um]
kfNPC 2.8E-7[um2.s-1.uM-2.molecules-1]
krNPC 8.7[s-1]
Clamin 100.0[kPa]

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