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Name - NucleationMechanism

BioModel ID - 217669650

Reaction Diagram

reactionDiagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
MonomerDimer	Dimerization Well	MassAction	MonomerDimer
		reaction rate (J): ((Kf * pow(Monomer,2.0)) - (Kr * Dimer))[uM.s-1] forward rate constant (Kf): 35.7[s-1.uM-1] reverse rate constant (Kr): 1.63E8[s-1]
Monomer+DimerTrimer	Trimerization Well	MassAction	Monomer+DimerTrimer
		reaction rate (J): (((Kf * Monomer) * Dimer) - (Kr * Trimer))[uM.s-1] forward rate constant (Kf): 2.18[s-1.uM-1] reverse rate constant (Kr): 1300.0[s-1]
MonomerFactin	AdditionToBarbedEnd Well	GeneralKinetics	MonomerFactin
		reaction rate (J): ((Kf * Monomer * EndsBarbed) - (Kr * EndsBarbed))[uM.s-1] user defined (Kr): 1.4[s-1] user defined (Kf): 11.6[uM-1.s-1]
Tetramer+MonomerEndsBarbed+EndsPointed	EndFormation(BarbedAddition) Well	MassAction	Tetramer+MonomerEndsBarbed+EndsPointed
		reaction rate (J): (((Kf * Tetramer) * Monomer) - ((Kr * EndsBarbed) * EndsPointed))[uM.s-1] forward rate constant (Kf): 11.6[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1.uM-1]
MonomerFactin	AdditionToPointedEnd Well	GeneralKinetics	MonomerFactin
		reaction rate (J): ((Kf * Monomer * EndsPointed) - (Kr * EndsPointed))[uM.s-1] user defined (Kr): 0.8[s-1] user defined (Kf): 1.3[s-1.uM-1]
Trimer+MonomerTetramer	Tetramerization(PointedAddition) Well	MassAction	Trimer+MonomerTetramer
		reaction rate (J): (((Kf * Trimer) * Monomer) - (Kr * Tetramer))[uM.s-1] forward rate constant (Kf): 1.3[s-1.uM-1] reverse rate constant (Kr): 0.8[s-1]
Trimer+MonomerTetramer	Tetramerization(BarbedAddition) Well	MassAction	Trimer+MonomerTetramer
		reaction rate (J): (((Kf * Trimer) * Monomer) - (Kr * Tetramer))[uM.s-1] forward rate constant (Kf): 11.6[s-1.uM-1] reverse rate constant (Kr): 1.4[s-1]
Tetramer+MonomerEndsPointed+EndsBarbed	EndFormation(PointedAddition) Well	MassAction	Tetramer+MonomerEndsPointed+EndsBarbed
		reaction rate (J): (((Kf * Tetramer) * Monomer) - ((Kr * EndsPointed) * EndsBarbed))[uM.s-1] forward rate constant (Kf): 1.3[s-1.uM-1] reverse rate constant (Kr): 0.0[s-1.uM-1]

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

Species See in Dashboard
Name	Structure	BioNetGen Definition
Monomer	Well

Dimer	Well

Trimer	Well

Factin	Well

EndsBarbed	Well

EndsPointed	Well

Tetramer	Well

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
Simulations of Sept and McCammon and this paper	Deterministic (ODE) Compartmental

Application - Simulations of Sept and McCammon and this paper

Specifications(Species) - Simulations of Sept and McCammon and this paper See in Dashboard
Species	Initial Condition	Diffusion Constant
Monomer	0.0 [uM]	0.0 [um2/s]
Dimer	0.0 [uM]	0.0 [um2/s]
Trimer	0.0 [uM]	0.0 [um2/s]
Factin	0.0 [uM]	0.0 [um2/s]
EndsBarbed	0.0 [uM]	0.0 [um2/s]
EndsPointed	0.0 [uM]	0.0 [um2/s]
Tetramer	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - Simulations of Sept and McCammon and this paper See in Dashboard
Name	Reaction Mapping
Dimerization	included
Trimerization	included
AdditionToBarbedEnd	included
EndFormation(BarbedAddition)	included
AdditionToPointedEnd	included
Tetramerization(PointedAddition)	included
Tetramerization(BarbedAddition)	included
EndFormation(PointedAddition)	included

Simulations - Simulations of Sept and McCammon and this paper See in Dashboard
Name	End Time	Output Options
Sept and McCammon 1 uM	50000.0 [s]	OutputTimeStep 10.0
Sept and McCammon 2.5 uM	7450.0 [s]	OutputTimeStep 10.0
Sept and McCammon 10 uM	1000.0 [s]	OutputTimeStep 10.0
This paper 1 uM	50000.0 [s]	OutputTimeStep 10.0
This paper 2.5 uM	7450.0 [s]	OutputTimeStep 10.0
This paper 10 uM	1000.0 [s]	OutputTimeStep 10.0
7.5% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0
15% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0
25% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0
50% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0
75% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0
100% pyrenyl-actin	7450.0 [s]	OutputTimeStep 10.0

Geometry non-spatial1610413133 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			Well

Global Parameters

Global Parameters See in Dashboard
Name	Expression