CA1 pyramidal neuron: synaptic plasticity during theta cycles (Saudargiene et al. 2015)

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Accession:157157
This NEURON code implements a microcircuit of CA1 pyramidal neuron and consists of a detailed model of CA1 pyramidal cell and four types of inhibitory interneurons (basket, bistratified, axoaxonic and oriens lacunosum-moleculare cells). Synaptic plasticity during theta cycles at a synapse in a single spine on the stratum radiatum dendrite of the CA1 pyramidal cell is modeled using a phenomenological model of synaptic plasticity (Graupner and Brunel, PNAS 109(20):3991-3996, 2012). The code is adapted from the Poirazi CA1 pyramidal cell (ModelDB accession number 20212) and the Cutsuridis microcircuit model (ModelDB accession number 123815)
Reference:
1 . Saudargiene A, Cobb S, Graham BP (2015) A computational study on plasticity during theta cycles at Schaffer collateral synapses on CA1 pyramidal cells in the hippocampus. Hippocampus 25:208-18 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal cell; Hippocampus CA1 basket cell; Hippocampus CA1 bistratified cell; Hippocampus CA1 axo-axonic cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Long-term Synaptic Plasticity; STDP;
Implementer(s): Saudargiene, Ausra [ausra.saudargiene at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell;
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SaudargieneEtAl2015
readme.html
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TITLE Calcium ion accumulation with longitudinal and radial diffusion

COMMENT
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.

ENDCOMMENT

NEURON {
	SUFFIX cadiffus
	USEION ca READ cai, ica WRITE cai
	GLOBAL vrat
}

DEFINE Nannuli  4

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

PARAMETER {
	DCa = 	0.23		(um2/ms) 
}

ASSIGNED {
	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)}

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

BREAKPOINT {
	SOLVE state METHOD sparse
}

LOCAL factors_done

INITIAL {
	if (factors_done == 0) {
		factors_done = 1
		factors()
	}

	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]
}

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