Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
cpxF+b_freecpxF_b cpxF_Binding cyto MassAction
b_free+cpxcpx_b cpx_Binding cyto MassAction

cpxF_Binding Universal ID's

cpxF_Binding Text Annotations

cpx_Binding Universal ID's

cpx_Binding Text Annotations

Expressions for cpxF_Binding

reaction rate

J

(((Kf * cpxF) * b_free) - (Kr * cpxF_b)) [uM.s-1]

forward rate constant

Kf

5.0 [s-1.uM-1]

reverse rate constant

Kr

(Kcpx * Kf) [s-1]

global

Kcpx

0.01 [uM]

Expressions for cpx_Binding

reaction rate

J

(((Kf * b_free) * cpx) - (Kr * cpx_b)) [uM.s-1]

forward rate constant

Kf

5.0 [s-1.uM-1]

reverse rate constant

Kr

(Kcpx * Kf) [s-1]

global

Kcpx

0.01 [uM]

Structures

Name
Type
Electrical
PM Membrane cyto(+)   EC(-)
cyto Compartment (+)   (-)
EC Compartment (+)   (-)

PM Universal ID's

PM Text Annotations

cyto Universal ID's

cyto Text Annotations

EC Universal ID's

EC Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
cpx_b cyto cyto
cpxF_b cyto cyto
cpx cyto cyto
b_free cyto cyto
cpxF cyto cyto

cpx_b Universal ID's

cpx_b Text Annotations

cpxF_b Universal ID's

cpxF_b Text Annotations

cpx Universal ID's

cpx Text Annotations

b_free Universal ID's

b_free Text Annotations

cpxF Universal ID's

cpxF Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Bouton R200 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)
R200 Steady Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)
Buffer in cylinder Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (3D)

Bouton R200 Universal ID's

Bouton R200 Text Annotations

R200 Steady Universal ID's

R200 Steady Text Annotations

Buffer in cylinder Universal ID's

Buffer in cylinder Text Annotations

Specifications (Species) - Bouton R200 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cpx_b (cpx_b0 * (Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] 0.0 [um2/s] cyto
cpxF_b (cpxF_b0 * Central_Synapse) [uM] 0.0 [um2/s] cyto
cpx (cpx0 * (HalfAxon_Neg || HalfAxon_Pos || Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] Dvalue [um2/s] cyto
b_free (b_free0 * (Central_Synapse || Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] 0.0 [um2/s] cyto
cpxF (cpxF0 * (Central_Synapse || ((y >= - 0.5) && (y <= 0.5) && (((x ^ 2.0) + (z ^ 2.0)) <= 0.01)))) [uM] Dvalue [um2/s] cyto

Specifications (Reaction) - Bouton R200 go to Simulations

Name
Enabled?
cpxF_Binding included
cpx_Binding included

Simulations - Bouton R200 go to Specifications

Name
End Time
Output Options
Short Sim 5.0

OutputTimeStep 0.05
Long Sim 25.0

OutputTimeStep 0.05

Bouton R200 Universal ID's

Bouton R200 Text Annotations

Bouton R200 Universal ID's

Bouton R200 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1868903692

(Origin: -0.2, -12.0, -0.2; Extent: 0.4, 24.0, 0.4 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain1 1.1351731200000001 [um3] cyto
Volume Analytical subdomain0 2.70482688 [um3] EC
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 18.528703902283166 [um2] PM

Events

Name Variable Rate Expression

Specifications (Species) - R200 Steady go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cpx_b (cpx_b0 * (Central_Synapse || Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] 0.0 [um2/s] cyto
cpxF_b 0.0 [uM] 0.0 [um2/s] cyto
cpx (cpx0 * (Axon || Central_Synapse || Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] Dvalue [um2/s] cyto
b_free (b_free0 * (Central_Synapse || Near_Neighbors || Next_Neighbors || Distant_Synapses)) [uM] 0.0 [um2/s] cyto
cpxF 0.0 [uM] 0.0 [um2/s] cyto

Specifications (Reaction) - R200 Steady go to Simulations

Name
Enabled?
cpxF_Binding included
cpx_Binding included

Simulations - R200 Steady go to Specifications

Name
End Time
Output Options
Simulation0 1.0

OutputTimeStep 0.05

R200 Steady Universal ID's

R200 Steady Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry2064458491

(Origin: -0.2, -25.0, -0.2; Extent: 0.4, 50.0, 0.4 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain1 1.891792 [um3] cyto
Volume Analytical subdomain0 6.108207999999999 [um3] EC
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 34.758421650959555 [um2] PM

Events

Name Variable Rate Expression

Specifications (Species) - Buffer in cylinder go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cpx_b (cpx_b0 * Central_Synapse) [uM] 0.0 [um2/s] cyto
cpxF_b 0.0 [uM] 0.0 [um2/s] cyto
cpx (cpx0 * Central_Synapse) [uM] Dvalue [um2/s] cyto
b_free (Btot - cpx_b) [uM] 0.0 [um2/s] cyto
cpxF 0.0 [uM] 0.0 [um2/s] cyto

Specifications (Reaction) - Buffer in cylinder go to Simulations

Name
Enabled?
cpxF_Binding included
cpx_Binding included

Simulations - Buffer in cylinder go to Specifications

Name
End Time
Output Options
Simulation1 3.0

OutputTimeStep 0.05

Buffer in cylinder Universal ID's

Buffer in cylinder Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1068243341

(Origin: -0.1, -25.0, -0.1; Extent: 0.2, 50.0, 0.2 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain1 1.567 [um3] cyto
Volume Analytical subdomain0 0.43299999999999994 [um3] EC
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 31.459453966422434 [um2] PM

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
Kcpx 0.01[uM]
cpx0 (Ctot - (0.5 * ((alpha * Btot) + Ctot + Kcpx - sqrt(((((alpha * Btot) + Ctot + Kcpx) ^ 2.0) - (4.0 * alpha * Btot * Ctot))))))[1]
cpxF0 (Ctot - (0.5 * ((alpha * Btot) + Ctot + Kcpx - sqrt(((((alpha * Btot) + Ctot + Kcpx) ^ 2.0) - (4.0 * alpha * Btot * Ctot))))))[1]
cpx_b0 (0.5 * ((alpha * Btot) + Ctot + Kcpx - sqrt(((((alpha * Btot) + Ctot + Kcpx) ^ 2.0) - (4.0 * alpha * Btot * Ctot)))) / alpha)[1]
cpxF_b0 (0.5 * ((alpha * Btot) + Ctot + Kcpx - sqrt(((((alpha * Btot) + Ctot + Kcpx) ^ 2.0) - (4.0 * alpha * Btot * Ctot)))) / alpha)[1]
Central_Synapse (((25.0 * (x ^ 2.0)) + (4.0 * (y ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0)[1]
Near_Neighbors ((((25.0 * (x ^ 2.0)) + (4.0 * (( - 3.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0) || (((25.0 * (x ^ 2.0)) + (4.0 * ((3.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0))[1]
Next_Neighbors ((((25.0 * (x ^ 2.0)) + (4.0 * (( - 6.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0) || (((25.0 * (x ^ 2.0)) + (4.0 * ((6.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0))[1]
Distant_Synapses ((((25.0 * (x ^ 2.0)) + (4.0 * (( - 9.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0) || (((25.0 * (x ^ 2.0)) + (4.0 * ((9.0 + y) ^ 2.0)) + (25.0 * (z ^ 2.0))) <= 1.0))[1]
HalfAxon_Neg ((((x ^ 2.0) + (z ^ 2.0)) <= 0.01) && (y < - 0.5))[1]
HalfAxon_Pos ((((x ^ 2.0) + (z ^ 2.0)) <= 0.01) && (y > 0.5))[1]
b_free0 (Btot - cpx_b0)[1]
Dvalue 2.0[1]
Btot 8.0[1]
Axon (((x ^ 2.0) + (z ^ 2.0)) <= 0.01)[1]
alpha 0.523[1]
Ctot 12.0[1]

Universal ID's

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