AP shape and parameter constraints in optimization of compartment models (Weaver and Wearne 2006)

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Accession:87473
"... We construct an objective function that includes both time-aligned action potential shape error and errors in firing rate and firing regularity. We then implement a variant of simulated annealing that introduces a recentering algorithm to handle infeasible points outside the boundary constraints. We show how our objective function captures essential features of neuronal firing patterns, and why our boundary management technique is superior to previous approaches."
Reference:
1 . Weaver CM, Wearne SL (2006) The role of action potential shape and parameter constraints in optimization of compartment models Neurocomputing 69:1053-1057
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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): Vestibular neuron;
Channel(s): I Na,p; I Na,t; I A; I K,Ca;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Parameter Fitting; Methods;
Implementer(s): Weaver, Christina [christina.weaver at fandm.edu];
Search NeuronDB for information about:  I Na,p; I Na,t; I A; I K,Ca;
COMMENT
	A-type transient K current for Av-Ron and Vidal 1999
	Implemented by C. Weaver, 2003

	Equation:

	I_A = gbar_A * ainf(V) * b * (v - v_K)

	db/dt = ( binf(V) - b ) / btau

	binf(V) = 1 / ( 1 + exp(-2ab*(V-Vhb)))

	ainf(V) similar.

ENDCOMMENT

UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)

}

PARAMETER {
	celsius 	(degC)
	gbar=.004 (mho/cm2)
	vha=-40 (mV)
	vhb=-70 (mV)
	aa=0.05	(/mV)
	ab=-0.1	(/mV)
	btau=10 (ms)
        v       (mV)
        ek      (mV)
	basic = 0
}


NEURON {
	SUFFIX ka
	USEION k READ ek WRITE ik
        RANGE gbar,gka
        RANGE ainf, binf, btau
	RANGE tot
}

STATE {
	b
}

ASSIGNED {
	ik (mA/cm2)
	tot (mA/cm2)
        gka  (mho/cm2)
	ainf
        binf
}

INITIAL {
        rates(v)
        b=binf
: printf( "ka ik=%g\n", ik)
}

BREAKPOINT {
	SOLVE state METHOD cnexp
	gka = gbar*ainf*b
	tot = gka*(v-ek)
	ik = gka*(v-ek)

}

FUNCTION expn(v (mV),a(/mV), vhalf(mV)) {
  	expn = exp(-2*a*(v-vhalf))
}

DERIVATIVE state {     : exact when v held constant; integrates over dt step
        rates(v)
        b' = (binf - b)/btau
}

PROCEDURE rates(v (mV)) { :callable from hoc
	binf = 1/(1 + expn(v,ab,vhb))
	ainf = 1/(1 + expn(v,aa,vha))
	if( basic > 0 ) {
		: in Av-Ron 1991, ainf = 1
	 	ainf = 1
	}
}