Reaction Diagram
Physiology
| Universal ID's | Text Annotations |
|---|---|
|
|
|
| Reaction |
Name
Structure
|
Kinetics | Depiction |
|---|---|---|---|
| cAMP_best+PDE_CytoPDE_cAMP |
r0
Cyto
|
MassAction | cAMP_best+PDE_CytoPDE_cAMP |
|
|
|
reaction rate (J): (((Kf * cAMP_best) * PDE_Cyto) - (Kr * PDE_cAMP))[uM.s-1]
forward rate constant (Kf): 12.0[s-1.uM-1] reverse rate constant (Kr): 58.82[s-1] |
|
| PDE_cAMPPDE_Cyto |
r1
Cyto
|
MassAction | PDE_cAMPPDE_Cyto |
|
|
|
reaction rate (J): ((Kf * PDE_cAMP) - (Kr * PDE_Cyto))[uM.s-1]
forward rate constant (Kf): 14.7[s-1] reverse rate constant (Kr): 0.0[s-1] |
|
| s0cAMP_best |
r2
Cyto
|
MassAction | s0cAMP_best |
|
|
|
reaction rate (J): ((Kf * s0) - (Kr * cAMP_best))[uM.s-1]
forward rate constant (Kf): (1.0 - ((1.0 / 2.0) + (1.0 / 3.14 * atan((100.0 * cAMP_best)))))[s-1] reverse rate constant (Kr): 0.0[s-1] |
| Name |
Type
Electrical (Membrane Polarity)
|
|---|---|
| SR |
Compartment
(+) (-)
|
|
|
|
| Unnamed compartment |
Compartment
(+) (-)
|
|
|
|
| ttube |
Compartment
(+) (-)
|
|
|
|
| mito2 |
Compartment
(+) (-)
|
|
|
|
| ttube2 |
Compartment
(+) (-)
|
|
|
|
| Cyto |
Compartment
(+) (-)
|
|
|
|
| mito |
Compartment
(+) (-)
|
|
|
|
| bests |
Membrane
N/A
|
|
|
|
| tttt |
Membrane
N/A
|
|
|
|
| Membrane0 |
Membrane
N/A
|
|
|
|
| Membrane1 |
Membrane
N/A
|
|
|
|
| Membrane2 |
Membrane
N/A
|
|
|
|
| Membrane3 |
Membrane
N/A
|
|
|
|
| Name | Structure | BioNetGen Definition |
|---|---|---|
| PDE_cAMP | Cyto | |
|
|
|
|
| PDE_Cyto | Cyto | |
|
|
|
|
| cAMP_best | Cyto | |
|
|
|
|
| s0 | Cyto | |
|
|
|
| Name | Text Annotations | BioNetGen Definition |
|---|
| Name |
Type
Count
|
BioNetGen Definition |
|---|
Applications
| Name | Math Type | Annotation |
|---|---|---|
| Correct PDE conc. with new geo with crop correct size | Deterministic (ODE) Spatial (3D) | cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user schaff cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test) |
| Copy of Correct PDE conc. with new geo with crop correct size | Deterministic (ODE) Spatial (3D) | cloned from 'Copy of Correct PDE conc. with new geo with crop correct size' owned by user schaff cloned from 'Copy of Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from Correct PDE conc. with new geo with crop correct size) (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test) |
| ode | Deterministic (ODE) Compartmental | cloned from 'ode' owned by user schaff (copied from Correct PDE conc. with new geo with crop correct size) cloned from 'Correct PDE conc. with new geo with crop correct size' owned by user bboras (copied from PDE's with new geo with crop correct size) (copied from PDE's with new geo with crop) (copied from PDE's with new geo) (copied from Copy of test 3) (copied from test 3) (copied from test) |
Application - Correct PDE conc. with new geo with crop correct size
| Species | Initial Condition | Diffusion Constant | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PDE_cAMP | (1000.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0))) [uM] | 0.0
[um2/s] | PDE_Cyto |
(5000.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0)))
[uM]
|
0.0
[um2/s] | cAMP_best |
0.99
[uM]
|
9.0
[um2/s] | s0 |
((((x < 0.01) || (x > 1.0)) || ((y < 0.01) || (y > 0.75)) || ((z < 0.01) || (z > 0.4))) * 500.0)
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| r0 | included |
| r1 | included |
| r2 | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 360000 elements | 10.0 [s] |
OutputTimeStep 0.5 |
| Simulation0 137826 elements diffusion 9 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Simulation0 137826 elements diffusion 75 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Simulation0 137826 elements diffusion 300 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Simulation0 137826 elements diffusion 9 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Copy of Simulation0 137826 elements diffusion 9 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Copy of Copy of Simulation0 137826 elements diffusion 9 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 | 10.0 [s] |
OutputTimeStep 0.5 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Volume | Image | cytosol | 0.2878215261413742 [um3] | Cyto | |
| Volume | Image | rest | 0.014342978016688063 [um3] | ||
| Surface | cytosol_rest_membrane | cytosol | rest | 0.36025610812006187 [um2] |
Application - Copy of Correct PDE conc. with new geo with crop correct size
| Species | Initial Condition | Diffusion Constant | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PDE_cAMP | 0.0 [uM] | 0.0
[um2/s] | PDE_Cyto |
((600.0 * (0.41 < x) * (x < 0.6) * (y > 0.28) * (y < 0.43) * (z > 0.03) * (z < 0.22)) - (600.0 * (0.46 < x) * (x < 0.55) * (y > 0.33) * (y < 0.38) * (z > 0.08) * (z < 0.17)))
[uM]
|
0.0
[um2/s] | cAMP_best |
0.0
[uM]
|
200.0
[um2/s] | s0 |
0.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| r0 | included |
| r1 | included |
| r2 | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation5 | 5.0 [s] |
OutputTimeStep 0.5 |
| Simulation6 | 1.0 [s] |
OutputTimeStep 0.5 |
| Simulation7 | 1.0 [s] |
OutputTimeStep 0.5 |
| Simulation8 | 10.0 [s] |
OutputTimeStep 0.5 |
| Simulation9 | 10.0 [s] |
OutputTimeStep 0.5 |
| Simulation10 | 10.0 [s] |
OutputTimeStep 0.5 |
| Simulation11 | 10.0 [s] |
OutputTimeStep 0.5 |
| Simulation12 | 1000.0 [s] |
OutputTimeStep 0.5 |
| Simulation13 | 10.0 [s] |
OutputTimeStep 0.5 |
| Copy of Simulation12 | 700.0 [s] |
OutputTimeStep 0.5 |
| Copy of Copy of Simulation12 | 700.0 [s] |
OutputTimeStep 0.5 |
| Copy of Simulation12 1 | 10.0 [s] |
OutputTimeStep 0.5 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Volume | Image | background | 0.2878215261413742 [um3] | Cyto | |
| Volume | Image | roi_255 | 0.00507383535190043 [um3] | ttube | |
| Volume | Image | mito | 0.006815278841323884 [um3] | mito | |
| Volume | Image | mito2 | 0.014342978016688063 [um3] | mito2 | |
| Volume | Image | SR | 0.011513772206563602 [um3] | SR | |
| Volume | Image | ttube2 | 0.004606609442149914 [um3] | ttube2 | |
| Surface | background_roi_255_membrane | background | roi_255 | 0.18949064675557042 [um2] | tttt | |
| Surface | SR_background_membrane | SR | background | 0.9515156362075461 [um2] | Membrane3 | |
| Surface | background_ttube2_membrane | background | ttube2 | 0.23305999926855114 [um2] | Membrane2 | |
| Surface | background_mito_membrane | background | mito | 0.19753629961257163 [um2] | Membrane0 | |
| Surface | background_mito2_membrane | background | mito2 | 0.36025610812006187 [um2] | Membrane1 |
Application - ode
| Species | Initial Condition | Diffusion Constant | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PDE_cAMP | 0.0 [uM] | 0.0
[um2/s] | PDE_Cyto |
7.0
[uM]
|
0.0
[um2/s] | cAMP_best |
1.0
[uM]
|
0.0
[um2/s] | s0 |
0.0
[uM]
|
0.0
[um2/s]
|
|
| Name | Reaction Mapping |
|---|---|
| r0 | included |
| r1 | included |
| r2 | included |
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 1.0 [s] |
OutputTimeStep 0.5 |
| Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
|---|---|---|---|---|---|
| Compartmental | Compartment | Membrane3 |
Global Parameters
| Name | Expression |
|---|---|
| g0 | 0.0[tbd] |
|
|
|
| C_kr | 2.3 [s-1] |
|
|
|
| C_kd | 3.8E-4 [uM] |
|
|
|
| B_factor | 5.0[tbd] |
|
|
|
| F_B_binding | 3.175[s-1] |
|
|
|
| B_kd | 0.013[tbd] |
|
|
|
| A_kd | 0.03[tbd] |
|
|
|
| spots | 2.0[tbd] |
|
|
|
| F_A_binding | 0.3[s-1] |
|
|
|
| A_factor | 23.0[tbd] |
|
|
|