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
s0cAMP_best r2 Cyto MassAction

r0 Universal ID's

r0 Text Annotations

r1 Universal ID's

r1 Text Annotations

r2 Universal ID's

r2 Text Annotations

Expressions for r0

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]

Expressions for r1

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]

Expressions for r2

reaction rate

J

((Kf * s0) - (Kr * cAMP_best)) [uM.s-1]

forward rate constant

Kf

(cAMP_best < 1.0) [s-1]

reverse rate constant

Kr

0.0 [s-1]

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(-)
ttube2 Compartment (+)   (-)
Cyto Compartment (+)   (-)
mito Compartment (+)   (-)
SR Compartment (+)   (-)
Unnamed compartment Compartment (+)   (-)
ttube Compartment (+)   (-)
mito2 Compartment (+)   (-)

bests Universal ID's

bests Text Annotations

tttt Universal ID's

tttt Text Annotations

Membrane0 Universal ID's

Membrane0 Text Annotations

Membrane1 Universal ID's

Membrane1 Text Annotations

Membrane2 Universal ID's

Membrane2 Text Annotations

Membrane3 Universal ID's

Membrane3 Text Annotations

ttube2 Universal ID's

ttube2 Text Annotations

Cyto Universal ID's

Cyto Text Annotations

mito Universal ID's

mito Text Annotations

SR Universal ID's

SR Text Annotations

Unnamed compartment Universal ID's

Unnamed compartment Text Annotations

ttube Universal ID's

ttube Text Annotations

mito2 Universal ID's

mito2 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
PDE_cAMP Cyto Cyto
PDE_Cyto Cyto Cyto
cAMP_best Cyto Cyto
s0 Cyto Cyto

PDE_cAMP Universal ID's

PDE_cAMP Text Annotations

PDE_Cyto Universal ID's

PDE_Cyto Text Annotations

cAMP_best Universal ID's

cAMP_best Text Annotations

s0 Universal ID's

s0 Text Annotations

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)

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

ode Universal ID's

ode Text Annotations

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

Species
Initial Condition
Diffusion Constant
Structure
PDE_cAMP (25000.0 * ((((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 (125000.0 * ((((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 1.02 [uM] 9.0 [um2/s] Cyto
s0 ((((x < 0.01) || (x > 1.0)) || ((y < 0.01) || (y > 0.75)) || ((z < 0.01) || (z > 0.4))) * 100.0) [uM] 0.0 [um2/s] Cyto

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

Name
Enabled?
r0 included
r1 included
r2 included

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

Name
End Time
Output Options
Simulation0 360000 elements 10.0

OutputTimeStep 0.5
Simulation0 137826 elements diffusion 9 10.0

OutputTimeStep 0.5
Copy of Simulation0 137826 elements diffusion 75 10.0

OutputTimeStep 0.5
Copy of Simulation0 137826 elements diffusion 300 10.0

OutputTimeStep 0.5
Copy of Simulation0 137826 elements diffusion 9 10.0

OutputTimeStep 0.5
Copy of Copy of Simulation0 137826 elements diffusion 9 10.0

OutputTimeStep 0.5
Copy of Copy of Copy of Simulation0 137826 elements diffusion 9 10.0

OutputTimeStep 0.5
Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 10.0

OutputTimeStep 0.5
Copy of Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 10 10.0

OutputTimeStep 0.5
Copy of Copy of Copy of Copy of Simulation0 137826 elements diffusion 9 10.0

OutputTimeStep 0.5

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

Correct PDE conc. with new geo with crop correct size Universal ID's

Correct PDE conc. with new geo with crop correct size Text Annotations

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
s0 0.0 [uM] 0.0 [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
r2 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

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

Copy of Correct PDE conc. with new geo with crop correct size Universal ID's

Copy of Correct PDE conc. with new geo with crop correct size Text Annotations

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
s0 0.0 [uM] 0.0 [um2/s] Cyto

Specifications (Reaction) - ode go to Simulations

Name
Enabled?
r0 included
r1 included
r2 included

Simulations - ode go to Specifications

Name
End Time
Output Options
Simulation0 1.0

OutputTimeStep 0.5

ode Universal ID's

ode Text Annotations

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]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations