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Name - CPX Binding

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
cpxF+b_freecpxF_b	cpxF_Binding cyto	MassAction	cpxF+b_freecpxF_b
		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]
b_free+cpxcpx_b	cpx_Binding cyto	MassAction	b_free+cpxcpx_b
		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]

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

EC	Compartment (+) (-)

PM	Membrane N/A

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Specifications(Species) - Bouton R200 See in Dashboard
Species	Initial Condition	Diffusion Constant
cpx_b	(cpx_b0 * (Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	0.0 [um2/s]
cpxF_b	(cpxF_b0 * Central_Synapse) [uM]	0.0 [um2/s]
cpx	(cpx0 * (HalfAxon_Neg \|\| HalfAxon_Pos \|\| Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	Dvalue [um2/s]
b_free	(b_free0 * (Central_Synapse \|\| Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	0.0 [um2/s]
cpxF	(cpxF0 * (Central_Synapse \|\| ((y >= - 0.5) && (y <= 0.5) && (((x ^ 2.0) + (z ^ 2.0)) <= 0.01)))) [uM]	Dvalue [um2/s]

Specifications(Reaction) - Bouton R200 See in Dashboard
Name	Reaction Mapping
cpxF_Binding	included
cpx_Binding	included

Simulations - Bouton R200 See in Dashboard
Name	End Time	Output Options
Short Sim	5.0 [s]	OutputTimeStep 0.05
Long Sim	25.0 [s]	OutputTimeStep 0.05

Geometry Geometry1868903692 See in Dashboard
(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

Specifications(Species) - R200 Steady See in Dashboard
Species	Initial Condition	Diffusion Constant
cpx_b	(cpx_b0 * (Central_Synapse \|\| Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	0.0 [um2/s]
cpxF_b	0.0 [uM]	0.0 [um2/s]
cpx	(cpx0 * (Axon \|\| Central_Synapse \|\| Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	Dvalue [um2/s]
b_free	(b_free0 * (Central_Synapse \|\| Near_Neighbors \|\| Next_Neighbors \|\| Distant_Synapses)) [uM]	0.0 [um2/s]
cpxF	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - R200 Steady See in Dashboard
Name	Reaction Mapping
cpxF_Binding	included
cpx_Binding	included

Simulations - R200 Steady See in Dashboard
Name	End Time	Output Options
Simulation0	1.0 [s]	OutputTimeStep 0.05

Geometry Geometry2064458491 See in Dashboard
(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

Specifications(Reaction) - Buffer in cylinder See in Dashboard
Name	Reaction Mapping
cpxF_Binding	included
cpx_Binding	included

Simulations - Buffer in cylinder See in Dashboard
Name	End Time	Output Options
Simulation1	3.0 [s]	OutputTimeStep 0.05

Geometry Geometry1068243341 See in Dashboard
(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

Global Parameters See in Dashboard
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]