Using Strahler`s analysis to reduce realistic models (Marasco et al, 2013)

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Accession:149000
Building on our previous work (Marasco et al., (2012)), we present a general reduction method based on Strahler's analysis of neuron morphologies. We show that, without any fitting or tuning procedures, it is possible to map any morphologically and biophysically accurate neuron model into an equivalent reduced version. Using this method for Purkinje cells, we demonstrate how run times can be reduced up to 200-fold, while accurately taking into account the effects of arbitrarily located and activated synaptic inputs.
Reference:
1 . Marasco A, Limongiello A, Migliore M (2013) Using Strahler's analysis to reduce up to 200-fold the run time of realistic neuron models. Sci Rep 3:2934 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Dendrite;
Brain Region(s)/Organism: Hippocampus; Cerebellum;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Cerebellum Purkinje GABA cell;
Channel(s): I Na,t; I T low threshold; I K; I Calcium; Ca pump;
Gap Junctions:
Receptor(s): AMPA;
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Action Potentials; Synaptic Integration;
Implementer(s): Limongiello, Alessandro [alessandro.limongiello at unina.it];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Cerebellum Purkinje GABA cell; AMPA; I Na,t; I T low threshold; I K; I Calcium; Ca pump; Glutamate;
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PurkReductionOnLine
morphologies
readme.txt
CaE.mod *
CalciumP.mod *
CaP.mod *
CaP2.mod *
CaT.mod *
K2.mod *
K22.mod *
K23.mod *
KA.mod *
KC.mod *
KC2.mod *
KC3.mod *
KD.mod *
Kdr.mod *
Kh.mod *
Khh.mod *
KM.mod *
Leak.mod *
NaF.mod *
NaP.mod *
pj.mod
clusterisingMethods.hoc
fixnseg.hoc
mergingMethods.hoc
mosinit.hoc
ranstream.hoc *
RedPurk.hoc
stimulation1.hoc
useful&InitProc.hoc
                            
TITLE decay of submembrane calcium concentration
: Internal calcium concentration due to calcium currents and pump.
: Differential equations.
:
: This file contains two mechanisms:
:
: 1. Simple model of ATPase pump with 3 kinetic constants (Destexhe 1992)
:
:      Cai + P <-> CaP -> Cao + P  (k1,k2,k3)
:
: A Michaelis-Menten approximation is assumed, which reduces the complexity
: of the system to 2 parameters:
:    kt = <tot enzyme concentration> * k3 -> TIME CONSTANT OF THE PUMP
:    kd = k2/k1 (dissociation constant)  -> EQUILIBRIUM CALCIUM VALE
: The values of these parameters are chosen assuming a high affinity of
: the pump to calcium and a low transport capacity (cfr. Blaustein,
: TINS, 11: 438, 1988, and references therein).
:
: For further information about this this mechanism, see Destexhe,A.
: Babloysntz,A. and Sejnowski,TJ. Ionic mechanisms for intrinsic slow
: oscillations in thalamic relay neurons. Biophys.J.65:1538-1552,1933.
:
:
: 2. Simple first-order decay or buffering:
:
:      Cai + B <->...
:
: which can be ritten as:
:
:      dCai/dt = (cainf-Cai) / taur
:
: where cainf is the equilibrium intracellular calcium value (usually
: inthe range of 200-300 nM) and tsur is the time constant of calcium
: removal. The dynamics of submembranal calcium is usually thought to
: be relativly fast, inthe 1-10 millisecond range (see Balaustein,
: TINS, 11:438,1988).
:
: All variables are range variables
:
: Written by Alain Destexhe, Salk Institute,Nov 12,1992 
: 

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

NEURON {
	SUFFIX cad
	USEION ca READ ica,cai WRITE cai
	RANGE depth,kt,kd,cainf,taur
}

UNITS {
	(molar) = (1/liter)      :moles do not appear in units
	(mM)	= (millimolar)
	(um)	= (micron)
	(mA)	= (milliamp)
	(msM)   = (ms mM)
}

CONSTANT{
	FARADAY = 96489 (coul)   : moles do not appear in units
}

PARAMETER {
	depth = .1	(um)     : depth of shell
	taur  = 1e10    (ms)     : remove first-order decay
	cainf = 2.4e-4	(mM)
	kt    = 1e-4	(mM/ms)
	kd    = 1e-4	(mM)
}

STATE {
	cai   (mM)
}

INITIAL {
	cai = kd
}

ASSIGNED{
	ica		(mA/cm2)
	drive_channel   (mM/ms)
	drive_pump	(mM/ms)
}

BREAKPOINT{
	SOLVE state METHOD derivimplicit
}

DERIVATIVE state {

	drive_channel = -(10000)*ica/(2*FARADAY*depth)

	if(drive_channel <= 0.) {drive_channel = 0.}:cannot pump inward

	drive_pump = -kt*cai/(cai+kd)  :Michaelis-Menten

	cai' =drive_channel+drive_pump+(cainf-cai)/taur
}

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