Spine neck plasticity controls postsynaptic calcium signals (Grunditz et al. 2008)

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This model was set up to dissect the relative contribution of different channels to the spine calcium transients measured at single spines.
1 . Grunditz A, Holbro N, Tian L, Zuo Y, Oertner TG (2008) Spine neck plasticity controls postsynaptic calcium signals through electrical compartmentalization. J Neurosci 28:13457-66 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Channel(s): I Calcium; I R;
Gap Junctions:
Receptor(s): AMPA; NMDA;
Transmitter(s): Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Calcium dynamics;
Implementer(s): Mueller, Asa [asa.mueller at fmi.ch];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; AMPA; NMDA; I Calcium; I R; Glutamate;
TITLE Calcium ion accumulation with longitudinal and radial diffusion

PROCEDURE factors_cadiffus() sets up the scale factors 
needed to model radial diffusion.
These scale factors do not have to be recomputed
when diam is changed.
The amount of calcium in an annulus is ca[i]*diam^2*vol[i] 
with ca[0] being the 2nd order correct concentration at the exact edge
and ca[NANN-1] being the concentration at the exact center.


	SUFFIX cadiffus
	USEION ca READ cai, ica WRITE cai
	GLOBAL vrat

DEFINE Nannuli  4

	(molar) =	(1/liter)
	(mM) =	(millimolar)
	(um) =	(micron)
	(mA) =	(milliamp)
	FARADAY =	(faraday)	(10000 coulomb)
	PI = (pi)	(1)

	DCa = 	0.23		(um2/ms) 

	diam	(um)
	ica		(mA/cm2)
	cai		(mM)
	vrat[Nannuli]		: numeric value of vrat[i] equals the volume
                        : of annulis i of a 1um diameter cylinder
                        : multiply by diam^2 to get volume per um length
	B0		(mM)

CONSTANT { volo = 1e10 (um2)}

	ca[Nannuli]		(mM) <1e-6>	: ca[0] is equivalent to cai

	SOLVE state METHOD sparse

LOCAL factors_done

	if (factors_done == 0) {
		factors_done = 1

	FROM i=0 TO Nannuli-1 {
		ca[i] = cai

LOCAL frat[Nannuli]

PROCEDURE factors() {
	LOCAL r, dr2
	r = 1/2			:starts at edge (half diam)
	dr2 = r/(Nannuli-1)/2	:half thickness of annulus
	vrat[0] = 0
	frat[0] = 2*r
	FROM i=0 TO Nannuli-2 {
		vrat[i] = vrat[i] + PI*(r-dr2/2)*2*dr2	:interior half
		r = r - dr2
		frat[i+1] = 2*PI*r/(2*dr2)	:exterior edge of annulus
					: divided by distance between centers
		r = r - dr2
		vrat[i+1] = PI*(r+dr2/2)*2*dr2	:outer half of annulus

LOCAL dsq, dsqvol	: can't define local variable in KINETIC block 
			: or use in COMPARTMENT

KINETIC state {
	COMPARTMENT i, diam*diam*vrat[i] {ca CaBuffer Buffer}
	LONGITUDINAL_DIFFUSION i, DCa*diam*diam*vrat[i] {ca}
	~ ca[0] << (-ica*PI*diam/(2*FARADAY))
	FROM i=0 TO Nannuli-2 {
		~ ca[i] <-> ca[i+1] (DCa*frat[i+1], DCa*frat[i+1])
cai = ca[0]