ModelBricks - Model Print Page

Name - Mohan chemotaxis 2017

BioModel ID - 113655498

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
RplasmaMembrane	Rsynthesis plasma_membrane	GeneralKinetics	RplasmaMembrane
		reaction rate (J): (kt * R0 * R_factor_plasmaMembrane)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
RplasmaMembrane	R_Turnover plasma_membrane	GeneralKinetics	RplasmaMembrane
		reaction rate (J): (kt * RplasmaMembrane)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
RplasmaMembraneC1_plasmaMembrane	PDGF_binding plasma_membrane	GeneralKinetics	RplasmaMembraneC1_plasmaMembrane
		reaction rate (J): (((kr / KD) * ((Lmid * PDGF_gradient_extracellular) + (Luni * PDGF_uniform_extracellular)) * RplasmaMembrane) - (kr * C1_plasmaMembrane))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
C1_plasmaMembrane	C1_turnover plasma_membrane	GeneralKinetics	C1_plasmaMembrane
		reaction rate (J): (kt * C1_plasmaMembrane)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
C1_plasmaMembraneC2_plasmaMembrane	C1_dimerization plasma_membrane	GeneralKinetics	C1_plasmaMembraneC2_plasmaMembrane
		reaction rate (J): ((kxR0 * (C1_plasmaMembrane ^ 2.0)) / R0)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
C2_plasmaMembraneC1_plasmaMembrane+RplasmaMembrane	C2_uncoupling plasma_membrane	GeneralKinetics	C2_plasmaMembraneC1_plasmaMembrane+RplasmaMembrane
		reaction rate (J): (kminusx * C2_plasmaMembrane)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
C2_plasmaMembrane	C2_Internalization plasma_membrane	GeneralKinetics	C2_plasmaMembrane
		reaction rate (J): (ke * C2_plasmaMembrane)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
E_inactive_PLCe_active_PLC	PLC_receptor_binding V_PLC plasma_membrane	GeneralKinetics	E_inactive_PLCe_active_PLC
		reaction rate (J): ((kone * C2_plasmaMembrane * E_inactive_PLC) - (koffe * e_active_PLC))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
pT_PIP2	PIP2_Synthesis plasma_membrane	GeneralKinetics	pT_PIP2
		reaction rate (J): (Vsynth0 * (1.0 + (alpha * C2_plasmaMembrane)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
pT_PIP2d_DAG	PLC catalyzed PIP2 hydrolysis plasma_membrane	GeneralKinetics	pT_PIP2d_DAG
		reaction rate (J): (k_hyd_PLC * e_active_PLC * ((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0 + sqrt(((((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0) ^ 2.0) + (4.0 * K_pip2 * pT_PIP2)))) / (2.0 * K_pip2))[molecules.um-2.s-1] inward current density (I): ((netValence * _F_ * J) * unitFactor)[pA.um-2] net charge valence (netValence): 1.0[1] electrical unit factor (unitFactor): (1.0 / 6.02214179E11)[pA.s.mol.molecules-1.C-1]
pT_PIP2	PIP2_hydrolysis plasma_membrane	GeneralKinetics	pT_PIP2
		reaction rate (J): (k_hyd0 * ((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0 + sqrt(((((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0) ^ 2.0) + (4.0 * K_pip2 * pT_PIP2)))) / (2.0 * K_pip2))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
d_DAG	DAG_consumption plasma_membrane	GeneralKinetics	d_DAG
		reaction rate (J): (k_DAGK * d_DAG)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
mMp	MARCKS phosphorylation by PKC plasma_membrane	GeneralKinetics	mMp
		reaction rate (J): (kpm * cStar * m)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
MpM_cytosolic_MARCKS	MARCKS dephosphorylation Cytosol	GeneralKinetics	MpM_cytosolic_MARCKS
		reaction rate (J): (kdpM * Mp)[uM.s-1]
M_cytosolic_MARCKSm	V_MARCKS plasma_membrane	GeneralKinetics	M_cytosolic_MARCKSm
		reaction rate (J): ((kon_m * M_cytosolic_MARCKS) - (koff_m * m / ((1.0 + (K_pip2 * ((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0 + sqrt(((((K_pip2 * pT_PIP2) - (3.0 * K_pip2 * m) - 1.0) ^ 2.0) + (4.0 * K_pip2 * pT_PIP2)))) / (2.0 * K_pip2))) ^ 3.0)))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
d_DAG+C_PKC_inactivecStar	V_PKC plasma_membrane	GeneralKinetics	d_DAG+C_PKC_inactivecStar
		reaction rate (J): ((konc * d_DAG * C_PKC_inactive) - (koffc1 * cStar))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (koffc1): 0.1[s-1]
cStarc_DAG_PKC	V_dpc plasma_membrane	GeneralKinetics	cStarc_DAG_PKC
		reaction rate (J): (kdpc * cStar)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
c_DAG_PKCcStar	Vpc1 plasma_membrane	GeneralKinetics	c_DAG_PKCcStar
		reaction rate (J): (kpc1 * c_DAG_PKC)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1] user defined (kpc1): 1.0[s-1]
c_DAG_PKCcStar	V_pc2 plasma_membrane	GeneralKinetics	c_DAG_PKCcStar
		reaction rate (J): (kpc2 * c_DAG_PKC * cStar)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]
c_DAG_PKCC_PKC_inactive+d_DAG	V_offc plasma_membrane	GeneralKinetics	c_DAG_PKCC_PKC_inactive+d_DAG
		reaction rate (J): (koffc * c_DAG_PKC)[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 1.0[1]

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

Nucleus	Compartment (+) (-)

Cytosol	Compartment (+) (-)

plasma_membrane	Membrane N/A

Nuclear_Membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
PDGF_gradient_extracellular	Extracellular

PDGF_uniform_extracellular	Extracellular

R_factor_plasmaMembrane	plasma_membrane

RplasmaMembrane	plasma_membrane

C1_plasmaMembrane	plasma_membrane

C2_plasmaMembrane	plasma_membrane

E_inactive_PLC	Cytosol

e_active_PLC	plasma_membrane

pT_PIP2	plasma_membrane

d_DAG	plasma_membrane

C_PKC_inactive	Cytosol

c_DAG_PKC	plasma_membrane

cStar	plasma_membrane

M_cytosolic_MARCKS	Cytosol

m	plasma_membrane

Mp	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
Relative_gradient_p67	Deterministic (ODE) Spatial (2D)	cloned from 'Relative_gradient_p67' owned by user kmohan cloned from 'Time_dep simulations' owned by user kmohan1 cloned from 'Time_dep simulations' owned by user kmohan2
Relative_gradient_0	Deterministic (ODE) Spatial (2D)	cloned from 'Relative_gradient_0' owned by user kmohan cloned from 'Relative_gradient_0' owned by user kmohan1 cloned from 'Relative_gradient_0' owned by user kmohan2 (copied from Time_dep simulations)
Relative_gradient_p1	Deterministic (ODE) Spatial (2D)	cloned from ' Relative_gradient_p1' owned by user kmohan cloned from ' Relative_gradient_p1' owned by user kmohan1 cloned from ' Relative_gradient_p1' owned by user kmohan2 (copied from Relative_gradient_p03) (copied from Relative_gradient_p01) (copied from Relative_gradient_0) (copied from Time_dep simulations)
Relative_gradient_p3	Deterministic (ODE) Spatial (2D)	cloned from ' Relative_gradient_p3' owned by user kmohan cloned from ' Relative_gradient_p3' owned by user kmohan1 cloned from ' Relative_gradient_p3' owned by user kmohan2 (copied from Relative_gradient_p1) (copied from Relative_gradient_p03) (copied from Relative_gradient_p01) (copied from Relative_gradient_0) (copied from Time_dep simulations)

Application - Relative_gradient_p67

Specifications(Species) - Relative_gradient_p67 See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_gradient_extracellular	((1.0 + (0.016666666666666666 * x)) * (t > 1200.0)) [uM]	10.0 [um2/s]
PDGF_uniform_extracellular	(t > 1200.0) [uM]	10.0 [um2/s]
E_inactive_PLC	0.03 [uM]	19.0 [um2/s]
C_PKC_inactive	0.3 [uM]	24.0 [um2/s]
M_cytosolic_MARCKS	1.0 [uM]	32.0 [um2/s]
Mp	0.0 [uM]	32.0 [um2/s]
R_factor_plasmaMembrane	1.0 [uM]	0.1 [um2/s]
RplasmaMembrane	130.0 [uM]	0.01 [um2/s]
C1_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
C2_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
e_active_PLC	0.0 [uM]	0.01 [um2/s]
pT_PIP2	5000.0 [uM]	0.5 [um2/s]
d_DAG	0.0 [uM]	0.5 [um2/s]
c_DAG_PKC	0.0 [uM]	0.5 [um2/s]
cStar	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Relative_gradient_p67 See in Dashboard
Name	Reaction Mapping
Rsynthesis	included
R_Turnover	included
PDGF_binding	included
C1_turnover	included
C1_dimerization	included
C2_uncoupling	included
C2_Internalization	included
PLC_receptor_binding V_PLC	included
PIP2_Synthesis	included
PLC catalyzed PIP2 hydrolysis	included
PIP2_hydrolysis	included
DAG_consumption	included
MARCKS phosphorylation by PKC	included
MARCKS dephosphorylation	included
V_MARCKS	included
V_PKC	included
V_dpc	included
Vpc1	included
V_pc2	included
V_offc	included

Simulations - Relative_gradient_p67 See in Dashboard
Name	End Time	Output Options
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, DM=scan, DMp=scan	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 1	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 2	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 3	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 4	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 5	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 6	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 7	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 8	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 9	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 10	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 11	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 12	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 13	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 14	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 15	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 16	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 17	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 18	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 19	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 20	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 21	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 22	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 23	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 24	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 25	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry602565730 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	subdomain1		1.235432 [um2]	Nucleus
Volume	Analytical	subdomain2		55.318912 [um2]	Cytosol
Volume	Analytical	subdomain0		32.325656 [um2]	Extracellular
Surface		subdomain0_subdomain2_membrane	subdomain0 \| subdomain2	80.43141559089119 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	15.061103475619058 [um]	Nuclear_Membrane

Application - Relative_gradient_0

Specifications(Species) - Relative_gradient_0 See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_gradient_extracellular	((1.0 + (0.0 * x)) * (t > 1200.0)) [uM]	10.0 [um2/s]
PDGF_uniform_extracellular	(t > 1200.0) [uM]	10.0 [um2/s]
E_inactive_PLC	0.03 [uM]	19.0 [um2/s]
C_PKC_inactive	0.3 [uM]	24.0 [um2/s]
M_cytosolic_MARCKS	1.0 [uM]	32.0 [um2/s]
Mp	0.0 [uM]	32.0 [um2/s]
R_factor_plasmaMembrane	1.0 [uM]	0.1 [um2/s]
RplasmaMembrane	130.0 [uM]	0.01 [um2/s]
C1_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
C2_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
e_active_PLC	0.0 [uM]	0.01 [um2/s]
pT_PIP2	5000.0 [uM]	0.5 [um2/s]
d_DAG	0.0 [uM]	0.5 [um2/s]
c_DAG_PKC	0.0 [uM]	0.5 [um2/s]
cStar	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Relative_gradient_0 See in Dashboard
Name	Reaction Mapping
Rsynthesis	included
R_Turnover	included
PDGF_binding	included
C1_turnover	included
C1_dimerization	included
C2_uncoupling	included
C2_Internalization	included
PLC_receptor_binding V_PLC	included
PIP2_Synthesis	included
PLC catalyzed PIP2 hydrolysis	included
PIP2_hydrolysis	included
DAG_consumption	included
MARCKS phosphorylation by PKC	included
MARCKS dephosphorylation	included
V_MARCKS	included
V_PKC	included
V_dpc	included
Vpc1	included
V_pc2	included
V_offc	included

Simulations - Relative_gradient_0 See in Dashboard
Name	End Time	Output Options
rel_grad=0, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry810115562 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	subdomain1		1.33064807219032 [um2]	Nucleus
Volume	Analytical	subdomain2		54.72062346185398 [um2]	Cytosol
Volume	Analytical	subdomain0		32.828728465955706 [um2]	Extracellular
Surface		subdomain0_subdomain2_membrane	subdomain0 \| subdomain2	80.29580232624156 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	13.908563234401484 [um]	Nuclear_Membrane

Application - Relative_gradient_p1

Specifications(Species) - Relative_gradient_p1 See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_gradient_extracellular	((1.0 + (0.0025 * x)) * (t > 1200.0)) [uM]	10.0 [um2/s]
PDGF_uniform_extracellular	(t > 1200.0) [uM]	10.0 [um2/s]
E_inactive_PLC	0.03 [uM]	19.0 [um2/s]
C_PKC_inactive	0.3 [uM]	24.0 [um2/s]
M_cytosolic_MARCKS	1.0 [uM]	32.0 [um2/s]
Mp	0.0 [uM]	32.0 [um2/s]
R_factor_plasmaMembrane	1.0 [uM]	0.1 [um2/s]
RplasmaMembrane	130.0 [uM]	0.01 [um2/s]
C1_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
C2_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
e_active_PLC	0.0 [uM]	0.01 [um2/s]
pT_PIP2	5000.0 [uM]	0.5 [um2/s]
d_DAG	0.0 [uM]	0.5 [um2/s]
c_DAG_PKC	0.0 [uM]	0.5 [um2/s]
cStar	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Relative_gradient_p1 See in Dashboard
Name	Reaction Mapping
Rsynthesis	included
R_Turnover	included
PDGF_binding	included
C1_turnover	included
C1_dimerization	included
C2_uncoupling	included
C2_Internalization	included
PLC_receptor_binding V_PLC	included
PIP2_Synthesis	included
PLC catalyzed PIP2 hydrolysis	included
PIP2_hydrolysis	included
DAG_consumption	included
MARCKS phosphorylation by PKC	included
MARCKS dephosphorylation	included
V_MARCKS	included
V_PKC	included
V_dpc	included
Vpc1	included
V_pc2	included
V_offc	included

Simulations - Relative_gradient_p1 See in Dashboard
Name	End Time	Output Options
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry1080403767 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	subdomain1		1.33064807219032 [um2]	Nucleus
Volume	Analytical	subdomain2		54.72062346185398 [um2]	Cytosol
Volume	Analytical	subdomain0		32.828728465955706 [um2]	Extracellular
Surface		subdomain0_subdomain2_membrane	subdomain0 \| subdomain2	80.29580232624156 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	13.908563234401484 [um]	Nuclear_Membrane

Application - Relative_gradient_p3

Specifications(Species) - Relative_gradient_p3 See in Dashboard
Species	Initial Condition	Diffusion Constant
PDGF_gradient_extracellular	((1.0 + (0.0075 * x)) * (t > 1200.0)) [uM]	10.0 [um2/s]
PDGF_uniform_extracellular	(t > 1200.0) [uM]	10.0 [um2/s]
E_inactive_PLC	0.03 [uM]	19.0 [um2/s]
C_PKC_inactive	0.3 [uM]	24.0 [um2/s]
M_cytosolic_MARCKS	1.0 [uM]	32.0 [um2/s]
Mp	0.0 [uM]	32.0 [um2/s]
R_factor_plasmaMembrane	1.0 [uM]	0.1 [um2/s]
RplasmaMembrane	130.0 [uM]	0.01 [um2/s]
C1_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
C2_plasmaMembrane	0.0 [uM]	0.01 [um2/s]
e_active_PLC	0.0 [uM]	0.01 [um2/s]
pT_PIP2	5000.0 [uM]	0.5 [um2/s]
d_DAG	0.0 [uM]	0.5 [um2/s]
c_DAG_PKC	0.0 [uM]	0.5 [um2/s]
cStar	0.0 [uM]	0.5 [um2/s]
m	3727.0 [uM]	0.5 [um2/s]

Specifications(Reaction) - Relative_gradient_p3 See in Dashboard
Name	Reaction Mapping
Rsynthesis	included
R_Turnover	included
PDGF_binding	included
C1_turnover	included
C1_dimerization	included
C2_uncoupling	included
C2_Internalization	included
PLC_receptor_binding V_PLC	included
PIP2_Synthesis	included
PLC catalyzed PIP2 hydrolysis	included
PIP2_hydrolysis	included
DAG_consumption	included
MARCKS phosphorylation by PKC	included
MARCKS dephosphorylation	included
V_MARCKS	included
V_PKC	included
V_dpc	included
Vpc1	included
V_pc2	included
V_offc	included

Simulations - Relative_gradient_p3 See in Dashboard
Name	End Time	Output Options
rel_grad=0.3, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1	20000.0 [s]	OutputTimeStep 100.0

Geometry Geometry1987800069 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	subdomain1		1.33064807219032 [um2]	Nucleus
Volume	Analytical	subdomain2		54.72062346185398 [um2]	Cytosol
Volume	Analytical	subdomain0		32.828728465955706 [um2]	Extracellular
Surface		subdomain0_subdomain2_membrane	subdomain0 \| subdomain2	80.29580232624156 [um]	plasma_membrane
Surface		subdomain1_subdomain2_membrane	subdomain1 \| subdomain2	13.908563234401484 [um]	Nuclear_Membrane

Global Parameters

Global Parameters See in Dashboard
Name	Expression
kt	3.33E-4[s-1]

R0	130.0[1]

kr	0.1[s-1]

KD	0.0015[uM]

kxR0	0.005[s-1]

kminusx	0.001166667[s-1]

ke	0.0025[s-1]

Lmid	1.0E-4[1]

Luni	1.0E-4[1]

kone	10.0[s-1.uM-1]

koffe	0.1[s-1]

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

konm	0.217[molecules.um-2.s-1]

Kpip2	((konm / koffm) * (h ^ - 1.0))[molecules.um-2.s-1]

koffm	10.0[molecules6.s-4.um-12]

k_hyd0	0.005[s-1]

h	0.003[um]

k_hyd_PLC	0.005[s-1]

Vsynth0	2.5[molecules.um-2.s-1]

alpha	0.0[um2.molecules-1]

k_DAGK	1.0[s-1]

kdpM	1.0[s-1]

koffc	0.1[s-1]

konc	1.0[s-1.uM-1]

kdC	1.0[s-1]

kac1	1.0[s-1]

K_pip2	0.00135[tbd]

kon_m	792.0[molecules.um-2.s-1.uM-1]

koff_m	1.0[tbd]

kdpc	1.0[s-1]

kpc2	0.0[um2.s-1.molecules-1]