Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
GactinGactin_PA r_PAforGa c0 GeneralKinetics

r_PAforGa Universal ID's

r_PAforGa Text Annotations

Expressions for r_PAforGa

reaction rate

J

(Gactin * (Gactin > 0.0) * K_PA * laser * (t > t_start) * (t < t_finish)) [uM.s-1]

global

t_start

0.0 [s]

global

t_finish

0.063 [s]

global

K_PA

1.0 [uM-1.s-1]

Structures

Name
Type
Electrical
Membrane0 Membrane c0(+)   c1(-)
c0 Compartment (+)   (-)
c1 Compartment (+)   (-)

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
laser c0 c0
Gactin_PA c0 c0
Gactin c0 c0

laser Universal ID's

laser Text Annotations

Gactin_PA Universal ID's

Gactin_PA Text Annotations

Gactin Universal ID's

Gactin Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application half-cell Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from Application1)
half-cell-smaller+tall Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from Application half-cell) (copied from Application1)

Application half-cell Universal ID's

Application half-cell Text Annotations

half-cell-smaller+tall Universal ID's

half-cell-smaller+tall Text Annotations

Specifications (Species) - Application half-cell go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
laser (sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM] 0.0 [um2/s] c0
Gactin_PA 0.0 [uM] 10.0 [um2/s] c0
Gactin 100.0 [uM] 10.0 [um2/s] c0

Specifications (Reaction) - Application half-cell go to Simulations

Name
Enabled?
r_PAforGa included

Simulations - Application half-cell go to Specifications

Name
End Time
Output Options
short D between 2 and 10 Gactin=100 0.2

OutputTimeStep 0.002
D=2 - 10 2.0

OutputTimeStep 0.002
short D= from 2 to 10 Gactin=1 0.2

OutputTimeStep 0.002
Copy of D=2 - 10 2.0

OutputTimeStep 0.002

Application half-cell Universal ID's

Application half-cell Text Annotations

Application half-cell Universal ID's

Application half-cell Text Annotations

Application half-cell Universal ID's

Application half-cell Text Annotations

Application half-cell Universal ID's

Application half-cell Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry 3D-half lamel cali-1

(Origin: -20.0, 0.0, -3.5; Extent: 40.0, 20.0, 3.5 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subVolume1 707.3967921228407 [um3] c0
Volume Analytical subVolume0 2092.6032078771595 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 1270.7539854953793 [um2] Membrane0

Events

Name Variable Rate Expression

Specifications (Species) - half-cell-smaller+tall go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
laser (sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM] 0.0 [um2/s] c0
Gactin_PA 0.0 [uM] 10.0 [um2/s] c0
Gactin 100.0 [uM] 10.0 [um2/s] c0

Specifications (Reaction) - half-cell-smaller+tall go to Simulations

Name
Enabled?
r_PAforGa included

Simulations - half-cell-smaller+tall go to Specifications

Name
End Time
Output Options
Simulation0 0.2

OutputTimeStep 0.002
Simulation1 2.0

OutputTimeStep 0.002
Simulation2 0.2

OutputTimeStep 0.002
Simulation3 2.0

OutputTimeStep 0.002

half-cell-smaller+tall Universal ID's

half-cell-smaller+tall Text Annotations

half-cell-smaller+tall Universal ID's

half-cell-smaller+tall Text Annotations

half-cell-smaller+tall Universal ID's

half-cell-smaller+tall Text Annotations

half-cell-smaller+tall Universal ID's

half-cell-smaller+tall Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry 3D-half lamel cali-1

(Origin: -15.0, 0.0, -7.0; Extent: 30.0, 15.0, 7.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subVolume1 641.8342290585618 [um3] c0
Volume Analytical subVolume0 2508.165770941438 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 745.886799368184 [um2] Membrane0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
t_start 0.0[s]
t_finish 0.063[s]
k_forw 0.1[uM-1.s-1]
k_f 0.1[uM-1.s-1]
k_r 0.1[s-1]
K_PA 1.0[uM-1.s-1]
K_polym 0.0[uM-1.s-1]
K_depol 1.0[uM-1.s-1]

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