Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
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] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
Well |
Compartment
(+) (-)
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
Monomer | Well | |
|
|
|
Dimer | Well | |
|
|
|
Trimer | Well | |
|
|
|
Factin | Well | |
|
|
|
EndsBarbed | Well | |
|
|
|
EndsPointed | Well | |
|
|
|
Tetramer | Well | |
|
|
Name | Text Annotations | BioNetGen Definition |
---|
Name |
Type
Count
|
BioNetGen Definition |
---|
Applications
Name | Math Type | Annotation |
---|---|---|
Simulations of Sept and McCammon and this paper | Deterministic (ODE) Compartmental |
Application - Simulations of Sept and McCammon and this paper
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]
|
|
Name | Reaction Mapping |
---|---|
Dimerization | included |
Trimerization | included |
AdditionToBarbedEnd | included |
EndFormation(BarbedAddition) | included |
AdditionToPointedEnd | included |
Tetramerization(PointedAddition) | included |
Tetramerization(BarbedAddition) | included |
EndFormation(PointedAddition) | included |
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 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | Well |
Global Parameters
Name | Expression |
---|