ModelBricks - Model Print Page

Dashboard

Name - Smoldyn

BioModel ID - 92705462

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
AB	r0 CM	MassAction	AB
		reaction rate (J): ((Kf * A) - (Kr * B))[molecules.um-2.s-1] inward current density (I): 0.0[pA.um-2] net charge valence (netValence): 0.0[1] forward rate constant (Kf): 1.0[s-1] reverse rate constant (Kr): 1.0[s-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
A	CM

B	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
Det	Deterministic (ODE) Spatial (3D)
stoch	Stochastic (SSA) Spatial (3D)	(copied from Det)

Application - Det

Specifications(Species) - Det See in Dashboard
Species	Initial Condition	Diffusion Constant
A	0.1 [uM]	0.1 [um2/s]
B	0.0 [uM]	0.1 [um2/s]

Specifications(Reaction) - Det See in Dashboard
Name	Reaction Mapping
r0	included

Simulations - Det See in Dashboard
Name	End Time	Output Options
Simulation1	10.0 [s]	OutputTimeStep 0.05

Geometry 3DLEGIStoch_Sayak 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

Application - stoch

Specifications(Species) - stoch See in Dashboard
Species	Initial Condition	Diffusion Constant
A	0.1 [uM]	0.1 [um2/s]
B	0.0 [uM]	0.1 [um2/s]

Specifications(Reaction) - stoch See in Dashboard
Name	Reaction Mapping
r0	included

Simulations - stoch See in Dashboard
Name	End Time	Output Options
Simulation0	10.0 [s]	OutputTimeStep 0.05

Geometry 3DLEGIStoch_Sayak 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