Reconstructing cerebellar granule layer evoked LFP using convolution (ReConv) (Diwakar et al. 2011)

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Accession:139883
The model allows reconstruction of evoked local field potentials as seen in the cerebellar granular layer. The approach uses a detailed model of cerebellar granule neuron to generate data traces and then uses a "ReConv" or jittered repetitive convolution technique to reproduce post-synaptic local field potentials in the granular layer. The algorithm was used to generate both in vitro and in vivo evoked LFP and reflected the changes seen during LTP and LTD, when such changes were induced in the underlying neurons by modulating release probability of synapses and sodium channel regulated intrinsic excitability of the cells.
Reference:
1 . Diwakar S, Lombardo P, Solinas S, Naldi G, D'Angelo E (2011) Local field potential modeling predicts dense activation in cerebellar granule cells clusters under LTP and LTD control PLoS ONE 6(7):e21928 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Cerebellum interneuron granule cell;
Channel(s): I K; I M; I K,Ca; I Sodium; I Calcium; I Cl, leak;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB; Octave;
Model Concept(s): Extracellular Fields; Evoked LFP;
Implementer(s): Diwakar, Shyam [shyam at amrita.edu];
Search NeuronDB for information about:  Cerebellum interneuron granule cell; GabaA; AMPA; NMDA; I K; I M; I K,Ca; I Sodium; I Calcium; I Cl, leak;
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ReConv
data
readme.html
AmpaCOD.mod *
GRC_CA.mod *
GRC_CALC.mod *
GRC_GABA.mod *
GRC_KA.mod *
GRC_KCA.mod *
GRC_KIR.mod *
GRC_KM.mod *
GRC_KV.mod *
GRC_LKG1.mod *
GRC_LKG2.mod *
GRC_NA.mod *
NmdaS.mod *
Pregen.mod *
ComPanel.hoc
Grc_Cell.hoc
mosinit.hoc
Parametri.hoc
ReConv_GrC.jpg
ReConv_invitro.jpg
ReConv_invivo.jpg
Record_vext.hoc
Start.hoc
                            
TITLE 

COMMENT
	Reference: Pugh JR and Raman I, Biophysical Journal Volume 88, March 2005 1740-1754
	Model adapted from patch to slice.
ENDCOMMENT

NEURON {
	POINT_PROCESS GRC_GABA
	NONSPECIFIC_CURRENT i
	RANGE g,Cdur,Erev,Open,OpenScaled,ScaleFactor

	:RANGE r1,r2,kon,koff,d1,d2,a1,a2,b1,b2
	RANGE kon,koff,d3,r3,d1d2,r1r2,a1,b1,a2,b2,r1,r2,d1,d2

	RANGE Tmax,gmax,onSET	
	
	RANGE tau_1,tau_rec,tau_facil,U,T 
	RANGE diff_flag,M,Rd,Diff,lamd
	RANGE diffusione,nd	
}

UNITS {
	(nA) 	= (nanoamp)
	(mV) 	= (millivolt)
	(umho)  = (micromho)
	(mM) 	= (milli/liter)
	(pS) 	= (picosiemens)
	PI   	= (pi)(1)
}

PARAMETER {
	: Parametri Postsinaptici
	gmax	=  756.35	(pS)	:1750 
	Cdur	= 0.3		(ms)	

	kon	= 20		(/ms/mM)	
	koff	= 2		(/ms) 		 
	d3	= 15		(/ms) 		 
	r3	= 3.75		(/ms) 		: 0.15, use 3.75 for slices 

	d1d2	= 15		(/ms/mM)	
	r1r2	= 0.007		(/ms)

	a1	= 0.06		(/ms)
	b1	= 0.03		(/ms)
	a2	= 0.4		(/ms)
	b2	= 10		(/ms)
	
	r1	= 7e-4		(/ms)
	r2	= 6e-3		(/ms)
	d1	= 3.3e-4	(/ms)
	d2	= 1.2		(/ms)

	Erev	= -65	(mV)

	: Parametri Presinaptici
	tau_1 		= 0.1 (ms) 	< 1e-9, 1e9 >
	tau_rec 	= 43.4 (ms) 	< 1e-9, 1e9 > 	:55.11 15.7	(first fit!)
	tau_facil 	= 6.22 (ms) 	< 0, 1e9 >    	:2.66 4.85  (first fit!)	
	U 		= 0.35		< 0, 1 >	:0.24  0.18	(first fit!)
	
	Tmax	= 1  (mM)	
	onSET	= 1
		
	: Diffusion parameters
	: Diffusion: M=21.500, R=1.033, D=0.223, lamd=0.02 as in excitatory synapses	

	M		= 52.76		:	46.93			: 20.95 (first fit!)
: numero di (kilo) molecole in una vescicola		
	Rd		= 4.79 (um)	:4.96	: 4.96 (first fit!)
	Diff		= 0.223 (um2/ms)
	lamd		= 20 	(nm)
	diff_flag	= 1			: flag diffusion on/off
	nd		= 1			: kernel exponent of diffusion

	ScaleFactor	= 1 			: for fit purposes
}


ASSIGNED {
	v		(mV)		: postsynaptic voltage
	i 		(nA)		: current = g*(v - Erev)
	g 		(pS)		: conductance
	Open
	OpenScaled	: for fit purposes
	
	T		(mM)	
	Trelease	(mM)
	Mres		(mM)	
	tpre		(ms)

	tspike[50]	(ms)	: will be initialized by the pointprocess
	PRE[50]
	numpulses
	tzero
}

STATE {	
	C
	CA1
	CA2
	DA1
	DA2
	DA2f
	OA1
	OA2	
}

INITIAL {
	C=1
	CA1=0
	CA2=0
	DA1=0
	DA2=0
	DA2f=0
	OA1=0  	
	OA2=0
	CA1=0
	CA2=0
	Open=0
	T=0 		(mM)
	:tpre=1e8	(ms)
		
	numpulses=0
	Mres=1e3* (1e3 * 1e15 / 6.022e23 * M)     : (M) to (mM) so 1e3, 1um^3=1dm^3*1e-15 so 1e15
	FROM i=1 TO 50{ PRE[i-1]=0 tspike[i-1]=0}
	tspike[0]=1e12	(ms)
	if(tau_1>=tau_rec){ 
		printf("Warning: tau_1 (%g) should never be higher neither equal to tau_rec (%g)!\n",tau_1,tau_rec)
		tau_rec=tau_1+1e-5
		:printf("tau_rec has been set to %g\n",tau_rec) 
	} 
}

FUNCTION diffusione(){
	LOCAL DifWave,i	
	DifWave=0
	FROM i=1 TO numpulses{
		tzero=tspike[i-1]
		if(t>tzero){
			DifWave=DifWave+PRE[i-1]*Mres*exp(-Rd*Rd/(4*Diff*(t-tzero)))/((4*PI*Diff*(1e-3)*lamd)*(t-tzero))^nd
		}
	}	
	diffusione=DifWave :Mres*exp(-Rd*Rd/(4*Diff*(t-tpre)))/((4*PI*Diff*(1e-3)*lamd)*(t-tpre))	
}


BREAKPOINT {
	SOLVE kstates METHOD sparse
	Open = OA1 + OA2
	OpenScaled=Open*ScaleFactor
	g = gmax * Open
	i = (1e-6) * g * (v - Erev)
}

KINETIC kstates {
	if ( diff_flag ) { Trelease = T + diff_flag * diffusione() } else { Trelease = T }
	: second row
	~	C  	<-> 	CA1	(2*kon*Trelease,koff)
	~	CA1 	<-> 	CA2	(kon*Trelease,2*koff)
	~	CA2	<->	DA2f	(d3,r3)
	: third row
	~ 	DA1  	<-> 	DA2	(d1d2*Trelease,r1r2)
	: first <=> second row
	~ 	OA1  	<-> 	CA1	(a1,b1)
	~ 	OA2  	<-> 	CA2	(a2,b2)
	: third <=> second row
	~	DA1	<->	CA1	(r1,d1)
	~	DA2	<->	CA2	(r2,d2)
	CONSERVE C+CA1+CA2+DA1+DA2+DA2f+OA1+OA2 = 1
}


NET_RECEIVE(weight, on, nspike, tzero (ms),x,y, z, u, tsyn (ms)) {

	INITIAL {
		x = 0
		y = 0
		z = 0
		u = 0 :u0
		tsyn = t
		nspike = 1
	}

	if(onSET){on=0 onSET=0}
        if (flag == 0) { 
		: Qui faccio rientrare la modulazione presinaptica
		nspike = nspike + 1
		if (!on) {
			tzero = t	
			tpre=t	: activates diffusion
			on = 1				
			z = z*exp(-(t - tsyn)/tau_rec)		
			z = z + ( y*(exp(-(t - tsyn)/tau_1) - exp(-(t - tsyn)/tau_rec)) / ((tau_1/tau_rec)-1) )
			y = y*exp(-(t - tsyn)/tau_1)			
			x = 1-y-z
				
			if (tau_facil > 0) { 
				u = u*exp(-(t - tsyn)/tau_facil)
				u = u + U * ( 1 - u )							
			} else { u = U }
			
			y = y + x * u
			T=Tmax*y
				
			PRE[numpulses]=y
			tspike[numpulses]=t
			numpulses=numpulses+1
			tsyn = t			
		}
		net_send(Cdur, nspike)
        }
	if (flag == nspike) { 
			T = 0
			on = 0
	}
}


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