Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Suc_f+H_fSuc_apo+H_apo UmSRT1 fungus membrane GeneralKinetics
Suc_P+H_PH_apo+Suc_apo ZmSUT1 Plant_Membrane GeneralKinetics

UmSRT1 Universal ID's

UmSRT1 Text Annotations

ZmSUT1 Universal ID's

ZmSUT1 Text Annotations

Expressions for UmSRT1

reaction rate

J

(I_HSf * (Voltage_fungus_membrane - (25.0 * log((H_apo * Suc_apo / (H_f * Suc_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 ZmSUT1

reaction rate

J

(I_HSP * (Voltage_Plant_Membrane - (25.0 * log((H_apo * Suc_apo / (H_P * Suc_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]

Structures

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

fungus membrane Universal ID's

fungus membrane Text Annotations

Plant_Membrane Universal ID's

Plant_Membrane Text Annotations

fungus Universal ID's

fungus Text Annotations

plant Universal ID's

plant Text Annotations

apoplast Universal ID's

apoplast Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
H_apo apoplast apoplast
Suc_apo apoplast apoplast
Suc_f fungus fungus
H_f fungus fungus
H_P plant plant
Suc_P plant plant
ion_f fungus fungus
ion_apo apoplast apoplast
ion_P plant plant

H_apo Universal ID's

H_apo Text Annotations

Suc_apo Universal ID's

Suc_apo Text Annotations

Suc_f Universal ID's

Suc_f Text Annotations

H_f Universal ID's

H_f Text Annotations

H_P Universal ID's

H_P Text Annotations

Suc_P Universal ID's

Suc_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
Suc_f 2000.0 [uM] 0.0 [um2/s] fungus
H_f 0.1 [uM] 0.0 [um2/s] fungus
ion_f 100000.0 [uM] 0.0 [um2/s] fungus
H_P 0.1 [uM] 0.0 [um2/s] plant
Suc_P 1000000.0 [uM] 0.0 [um2/s] plant
ion_P 100000.0 [uM] 0.0 [um2/s] plant
H_apo 10.0 [uM] 0.0 [um2/s] apoplast
Suc_apo 2000.0 [uM] 0.0 [um2/s] apoplast
ion_apo 2000.0 [uM] 0.0 [um2/s] apoplast

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
UmSRT1 included
ZmSUT1 included
Background_fungus included
Background_Plant included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
standard condition 5.0

KeepEvery 1

KeepAtMost 1000
A, slope_ZmSUT1 20.0

KeepEvery 1

KeepAtMost 1000
D, slope_UmSRT1 20.0

KeepEvery 1

KeepAtMost 1000
G, slope_BG_p 20.0

KeepEvery 1

KeepAtMost 1000
K, slope_BG_f 20.0

KeepEvery 1

KeepAtMost 1000
V0_p, Vrev_BG_p 20.0

KeepEvery 1

KeepAtMost 1000
V0_f, Vrev_BG_f 20.0

KeepEvery 1

KeepAtMost 1000
H_apo 20.0

KeepEvery 1

KeepAtMost 1000

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

Application0 Universal ID's

Application0 Text Annotations

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