Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RplasmaMembrane Rsynthesis plasma_membrane GeneralKinetics
RplasmaMembrane R_Turnover plasma_membrane GeneralKinetics
RplasmaMembraneC1_plasmaMembrane PDGF_binding plasma_membrane GeneralKinetics
C1_plasmaMembrane C1_turnover plasma_membrane GeneralKinetics
C1_plasmaMembraneC2_plasmaMembrane C1_dimerization plasma_membrane GeneralKinetics
C2_plasmaMembraneC1_plasmaMembrane+RplasmaMembrane C2_uncoupling plasma_membrane GeneralKinetics
C2_plasmaMembrane C2_Internalization plasma_membrane GeneralKinetics
E_inactive_PLCe_active_PLC PLC_receptor_binding V_PLC plasma_membrane GeneralKinetics
pT_PIP2 PIP2_Synthesis plasma_membrane GeneralKinetics
pT_PIP2d_DAG PLC catalyzed PIP2 hydrolysis plasma_membrane GeneralKinetics
pT_PIP2 PIP2_hydrolysis plasma_membrane GeneralKinetics
d_DAG DAG_consumption plasma_membrane GeneralKinetics
mMp MARCKS phosphorylation by PKC plasma_membrane GeneralKinetics
MpM_cytosolic_MARCKS MARCKS dephosphorylation Cytosol GeneralKinetics
M_cytosolic_MARCKSm V_MARCKS plasma_membrane GeneralKinetics
d_DAG+C_PKC_inactivecStar V_PKC plasma_membrane GeneralKinetics
cStarc_DAG_PKC V_dpc plasma_membrane GeneralKinetics
c_DAG_PKCcStar Vpc1 plasma_membrane GeneralKinetics
c_DAG_PKCcStar V_pc2 plasma_membrane GeneralKinetics
c_DAG_PKCC_PKC_inactive+d_DAG V_offc plasma_membrane GeneralKinetics

Rsynthesis Universal ID's

Rsynthesis Text Annotations

R_Turnover Universal ID's

R_Turnover Text Annotations

PDGF_binding Universal ID's

PDGF_binding Text Annotations

C1_turnover Universal ID's

C1_turnover Text Annotations

C1_dimerization Universal ID's

C1_dimerization Text Annotations

C2_uncoupling Universal ID's

C2_uncoupling Text Annotations

C2_Internalization Universal ID's

C2_Internalization Text Annotations

PLC_receptor_binding V_PLC Universal ID's

PLC_receptor_binding V_PLC Text Annotations

PIP2_Synthesis Universal ID's

PIP2_Synthesis Text Annotations

PLC catalyzed PIP2 hydrolysis Universal ID's

PLC catalyzed PIP2 hydrolysis Text Annotations

PIP2_hydrolysis Universal ID's

PIP2_hydrolysis Text Annotations

DAG_consumption Universal ID's

DAG_consumption Text Annotations

MARCKS phosphorylation by PKC Universal ID's

MARCKS phosphorylation by PKC Text Annotations

MARCKS dephosphorylation Universal ID's

MARCKS dephosphorylation Text Annotations

V_MARCKS Universal ID's

V_MARCKS Text Annotations

V_PKC Universal ID's

V_PKC Text Annotations

V_dpc Universal ID's

V_dpc Text Annotations

Vpc1 Universal ID's

Vpc1 Text Annotations

V_pc2 Universal ID's

V_pc2 Text Annotations

V_offc Universal ID's

V_offc Text Annotations

Expressions for Rsynthesis

reaction rate

J

(kt * R0 * R_factor_plasmaMembrane) [molecules.um-2.s-1]

global

kt

3.33E-4 [s-1]

global

R0

130.0 [1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for R_Turnover

reaction rate

J

(kt * RplasmaMembrane) [molecules.um-2.s-1]

global

kt

3.33E-4 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for PDGF_binding

reaction rate

J

(((kr / KD) * ((Lmid * PDGF_gradient_extracellular) + (Luni * PDGF_uniform_extracellular)) * RplasmaMembrane) - (kr * C1_plasmaMembrane)) [molecules.um-2.s-1]

global

kr

0.1 [s-1]

global

KD

0.0015 [uM]

global

Lmid

1.0E-4 [1]

global

Luni

1.0E-4 [1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for C1_turnover

reaction rate

J

(kt * C1_plasmaMembrane) [molecules.um-2.s-1]

global

kt

3.33E-4 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for C1_dimerization

reaction rate

J

((kxR0 * (C1_plasmaMembrane ^ 2.0)) / R0) [molecules.um-2.s-1]

global

R0

130.0 [1]

global

kxR0

0.005 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for C2_uncoupling

reaction rate

J

(kminusx * C2_plasmaMembrane) [molecules.um-2.s-1]

global

kminusx

0.001166667 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for C2_Internalization

reaction rate

J

(ke * C2_plasmaMembrane) [molecules.um-2.s-1]

global

ke

0.0025 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for PLC_receptor_binding V_PLC

reaction rate

J

((kone * C2_plasmaMembrane * E_inactive_PLC) - (koffe * e_active_PLC)) [molecules.um-2.s-1]

global

kone

10.0 [s-1.uM-1]

global

koffe

0.1 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for PIP2_Synthesis

reaction rate

J

(Vsynth0 * (1.0 + (alpha * C2_plasmaMembrane))) [molecules.um-2.s-1]

global

h

0.003 [um]

global

Vsynth0

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

global

alpha

0.0 [um2.molecules-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for PLC catalyzed PIP2 hydrolysis

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]

global

h

0.003 [um]

global

k_hyd_PLC

0.005 [s-1]

global

K_pip2

0.00135 [tbd]

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]

Expressions for PIP2_hydrolysis

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]

global

k_hyd0

0.005 [s-1]

global

h

0.003 [um]

global

K_pip2

0.00135 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for DAG_consumption

reaction rate

J

(k_DAGK * d_DAG) [molecules.um-2.s-1]

global

k_DAGK

1.0 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for MARCKS phosphorylation by PKC

reaction rate

J

(kpm * cStar * m) [molecules.um-2.s-1]

global

kpm

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

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for MARCKS dephosphorylation

reaction rate

J

(kdpM * Mp) [uM.s-1]

global

kdpM

1.0 [s-1]

Expressions for V_MARCKS

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]

global

K_pip2

0.00135 [tbd]

global

kon_m

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

global

koff_m

1.0 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for V_PKC

reaction rate

J

((konc * d_DAG * C_PKC_inactive) - (koffc1 * cStar)) [molecules.um-2.s-1]

global

koffc

0.1 [s-1]

global

konc

1.0 [s-1.uM-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

koffc1

0.1 [s-1]

Expressions for V_dpc

reaction rate

J

(kdpc * cStar) [molecules.um-2.s-1]

global

kdpc

1.0 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for Vpc1

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]

local

kpc1

1.0 [s-1]

Expressions for V_pc2

reaction rate

J

(kpc2 * c_DAG_PKC * cStar) [molecules.um-2.s-1]

global

kpc2

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

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for V_offc

reaction rate

J

(koffc * c_DAG_PKC) [molecules.um-2.s-1]

global

koffc

0.1 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Structures

Name
Type
Electrical
plasma_membrane Membrane Cytosol(+)   Extracellular(-)
Nuclear_Membrane Membrane Nucleus(+)   Cytosol(-)
Extracellular Compartment (+)   (-)
Nucleus Compartment (+)   (-)
Cytosol Compartment (+)   (-)

plasma_membrane Universal ID's

plasma_membrane Text Annotations

Nuclear_Membrane Universal ID's

Nuclear_Membrane Text Annotations

Extracellular Universal ID's

Extracellular Text Annotations

Nucleus Universal ID's

Nucleus Text Annotations

Cytosol Universal ID's

Cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
PDGF_gradient_extracellular Extracellular Extracellular
PDGF_uniform_extracellular Extracellular Extracellular
R_factor_plasmaMembrane plasma_membrane plasma_membrane
RplasmaMembrane plasma_membrane plasma_membrane
C1_plasmaMembrane plasma_membrane plasma_membrane
C2_plasmaMembrane plasma_membrane plasma_membrane
E_inactive_PLC Cytosol Cytosol
e_active_PLC plasma_membrane plasma_membrane
pT_PIP2 plasma_membrane plasma_membrane
d_DAG plasma_membrane plasma_membrane
C_PKC_inactive Cytosol Cytosol
c_DAG_PKC plasma_membrane plasma_membrane
cStar plasma_membrane plasma_membrane
M_cytosolic_MARCKS Cytosol Cytosol
m plasma_membrane plasma_membrane
Mp Cytosol Cytosol

PDGF_gradient_extracellular Universal ID's

PDGF_gradient_extracellular Text Annotations

PDGF_uniform_extracellular Universal ID's

PDGF_uniform_extracellular Text Annotations

R_factor_plasmaMembrane Universal ID's

R_factor_plasmaMembrane Text Annotations

RplasmaMembrane Universal ID's

RplasmaMembrane Text Annotations

C1_plasmaMembrane Universal ID's

C1_plasmaMembrane Text Annotations

C2_plasmaMembrane Universal ID's

C2_plasmaMembrane Text Annotations

E_inactive_PLC Universal ID's

E_inactive_PLC Text Annotations

e_active_PLC Universal ID's

e_active_PLC Text Annotations

pT_PIP2 Universal ID's

pT_PIP2 Text Annotations

d_DAG Universal ID's

d_DAG Text Annotations

C_PKC_inactive Universal ID's

C_PKC_inactive Text Annotations

c_DAG_PKC Universal ID's

c_DAG_PKC Text Annotations

cStar Universal ID's

cStar Text Annotations

M_cytosolic_MARCKS Universal ID's

M_cytosolic_MARCKS Text Annotations

m Universal ID's

m Text Annotations

Mp Universal ID's

Mp Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Relative_gradient_p67 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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 Specs - Species
Specs - Reaction
Simulations 		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)

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_0 Universal ID's

Relative_gradient_0 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p3 Universal ID's

Relative_gradient_p3 Text Annotations

Specifications (Species) - Relative_gradient_p67 go to Simulations

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

Specifications (Reaction) - Relative_gradient_p67 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, DM=scan, DMp=scan 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0 20000.0

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

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 1 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 2 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 3 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 4 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 5 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 6 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 7 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 8 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 9 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 10 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 11 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 12 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 13 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 14 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 15 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 16 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 17 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 18 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 19 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 20 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 21 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 22 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 23 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 24 20000.0

OutputTimeStep 100.0
rel_grad=0.67, Lmid=3e-5, kpm=scan, kdpm=scan, kpc1=1, kpc2=0, 25 20000.0

OutputTimeStep 100.0

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Relative_gradient_p67 Universal ID's

Relative_gradient_p67 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry602565730

(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

Events

Name Variable Rate Expression

Specifications (Species) - Relative_gradient_0 go to Simulations

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

Specifications (Reaction) - Relative_gradient_0 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
rel_grad=0, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1 20000.0

OutputTimeStep 100.0

Relative_gradient_0 Universal ID's

Relative_gradient_0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry810115562

(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

Events

Name Variable Rate Expression

Specifications (Species) - Relative_gradient_p1 go to Simulations

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

Specifications (Reaction) - Relative_gradient_p1 go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0 20000.0

OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=0.01, kpc2=1 20000.0

OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=0.03, kdpm=0.01, kpc1=0.01, kpc2=1 20000.0

OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=1, kpc2=0, konm=0, koffm=0 20000.0

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

OutputTimeStep 100.0
rel_grad=0.1, Lmid=3e-5, kpm=1, kdpm=1, kpc1=scan, kpc2=scan, konm=0, koffm=0 20000.0

OutputTimeStep 100.0

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Relative_gradient_p1 Universal ID's

Relative_gradient_p1 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1080403767

(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

Events

Name Variable Rate Expression

Specifications (Species) - Relative_gradient_p3 go to Simulations

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

Specifications (Reaction) - Relative_gradient_p3 go to Simulations

Name
Enabled?
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 go to Specifications

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

OutputTimeStep 100.0

Relative_gradient_p3 Universal ID's

Relative_gradient_p3 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1987800069

(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

Events

Name Variable Rate Expression

Global Parameters

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]

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