Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
GactinFactin r_polym c0 GeneralKinetics
Gactin_PAFactin_PA r_polymer_PA c0 GeneralKinetics
Factin_PAGactin_PA r_depolym-PA c0 GeneralKinetics
FactinGactin r_depolym c0 GeneralKinetics
FactinFactin_PA r_PAforFa c0 GeneralKinetics
GactinGactin_PA r_PAforGa c0 GeneralKinetics

r_polym Universal ID's

r_polym Text Annotations

r_polymer_PA Universal ID's

r_polymer_PA Text Annotations

r_depolym-PA Universal ID's

r_depolym-PA Text Annotations

r_depolym Universal ID's

r_depolym Text Annotations

r_PAforFa Universal ID's

r_PAforFa Text Annotations

r_PAforGa Universal ID's

r_PAforGa Text Annotations

Expressions for r_polym

reaction rate

J_Polymer

(K_polym * Gactin * nucleator) [uM.s-1]

global

K_polym

1.0 [uM-1.s-1]

Expressions for r_polymer_PA

reaction rate

J_polym_PA

(K_polym * Gactin_PA * nucleator) [uM.s-1]

global

K_polym

1.0 [uM-1.s-1]

Expressions for r_depolym-PA

reaction rate

J_depol_PA

(K_depol * Factin_PA * denucl) [uM.s-1]

global

K_depol

1.0 [uM-1.s-1]

Expressions for r_depolym

reaction rate

J_depol

(K_depol * Factin * denucl) [uM.s-1]

global

K_depol

1.0 [uM-1.s-1]

Expressions for r_PAforFa

reaction rate

J

(Factin * (Factin > 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]

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
Factin_PA c0 c0
Gactin_PA c0 c0
nucleator c0 c0
Gactin c0 c0
Factin c0 c0
denucl c0 c0

laser Universal ID's

laser Text Annotations

Factin_PA Universal ID's

Factin_PA Text Annotations

Gactin_PA Universal ID's

Gactin_PA Text Annotations

nucleator Universal ID's

nucleator Text Annotations

Gactin Universal ID's

Gactin Text Annotations

Factin Universal ID's

Factin Text Annotations

denucl Universal ID's

denucl Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
wt D=3 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from FRAP-wt more) (copied from FRAP-wt-start) (copied from Application half-cell) (copied from Application1)
smaller+tall Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from wt uniform) (copied from FRAP-wt more) (copied from FRAP-wt-start) (copied from Application half-cell) (copied from Application1)
wt D=5 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D) (copied from wt uniform) (copied from FRAP-wt more) (copied from FRAP-wt-start) (copied from Application half-cell) (copied from Application1)

wt D=3 Universal ID's

wt D=3 Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

Specifications (Species) - wt D=3 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
Factin_PA 0.0 [uM] 0.01 [um2/s] c0
Gactin_PA 0.0 [uM] 5.0 [um2/s] c0
nucleator 1.0 [uM] 0.0 [um2/s] c0
Gactin 100.0 [uM] 5.0 [um2/s] c0
Factin 100.0 [uM] 0.01 [um2/s] c0
denucl 1.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - wt D=3 go to Simulations

Name
Enabled?
r_PAforFa included
r_PAforGa included
r_polym included
r_polymer_PA included
r_depolym-PA included
r_depolym included

Simulations - wt D=3 go to Specifications

Name
End Time
Output Options
F/G=10/190, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=20-30 , Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=40-50, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=60-70, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=80-90, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=100-110, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=120-130, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=140-150, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=160-170, Kd=0.01-0.2 30.0

OutputTimeStep 0.2
Factin=180-190, Kd=0.01-0.2 30.0

OutputTimeStep 0.2

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 Text Annotations

wt D=3 Universal ID's

wt D=3 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 672.8210196853636 [um3] c0
Volume Analytical subVolume0 2127.178980314636 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 1264.1530845472296 [um2] Membrane0

Events

Name Variable Rate Expression

Specifications (Species) - 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
Factin_PA 0.0 [uM] 0.01 [um2/s] c0
Gactin_PA 0.0 [uM] 5.0 [um2/s] c0
nucleator 1.0 [uM] 0.0 [um2/s] c0
Gactin 100.0 [uM] 5.0 [um2/s] c0
Factin 100.0 [uM] 0.01 [um2/s] c0
denucl 1.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - smaller+tall go to Simulations

Name
Enabled?
r_PAforFa included
r_PAforGa included
r_polym included
r_polymer_PA included
r_depolym-PA included
r_depolym included

Simulations - smaller+tall go to Specifications

Name
End Time
Output Options
Simulation0 30.0

OutputTimeStep 0.2
Simulation1 30.0

OutputTimeStep 0.2
Simulation2 30.0

OutputTimeStep 0.2
Simulation3 30.0

OutputTimeStep 0.2
Simulation4 30.0

OutputTimeStep 0.2
Simulation5 30.0

OutputTimeStep 0.2
Simulation6 30.0

OutputTimeStep 0.2
Simulation7 30.0

OutputTimeStep 0.2
Simulation8 30.0

OutputTimeStep 0.2
Simulation9 30.0

OutputTimeStep 0.2

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

smaller+tall Text Annotations

smaller+tall Universal ID's

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

Specifications (Species) - wt D=5 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
Factin_PA 0.0 [uM] 0.01 [um2/s] c0
Gactin_PA 0.0 [uM] 5.0 [um2/s] c0
nucleator 1.0 [uM] 0.0 [um2/s] c0
Gactin 100.0 [uM] 5.0 [um2/s] c0
Factin 100.0 [uM] 0.01 [um2/s] c0
denucl 1.0 [uM] 0.0 [um2/s] c0

Specifications (Reaction) - wt D=5 go to Simulations

Name
Enabled?
r_PAforFa included
r_PAforGa included
r_polym included
r_polymer_PA included
r_depolym-PA included
r_depolym included

Simulations - wt D=5 go to Specifications

Name
End Time
Output Options
Simulation20 30.0

OutputTimeStep 0.2
Simulation21 30.0

OutputTimeStep 0.2
Simulation22 30.0

OutputTimeStep 0.2
Simulation23 30.0

OutputTimeStep 0.2
Simulation24 30.0

OutputTimeStep 0.2
Simulation25 30.0

OutputTimeStep 0.2
Simulation26 30.0

OutputTimeStep 0.2
Simulation27 30.0

OutputTimeStep 0.2
Simulation28 30.0

OutputTimeStep 0.2
Simulation29 30.0

OutputTimeStep 0.2
F=100 D=10 25.0

OutputTimeStep 0.2

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 Text Annotations

wt D=5 Universal ID's

wt D=5 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 672.8210196853636 [um3] c0
Volume Analytical subVolume0 2127.178980314636 [um3] c1
Surface subVolume0_subVolume1_membrane subVolume0 | subVolume1 1264.1530845472296 [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 1.0[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

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL wt D=3.bngl , smaller+tall.bngl , wt D=5.bngl
SBML wt D=3.sbml , smaller+tall.sbml , wt D=5.sbml
Matlab wt D=3.m , smaller+tall.m , wt D=5.m
NFSim XML wt D=3.xml , smaller+tall.xml , wt D=5.xml