ModelBricks - Model Print Page

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

BioModel ID - 200301683

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
RhoAGTP_MEMRhoAGDP	r3 PM	MassAction	RhoAGTP_MEMRhoAGDP
		reaction rate (J): ((Kf * RhoAGTP_MEM) - (Kr * RhoAGDP))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): kdp[s-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1]
ROCKROCKA	r4 PM	MassAction	ROCKROCKA
		reaction rate (J): ((Kf * ROCK) - (Kr * ROCKA))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (krp * RhoAGTP_MEM)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1]
mDiamDiaA	r5 PM	MassAction	mDiamDiaA
		reaction rate (J): ((Kf * mDia) - (Kr * mDiaA))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kmp * RhoAGTP_MEM)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1]
ROCKAROCK	r6 Cyto	MassAction	ROCKAROCK
		reaction rate (J): ((Kf * ROCKA) - (Kr * ROCK))[uM.s-1] forward rate constant (Kf): kdrock[s-1] reverse rate constant (Kr): 0.0[s-1]
LIMKLIMKA	r8 Cyto	MassAction	LIMKLIMKA
		reaction rate (J): ((Kf * LIMK) - (Kr * LIMKA))[uM.s-1] forward rate constant (Kf): (klr * (1.0 + (0.5 * tau * (1.0 + tanh((20.0 * (ROCKA - ROCKB)))) * ROCKA)))[s-1] reverse rate constant (Kr): kdl[s-1]
MyoMyoA	r9 Cyto	MassAction	MyoMyoA
		reaction rate (J): ((Kf * Myo) - (Kr * MyoA))[uM.s-1] forward rate constant (Kf): (kmr * (1.0 + (0.5 * epsilon * (1.0 + tanh((20.0 * (ROCKA - ROCKB)))) * ROCKA)))[s-1] reverse rate constant (Kr): kdmy[s-1]
CofilinPCofilinNP	r10 Cyto	MassAction	CofilinPCofilinNP
		reaction rate (J): ((Kf * CofilinP) - (Kr * CofilinNP))[uM.s-1] forward rate constant (Kf): kturnover[s-1] reverse rate constant (Kr): (kcatcof * LIMKA / (kmCof + CofilinNP))[s-1] user defined (kcatcof): 0.34[s-1.uM-1] user defined (kmCof): 4.0[uM]
GactinFcyto	r11 Cyto	MassAction	GactinFcyto
		reaction rate (J): ((Kf * Gactin) - (Kr * Fcyto))[uM.s-1] forward rate constant (Kf): (kra * (1.0 + (0.5 * alpha * (1.0 + tanh((20.0 * (mDiaA - mDiaB)))) * mDiaA)))[s-1] reverse rate constant (Kr): (kdep + (kfc1 * CofilinNP))[s-1]
mDiaAmDia	r7 Cyto	MassAction	mDiaAmDia
		reaction rate (J): ((Kf * mDiaA) - (Kr * mDia))[uM.s-1] forward rate constant (Kf): kdmdia[s-1] reverse rate constant (Kr): 0.0[s-1]
YAPTAZPYAPTAZN	r13 Cyto	MassAction	YAPTAZPYAPTAZN
		reaction rate (J): ((Kf * YAPTAZP) - (Kr * YAPTAZN))[uM.s-1] forward rate constant (Kf): (kCN + (kCY * MyoA * Fcyto))[s-1] reverse rate constant (Kr): kNC[s-1]
FakFakp	r12 PM	MassAction	FakFakp
		reaction rate (J): ((Kf * Fak) - (Kr * Fakp))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (ksf * Emol * unitconversionfactor * SAV * Positionboolean / (C + Emol))[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[molecules.um-2.s-1.uM-1]
FakpFak	r0 Cyto	MassAction	FakpFak
		reaction rate (J): ((Kf * Fakp) - (Kr * Fak))[uM.s-1] forward rate constant (Kf): kdf[s-1] reverse rate constant (Kr): 0.0[s-1]
RhoAGDPRhoAGTP_MEM	r1 PM	MassAction	RhoAGDPRhoAGTP_MEM
		reaction rate (J): ((Kf * RhoAGDP) - (Kr * RhoAGTP_MEM))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kfkp * (1.0 + (gamma * (Fakp ^ n2))) * unitconversionfactor * SAV * Positionboolean)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): 0.0[s-1] user defined (n2): 5.0[1]
FakFakp	r2 Cyto	MassAction	FakFakp
		reaction rate (J): ((Kf * Fak) - (Kr * Fakp))[uM.s-1] forward rate constant (Kf): kf[s-1] reverse rate constant (Kr): 0.0[s-1]
NPCNPCA	r14 NM	MassAction	NPCNPCA
		reaction rate (J): ((Kf * NPC) - (Kr * NPCA))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kfNPC * MyoA * Fcyto * LaminA)[s-1] reverse rate constant (Kr): krNPC[s-1]
LaminApLaminA	r15 NM	MassAction	LaminApLaminA
		reaction rate (J): ((Kf * LaminAp) - (Kr * LaminA))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): (kflaminA * Ecytosol / (Clamin + Ecytosol))[s-1] reverse rate constant (Kr): 0.001[s-1] user defined (kflaminA): 0.46[s-1] user defined (Ecytosol): (p * (Fcyto ^ 2.6))[1] user defined (p): 9.0E-6[tbd]
YAPTAZNYAPTAZnuc	r16 NM	MassAction	YAPTAZNYAPTAZnuc
		reaction rate (J): ((Kf * YAPTAZN) - (Kr * YAPTAZnuc))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] forward rate constant (Kf): ((kin2 * NPCA) + kinSolo2)[molecules.um-2.s-1.uM-1] reverse rate constant (Kr): kout2[molecules.um-2.s-1.uM-1] user defined (kin2): 10.0[s-1.uM-1] user defined (kinSolo2): 1.0[molecules.um-2.s-1.uM-1] user defined (kout2): 1.0[molecules.um-2.s-1.uM-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
Cyto	Compartment (+) (-)

Nuc	Compartment (+) (-)

ECM	Compartment (+) (-)

NM	Membrane N/A

PM	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
RhoAGTP_MEM	PM

Fakp	Cyto

RhoAGDP	Cyto

Fak	Cyto

ROCKA	Cyto

ROCK	Cyto

mDia	Cyto

mDiaA	Cyto

Myo	Cyto

MyoA	Cyto

LIMK	Cyto

CofilinP	Cyto

LIMKA	Cyto

CofilinNP	Cyto

Fcyto	Cyto

Gactin	Cyto

YAPTAZP	Cyto

YAPTAZN	Cyto

YAPTAZnuc	Nuc

Positionboolean	PM

NPCA	NM

NPC	NM

LaminA	NM

LaminAp	NM

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

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]