Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Pi_f+H_fPi_apo+H_apo H_P_f_Co_Transport fungus membrane GeneralKinetics
Pi_P+H_PPi_apo+H_apo H_P_p_Co_Transport Plant_Membrane GeneralKinetics
C_f+H_fC_apo+H_apo H_C_f_Co_Transport fungus membrane GeneralKinetics
C_P+H_PH_apo+C_apo H_C_p_Co_Transport Plant_Membrane GeneralKinetics
C_PC_apo SWEET Plant_Membrane GeneralKinetics

H_P_f_Co_Transport Universal ID's

H_P_f_Co_Transport Text Annotations

H_P_p_Co_Transport Universal ID's

H_P_p_Co_Transport Text Annotations

H_C_f_Co_Transport Universal ID's

H_C_f_Co_Transport Text Annotations

H_C_p_Co_Transport Universal ID's

H_C_p_Co_Transport Text Annotations

SWEET Universal ID's

SWEET Text Annotations

Expressions for H_P_f_Co_Transport

reaction rate

J

(I_HPf * (Voltage_fungus_membrane - (25.0 * log((H_apo * H_apo * Pi_apo / (H_f * H_f * Pi_f)))))) [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

I_HPf

(E * number_transporters) [molecules.um-2.s-1.mV-1]

global

number_transporters

(625.0 * 2.0) [molecules.um-2.s-1.mV-1]

local

E

1.0 [1]

Expressions for H_P_p_Co_Transport

reaction rate

J

(I_HPP * (Voltage_Plant_Membrane - (25.0 * log((H_apo * H_apo * Pi_apo / (H_P * H_P * Pi_P)))))) [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

I_HPP

(B * number_transporters) [molecules.um-2.s-1.mV-1]

global

number_transporters

(625.0 * 2.0) [molecules.um-2.s-1.mV-1]

local

B

1.0 [1]

Expressions for H_C_f_Co_Transport

reaction rate

J

(I_HSf * (Voltage_fungus_membrane - (25.0 * log((H_apo * C_apo / (H_f * C_f)))))) [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

I_HSf

(D * number_transporters) [molecules.um-2.s-1.mV-1]

global

number_transporters

(625.0 * 2.0) [molecules.um-2.s-1.mV-1]

local

D

1.0 [1]

Expressions for H_C_p_Co_Transport

reaction rate

J

(I_HSP * (Voltage_Plant_Membrane - (25.0 * log((H_apo * C_apo / (H_P * C_P)))))) [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

I_HSP

(A * number_transporters) [molecules.um-2.s-1.mV-1]

global

number_transporters

(625.0 * 2.0) [molecules.um-2.s-1.mV-1]

local

A

1.0 [1]

Expressions for SWEET

reaction rate

J

(Diff_Sweet * (C_P - C_apo)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

1.0 [1]

local

Diff_Sweet

(M * 100.0) [molecules.um-2.s-1.uM-1]

local

M

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

Structures

Name
Type
Electrical
fungus membrane Membrane apoplast(+)   fungus(-)
Plant_Membrane Membrane apoplast(+)   plant(-)
apoplast Compartment (+)   (-)
plant Compartment (+)   (-)
fungus Compartment (+)   (-)

fungus membrane Universal ID's

fungus membrane Text Annotations

Plant_Membrane Universal ID's

Plant_Membrane Text Annotations

apoplast Universal ID's

apoplast Text Annotations

plant Universal ID's

plant Text Annotations

fungus Universal ID's

fungus Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
H_apo apoplast apoplast
Pi_apo apoplast apoplast
C_apo apoplast apoplast
C_f fungus fungus
H_f fungus fungus
Pi_f fungus fungus
H_P plant plant
Pi_P plant plant
C_P plant plant
ion_f fungus fungus
ion_apo apoplast apoplast
ion_P plant plant

H_apo Universal ID's

H_apo Text Annotations

Pi_apo Universal ID's

Pi_apo Text Annotations

C_apo Universal ID's

C_apo Text Annotations

C_f Universal ID's

C_f Text Annotations

H_f Universal ID's

H_f Text Annotations

Pi_f Universal ID's

Pi_f Text Annotations

H_P Universal ID's

H_P Text Annotations

Pi_P Universal ID's

Pi_P Text Annotations

C_P Universal ID's

C_P Text Annotations

ion_f Universal ID's

ion_f Text Annotations

ion_apo Universal ID's

ion_apo Text Annotations

ion_P Universal ID's

ion_P Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
H_apo 1.0 [uM] 0.0 [um2/s] apoplast
Pi_apo 1.0 [uM] 0.0 [um2/s] apoplast
C_apo 7.0 [uM] 0.0 [um2/s] apoplast
ion_apo 2000.0 [uM] 0.0 [um2/s] apoplast
H_P 0.1 [uM] 0.0 [um2/s] plant
Pi_P 1500.0 [uM] 0.0 [um2/s] plant
C_P 2000.0 [uM] 0.0 [um2/s] plant
ion_P 100000.0 [uM] 0.0 [um2/s] plant
C_f 1000.0 [uM] 0.0 [um2/s] fungus
H_f 0.1 [uM] 0.0 [um2/s] fungus
Pi_f 3000.0 [uM] 0.0 [um2/s] fungus
ion_f 100000.0 [uM] 0.0 [um2/s] fungus

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
H_P_f_Co_Transport included
H_P_p_Co_Transport included
H_C_f_Co_Transport included
H_C_p_Co_Transport included
SWEET included
Background_fungus included
Background_Plant included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Simulation0 5.0

KeepEvery 1

KeepAtMost 1000

Application0 Universal ID's

Application0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial103398121

(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 Plant_Membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
number_transporters (625.0 * 2.0)[molecules.um-2.s-1.mV-1]

Universal ID's

Text Annotations

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 Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml