Hippocampal CA1 NN with spontaneous theta, gamma: full scale & network clamp (Bezaire et al 2016)

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This model is a full-scale, biologically constrained rodent hippocampal CA1 network model that includes 9 cells types (pyramidal cells and 8 interneurons) with realistic proportions of each and realistic connectivity between the cells. In addition, the model receives realistic numbers of afferents from artificial cells representing hippocampal CA3 and entorhinal cortical layer III. The model is fully scaleable and parallelized so that it can be run at small scale on a personal computer or large scale on a supercomputer. The model network exhibits spontaneous theta and gamma rhythms without any rhythmic input. The model network can be perturbed in a variety of ways to better study the mechanisms of CA1 network dynamics. Also see online code at http://bitbucket.org/mbezaire/ca1 and further information at http://mariannebezaire.com/models/ca1
1 . Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I (2016) Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit. Elife [PubMed]
2 . Bezaire M, Raikov I, Burk K, Armstrong C, Soltesz I (2016) SimTracker tool and code template to design, manage and analyze neural network model simulations in parallel NEURON bioRxiv
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 interneuron oriens alveus GABA cell; Hippocampus CA1 basket cell; Hippocampus CA1 stratum radiatum interneuron; Hippocampus CA1 bistratified cell; Hippocampus CA1 axo-axonic cell; Hippocampus CA1 PV+ fast-firing interneuron;
Channel(s): I Na,t; I K; I K,leak; I h; I K,Ca; I Calcium;
Gap Junctions:
Receptor(s): GabaA; GabaB; Glutamate; Gaba;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; NEURON (web link to model);
Model Concept(s): Oscillations; Methods; Connectivity matrix; Laminar Connectivity; Gamma oscillations;
Implementer(s): Bezaire, Marianne [mariannejcase at gmail.com]; Raikov, Ivan [ivan.g.raikov at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 interneuron oriens alveus GABA cell; GabaA; GabaB; Glutamate; Gaba; I Na,t; I K; I K,leak; I h; I K,Ca; I Calcium; Gaba; Glutamate;
TITLE N-type calcium channel (voltage dependent)
N-Type Ca2+ channel (voltage dependent)

Ions: ca

Style: quasi-ohmic

From: Aradi and Holmes, 1999

2014 December (Marianne Bezaire): documented

#include <stdlib.h> /* 	Include this library so that the following
						(innocuous) warning does not appear:
						 In function '_thread_cleanup':
						 warning: incompatible implicit declaration of 
						          built-in function 'free'  */
	(mA) =(milliamp)
	(mV) =(millivolt)
	(molar) = (1/liter)
	(mM) = (millimolar)
	FARADAY = 96520 (coul)
	R = 8.3134	(joule/degC)
	SUFFIX ch_CavN				: The name of the mechanism
	RANGE gmax
	RANGE cinf, ctau, dinf, dtau
	RANGE myi
INDEPENDENT {t FROM 0 TO 100 WITH 100 (ms)}

	v (mV) 					: membrane potential
      celsius (degC) : temperature - set in hoc; default is 6.3
	gmax (mho/cm2)		: conductance flux - defined in CavT but not here
	c d		
ASSIGNED {			: assigned (where?)
	dt (ms) 				: simulation time step

	ica (mA/cm2)	: current flux
	g (mho/cm2)	: conductance flux
	eca (mV)		: reversal potential

	cinf dinf
	ctau (ms)
	dtau (ms) 
	cexp dexp      
	myi (mA/cm2)

	SOLVE states : what is the method? let's specify one
    g = gmax*c*c*d
	ica = g*(v-eca)
	myi = ica
	c = cinf
	d = dinf

? states : verbatim blocks are not thread safe (perhaps related, this mechanism cannot be used with cvode)
PROCEDURE states() {	:Computes state variables m, h, and n 
        trates(v)	:      at the current v and dt.
	c = c + cexp*(cinf-c)
	d = d + dexp*(dinf-d)
        :return 0;

PROCEDURE rates(v) {  :Computes rate and other constants at current v.
                      :Call once from HOC to initialize inf at resting v.
        LOCAL  alpha, beta, sum
       :q10 = 3^((celsius - 6.3)/10)
       q10 = 3^((celsius - 34)/10)
                :"c" NCa activation system
        alpha = -0.19*vtrap(v-19.88,-10)
	beta = 0.046*exp(-v/20.73)
	sum = alpha+beta        
	ctau = 1/sum      cinf = alpha/sum
                :"d" NCa inactivation system
	alpha = 0.00016*exp(-v/48.4) : this is multiplied, not divided in Aradi & Holmes formula
	beta = 1/(exp((-v+39)/10)+1)
	sum = alpha+beta        
	dtau = 1/sum      dinf = alpha/sum

PROCEDURE trates(v) {  :Computes rate and other constants at current v.
                      :Call once from HOC to initialize inf at resting v.
	LOCAL tinc
	TABLE  cinf, cexp, dinf, dexp, ctau, dtau
	DEPEND dt, celsius FROM -100 TO 100 WITH 200
	rates(v)	: not consistently executed from here if usetable_hh == 1
				: so don't expect the tau values to be tracking along with
				: the inf values in hoc

	tinc = -dt * q10
	cexp = 1 - exp(tinc/ctau)
	dexp = 1 - exp(tinc/dtau)

FUNCTION vtrap(x,y) {  :Traps for 0 in denominator of rate eqns.
	if (fabs(x/y) < 1e-6) {
		vtrap = y*(1 - x/y/2)
		vtrap = x/(exp(x/y) - 1)