Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
cAMP_best+PDE_CytoPDE_cAMP r0 Cyto MassAction
PDE_cAMPPDE_Cyto r1 Cyto MassAction

Structures

Name
Type
Electrical
bests Membrane Cyto(+)   Unnamed compartment(-)
tttt Membrane ttube(+)   Cyto(-)
Membrane0 Membrane mito(+)   Cyto(-)
Membrane1 Membrane mito2(+)   Cyto(-)
Membrane2 Membrane ttube2(+)   Cyto(-)
Membrane3 Membrane SR(+)   Cyto(-)
mito Compartment (+)   (-)
SR Compartment (+)   (-)
Unnamed compartment Compartment (+)   (-)
ttube Compartment (+)   (-)
mito2 Compartment (+)   (-)
ttube2 Compartment (+)   (-)
Cyto Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
PDE_cAMP Cyto Cyto
PDE_Cyto Cyto Cyto
cAMP_best Cyto Cyto

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Correct PDE conc. with new geo with crop correct size Specs - Species
Specs - Reaction
Simulations
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 Specs - Species
Specs - Reaction
Simulations
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 Specs - Species
Specs - Reaction
Simulations
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)

Specifications (Species) - Correct PDE conc. with new geo with crop correct size go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDE_cAMP (8400.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0))) [uM] 0.0 [um2/s] Cyto
PDE_Cyto (51600.0 * ((((x - 0.57) ^ 2.0) + ((y - 0.35) ^ 2.0) + ((z - 0.18) ^ 2.0)) < (0.025 ^ 2.0))) [uM] 0.0 [um2/s] Cyto
cAMP_best 1.0 [uM] 9.0 [um2/s] Cyto

Specifications (Reaction) - Correct PDE conc. with new geo with crop correct size go to Simulations

Name
Enabled?
r0 included
r1 included

Simulations - Correct PDE conc. with new geo with crop correct size go to Specifications

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20150608_114218

(Origin: 0.0, 0.0, 0.0; Extent: 1.04, 0.765, 0.41500000000000004 [um])

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]

Events

Name Variable Rate Expression

Specifications (Species) - Copy of Correct PDE conc. with new geo with crop correct size go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDE_cAMP 0.0 [uM] 0.0 [um2/s] Cyto
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] Cyto
cAMP_best 0.0 [uM] 200.0 [um2/s] Cyto

Specifications (Reaction) - Copy of Correct PDE conc. with new geo with crop correct size go to Simulations

Name
Enabled?
r0 included
r1 included

Simulations - Copy of Correct PDE conc. with new geo with crop correct size go to Specifications

Name
End Time
Output Options
Simulation5 5.0

OutputTimeStep 0.5

Simulation6 1.0

OutputTimeStep 0.5

Simulation7 1.0

OutputTimeStep 0.5

Simulation8 10.0

OutputTimeStep 0.5

Simulation9 10.0

OutputTimeStep 0.5

Simulation10 10.0

OutputTimeStep 0.5

Simulation11 10.0

OutputTimeStep 0.5

Simulation12 1000.0

OutputTimeStep 0.5

Simulation13 10.0

OutputTimeStep 0.5

Copy of Simulation12 700.0

OutputTimeStep 0.5

Copy of Copy of Simulation12 700.0

OutputTimeStep 0.5

Copy of Simulation12 1 10.0

OutputTimeStep 0.5

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry cAMP-diffusion_with EPAC_V_cell_short11_including PKA_Correct PDE conc. with new geo with crop correct size_20110706_826393532

(Origin: 0.0, 0.0, 0.0; Extent: 1.04, 0.765, 0.41500000000000004 [um])

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

Events

Name Variable Rate Expression

Specifications (Species) - ode go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDE_cAMP 0.0 [uM] 0.0 [um2/s] Cyto
PDE_Cyto 7.0 [uM] 0.0 [um2/s] Cyto
cAMP_best 1.0 [uM] 0.0 [um2/s] Cyto

Specifications (Reaction) - ode go to Simulations

Name
Enabled?
r0 included
r1 included

Simulations - ode go to Specifications

Name
End Time
Output Options
Simulation0 1.0

OutputTimeStep 0.5

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry nonspatial1893829213

(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 Membrane3

Events

Name Variable Rate Expression

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]