Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| GaFa | posFeed | c1 | MassAction | |
| FaBundle | nuclS | c1 | MassAction | |
| BundleGa | r2 | c1 | MassAction | |
| Ga+FaFa | basal | c1 | MassAction | |
| C1Fa | nucl_corr | c1 | MassAction | |
| C2Bundle | nuclS_corr | c1 | MassAction | |
| C1Fa | basal_corr | c1 | MassAction | |
| C0Bundle | basalSF_corr | c1 | MassAction | |
| GaFa | nucl | c1 | MassAction | |
| FaGa | dep | c1 | MassAction | |
| Ga+BundleBundle | basalSF | c1 | MassAction | |
| C2Bundle | basalFS_corr | c1 | MassAction | |
| Fa+BundleBundle | basalFS | c1 | MassAction |
posFeed Universal ID's
posFeed Text Annotations
nuclS Universal ID's
nuclS Text Annotations
r2 Universal ID's
r2 Text Annotations
basal Universal ID's
basal Text Annotations
nucl_corr Universal ID's
nucl_corr Text Annotations
nuclS_corr Universal ID's
nuclS_corr Text Annotations
basal_corr Universal ID's
basal_corr Text Annotations
basalSF_corr Universal ID's
basalSF_corr Text Annotations
nucl Universal ID's
nucl Text Annotations
dep Universal ID's
dep Text Annotations
basalSF Universal ID's
basalSF Text Annotations
basalFS_corr Universal ID's
basalFS_corr Text Annotations
basalFS Universal ID's
basalFS Text Annotations
Expressions for posFeed
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]
global
alphaT
(alpha0 + (perturb1 * coef_alpha_p1 * funcoftime1) + (perturb2 * coef_alpha_p2 * funcoftime2)) [tbd]
global
k
0.22 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for nuclS
reaction rate
J
((Kf * pow(Fa,2.0)) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
alpha2T [s-1.uM-1]
global
alpha2T
(alpha2 + (perturb1 * coef_alpha2_p1 * funcoftime1) + (perturb2 * coef_alpha2_p2 * funcoftime2)) [tbd]
global
alpha2
0.03 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for r2
reaction rate
J
((Kf * Bundle) - (Kr * Ga)) [uM.s-1]
forward rate constant
Kf
beta2T [s-1]
global
beta2T
(beta2 + (perturb1 * coef_beta2_p1 * funcoftime1) + (perturb2 * coef_beta2_p2 * funcoftime2)) [s-1]
global
beta
0.3 [tbd]
global
beta2
0.015 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basal
reaction rate
J
(((Kf * Ga) * Fa) - (Kr * Fa)) [uM.s-1]
forward rate constant
Kf
gammaT [s-1.uM-1]
global
gammaT
(gamma0 + (perturb1 * coef_gamma_p1 * funcoftime1) + (perturb2 * coef_gamma_p2 * funcoftime2)) [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for nucl_corr
reaction rate
J
((Kf * C1) - (Kr * Fa)) [uM.s-1]
forward rate constant
Kf
(gammaT * (Ga ^ 2.0)) [s-1]
global
gammaT
(gamma0 + (perturb1 * coef_gamma_p1 * funcoftime1) + (perturb2 * coef_gamma_p2 * funcoftime2)) [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for nuclS_corr
reaction rate
J
((Kf * C2) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
(alpha2T * (Fa ^ 2.0)) [s-1]
global
alpha2T
(alpha2 + (perturb1 * coef_alpha2_p1 * funcoftime1) + (perturb2 * coef_alpha2_p2 * funcoftime2)) [tbd]
global
alpha2
0.03 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basal_corr
reaction rate
J
((Kf * C1) - (Kr * Fa)) [uM.s-1]
forward rate constant
Kf
(gammaT * Ga * Fa) [s-1]
global
gammaT
(gamma0 + (perturb1 * coef_gamma_p1 * funcoftime1) + (perturb2 * coef_gamma_p2 * funcoftime2)) [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basalSF_corr
reaction rate
J
((Kf * C0) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
(Ga * Bundle * gamma2T) [s-1]
global
gamma2T
(gamma2 + (perturb1 * coef_gamma2_p1 * funcoftime1) + (perturb2 * coef_gamma2_p2 * funcoftime2)) [s-1.uM-1]
global
gamma2
5.0E-4 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for nucl
reaction rate
J
((Kf * pow(Ga,2.0)) - (Kr * Fa)) [uM.s-1]
forward rate constant
Kf
gammaT [s-1.uM-1]
global
gammaT
(gamma0 + (perturb1 * coef_gamma_p1 * funcoftime1) + (perturb2 * coef_gamma_p2 * funcoftime2)) [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for dep
reaction rate
J
((Kf * Fa) - (Kr * Ga)) [uM.s-1]
forward rate constant
Kf
betaT [s-1]
global
betaT
(beta + (perturb1 * coef_beta_p1 * funcoftime1) + (perturb2 * coef_beta_p2 * funcoftime2)) [s-1]
global
beta
0.3 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basalSF
reaction rate
J
(((Kf * Ga) * Bundle) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
gamma2T [s-1.uM-1]
global
gamma2T
(gamma2 + (perturb1 * coef_gamma2_p1 * funcoftime1) + (perturb2 * coef_gamma2_p2 * funcoftime2)) [s-1.uM-1]
global
gamma2
5.0E-4 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basalFS_corr
reaction rate
J
((Kf * C2) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
(alpha2T * Fa * Bundle) [s-1]
global
alpha2T
(alpha2 + (perturb1 * coef_alpha2_p1 * funcoftime1) + (perturb2 * coef_alpha2_p2 * funcoftime2)) [tbd]
global
alpha2
0.03 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Expressions for basalFS
reaction rate
J
(((Kf * Fa) * Bundle) - (Kr * Bundle)) [uM.s-1]
forward rate constant
Kf
alpha2T [s-1.uM-1]
global
alpha2T
(alpha2 + (perturb1 * coef_alpha2_p1 * funcoftime1) + (perturb2 * coef_alpha2_p2 * funcoftime2)) [tbd]
global
alpha2
0.03 [tbd]
reverse rate constant
Kr
0.0 [s-1]
Structures
Membrane0 Universal ID's
Membrane0 Text Annotations
c0 Universal ID's
c0 Text Annotations
c1 Universal ID's
c1 Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| 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 |
C2 Universal ID's
C2 Text Annotations
Loc Universal ID's
Loc Text Annotations
Ga Universal ID's
Ga Text Annotations
Fa Universal ID's
Fa Text Annotations
skeleton2 Universal ID's
skeleton2 Text Annotations
skeleton Universal ID's
skeleton Text Annotations
Bundle Universal ID's
Bundle Text Annotations
Loc1 Universal ID's
Loc1 Text Annotations
perturb2 Universal ID's
perturb2 Text Annotations
perturb1 Universal ID's
perturb1 Text Annotations
locCorrection Universal ID's
locCorrection Text Annotations
C1 Universal ID's
C1 Text Annotations
C0 Universal ID's
C0 Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| non-spatial |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | |
| extra: simple test geometry. "few fingers" |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (3D) | (copied from non-spat) |
| extra: generate initial condition; full geometry,no LocCorr |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Spatial (3D) | (copied from few fingers) (copied from non-spat) |
| extra: tests, full geometry, no LocCorr: smaller pert region |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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) |
Specs -
Species Specs - Reaction Simulations |
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) |
Specs -
Species Specs - Reaction Simulations |
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) |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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 |
Specs -
Species Specs - Reaction Simulations |
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' |
non-spatial Universal ID's
non-spatial Text Annotations
extra: simple test geometry. "few fingers" Universal ID's
extra: simple test geometry. "few fingers" Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: test, import ic: of few fingers: uniform, pert n fix Universal ID's
extra: test, import ic: of few fingers: uniform, pert n fix Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Text Annotations
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) Universal ID's
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Universal ID's
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Text Annotations
extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 Universal ID's
extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 Text Annotations
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Universal ID's
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Text Annotations
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Universal ID's
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Text Annotations
Specifications (Species) - non-spatial go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 0.0 [um2/s] | c1 |
| Loc | 1.0 [uM] | 0.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 0.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.0 [um2/s] | c1 |
| skeleton2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| skeleton | 0.0 [uM] | 0.0 [um2/s] | c1 |
| Bundle | 0.0 [uM] | 0.0 [um2/s] | c1 |
| Loc1 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | 1.0 [uM] | 0.0 [um2/s] | c1 |
| locCorrection | 0.0 [uM] | 0.0 [um2/s] | c1 |
| C1 | 1.0 [uM] | 0.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 0.0 [um2/s] | c1 |
Specifications (Reaction) - non-spatial go to Simulations
Simulations - non-spatial go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 500.0 |
KeepEvery 1 KeepAtMost 1000 |
| high alpha2, followed by high alpha | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| high alpha2 followed by higher alpha | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| low beta2 followed by highr alpha | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
non-spatial Universal ID's
non-spatial Text Annotations
non-spatial Universal ID's
non-spatial Text Annotations
non-spatial Universal ID's
non-spatial Text Annotations
non-spatial Universal ID's
non-spatial Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1601727147
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: simple test geometry. "few fingers" go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | ((z <= 0.1) && (y >= 2.1)) [uM] | 10.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.005 [um2/s] | c1 |
| skeleton2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| skeleton | 0.0 [uM] | 0.0 [um2/s] | c1 |
| Bundle | 0.0 [uM] | (1.0E-20 + (0.005 * (y > 2.0))) [um2/s] | c1 |
| Loc1 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb2 | ((y > 2.0) && (y < 3.5) && (x > 0.5) && (x < 1.1)) [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((y > 2.0) && (x > 0.5) && (x < 1.1)) [uM] | 0.0 [um2/s] | c1 |
| locCorrection | 0.0 [uM] | 0.0 [um2/s] | c1 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: simple test geometry. "few fingers" go to Simulations
Simulations - extra: simple test geometry. "few fingers" go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| stable - test localization | 500.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of stable - test localization | 500.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of stable - test localization | 500.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: simple test geometry. "few fingers" Universal ID's
extra: simple test geometry. "few fingers" Text Annotations
extra: simple test geometry. "few fingers" Universal ID's
extra: simple test geometry. "few fingers" Text Annotations
extra: simple test geometry. "few fingers" Universal ID's
extra: simple test geometry. "few fingers" Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry Geometry1511204787
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: generate initial condition; full geometry,no LocCorr go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.005 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| Bundle | 0.0 [uM] | (1.0E-20 + (0.005 * Loc)) [um2/s] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | (z > 3.5) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: generate initial condition; full geometry,no LocCorr go to Simulations
Simulations - extra: generate initial condition; full geometry,no LocCorr go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| good mesh (GM0): check loc | 2.0E-5 |
KeepEvery 1 KeepAtMost 1000 |
| GM0: try single stable point | 2.0E-5 |
KeepEvery 1 KeepAtMost 1000 |
| short, to check details | 0.01 |
KeepEvery 1 KeepAtMost 1000 |
| My19, increase alpha z>3.5; tmax=200 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| My19, increase alpha z>3.5; (forgot coefAlp1!!) - almost SS, will use as IC | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of My19, increase alpha z>3.5; | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of My19, increase alpha z>3.5; change ic | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
extra: generate initial condition; full geometry,no LocCorr Universal ID's
extra: generate initial condition; full geometry,no LocCorr Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: tests, full geometry, no LocCorr: smaller pert region go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.005 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| Bundle | 0.0 [uM] | (1.0E-20 + (0.005 * Loc)) [um2/s] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((z > 7.0) && (z < 13.0) && (x > 15.0)) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: tests, full geometry, no LocCorr: smaller pert region go to Simulations
Simulations - extra: tests, full geometry, no LocCorr: smaller pert region go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| My19, increase alpha (7>z>13)&&(x>15); | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of My19, increase alpha (7>z>13)&&(x>15); | 0.01 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of My19, increase alpha (7>z>13)&&(x>15); 1 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of My19, increase alpha (7>z>13)&&(x>15); 1, change ic | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| Copy of Copy of Copy of My19, increase alpha (7>z>13)&&(x>15); - later trigger | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
extra: tests, full geometry, no LocCorr: smaller pert region Universal ID's
extra: tests, full geometry, no LocCorr: smaller pert region Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: tests, full geometry, no LocCorr: uniform go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.005 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| Bundle | 0.0 [uM] | (1.0E-20 + (0.005 * Loc)) [um2/s] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | Loc [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: tests, full geometry, no LocCorr: uniform go to Simulations
Simulations - extra: tests, full geometry, no LocCorr: uniform go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| testloc | 0.01 |
KeepEvery 1 KeepAtMost 1000 |
| peak in alpha | 1200.0 |
KeepEvery 1 KeepAtMost 1000 |
| change ic | 1200.0 |
KeepEvery 1 KeepAtMost 1000 |
| triggger at 800 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| change ic, tr 800 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
extra: tests, full geometry, no LocCorr: uniform Universal ID's
extra: tests, full geometry, no LocCorr: uniform Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: simple test geometry. few fingers: uniform, pert n fix go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (y >= 2.1) [uM] | 10.0 [um2/s] | c1 |
| Ga | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Fa | 0.0 [uM] | 0.005 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| Bundle | 0.0 [uM] | (1.0E-20 + (0.005 * Loc)) [um2/s] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | Loc [uM] | 0.0 [um2/s] | c1 |
| perturb1 | Loc [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: simple test geometry. few fingers: uniform, pert n fix go to Simulations
Simulations - extra: simple test geometry. few fingers: uniform, pert n fix go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| delay 200 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| delay 40 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| delay 500 - recovered | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| low beta2 - delay 200 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| low beta2 - delay 40 | 1500.0 |
KeepEvery 1 KeepAtMost 1000 |
| low beta2 - delay 500 - recovered | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay3000 (st)-(p5)-(p6): still OK | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (b) low beta2 - delay 2500 (st)-(p0)-(p4): too late | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (b) low beta2 - delay 1500 (st)-(p0)-(p4): dt2=2500 | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (b) low beta2 - delay 2000 (st)-(p0)-(p4): dt2=3000 | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay 4000 (st)-(p5)-(p6): | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay 6000 (st)-(p5)-(p6): | 9000.0 |
KeepEvery 1 KeepAtMost 1000 |
| damage: p5 (IIA) ; recover delay3000 | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| damage: p5 (IIA) ; recover delay4500 | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| damage: p0 (IIB) ; recover delay 500 | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| damage: p0 (IIB) ; recover delay 1500 | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ia) delay3000 (st)-(p5)-(p7) | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ia) delay4500 (st)-(p5)-(p7) | 7000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ib) delay 500 (st)-(p0)-(p3) | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ib) delay 1500 (st)-(p0)-(p3) | 5000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
extra: simple test geometry. few fingers: uniform, pert n fix Universal ID's
extra: simple test geometry. few fingers: uniform, pert n fix Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry Geometry1511204787
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: test, import ic: of few fingers: uniform, pert n fix go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (y >= 2.1) [uM] | 10.0 [um2/s] | c1 |
| Ga | vcField('__b___low_beta2___delay_2500__st___p0___p4___too_late', 'Ga', 5000.0, 'Volume') [uM] | 10.0 [um2/s] | c1 |
| Fa | vcField('__b___low_beta2___delay_2500__st___p0___p4___too_late', 'Fa', 5000.0, 'Volume') [uM] | 0.005 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | Loc [uM] | 0.0 [um2/s] | c1 |
| perturb1 | Loc [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: test, import ic: of few fingers: uniform, pert n fix go to Simulations
Simulations - extra: test, import ic: of few fingers: uniform, pert n fix go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| try to copy ic | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: test, import ic: of few fingers: uniform, pert n fix Universal ID's
extra: test, import ic: of few fingers: uniform, pert n fix Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry Geometry1511204787
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - Figures 3 and 6; with SS ic: full geometry,no LocCorr go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | Loc [uM] | 0.0 [um2/s] | c1 |
| perturb1 | Loc [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - Figures 3 and 6; with SS ic: full geometry,no LocCorr go to Simulations
Simulations - Figures 3 and 6; with SS ic: full geometry,no LocCorr go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| keep extending to SS | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay3000 - Figure 3 | 4500.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay4500 | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ia) delay3000 | 4500.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ia) delay4500 | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (IIa) delay3000 | 4500.0 |
KeepEvery 1 KeepAtMost 1000 |
| (IIa) delay4500 | 6000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (b) delay500 - Figure6 ( i, j) | 2000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (b) delay1500 | 3000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ib) delay500 - Figure 6 (f,g) | 2000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (Ib) delay1500 | 3000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (IIb) delay500 - Figure 6 (d, e) | 2000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (IIb) delay1500 | 3000.0 |
KeepEvery 1 KeepAtMost 1000 |
| (a) delay3000 -fast diffusion G | 4500.0 |
KeepEvery 1 KeepAtMost 1000 |
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Figures 3 and 6; with SS ic: full geometry,no LocCorr Universal ID's
Figures 3 and 6; with SS ic: full geometry,no LocCorr Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | ((Loc1 && !((skeleton2 || skeleton))) * (1.0 + (Amp_SpatLocPert * (sin((0.5 * (x + z))) ^ 2.0)))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | (z > 3.5) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) go to Simulations
Simulations - extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| keep alpha=0.32+(1+0.1*(Sin(x/2...)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| keep alpha=0.32+(1+0.5*(Sin(x/2...) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| keep alpha=0.32+(1 - 0.5*(Sin(x/2...)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(x,z) Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((z < - 8.0) && (z > - 13.0) && (x > 7.0) && (x < 10.0)) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) go to Simulations
Simulations - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| -13<z<-7, 7>x>10 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) Universal ID's
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t) Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | ((Loc1 && !((skeleton2 || skeleton))) * (1.0 + (Amp_SpatLocPert * exp( - (0.03333333333333333 * sqrt(((x ^ 2.0) + (z ^ 2.0)))))))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | (z > 3.5) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) go to Simulations
Simulations - extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| amplitude (1+0.1exp(-r/30)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| amplitude (1+0.5 exp(-r/30)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| amplitude (1+0.75 exp(-r/30)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| amplitude (1+1 exp(-r/30)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| amplitude (1-0.5 exp(-r/30)) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Universal ID's
extra: with SS ic: full geometry,no LocCorr; perturb alpha(r) Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((z < - 6.6) && (z > - 13.0) && (x > 7.0) && (x < 10.0)) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 go to Simulations
Simulations - extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| -13<z < - 6.6, 7.0<x < 10.0 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| -13<z < - 6.6, 7.0<x < 10.0 (weaker stim) | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Universal ID's
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Text Annotations
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Universal ID's
extra: variation of Fig.5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region1 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((z < - 8.0) && (z > - 12.8) && (x > 1.5) && (x < 3.5)) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 go to Simulations
Simulations - extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| -12.8<z<-8, 1.5>x>3.5 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 Universal ID's
extra: variation of Fig5. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 2 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | ((z > 6.7) && (z < 13.0) && (x > 17.0) && (x < 18.5)) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 go to Simulations
Simulations - Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation3 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| slower diff Ga: 5um2/s, as in BJ 2008, 95:1627-1638; Biophys. J. 75:2070�2078 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| faster diff Ga: 20um2/s | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Universal ID's
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Text Annotations
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Universal ID's
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Text Annotations
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Universal ID's
Figure 5 and Movie2. with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 3 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| C2 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| Loc | (Loc1 && !((skeleton2 || skeleton))) [uM] | 10.0 [um2/s] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| 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] | c1 |
| Loc1 | (y > 1.1) [uM] | 0.0 [um2/s] | c1 |
| perturb2 | 0.0 [uM] | 0.0 [um2/s] | c1 |
| perturb1 | (z > 3.5) [uM] | 0.0 [um2/s] | c1 |
| 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 |
| C1 | 1.0 [uM] | 10.0 [um2/s] | c1 |
| C0 | 1.0 [uM] | 10.0 [um2/s] | c1 |
Specifications (Reaction) - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 go to Simulations
Simulations - Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation6 | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
| weaker pert | 1000.0 |
KeepEvery 1 KeepAtMost 1000 |
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Universal ID's
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Text Annotations
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Universal ID's
Movie3 (variation of Fig. 5). with SS ic: full geometry,no LocCorr; perturb alpha(x,z,t), region 4 Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry geom_20131101_170017
(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 |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| 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] |