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Name - Kerbai_PLoSone_2021_teardrop_polarization_extended

BioModel ID - 203656156

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
cdc42_inactcdc42_act	r0 cytosol	GeneralKinetics	cdc42_inactcdc42_act
		reaction rate (J): ((Ic / (1.0 + ((Rho_act / a1) ^ n)) * (cdc42_inact / cdc42_tot) * ((1.0 - f) + (f * P3 / P3b))) - (d_cdc42 * cdc42_act))[uM.s-1] user defined (a1): 1.25[uM] user defined (d_cdc42): 1.0[s-1]
Rac_inactRac_act	r1 cytosol	GeneralKinetics	Rac_inactRac_act
		reaction rate (J): (((Ir + (alpha * cdc42_act)) * (Rac_inact / Rac_tot) * ((1.0 - f) + (f * P3 / P3b))) - (d_rac * Rac_act))[uM.s-1] user defined (alpha): 4.5[s-1] user defined (d_rac): 1.0[s-1] user defined (Ir): 0.5[uM.s-1]
Rho_inactRho_act	r2 cytosol	GeneralKinetics	Rho_inactRho_act
		reaction rate (J): (((Ip + (Beta * Rac_act)) / (1.0 + ((cdc42_act / a2) ^ n)) * (Rho_inact / Rho_tot)) - (d_rho * Rho_act))[uM.s-1] user defined (d_rho): 1.0[s-1] user defined (a2): 1.0[uM] user defined (Ip): 3.3[uM.s-1] user defined (Beta): 0.3[s-1]
P1P2	r3 cytosol	GeneralKinetics	P1P2
		reaction rate (J): (( - k21 * P2) + (k_PI5K / 2.0 * (1.0 + (Rac_act / Rb)) * P1))[uM.s-1] user defined (k_PI5K): 0.084[microM.s-1.uM-1] user defined (k21): 0.014[s-1]
P2P3	r4 cytosol	GeneralKinetics	P2P3
		reaction rate (J): ((k_PI3K / 2.0 * (1.0 + (Rac_act / Rb)) * P2) - (k_PTEN / 2.0 * (1.0 + (Rho_act / Rho_b)) * P3))[uM.s-1] user defined (k_PI3K): 7.2E-4[microM.s-1.uM-1] user defined (k_PTEN): 0.432[microM.s-1.uM-1] user defined (Rho_b): 1.25[microM]
PIP1	r5 cytosol	GeneralKinetics	PIP1
		reaction rate (J): (Ip1 - (delta_P1 * P1))[uM.s-1] user defined (Ip1): 10.5[uM.s-1] user defined (delta_P1): 0.21[s-1]

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

cytosol	Compartment (+) (-)

plasma membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
cdc42_inact	cytosol

cdc42_act	cytosol

Rac_inact	cytosol

Rac_act	cytosol

Rho_inact	cytosol

Rho_act	cytosol

P1	cytosol

P2	cytosol

P3	cytosol

PI5K	cytosol

PI3K	cytosol

PTEN	cytosol

PI	cytosol

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
real cell	Deterministic (ODE) Spatial (2D)	cloned from 'real cell' owned by user aureliecarlier (copied from real cell) (copied from Application0)

Application - real cell

Specifications(Species) - real cell See in Dashboard
Species	Initial Condition	Diffusion Constant
cdc42_inact	1.4 [uM]	50.0 [um2/s]
cdc42_act	1.0 [uM]	0.1 [um2/s]
Rac_inact	4.5 [uM]	50.0 [um2/s]
Rac_act	3.0 [uM]	0.1 [um2/s]
Rho_inact	1.85 [uM]	50.0 [um2/s]
Rho_act	1.25 [uM]	0.1 [um2/s]
P1	55.0 [uM]	5.0 [um2/s]
P2	30.0 [uM]	5.0 [um2/s]
P3	0.05 [uM]	5.0 [um2/s]
PI5K	10.0 [uM]	10.0 [um2/s]
PI3K	10.0 [uM]	10.0 [um2/s]
PTEN	10.0 [uM]	10.0 [um2/s]
PI	10.0 [uM]	10.0 [um2/s]

Specifications(Reaction) - real cell See in Dashboard
Name	Reaction Mapping
r0	included
r1	included
r2	included
r3	included
r4	included
r5	included

Simulations - real cell See in Dashboard
Name	End Time	Output Options
simulation1	500.0 [s]	OutputTimeStep 5.0
simulation2	100.0 [s]	OutputTimeStep 5.0
simulation3	1000.0 [s]	OutputTimeStep 5.0

Geometry geom_20171120_183216 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 50.0, 20.0, 9.0E-7[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Image	Cell		640.0005147077745 [um2]	cytosol
Volume	Image	EC		34.62053169313122 [um2]	extracellular space
Surface		Cell_EC_membrane	Cell \| EC	19.36700981687842 [um]	plasma membrane

Global Parameters

Global Parameters See in Dashboard
Name	Expression
n	3.0[1]

Ic	(((2.6 + (0.05 * x)) * (t <= 10.0)) + (2.95 * (t > 10.0)))[uM.s-1]

P3b	0.05[uM]

f	0.4[1]

cdc42_tot	2.4[uM]

Rac_tot	7.5[uM]

Rho_tot	3.1[uM]

Rb	3.0[microM]