ModelBricks - Model Print Page

Dashboard

Name - GF-actin FDAP

BioModel ID - 101981216

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
GactinFactin	r_polym c0	GeneralKinetics	GactinFactin
		reaction rate (J_Polymer): (K_polym * Gactin * nucleator)[uM.s-1]
Gactin_PAFactin_PA	r_polymer_PA c0	GeneralKinetics	Gactin_PAFactin_PA
		reaction rate (J_polym_PA): (K_polym * Gactin_PA * nucleator)[uM.s-1]
Factin_PAGactin_PA	r_depolym-PA c0	GeneralKinetics	Factin_PAGactin_PA
		reaction rate (J_depol_PA): (K_depol * Factin_PA * denucl)[uM.s-1]
FactinGactin	r_depolym c0	GeneralKinetics	FactinGactin
		reaction rate (J_depol): (K_depol * Factin * denucl)[uM.s-1]
FactinFactin_PA	r_PAforFa c0	GeneralKinetics	FactinFactin_PA
		reaction rate (J): (Factin * (Factin > 0.0) * K_PA * laser * (t > t_start) * (t < t_finish))[uM.s-1]
GactinGactin_PA	r_PAforGa c0	GeneralKinetics	GactinGactin_PA
		reaction rate (J): (Gactin * (Gactin > 0.0) * K_PA * laser * (t > t_start) * (t < t_finish))[uM.s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
c0	Compartment (+) (-)

c1	Compartment (+) (-)

Membrane0	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
laser	c0

Factin_PA	c0

Gactin_PA	c0

nucleator	c0

Gactin	c0

Factin	c0

denucl	c0

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
wt D=3	Deterministic (ODE) Spatial (3D)	(copied from FRAP-wt more) (copied from FRAP-wt-start) (copied from Application half-cell) (copied from Application1)
smaller+tall	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	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)

Application - wt D=3

Specifications(Species) - wt D=3 See in Dashboard
Species	Initial Condition	Diffusion Constant
laser	(sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM]	0.0 [um2/s]
Factin_PA	0.0 [uM]	0.01 [um2/s]
Gactin_PA	0.0 [uM]	5.0 [um2/s]
nucleator	1.0 [uM]	0.0 [um2/s]
Gactin	100.0 [uM]	5.0 [um2/s]
Factin	100.0 [uM]	0.01 [um2/s]
denucl	1.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - wt D=3 See in Dashboard
Name	Reaction Mapping
r_PAforFa	included
r_PAforGa	included
r_polym	included
r_polymer_PA	included
r_depolym-PA	included
r_depolym	included

Simulations - wt D=3 See in Dashboard
Name	End Time	Output Options
F/G=10/190, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=20-30 , Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=40-50, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=60-70, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=80-90, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=100-110, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=120-130, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=140-150, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=160-170, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2
Factin=180-190, Kd=0.01-0.2	30.0 [s]	OutputTimeStep 0.2

Geometry 3D-half lamel cali-1 See in Dashboard
(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

Application - smaller+tall

Specifications(Species) - smaller+tall See in Dashboard
Species	Initial Condition	Diffusion Constant
laser	(sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM]	0.0 [um2/s]
Factin_PA	0.0 [uM]	0.01 [um2/s]
Gactin_PA	0.0 [uM]	5.0 [um2/s]
nucleator	1.0 [uM]	0.0 [um2/s]
Gactin	100.0 [uM]	5.0 [um2/s]
Factin	100.0 [uM]	0.01 [um2/s]
denucl	1.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - smaller+tall See in Dashboard
Name	Reaction Mapping
r_PAforFa	included
r_PAforGa	included
r_polym	included
r_polymer_PA	included
r_depolym-PA	included
r_depolym	included

Simulations - smaller+tall See in Dashboard
Name	End Time	Output Options
Simulation0	30.0 [s]	OutputTimeStep 0.2
Simulation1	30.0 [s]	OutputTimeStep 0.2
Simulation2	30.0 [s]	OutputTimeStep 0.2
Simulation3	30.0 [s]	OutputTimeStep 0.2
Simulation4	30.0 [s]	OutputTimeStep 0.2
Simulation5	30.0 [s]	OutputTimeStep 0.2
Simulation6	30.0 [s]	OutputTimeStep 0.2
Simulation7	30.0 [s]	OutputTimeStep 0.2
Simulation8	30.0 [s]	OutputTimeStep 0.2
Simulation9	30.0 [s]	OutputTimeStep 0.2

Geometry 3D-half lamel cali-1 See in Dashboard
(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

Application - wt D=5

Specifications(Species) - wt D=5 See in Dashboard
Species	Initial Condition	Diffusion Constant
laser	(sqrt(((x * x) + (( - 10.0 + y) * ( - 10.0 + y)))) < 1.0) [uM]	0.0 [um2/s]
Factin_PA	0.0 [uM]	0.01 [um2/s]
Gactin_PA	0.0 [uM]	5.0 [um2/s]
nucleator	1.0 [uM]	0.0 [um2/s]
Gactin	100.0 [uM]	5.0 [um2/s]
Factin	100.0 [uM]	0.01 [um2/s]
denucl	1.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - wt D=5 See in Dashboard
Name	Reaction Mapping
r_PAforFa	included
r_PAforGa	included
r_polym	included
r_polymer_PA	included
r_depolym-PA	included
r_depolym	included

Simulations - wt D=5 See in Dashboard
Name	End Time	Output Options
Simulation20	30.0 [s]	OutputTimeStep 0.2
Simulation21	30.0 [s]	OutputTimeStep 0.2
Simulation22	30.0 [s]	OutputTimeStep 0.2
Simulation23	30.0 [s]	OutputTimeStep 0.2
Simulation24	30.0 [s]	OutputTimeStep 0.2
Simulation25	30.0 [s]	OutputTimeStep 0.2
Simulation26	30.0 [s]	OutputTimeStep 0.2
Simulation27	30.0 [s]	OutputTimeStep 0.2
Simulation28	30.0 [s]	OutputTimeStep 0.2
Simulation29	30.0 [s]	OutputTimeStep 0.2
F=100 D=10	25.0 [s]	OutputTimeStep 0.2

Geometry 3D-half lamel cali-1 See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
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]