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Name - Dreyer_2017_AIMS Biophysics

BioModel ID - 116929912

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
K_extK_int	Kin_channel membrane	GeneralKinetics	K_extK_int
		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] user defined (N_Kin): 1.0[molecules.C.um-2.s-1.mV-1.uM-1.mol-1]
H_extH_int	H_Pump membrane	GeneralKinetics	H_extH_int
		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] user defined (N_Pump): 1.0[molecules.C.um-2.s-1.mol-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
apoplast	Compartment (+) (-)

Cell	Compartment (+) (-)

membrane	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
K_ext	apoplast

K_int	Cell

H_int	Cell

H_ext	apoplast

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Channel_test	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

Application - Channel_test

Specifications(Species) - Channel_test See in Dashboard
Species	Initial Condition	Diffusion Constant
K_ext	10.0 [uM]	0.0 [um2/s]
H_ext	3.16 [uM]	0.0 [um2/s]
K_int	1000.0 [uM]	0.0 [um2/s]
H_int	0.1 [uM]	0.0 [um2/s]

Specifications(Reaction) - Channel_test See in Dashboard
Name	Reaction Mapping
Kin_channel	included
H_Pump	included

Simulations - Channel_test See in Dashboard
Name	End Time	Output Options
Simulation0	15000.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry non-spatial844989218 See in Dashboard
(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

Global Parameters

Global Parameters See in Dashboard
Name	Expression