ModelBricks - Model Print Page

Dashboard

Name - BEN

BioModel ID - 93386467

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
X_CMX_CM+X_CM	r2 CM	GeneralKinetics	X_CMX_CM+X_CM
		reaction rate (J): (0.04 + (0.4 * N_CM) + (2.0 * X_CM * X_CM / (1.0 + (X_CM * X_CM))) - (0.4 * X_CM * Y_CM) + (0.008 * X_CM * S_CM))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1]
Y_CMY_CM+Y_CM	r3 CM	GeneralKinetics	Y_CMY_CM+Y_CM
		reaction rate (J): ((0.4 * X_CM) - (0.028 * Y_CM))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1]
L_sourceL_EC	rx EC	GeneralKinetics	L_sourceL_EC
		reaction rate (J): ((kf * L_source) - (kr * L_EC))[uM.s-1] user defined (kr): 1.0[s-1] user defined (kf): 10.0[s-1]
L_EC+R_CMS_CM	r1 CM	GeneralKinetics	L_EC+R_CMS_CM
		reaction rate (J): ((kf * L_EC * R_CM) - (kr * S_CM))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] user defined (kr): 1.0[s-1] user defined (kf): 2.0[s-1.uM-1]

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

EC	Compartment (+) (-)

CM	Membrane N/A

Species See in Dashboard
Name	Structure	BioNetGen Definition
L_EC	EC

L_source	EC

N_CM	CM

Y_CM	CM

X_CM	CM

S_CM	CM

R_CM	CM

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
Needle	Deterministic (ODE) Spatial (3D)

Application - Needle

Specifications(Species) - Needle See in Dashboard
Species	Initial Condition	Diffusion Constant
L_EC	0.0 [uM]	15.0 [um2/s]
L_source	(((( - 5.0 + x) * ( - 5.0 + x)) + (( - 5.0 + y) * ( - 5.0 + y)) + (( - 2.5 + z) * ( - 2.5 + z))) < 1.0) [uM]	10.0 [um2/s]
N_CM	(0.2 * ((t >= 15.0) && (t <= 16.0))) [uM]	0.1 [um2/s]
Y_CM	2.0 [uM]	0.0 [um2/s]
X_CM	0.14 [uM]	0.0 [um2/s]
S_CM	0.0 [uM]	0.0 [um2/s]
R_CM	100.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - Needle See in Dashboard
Name	Reaction Mapping
r2	included
r3	included
rx	included
r1	included

Simulations - Needle See in Dashboard
Name	End Time	Output Options
Simulation0	100.0 [s]	OutputTimeStep 1.0

Geometry 3DLEGI_BEN See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 5.0, 5.0, 5.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
Volume	Analytical	IC		11.821125 [um3]	IC
Volume	Analytical	EC		113.17887499999999 [um3]	EC
Surface		EC_IC_membrane	EC \| IC	25.03574790171551 [um2]	CM

Global Parameters

Global Parameters See in Dashboard
Name	Expression