Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
d+Cc_active V_PKC plasma_membrane GeneralKinetics
Ee V_PLC plasma_membrane GeneralKinetics
M_pM V_dpm cytosol GeneralKinetics
pT V_basal_p plasma_membrane GeneralKinetics
pT Vsynth,p plasma_membrane GeneralKinetics
pTd V_hyd_PLC plasma_membrane GeneralKinetics
Mm V_MARCKS plasma_membrane GeneralKinetics
mM_p V_pm plasma_membrane GeneralKinetics
c_activec V_dpc plasma_membrane GeneralKinetics
cc_active V_pc plasma_membrane GeneralKinetics
cd+C V_off,c plasma_membrane GeneralKinetics
d_p Vsynth,dp plasma_membrane GeneralKinetics
d_p V_basal_dp plasma_membrane GeneralKinetics
d_pd V_PAP plasma_membrane GeneralKinetics
dd_p V_DAGK plasma_membrane GeneralKinetics

V_PKC Universal ID's

V_PKC Text Annotations

V_PLC Universal ID's

V_PLC Text Annotations

V_dpm Universal ID's

V_dpm Text Annotations

V_basal_p Universal ID's

V_basal_p Text Annotations

Vsynth,p Universal ID's

Vsynth,p Text Annotations

V_hyd_PLC Universal ID's

V_hyd_PLC Text Annotations

V_MARCKS Universal ID's

V_MARCKS Text Annotations

V_pm Universal ID's

V_pm Text Annotations

V_dpc Universal ID's

V_dpc Text Annotations

V_pc Universal ID's

V_pc Text Annotations

V_off,c Universal ID's

V_off,c Text Annotations

Vsynth,dp Universal ID's

Vsynth,dp Text Annotations

V_basal_dp Universal ID's

V_basal_dp Text Annotations

V_PAP Universal ID's

V_PAP Text Annotations

V_DAGK Universal ID's

V_DAGK Text Annotations

Expressions for V_PKC

reaction rate

J

((kon_c * d * C) - (koff_c * c_active)) [molecules.um-2.s-1]

global

n

2.0 [1]

global

koff_c

0.1 [s-1]

global

kon_c

1.0 [s-1.uM-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for V_PLC

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]

global

n

2.0 [1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

rsteep2

0.0 [tbd]

local

epsilon

0.01 [1]

local

rsteep1

0.0 [tbd]

local

rfrac

0.0 [tbd]

local

kon_e

0.1 [s-1.uM-1]

local

k_PA

10.0 [um2.molecules-1]

local

koff_e

0.1 [s-1]

Expressions for V_dpm

reaction rate

J

(k_dpm * M_p) [uM.s-1]

local

k_dpm

0.3 [s-1]

Expressions for V_basal_p

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]

global

k_PIP2

0.00135 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

k_basal_p

0.005 [tbd]

Expressions for Vsynth,p

reaction rate

J

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

global

n

2.0 [1]

global

h

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

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

Vsynth_p

2.5 [s-1]

Expressions for V_hyd_PLC

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]

global

h

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

global

k_PIP2

0.00135 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

k_hyd_PLC

5.0E-4 [s-1]

Expressions for V_MARCKS

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]

global

n

2.0 [1]

global

koff_m

1.0 [s-1]

global

kon_m

792.0 [s-1.uM-1]

global

k_PIP2

0.00135 [tbd]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for V_pm

reaction rate

J

(k_pm * c_active * m) [molecules.um-2.s-1]

global

k_pm

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 V_dpc

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]

local

k_dpc

1.0 [s-1]

Expressions for V_pc

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]

local

k_pc

1.0 [s-1]

Expressions for V_off,c

reaction rate

J

(koff_c * c) [molecules.um-2.s-1]

global

koff_c

0.1 [s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

Expressions for Vsynth,dp

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]

global

n

2.0 [1]

global

h

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

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

k_PLD

0.1 [um2.molecules-1]

local

Vsynth_dp

1.0E-4 [tbd]

local

gamma

100000.0 [tbd]

Expressions for V_basal_dp

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]

local

k_basal_dp

1.0 [s-1]

Expressions for V_PAP

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]

local

k_PAP

1.0 [s-1]

Expressions for V_DAGK

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]

local

k_DAGK

1.0 [s-1]

Structures

Name
Type
Electrical
plasma_membrane Membrane cytosol(+)   extracellular(-)
nuclear_membrane Membrane nucleus(+)   cytosol(-)
nucleus Compartment (+)   (-)
extracellular Compartment (+)   (-)
cytosol Compartment (+)   (-)

plasma_membrane Universal ID's

plasma_membrane Text Annotations

nuclear_membrane Universal ID's

nuclear_membrane Text Annotations

nucleus Universal ID's

nucleus Text Annotations

extracellular Universal ID's

extracellular Text Annotations

cytosol Universal ID's

cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
pT plasma_membrane plasma_membrane
d plasma_membrane plasma_membrane
c_active plasma_membrane plasma_membrane
M cytosol cytosol
M_p cytosol cytosol
E cytosol cytosol
e plasma_membrane plasma_membrane
C cytosol cytosol
c plasma_membrane plasma_membrane
m plasma_membrane plasma_membrane
d_p plasma_membrane plasma_membrane

pT Universal ID's

pT Text Annotations

d Universal ID's

d Text Annotations

c_active Universal ID's

c_active Text Annotations

M Universal ID's

M Text Annotations

M_p Universal ID's

M_p Text Annotations

E Universal ID's

E Text Annotations

e Universal ID's

e Text Annotations

C Universal ID's

C Text Annotations

c Universal ID's

c Text Annotations

m Universal ID's

m Text Annotations

d_p Universal ID's

d_p Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Symmetric Geometry Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D)
Asymmetric Geometry Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D) (copied from Symmetric Geometry)

Symmetric Geometry Universal ID's

Symmetric Geometry Text Annotations

Asymmetric Geometry Universal ID's

Asymmetric Geometry Text Annotations

Specifications (Species) - Symmetric Geometry go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
M 1.0 [uM] 32.0 [um2/s] cytosol
M_p 0.0 [uM] 32.0 [um2/s] cytosol
E 0.02 [uM] 19.0 [um2/s] cytosol
C 0.3 [uM] 24.0 [um2/s] cytosol
pT 5000.0 [uM] 0.5 [um2/s] plasma_membrane
d 0.0 [uM] 0.5 [um2/s] plasma_membrane
c_active 0.0 [uM] 0.5 [um2/s] plasma_membrane
e 0.0 [uM] 0.01 [um2/s] plasma_membrane
c 0.0 [uM] 0.5 [um2/s] plasma_membrane
m 3727.0 [uM] 0.5 [um2/s] plasma_membrane
d_p 0.0 [uM] 0.5 [um2/s] plasma_membrane

Specifications (Reaction) - Symmetric Geometry go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Fig 2A: PFL 1 scan 0% gradient 40000.0

OutputTimeStep 100.0
Fig 2A: PFL 1 scan 3% gradient 40000.0

OutputTimeStep 100.0
Fig 2A: PFL 1 scan 10% gradient 40000.0

OutputTimeStep 100.0
Fig 2A: PFL 1 scan 30% gradient 40000.0

OutputTimeStep 100.0
Fig 2A: PFL 1 scan 67% gradient 40000.0

OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 0% gradient 20000.0

OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 3% gradient 20000.0

OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 10% gradient 20000.0

OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 30% gradient 20000.0

OutputTimeStep 100.0
Fig 2B: PFL 1 scan without MARCKS 67% gradient 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.1 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.2 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 0.5 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 2.0 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 5.0 20000.0

OutputTimeStep 100.0
Fig 3A: M and Mp diffusivity scan x 10 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.1 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.2 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 0.5 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 2.0 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 5.0 20000.0

OutputTimeStep 100.0
Fig 3B: pT and mT diffusivity scan x 10 20000.0

OutputTimeStep 100.0
Fig 5B: 0.3 x kDAGK scan 10% gradient 40000.0

OutputTimeStep 100.0
Fig 5B: 3.0 x kDAGK scan 10% gradient 40000.0

OutputTimeStep 100.0
Fig 5D: 3.0 x kDAGK scan 3% gradient 40000.0

OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.1 20000.0

OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.2 20000.0

OutputTimeStep 100.0
Fig 5E: Variation of DAG and PA scan x 0.5 20000.0

OutputTimeStep 100.0
Fig 6A: PFL 2 + MARCKS 40000.0

OutputTimeStep 100.0
Fig 6B: PFL 1+ PFL 2 40000.0

OutputTimeStep 100.0
Fig 6C: PFL 1+ PFL 2 + MARCKS 40000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kon,e 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans koff,e 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans epsilon 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans KPA 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans khyd,PLC 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kpm 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kdpm 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kbasal,dp 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kDAGK 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kPAP 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kon,c 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans koff,c 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kdpc 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans kpc 20000.0

OutputTimeStep 100.0
Fig S4: Parameter scans Vsynth,dp 20000.0

OutputTimeStep 100.0
Fig S5: PFL 2 + MARCKS, kDAGK 20000.0

OutputTimeStep 100.0
Fig S5: PFL 2 + MARCKS, KPLD 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, kDAGK 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, KPA 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2, KPLD 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, kDAGK 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, KPA 20000.0

OutputTimeStep 100.0
Fig S5: PFL 1 + PFL 2 + MARCKS, KPLD 20000.0

OutputTimeStep 100.0

Symmetric Geometry Universal ID's

Symmetric Geometry Text Annotations

Symmetric Geometry Universal ID's

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Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry2

(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

Events

Name Variable Rate Expression

Specifications (Species) - Asymmetric Geometry go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
M 1.0 [uM] 32.0 [um2/s] cytosol
M_p 0.0 [uM] 32.0 [um2/s] cytosol
E 0.02 [uM] 19.0 [um2/s] cytosol
C 0.3 [uM] 24.0 [um2/s] cytosol
pT 5000.0 [uM] 0.5 [um2/s] plasma_membrane
d 0.0 [uM] 0.5 [um2/s] plasma_membrane
c_active 0.0 [uM] 0.5 [um2/s] plasma_membrane
e 0.0 [uM] 0.01 [um2/s] plasma_membrane
c 0.0 [uM] 0.5 [um2/s] plasma_membrane
m 3727.0 [uM] 0.5 [um2/s] plasma_membrane
d_p 0.0 [uM] 0.5 [um2/s] plasma_membrane

Specifications (Reaction) - Asymmetric Geometry go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Fig 4B: PFL 1 scan 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.1 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.2 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 0.5 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 2.0 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 5.0 20000.0

OutputTimeStep 100.0
Fig 4C: M and Mp diffusivity scan x 10 20000.0

OutputTimeStep 100.0
Fig 4D: Back end blunted scan 3% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Back end blunted scan 10% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Back end blunted scan 30% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Back end blunted scan 67% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Front end blunted scan 3% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Front end blunted scan 10% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Front end blunted scan 30% gradient 20000.0

OutputTimeStep 100.0
Fig 4D: Front end blunted scan 67% gradient 20000.0

OutputTimeStep 100.0

Asymmetric Geometry Universal ID's

Asymmetric Geometry Text Annotations

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Asymmetric Geometry Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry2

(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

Events

Name Variable Rate Expression

Global Parameters

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]

Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Symmetric Geometry.bngl , Asymmetric Geometry.bngl
SBML Symmetric Geometry.sbml , Asymmetric Geometry.sbml
Matlab Symmetric Geometry.m , Asymmetric Geometry.m
NFSim XML Symmetric Geometry.xml , Asymmetric Geometry.xml