ModelBricks - Model Print Page

Name - Nosbisch chemotaxis 2020

BioModel ID - 172076998

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
d+Cc_active	V_PKC plasma_membrane	GeneralKinetics	d+Cc_active
		reaction rate (J): ((kon_c * d * C) - (koff_c * c_active))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
Ee	V_PLC plasma_membrane	GeneralKinetics	Ee
		reaction rate (J): ((kon_e * (((130.0 * rfrac * (1.0 + (rsteep1 * x / 40.0)) * ((t > 2000.0) && (t < 20000.0))) + (130.0 * rfrac * (1.0 + (rsteep2 * x / 40.0)) * (t > 20000.0)) - e) * E)) - ((koff_e * (1.0 + (epsilon * k_PA * d_p)) / (1.0 + (k_PA * d_p))) * e))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (rsteep2): 0.0[tbd] user defined (epsilon): 0.01[1] user defined (rsteep1): 0.0[tbd] user defined (rfrac): 0.0[tbd] user defined (kon_e): 0.1[s-1.uM-1] user defined (k_PA): 10.0[um2.molecules-1] user defined (koff_e): 0.1[s-1]
M_pM	V_dpm cytosol	GeneralKinetics	M_pM
		reaction rate (J): (k_dpm * M_p)[uM.s-1] user defined (k_dpm): 0.3[s-1]
pT	V_basal_p plasma_membrane	GeneralKinetics	pT
		reaction rate (J): (k_basal_p * ( - (1.0 / 2.0) * ((3.0 * k_PIP2 * m) - (k_PIP2 * pT) - sqrt(((9.0 * (k_PIP2 ^ 2.0) * (m ^ 2.0)) - (6.0 * (k_PIP2 ^ 2.0) * m * pT) + ((k_PIP2 ^ 2.0) * (pT ^ 2.0)) + (6.0 * k_PIP2 * m) + (2.0 * k_PIP2 * pT) + 1.0)) + 1.0) / k_PIP2))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_basal_p): 0.005[tbd]
pT	Vsynth,p plasma_membrane	GeneralKinetics	pT
		reaction rate (J): Vsynth_p[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (Vsynth_p): 2.5[s-1]
pTd	V_hyd_PLC plasma_membrane	GeneralKinetics	pTd
		reaction rate (J): (k_hyd_PLC * e * ( - (1.0 / 2.0) * ((3.0 * k_PIP2 * m) - (k_PIP2 * pT) - sqrt(((9.0 * (k_PIP2 ^ 2.0) * (m ^ 2.0)) - (6.0 * (k_PIP2 ^ 2.0) * m * pT) + ((k_PIP2 ^ 2.0) * (pT ^ 2.0)) + (6.0 * k_PIP2 * m) + (2.0 * k_PIP2 * pT) + 1.0)) + 1.0) / k_PIP2))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_hyd_PLC): 5.0E-4[s-1]
Mm	V_MARCKS plasma_membrane	GeneralKinetics	Mm
		reaction rate (J): ((kon_m * M) - ((koff_m * m) / (1.0 - ((1.0 / 2.0 * ((3.0 * k_PIP2 * m) - (k_PIP2 * pT) - sqrt(((9.0 * (k_PIP2 ^ 2.0) * (m ^ 2.0)) - (6.0 * (k_PIP2 ^ 2.0) * m * pT) + ((k_PIP2 ^ 2.0) * (pT ^ 2.0)) + (6.0 * k_PIP2 * m) + (2.0 * k_PIP2 * pT) + 1.0)) + 1.0)) * (3.0 - ((1.0 / 2.0 * ((3.0 * k_PIP2 * m) - (k_PIP2 * pT) - sqrt(((9.0 * (k_PIP2 ^ 2.0) * (m ^ 2.0)) - (6.0 * (k_PIP2 ^ 2.0) * m * pT) + ((k_PIP2 ^ 2.0) * (pT ^ 2.0)) + (6.0 * k_PIP2 * m) + (2.0 * k_PIP2 * pT) + 1.0)) + 1.0)) * (( - (3.0 / 2.0) * k_PIP2 * m) + ((1.0 / 2.0) * k_PIP2 * pT) + ((1.0 / 2.0) * sqrt(((9.0 * (k_PIP2 ^ 2.0) * (m ^ 2.0)) - (6.0 * (k_PIP2 ^ 2.0) * m * pT) + ((k_PIP2 ^ 2.0) * (pT ^ 2.0)) + (6.0 * k_PIP2 * m) + (2.0 * k_PIP2 * pT) + 1.0))) + (5.0 / 2.0))))))))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
mM_p	V_pm plasma_membrane	GeneralKinetics	mM_p
		reaction rate (J): (k_pm * c_active * m)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
c_activec	V_dpc plasma_membrane	GeneralKinetics	c_activec
		reaction rate (J): (k_dpc * c_active)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_dpc): 1.0[s-1]
cc_active	V_pc plasma_membrane	GeneralKinetics	cc_active
		reaction rate (J): (k_pc * c)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_pc): 1.0[s-1]
cd+C	V_off,c plasma_membrane	GeneralKinetics	cd+C
		reaction rate (J): (koff_c * c)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
d_p	Vsynth,dp plasma_membrane	GeneralKinetics	d_p
		reaction rate (J): (Vsynth_dp * (1.0 + (gamma * ((k_PLD * c_active) ^ n))) / (1.0 + ((k_PLD * c_active) ^ n)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_PLD): 0.1[um2.molecules-1] user defined (Vsynth_dp): 1.0E-4[tbd] user defined (gamma): 100000.0[tbd]
d_p	V_basal_dp plasma_membrane	GeneralKinetics	d_p
		reaction rate (J): (k_basal_dp * d_p)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_basal_dp): 1.0[s-1]
d_pd	V_PAP plasma_membrane	GeneralKinetics	d_pd
		reaction rate (J): (k_PAP * d_p)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_PAP): 1.0[s-1]
dd_p	V_DAGK plasma_membrane	GeneralKinetics	dd_p
		reaction rate (J): (k_DAGK * d)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (k_DAGK): 1.0[s-1]

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

extracellular	Compartment (+) (-)

cytosol	Compartment (+) (-)

plasma_membrane	Membrane N/A

nuclear_membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
pT	plasma_membrane

d	plasma_membrane

c_active	plasma_membrane

M	cytosol

M_p	cytosol

E	cytosol

e	plasma_membrane

C	cytosol

c	plasma_membrane

m	plasma_membrane

d_p	plasma_membrane

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
Symmetric Geometry	Deterministic (ODE) Spatial (2D)
Asymmetric Geometry	Deterministic (ODE) Spatial (2D)	(copied from Symmetric Geometry)

Application - Symmetric Geometry

Specifications(Species) - Symmetric Geometry See in Dashboard
Species	Initial Condition	Diffusion Constant
M	1.0 [uM]	32.0 [um2/s]
M_p	0.0 [uM]	32.0 [um2/s]
E	0.02 [uM]	19.0 [um2/s]
C	0.3 [uM]	24.0 [um2/s]
pT	5000.0 [uM]	0.5 [um2/s]
d	0.0 [uM]	0.5 [um2/s]
c_active	0.0 [uM]	0.5 [um2/s]
e	0.0 [uM]	0.01 [um2/s]
c	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]
d_p	0.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Symmetric Geometry See in Dashboard
Name	Reaction Mapping
V_PKC	included
V_PLC	included
V_dpm	included
V_basal_p	included
Vsynth,p	included
V_hyd_PLC	included
V_MARCKS	included
V_pm	included
V_dpc	included
V_pc	included
V_off,c	included
Vsynth,dp	included
V_basal_dp	included
V_PAP	included
V_DAGK	included

Simulations - Symmetric Geometry See in Dashboard
Name	End Time	Output Options
Fig 2A: PFL 1 scan 0% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 2A: PFL 1 scan 3% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 2A: PFL 1 scan 10% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 2A: PFL 1 scan 30% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 2A: PFL 1 scan 67% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 0% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 3% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 10% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 30% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 67% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.1	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.2	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.5	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 2.0	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 5.0	20000.0 [s]	OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 10	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.1	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.2	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.5	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 2.0	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 5.0	20000.0 [s]	OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 10	20000.0 [s]	OutputTimeStep 100.0
Fig 5B: 0.3 x kDAGK scan 10% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 5B: 3.0 x kDAGK scan 10% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 5D: 3.0 x kDAGK scan 3% gradient	40000.0 [s]	OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.1	20000.0 [s]	OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.2	20000.0 [s]	OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.5	20000.0 [s]	OutputTimeStep 100.0
Fig 6A: PFL 2 + MARCKS	40000.0 [s]	OutputTimeStep 100.0
Fig 6B: PFL 1+ PFL 2	40000.0 [s]	OutputTimeStep 100.0
Fig 6C: PFL 1+ PFL 2 + MARCKS	40000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kon,e	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans koff,e	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans epsilon	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans KPA	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans khyd,PLC	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kpm	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kdpm	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kbasal,dp	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kDAGK	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kPAP	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kon,c	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans koff,c	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kdpc	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans kpc	20000.0 [s]	OutputTimeStep 100.0
Fig S4: Parameter scans Vsynth,dp	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 2 + MARCKS, kDAGK	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 2 + MARCKS, KPLD	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, kDAGK	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, KPA	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, KPLD	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, kDAGK	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, KPA	20000.0 [s]	OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, KPLD	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry2 See in Dashboard
(Origin: -20.2, -1.1, 0.0; Extent: 40.4, 2.2, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain2		1.235432 [um2]	nucleus
Volume	Analytical	subdomain1		55.318912 [um2]	cytosol
Volume	Analytical	subdomain0		32.325656 [um2]	extracellular
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	80.43141559089119 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	15.061103475619058 [um]	nuclear_membrane

Application - Asymmetric Geometry

Specifications(Species) - Asymmetric Geometry See in Dashboard
Species	Initial Condition	Diffusion Constant
M	1.0 [uM]	32.0 [um2/s]
M_p	0.0 [uM]	32.0 [um2/s]
E	0.02 [uM]	19.0 [um2/s]
C	0.3 [uM]	24.0 [um2/s]
pT	5000.0 [uM]	0.5 [um2/s]
d	0.0 [uM]	0.5 [um2/s]
c_active	0.0 [uM]	0.5 [um2/s]
e	0.0 [uM]	0.01 [um2/s]
c	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]
d_p	0.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Asymmetric Geometry See in Dashboard
Name	Reaction Mapping
V_PKC	included
V_PLC	included
V_dpm	included
V_basal_p	included
Vsynth,p	included
V_hyd_PLC	included
V_MARCKS	included
V_pm	included
V_dpc	included
V_pc	included
V_off,c	included
Vsynth,dp	included
V_basal_dp	included
V_PAP	included
V_DAGK	included

Simulations - Asymmetric Geometry See in Dashboard
Name	End Time	Output Options
Fig 4B: PFL 1 scan	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.1	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.2	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.5	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 2.0	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 5.0	20000.0 [s]	OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 10	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Back end blunted scan 3% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Back end blunted scan 10% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Back end blunted scan 30% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Back end blunted scan 67% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Front end blunted scan 3% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Front end blunted scan 10% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Front end blunted scan 30% gradient	20000.0 [s]	OutputTimeStep 100.0
Fig 4D: Front end blunted scan 67% gradient	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry2 See in Dashboard
(Origin: -20.2, -1.1, 0.0; Extent: 40.4, 2.2, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	subdomain2		1.235432 [um2]	nucleus
Volume	Analytical	subdomain1		59.798464 [um2]	cytosol
Volume	Analytical	subdomain0		27.846104 [um2]	extracellular
Surface		subdomain0_subdomain1_membrane	subdomain0 \| subdomain1	81.09121310386575 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	15.061103475619058 [um]	nuclear_membrane

Global Parameters

Global Parameters See in Dashboard
Name	Expression
n	2.0[1]

k_dc	1.0[s-1]

koff_c	0.1[s-1]

kon_c	1.0[s-1.uM-1]

koff_m	1.0[s-1]

kon_m	792.0[s-1.uM-1]

h	0.003[molecules.uM-1.um-2]

k_pm	1.0[um2.s-1.molecules-1]

k_PIP2	0.00135[tbd]