Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
K_extK_int Kin_channel membrane GeneralKinetics
H_extH_int H_Pump membrane GeneralKinetics

Kin_channel Universal ID's

Kin_channel Text Annotations

H_Pump Universal ID's

H_Pump Text Annotations

Expressions for Kin_channel

reaction rate

J

- (N_Kin / 100.0 * 6.02E11 / _F_ * Voltage_membrane / 25.0 * (K_int - (K_ext * exp(( - 0.04 * Voltage_membrane)))) / ((1.0 + (0.03 * Voltage_membrane) - exp(( - 0.04 * Voltage_membrane))) * (1.0 + exp((6.0 + (0.04 * Voltage_membrane)))))) [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]

local

N_Kin

1.0 [molecules.C.um-2.s-1.mV-1.uM-1.mol-1]

Expressions for H_Pump

reaction rate

J

- (N_Pump * 6.02E11 / _F_ * (1.0 - exp(( - 10.0 - (0.04 * Voltage_membrane)))) / (1.0 + exp(( - 8.0 - (0.04 * Voltage_membrane))) + exp(( - 2.5 - (0.0128 * Voltage_membrane))))) [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]

local

N_Pump

1.0 [molecules.C.um-2.s-1.mol-1]

Structures

Name
Type
Electrical
membrane Membrane Cell(+)   apoplast(-)
apoplast Compartment (+)   (-)
Cell Compartment (+)   (-)

membrane Universal ID's

membrane Text Annotations

apoplast Universal ID's

apoplast Text Annotations

Cell Universal ID's

Cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
K_ext apoplast apoplast
K_int Cell Cell
H_int Cell Cell
H_ext apoplast apoplast

K_ext Universal ID's

K_ext Text Annotations

K_int Universal ID's

K_int Text Annotations

H_int Universal ID's

H_int Text Annotations

H_ext Universal ID's

H_ext Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Channel_test Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'phloem_test' owned by user IngoDreyer cloned from 'phloem_test' owned by user Sandmann cloned from 'phloem_test' owned by user Jgomez

Channel_test Universal ID's

Channel_test Text Annotations

Specifications (Species) - Channel_test go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
K_ext 10.0 [uM] 0.0 [um2/s] apoplast
H_ext 3.16 [uM] 0.0 [um2/s] apoplast
K_int 1000.0 [uM] 0.0 [um2/s] Cell
H_int 0.1 [uM] 0.0 [um2/s] Cell

Specifications (Reaction) - Channel_test go to Simulations

Name
Enabled?
Kin_channel included
H_Pump included

Simulations - Channel_test go to Specifications

Name
End Time
Output Options
Simulation0 15000.0

KeepEvery 1

KeepAtMost 1000

Channel_test Universal ID's

Channel_test Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial844989218

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

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 Channel_test.bngl
SBML Channel_test.sbml
Matlab Channel_test.m
NFSim XML Channel_test.xml