MyFirstNEURON (Houweling, Sejnowski 1997)

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Accession:3808
MyFirstNEURON is a NEURON demo by Arthur Houweling and Terry Sejnowski. Perform experiments from the book 'Electrophysiology of the Neuron, A Companion to Shepherd's Neurobiology, An Interactive Tutorial' by John Huguenard & David McCormick, Oxford University Press 1997, or design your own one or two cell simulation.
References:
1 . Huguenard J, McCormick DA, Shepherd GM (1997) Electrophysiology of the Neuron, A Companion to Shepherd's Neurobiology, An Interactive Tutorial. Electrophysiology of the Neuron
2 . Houweling AR, Sejnowski TJ (1997) Personal communication from Arthur Houweling.
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s): I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I K,Ca; I CAN; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; GabaB; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Activity Patterns; Bursting; Ion Channel Kinetics; Temporal Pattern Generation; Oscillations; Parameter Fitting; Detailed Neuronal Models; Tutorial/Teaching; Action Potentials; Sleep; Calcium dynamics;
Implementer(s): Houweling, Arthur [Arthur at Salk.edu];
Search NeuronDB for information about:  GabaA; GabaB; AMPA; NMDA; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I K,Ca; I CAN; I Sodium; I Calcium; I Potassium;
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MyFirstNEURON
MyFirstNEURONmanual_files
readme.txt
ampa.mod
ampa2.mod
cadyn.mod
gabaA.mod
gabaA2.mod
gabaB.mod
gabaB2.mod
HH1.mod
HH2.mod
ia.mod *
iahp.mod
iahp2.mod *
ic.mod *
ican.mod
ih.mod *
il.mod *
im.mod *
it.mod *
it2.mod
leak.mod *
nmda.mod
nmda2.mod
synstim.mod
about.hoc
e1.par
e10.par
e11a.par
e11b.par
e12.par
e13.par
e14.par
e15a.par
e15b.par
e16a.par
e16b.par
e16c.par
e17a.par
e17b.par
e3.par
e5.par
e7.par
manual.htm
mcontrl1.hoc
mcontrl2.hoc
mcontrl3.hoc
methods.htm
mosinit.hoc
my1stnrn.hoc
parpanl1.hoc
parpanl2.hoc
parpanl3.hoc
plotcurr.hoc
                            
TITLE hyperpolarization-activated current (H-current) 

COMMENT
	Two distinct activation gates are assumed with the same asymptotic 
	opening values, a fast gate (F) and a slow gate (S). The following 
	kinetic scheme is assumed

	s0  --(Alpha)--> s1 + n Cai  --(k1)--> s2
           <--(Beta)---             <--(k2)--
 
 	f0  --(Alpha)--> f1 + n Cai  --(k1)--> f2
           <--(Beta)---             <--(k2)--

	where s0/f0, s1/f1, and s2/f2 are resp. fraction of closed slow/fast 
	gates, fraction of open unbound slow/fast gates, and fraction of open 
	calcium-bound slow/fast	gates, n is taken 2, and k1 = k2*C where 
	C = (cai/cac)^n and cac is the critical value at which Ca2+ binding 
	is half-activated.
	
	The total current is computed according

	ih = ghbar * (s1+s2) * (f1+f2) * (v-eh)

        *********************************************
        reference:      Destexhe, Babloyantz & Sejnowski (1993)
			Biophys.J. 65, 1538-1552
        found in:       thalamocortical neurons
        *********************************************
	Maxim Bazhenov's first mod file
        Rewritten for MyFirstNEURON by Arthur Houweling 
ENDCOMMENT

INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

NEURON {
	SUFFIX iH
	USEION h READ eh WRITE ih VALENCE 1
	USEION ca READ cai
        RANGE ghbar, tau_s, tau_f, tau_c, ih
	GLOBAL cac
}

UNITS {
	(mA) 	= (milliamp)
	(mV) 	= (millivolt)
	(molar)	= (1/liter)
	(mM) 	= (millimolar)
}

PARAMETER {
	v		(mV)
	cai		(mM)
	celsius		(degC)
	eh	= -43	(mV)
	ghbar	= 4e-5	(mho/cm2)
	cac 	= 5e-4	(mM)
}

STATE {
	s1			: fraction of open unbound slow gates 
	s2 			: fraction of open calcium-bound slow gates
	f1	 		: fraction of open unbound fast gates
	f2			: fraction of open calcium-bound fast gates
}

ASSIGNED {
	ih		(mA/cm2)
        h_inf
        tau_s		(ms)	: time constant slow gate
        tau_f 		(ms)	: time constant fast gate
	tau_c		(ms)	: time constant calcium binding 
        alpha_s		(1/ms)
        alpha_f 	(1/ms)
        beta_s 		(1/ms)
        beta_f		(1/ms)
	C
	k2		(1/ms)
	tadj
	s0			: fraction of closed slow gates 
	f0			: fraction of closed fast gates
}

BREAKPOINT { 
	SOLVE states METHOD euler
	ih = ghbar * (s1+s2) * (f1+f2) * (v-eh)
}

UNITSOFF
DERIVATIVE states { 
	evaluate_fct(v,cai)

	s1' = alpha_s*s0 - beta_s*s1 + k2*(s2-C*s1)
        f1' = alpha_f*f0 - beta_f*f1 + k2*(f2-C*f1)
        s2' = -k2*(s2-C*s1)
        f2' = -k2*(f2-C*f1)

        s0 = 1-s1-s2
        f0 = 1-f1-f2
}

INITIAL {
	: Q10 assumed to be 3
	tadj = 3^((celsius-35.5)/10)
	evaluate_fct(v,cai)

	s1 = alpha_s / (beta_s+alpha_s*(1+C))
	s2 = alpha_s*C / (beta_s+alpha_s*(1+C))
	s0 = 1-s1-s2
	f1 = alpha_f / (beta_f+alpha_f*(1+C))
	f2 = alpha_f*C / (beta_f+alpha_f*(1+C))
	f0 = 1-f1-f2

	tau_c = 1 / (1+C) / k2	: for plotting purposes
}

PROCEDURE evaluate_fct( v(mV), cai(mM)) {
	h_inf = 1 / (1+exp((v+68.9)/6.5))
	tau_s = exp((v+183.6)/15.24) / tadj
	tau_f = exp((v+158.6)/11.2) / (1+exp((v+75)/5.5)) / tadj

	alpha_s = h_inf / tau_s 
	alpha_f = h_inf / tau_f 
	beta_s = (1-h_inf) / tau_s
	beta_f = (1-h_inf) / tau_f

        C = cai*cai/(cac*cac)
	k2 = 4e-4 * tadj	
}	
UNITSON







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