ModelBricks - Model Print Page

Name - Falkenberg_PodocyteStability

BioModel ID - 101963252

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
GaFa	posFeed c1	MassAction	GaFa
		reaction rate (J): ((Kf * Ga) - (Kr * Fa))[uM.s-1] forward rate constant (Kf): (alphaT * Loc * (Fa ^ 2.0) / ((k ^ 2.0) + (Fa ^ 2.0)))[s-1] reverse rate constant (Kr): 0.0[s-1]
FaBundle	nuclS c1	MassAction	FaBundle
		reaction rate (J): ((Kf * pow(Fa,2.0)) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): alpha2T[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1]
BundleGa	r2 c1	MassAction	BundleGa
		reaction rate (J): ((Kf * Bundle) - (Kr * Ga))[uM.s-1] forward rate constant (Kf): beta2T[s-1] reverse rate constant (Kr): 0.0[s-1]
Ga+FaFa	basal c1	MassAction	Ga+FaFa
		reaction rate (J): (((Kf * Ga) * Fa) - (Kr * Fa))[uM.s-1] forward rate constant (Kf): gammaT[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1]
C1Fa	nucl_corr c1	MassAction	C1Fa
		reaction rate (J): ((Kf * C1) - (Kr * Fa))[uM.s-1] forward rate constant (Kf): (gammaT * (Ga ^ 2.0))[s-1] reverse rate constant (Kr): 0.0[s-1]
C2Bundle	nuclS_corr c1	MassAction	C2Bundle
		reaction rate (J): ((Kf * C2) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): (alpha2T * (Fa ^ 2.0))[s-1] reverse rate constant (Kr): 0.0[s-1]
C1Fa	basal_corr c1	MassAction	C1Fa
		reaction rate (J): ((Kf * C1) - (Kr * Fa))[uM.s-1] forward rate constant (Kf): (gammaT * Ga * Fa)[s-1] reverse rate constant (Kr): 0.0[s-1]
C0Bundle	basalSF_corr c1	MassAction	C0Bundle
		reaction rate (J): ((Kf * C0) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): (Ga * Bundle * gamma2T)[s-1] reverse rate constant (Kr): 0.0[s-1]
GaFa	nucl c1	MassAction	GaFa
		reaction rate (J): ((Kf * pow(Ga,2.0)) - (Kr * Fa))[uM.s-1] forward rate constant (Kf): gammaT[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1]
FaGa	dep c1	MassAction	FaGa
		reaction rate (J): ((Kf * Fa) - (Kr * Ga))[uM.s-1] forward rate constant (Kf): betaT[s-1] reverse rate constant (Kr): 0.0[s-1]
Ga+BundleBundle	basalSF c1	MassAction	Ga+BundleBundle
		reaction rate (J): (((Kf * Ga) * Bundle) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): gamma2T[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1]
C2Bundle	basalFS_corr c1	MassAction	C2Bundle
		reaction rate (J): ((Kf * C2) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): (alpha2T * Fa * Bundle)[s-1] reverse rate constant (Kr): 0.0[s-1]
Fa+BundleBundle	basalFS c1	MassAction	Fa+BundleBundle
		reaction rate (J): (((Kf * Fa) * Bundle) - (Kr * Bundle))[uM.s-1] forward rate constant (Kf): alpha2T[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
c0	Compartment (+) (-)

c1	Compartment (+) (-)

Membrane0	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
C2	c1

Loc	c1

Ga	c1

Fa	c1

skeleton2	c1

skeleton	c1

Bundle	c1

Loc1	c1

perturb2	c1

perturb1	c1

locCorrection	c1

C1	c1

C0	c1

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
non-spatial	Deterministic (ODE) Compartmental
extra: simple test geometry. "few fingers"	Deterministic (ODE) Spatial (3D)	(copied from non-spat)
extra: generate initial condition; full geometry,no LocCorr	Deterministic (ODE) Spatial (3D)	(copied from few fingers) (copied from non-spat)
extra: tests, full geometry, no LocCorr: smaller pert region	Deterministic (ODE) Spatial (3D)	(copied from full geometry, no LocCorr) (copied from few fingers) (copied from non-spat)
extra: tests, full geometry, no LocCorr: uniform	Deterministic (ODE) Spatial (3D)	(copied from full geometry, no LocCorr: smaller pert region) (copied from full geometry, no LocCorr) (copied from few fingers) (copied from non-spat)
extra: simple test geometry. few fingers: uniform, pert n fix	Deterministic (ODE) Spatial (3D)	(copied from full geometry, no LocCorr: uniform, pert n fix) (copied from full geometry, no LocCorr: uniform) (copied from full geometry, no LocCorr: smaller pert region) (copied from full geometry, no LocCorr) (copied from few fingers) (copied from non-spat)
extra: test, import ic: of few fingers: uniform, pert n fix	Deterministic (ODE) Spatial (3D)	(copied from few fingers: uniform, pert n fix) (copied from full geometry, no LocCorr: uniform, pert n fix) (copied from full geometry, no LocCorr: uniform) (copied from full geometry, no LocCorr: smaller pert region) (copied from full geometry, no LocCorr) (copied from few fingers) (copied from non-spat)
Figures 3 and 6; with SS ic: full geometry,no LocCorr	Deterministic (ODE) Spatial (3D)	(copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z)	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)) (copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)) (copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)) (copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4	Deterministic (ODE) Spatial (3D)	(copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2) (copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)) (copied from with SS ic: full geometry,no LocCorr; perturb alpha(x,z)) (copied from with SS ic: full geometry,no LocCorr) (copied from full geometry,no LocCorr) (copied from few fingers) (copied from non-spat) use simulation ' My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC'

Application - non-spatial

Specifications(Species) - non-spatial See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	0.0 [um2/s]
Loc	1.0 [uM]	0.0 [um2/s]
Ga	1.0 [uM]	0.0 [um2/s]
Fa	0.0 [uM]	0.0 [um2/s]
skeleton2	0.0 [uM]	0.0 [um2/s]
skeleton	0.0 [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	0.0 [um2/s]
Loc1	0.0 [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	1.0 [uM]	0.0 [um2/s]
locCorrection	0.0 [uM]	0.0 [um2/s]
C1	1.0 [uM]	0.0 [um2/s]
C0	1.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - non-spatial See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - non-spatial See in Dashboard
Name	End Time	Output Options
Simulation0	500.0 [s]	KeepEvery 1 KeepAtMost 1000
high alpha2, followed by high alpha	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
high alpha2 followed by higher alpha	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
low beta2 followed by highr alpha	1500.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry non-spatial1601727147 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			Membrane0

Application - extra: simple test geometry. "few fingers"

Specifications(Species) - extra: simple test geometry. "few fingers" See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	((z <= 0.1) && (y >= 2.1)) [uM]	10.0 [um2/s]
Ga	1.0 [uM]	10.0 [um2/s]
Fa	0.0 [uM]	0.005 [um2/s]
skeleton2	0.0 [uM]	0.0 [um2/s]
skeleton	0.0 [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	(1.0E-20 + (0.005 * (y > 2.0))) [um2/s]
Loc1	0.0 [uM]	0.0 [um2/s]
perturb2	((y > 2.0) && (y < 3.5) && (x > 0.5) && (x < 1.1)) [uM]	0.0 [um2/s]
perturb1	((y > 2.0) && (x > 0.5) && (x < 1.1)) [uM]	0.0 [um2/s]
locCorrection	0.0 [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: simple test geometry. "few fingers" See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: simple test geometry. "few fingers" See in Dashboard
Name	End Time	Output Options
stable - test localization	500.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of stable - test localization	500.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of Copy of stable - test localization	500.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Geometry1511204787 See in Dashboard
(Origin: -0.9, 0.0, 0.0; Extent: 2.8, 5.0, 1.1[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain1		7.312150999999999 [um3]	c1
Volume	CSGObject	subdomain0		8.087848999999999 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	22.576389710071396 [um2]	Membrane0

Application - extra: generate initial condition; full geometry,no LocCorr

Specifications(Species) - extra: generate initial condition; full geometry,no LocCorr See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	1.0 [uM]	10.0 [um2/s]
Fa	0.0 [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	(z > 3.5) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: generate initial condition; full geometry,no LocCorr See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: generate initial condition; full geometry,no LocCorr See in Dashboard
Name	End Time	Output Options
good mesh (GM0): check loc	2.0E-5 [s]	KeepEvery 1 KeepAtMost 1000
GM0: try single stable point	2.0E-5 [s]	KeepEvery 1 KeepAtMost 1000
short, to check details	0.01 [s]	KeepEvery 1 KeepAtMost 1000
My19, increase alpha z>3.5; tmax=200	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of My19, increase alpha z>3.5;	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of My19, increase alpha z>3.5; change ic	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: tests, full geometry, no LocCorr: smaller pert region

Specifications(Species) - extra: tests, full geometry, no LocCorr: smaller pert region See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	1.0 [uM]	10.0 [um2/s]
Fa	0.0 [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	((z > 7.0) && (z < 13.0) && (x > 15.0)) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: tests, full geometry, no LocCorr: smaller pert region See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: tests, full geometry, no LocCorr: smaller pert region See in Dashboard
Name	End Time	Output Options
My19, increase alpha (7>z>13)&&(x>15);	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of My19, increase alpha (7>z>13)&&(x>15);	0.01 [s]	KeepEvery 1 KeepAtMost 1000
Copy of My19, increase alpha (7>z>13)&&(x>15); 1	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of My19, increase alpha (7>z>13)&&(x>15); 1, change ic	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
Copy of Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger	1500.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: tests, full geometry, no LocCorr: uniform

Specifications(Species) - extra: tests, full geometry, no LocCorr: uniform See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	1.0 [uM]	10.0 [um2/s]
Fa	0.0 [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	Loc [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: tests, full geometry, no LocCorr: uniform See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: tests, full geometry, no LocCorr: uniform See in Dashboard
Name	End Time	Output Options
testloc	0.01 [s]	KeepEvery 1 KeepAtMost 1000
peak in alpha	1200.0 [s]	KeepEvery 1 KeepAtMost 1000
change ic	1200.0 [s]	KeepEvery 1 KeepAtMost 1000
triggger at 800	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
change ic, tr 800	1500.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: simple test geometry. few fingers: uniform, pert n fix

Specifications(Species) - extra: simple test geometry. few fingers: uniform, pert n fix See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(y >= 2.1) [uM]	10.0 [um2/s]
Ga	1.0 [uM]	10.0 [um2/s]
Fa	0.0 [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	0.0 [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	Loc [uM]	0.0 [um2/s]
perturb1	Loc [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: simple test geometry. few fingers: uniform, pert n fix See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: simple test geometry. few fingers: uniform, pert n fix See in Dashboard
Name	End Time	Output Options
delay 200	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
delay 40	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
delay 500 - recovered	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
low beta2 - delay 200	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
low beta2 - delay 40	1500.0 [s]	KeepEvery 1 KeepAtMost 1000
low beta2 - delay 500 - recovered	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay3000 (st)-(p5)-(p6): still OK	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
(b) low beta2 - delay 2500 (st)-(p0)-(p4): too late	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(b) low beta2 - delay 1500 (st)-(p0)-(p4): dt2=2500	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(b) low beta2 - delay 2000 (st)-(p0)-(p4): dt2=3000	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay 4000 (st)-(p5)-(p6):	7000.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay 6000 (st)-(p5)-(p6):	9000.0 [s]	KeepEvery 1 KeepAtMost 1000
damage: p5 (IIA) ; recover delay3000	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
damage: p5 (IIA) ; recover delay4500	7000.0 [s]	KeepEvery 1 KeepAtMost 1000
damage: p0 (IIB) ; recover delay 500	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
damage: p0 (IIB) ; recover delay 1500	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ia) delay3000 (st)-(p5)-(p7)	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ia) delay4500 (st)-(p5)-(p7)	7000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ib) delay 500 (st)-(p0)-(p3)	5000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ib) delay 1500 (st)-(p0)-(p3)	5000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Geometry1511204787 See in Dashboard
(Origin: -0.9, 0.0, 0.0; Extent: 2.8, 5.0, 1.1[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain1		7.312150999999999 [um3]	c1
Volume	CSGObject	subdomain0		8.087848999999999 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	22.576389710071396 [um2]	Membrane0

Application - extra: test, import ic: of few fingers: uniform, pert n fix

Specifications(Species) - extra: test, import ic: of few fingers: uniform, pert n fix See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(y >= 2.1) [uM]	10.0 [um2/s]
Ga	vcField('__b___low_beta2___delay_2500__st___p0___p4___too_late', 'Ga', 5000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('__b___low_beta2___delay_2500__st___p0___p4___too_late', 'Fa', 5000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('__b___low_beta2___delay_2500__st___p0___p4___too_late', 'Bundle', 5000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	Loc [uM]	0.0 [um2/s]
perturb1	Loc [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: test, import ic: of few fingers: uniform, pert n fix See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: test, import ic: of few fingers: uniform, pert n fix See in Dashboard
Name	End Time	Output Options
try to copy ic	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry Geometry1511204787 See in Dashboard
(Origin: -0.9, 0.0, 0.0; Extent: 2.8, 5.0, 1.1[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain1		7.4771639576883375 [um3]	c1
Volume	CSGObject	subdomain0		7.922836042311659 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	22.952655091434444 [um2]	Membrane0

Application - Figures 3 and 6; with SS ic: full geometry,no LocCorr

Specifications(Species) - Figures 3 and 6; with SS ic: full geometry,no LocCorr See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	Loc [uM]	0.0 [um2/s]
perturb1	Loc [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - Figures 3 and 6; with SS ic: full geometry,no LocCorr See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - Figures 3 and 6; with SS ic: full geometry,no LocCorr See in Dashboard
Name	End Time	Output Options
keep extending to SS	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay3000 - Figure 3	4500.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay4500	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ia) delay3000	4500.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ia) delay4500	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
(IIa) delay3000	4500.0 [s]	KeepEvery 1 KeepAtMost 1000
(IIa) delay4500	6000.0 [s]	KeepEvery 1 KeepAtMost 1000
(b) delay500 - Figure6 ( i, j)	2000.0 [s]	KeepEvery 1 KeepAtMost 1000
(b) delay1500	3000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ib) delay500 - Figure 6 (f,g)	2000.0 [s]	KeepEvery 1 KeepAtMost 1000
(Ib) delay1500	3000.0 [s]	KeepEvery 1 KeepAtMost 1000
(IIb) delay500 - Figure 6 (d, e)	2000.0 [s]	KeepEvery 1 KeepAtMost 1000
(IIb) delay1500	3000.0 [s]	KeepEvery 1 KeepAtMost 1000
(a) delay3000 -fast diffusion G	4500.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z)

Specifications(Species) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	((Loc1 && !((skeleton2 \|\| skeleton))) * (1.0 + (Amp_SpatLocPert * (sin((0.5 * (x + z))) ^ 2.0)))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	(z > 3.5) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) See in Dashboard
Name	End Time	Output Options
keep alpha=0.32+(1+0.1*(Sin(x/2...))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
keep alpha=0.32+(1+0.5*(Sin(x/2...)	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
keep alpha=0.32+(1 - 0.5*(Sin(x/2...))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t)

Specifications(Species) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	((z < - 8.0) && (z > - 13.0) && (x > 7.0) && (x < 10.0)) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) See in Dashboard
Name	End Time	Output Options
-13<z<-7, 7>x>10	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r)

Specifications(Species) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	((Loc1 && !((skeleton2 \|\| skeleton))) * (1.0 + (Amp_SpatLocPert * exp( - (0.03333333333333333 * sqrt(((x ^ 2.0) + (z ^ 2.0)))))))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	(z > 3.5) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) See in Dashboard
Name	End Time	Output Options
amplitude (1+0.1exp(-r/30))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
amplitude (1+0.5 exp(-r/30))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
amplitude (1+0.75 exp(-r/30))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
amplitude (1+1 exp(-r/30))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
amplitude (1-0.5 exp(-r/30))	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1

Specifications(Species) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	((z < - 6.6) && (z > - 13.0) && (x > 7.0) && (x < 10.0)) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 See in Dashboard
Name	End Time	Output Options
-13<z < - 6.6, 7.0<x < 10.0	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
-13<z < - 6.6, 7.0<x < 10.0 (weaker stim)	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2

Specifications(Species) - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	((z < - 8.0) && (z > - 12.8) && (x > 1.5) && (x < 3.5)) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 See in Dashboard
Name	End Time	Output Options
-12.8<z<-8, 1.5>x>3.5	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3

Specifications(Species) - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	((z > 6.7) && (z < 13.0) && (x > 17.0) && (x < 18.5)) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 See in Dashboard
Name	End Time	Output Options
Simulation3	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
slower diff Ga: 5um2/s, as in BJ 2008, 95:1627-1638; Biophys. J. 75:2070�2078	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
faster diff Ga: 20um2/s	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Application - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4

Specifications(Species) - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 See in Dashboard
Species	Initial Condition	Diffusion Constant
C2	1.0 [uM]	10.0 [um2/s]
Loc	(Loc1 && !((skeleton2 \|\| skeleton))) [uM]	10.0 [um2/s]
Ga	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Ga', 1000.0, 'Volume') [uM]	10.0 [um2/s]
Fa	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Fa', 1000.0, 'Volume') [uM]	0.005 [um2/s]
skeleton2	(((z >= 3.5) && (z <= 18.0) && ((((( - 6.0 + x) / (0.8 * (1.92 - (0.055 * z)))) ^ 2.0) + ((y / (1.15 * (1.92 - (0.055 * z)))) ^ 2.0)) < 1.0)) \|\| ((y <= 2.0) && (((x >= 8.5) && (x <= 18.5) && ((((( - 3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * ( - 3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0)) + ((x >= 8.5) && (x <= 18.5) && (((((3.0 + z) / (0.8 * (2.252 - (0.072 * x)))) ^ 2.0) + ((y / (1.2 * (2.252 - (0.072 * x)))) ^ 2.0)) < 1.0)) + ((x >= 4.0) && (x <= 8.5) && ((((0.7621951219512196 * (3.0 + z)) ^ 2.0) + ((0.5081300813008132 * y) ^ 2.0)) < 1.0))))) [uM]	(1.0E-20 + (0.005 * Loc1)) [um2/s]
skeleton	((((z >= 4.0) && (z <= 14.0) && ((((1.3333333333333333 * ( - 12.5 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z >= - 1.9) && (z <= 11.0) && ((((1.4285714285714286 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((((0.015625 * (x ^ 2.0)) + (0.14792899408284022 * (y ^ 2.0)) + (0.015625 * (z ^ 2.0))) <= 1.0) && (y <= 2.0)) \|\| (((z >= 7.0) && (z <= 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0)) + ((z <= - 7.0) && (z >= - 20.0) && ((((1.5384615384615383 * ( - 2.75 + x)) ^ 2.0) + ((0.8333333333333334 * y) ^ 2.0)) < 1.0))) \|\| (((z <= - 3.0) && (z >= - 16.5) && ((((1.3333333333333333 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 16.5) && (z >= - 21.0) && ((((1.4285714285714286 * ( - 9.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 14.0) && ((((1.3333333333333333 * ( - 18.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0)) + ((z <= - 3.0) && (z >= - 9.0) && ((((1.4285714285714286 * ( - 25.0 + x)) ^ 2.0) + ((0.9090909090909091 * y) ^ 2.0)) < 1.0))) \|\| ((x >= 4.0) && (x <= 25.5) && ((((0.8695652173913044 * y) ^ 2.0) + ((1.4285714285714286 * (16.5 + z)) ^ 2.0)) < 1.0)) \|\| (((x >= 17.5) && (x <= 38.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 17.5) && (x <= 32.5) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * (3.0 + z)) ^ 2.0)) < 1.0)) + ((x >= 5.5) && (x <= 24.0) && ((((0.8333333333333334 * y) ^ 2.0) + ((1.5384615384615383 * ( - 17.3 + z)) ^ 2.0)) < 1.0)))) [uM]	0.0 [um2/s]
Bundle	vcField('My19__increase_alpha_z_3_5___forgot_coefAlp1______almost_SS__will_use_as_IC', 'Bundle', 1000.0, 'Volume') [uM]	(1.0E-20 + (0.005 * Loc)) [um2/s]
Loc1	(y > 1.1) [uM]	0.0 [um2/s]
perturb2	0.0 [uM]	0.0 [um2/s]
perturb1	(z > 3.5) [uM]	0.0 [um2/s]
locCorrection	(((x >= 5.4) && (x < 8.0) && (z > 7.0) && (z < 9.9)) \|\| ((x >= 5.5) && (x < 8.0) && (z >= 9.9) && (z < 13.9)) \|\| ((x >= 5.7) && (x < 8.0) && (z >= 13.9) && (z < 15.6)) \|\| ((z > - 7.8) && (z < 7.8) && (x < 8.0)) \|\| ((x > 7.0) && (x < 17.0) && (z > - 4.3) && (z < 3.8))) [uM]	0.0 [um2/s]
C1	1.0 [uM]	10.0 [um2/s]
C0	1.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 See in Dashboard
Name	Reaction Mapping
basalSF	included
basalFS_corr	included
posFeed	included
nuclS	included
r2	included
basal	included
nucl_corr	included
nuclS_corr	included
basal_corr	included
basalSF_corr	included
nucl	included
dep	included
basalFS	included

Simulations - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 See in Dashboard
Name	End Time	Output Options
Simulation6	1000.0 [s]	KeepEvery 1 KeepAtMost 1000
weaker pert	1000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry geom_20131101_170017 See in Dashboard
(Origin: 1.0, 0.0, -22.0; Extent: 40.0, 4.5, 43.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	subdomain1		529.9964622689193 [um3]	c1
Volume	Image	subdomain0		7210.0035377310805 [um3]	c0
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	1683.1412599207792 [um2]	Membrane0

Global Parameters

Global Parameters See in Dashboard
Name	Expression
gammaT	(gamma0 + (perturb1 * coef_gamma_p1 * funcoftime1) + (perturb2 * coef_gamma_p2 * funcoftime2))[tbd]

alphaT	(alpha0 + (perturb1 * coef_alpha_p1 * funcoftime1) + (perturb2 * coef_alpha_p2 * funcoftime2))[tbd]

k	0.22[tbd]

betaT	(beta + (perturb1 * coef_beta_p1 * funcoftime1) + (perturb2 * coef_beta_p2 * funcoftime2))[s-1]

beta2T	(beta2 + (perturb1 * coef_beta2_p1 * funcoftime1) + (perturb2 * coef_beta2_p2 * funcoftime2))[s-1]

alpha2T	(alpha2 + (perturb1 * coef_alpha2_p1 * funcoftime1) + (perturb2 * coef_alpha2_p2 * funcoftime2))[tbd]

gamma2T	(gamma2 + (perturb1 * coef_gamma2_p1 * funcoftime1) + (perturb2 * coef_gamma2_p2 * funcoftime2))[s-1.uM-1]

alpha0	0.3[tbd]

funcoftime	(1.0 + (on * (0.2 + (exp( - (0.01 * ( - 1000.0 + t))) * sin((0.01 * ( - 1000.0 + t))))) * (t > 1000.0)))[tbd]

tau	50.0[tbd]

tau2	10.0[tbd]

on	1.0[tbd]

coef_alpha_p1	0.0[tbd]

coef_alpha_p2	0.0[tbd]

coef_alpha2_p1	0.0[tbd]

coef_alpha2_p2	0.0[tbd]

coef_beta_p1	0.0[tbd]

coef_beta_p2	0.0[tbd]

coef_beta2_p1	0.0[tbd]

coef_beta2_p2	0.0[tbd]

coef_gamma_p1	0.0[tbd]

coef_gamma_p2	0.0[tbd]

coef_gamma2_p1	0.0[tbd]

coef_gamma2_p2	0.0[tbd]

gamma0	0.001[tbd]

tt1	100.0[tbd]

tt2	50.0[tbd]

funcoftime1	((t > trigger1) * ((exp( - (5.0 * (t - trigger1) / tt1)) * amp1_1 * sin(((t - trigger1) * _PI_ / tt1))) + (amp1_2 * (1.0 - exp( - (5.0 * (t - trigger1) / tt1))))))[tbd]

funcoftime2	((t > trigger2) * ((exp( - (5.0 * (t - trigger2) / tt2)) * amp2_1 * sin(((t - trigger2) * _PI_ / tt2))) + (amp2_2 * (1.0 - exp( - (5.0 * (t - trigger2) / tt2))))))[tbd]

amp1_1	1.0[tbd]

amp1_2	0.0[tbd]

amp2_1	1.0[tbd]

amp2_2	0.0[tbd]

trigger1	200.0[tbd]

trigger2	300.0[tbd]

beta	0.3[tbd]

gamma2	5.0E-4[tbd]

beta2	0.015[tbd]

alpha2	0.03[tbd]

Amp_SpatLocPert	0.1[tbd]