Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
MonomerDimer Dimerization Well MassAction
Monomer+DimerTrimer Trimerization Well MassAction
MonomerFactin AdditionToBarbedEnd Well GeneralKinetics
Tetramer+MonomerEndsBarbed+EndsPointed EndFormation(BarbedAddition) Well MassAction
MonomerFactin AdditionToPointedEnd Well GeneralKinetics
Trimer+MonomerTetramer Tetramerization(PointedAddition) Well MassAction
Trimer+MonomerTetramer Tetramerization(BarbedAddition) Well MassAction
Tetramer+MonomerEndsPointed+EndsBarbed EndFormation(PointedAddition) Well MassAction

Dimerization Universal ID's

Dimerization Text Annotations

Trimerization Universal ID's

Trimerization Text Annotations

AdditionToBarbedEnd Universal ID's

AdditionToBarbedEnd Text Annotations

EndFormation(BarbedAddition) Universal ID's

EndFormation(BarbedAddition) Text Annotations

AdditionToPointedEnd Universal ID's

AdditionToPointedEnd Text Annotations

Tetramerization(PointedAddition) Universal ID's

Tetramerization(PointedAddition) Text Annotations

Tetramerization(BarbedAddition) Universal ID's

Tetramerization(BarbedAddition) Text Annotations

EndFormation(PointedAddition) Universal ID's

EndFormation(PointedAddition) Text Annotations

Expressions for Dimerization

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]

Expressions for Trimerization

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]

Expressions for AdditionToBarbedEnd

reaction rate

J

((Kf * Monomer * EndsBarbed) - (Kr * EndsBarbed)) [uM.s-1]

local

Kr

1.4 [s-1]

local

Kf

11.6 [uM-1.s-1]

Expressions for EndFormation(BarbedAddition)

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]

Expressions for AdditionToPointedEnd

reaction rate

J

((Kf * Monomer * EndsPointed) - (Kr * EndsPointed)) [uM.s-1]

local

Kr

0.8 [s-1]

local

Kf

1.3 [s-1.uM-1]

Expressions for Tetramerization(PointedAddition)

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]

Expressions for Tetramerization(BarbedAddition)

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]

Expressions for EndFormation(PointedAddition)

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

Name
Type
Electrical
Well Compartment (+)   (-)

Well Universal ID's

Well Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Monomer Well Well
Dimer Well Well
Trimer Well Well
Factin Well Well
EndsBarbed Well Well
EndsPointed Well Well
Tetramer Well Well

Monomer Universal ID's

Monomer Text Annotations

Dimer Universal ID's

Dimer Text Annotations

Trimer Universal ID's

Trimer Text Annotations

Factin Universal ID's

Factin Text Annotations

EndsBarbed Universal ID's

EndsBarbed Text Annotations

EndsPointed Universal ID's

EndsPointed Text Annotations

Tetramer Universal ID's

Tetramer Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Simulations of Sept and McCammon and this paper Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Specifications (Species) - Simulations of Sept and McCammon and this paper go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Monomer 0.0 [uM] 0.0 [um2/s] Well
Dimer 0.0 [uM] 0.0 [um2/s] Well
Trimer 0.0 [uM] 0.0 [um2/s] Well
Factin 0.0 [uM] 0.0 [um2/s] Well
EndsBarbed 0.0 [uM] 0.0 [um2/s] Well
EndsPointed 0.0 [uM] 0.0 [um2/s] Well
Tetramer 0.0 [uM] 0.0 [um2/s] Well

Specifications (Reaction) - Simulations of Sept and McCammon and this paper go to Simulations

Name
Enabled?
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 go to Specifications

Name
End Time
Output Options
Sept and McCammon 1 uM 50000.0

OutputTimeStep 10.0
Sept and McCammon 2.5 uM 7450.0

OutputTimeStep 10.0
Sept and McCammon 10 uM 1000.0

OutputTimeStep 10.0
This paper 1 uM 50000.0

OutputTimeStep 10.0
This paper 2.5 uM 7450.0

OutputTimeStep 10.0
This paper 10 uM 1000.0

OutputTimeStep 10.0
7.5% pyrenyl-actin 7450.0

OutputTimeStep 10.0
15% pyrenyl-actin 7450.0

OutputTimeStep 10.0
25% pyrenyl-actin 7450.0

OutputTimeStep 10.0
50% pyrenyl-actin 7450.0

OutputTimeStep 10.0
75% pyrenyl-actin 7450.0

OutputTimeStep 10.0
100% pyrenyl-actin 7450.0

OutputTimeStep 10.0

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Simulations of Sept and McCammon and this paper Universal ID's

Simulations of Sept and McCammon and this paper Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial1610413133

(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

Events

Name Variable Rate Expression

Global Parameters

Name
Expression