Rhesus Monkey Young and Aged L3 PFC Pyramidal Neurons (Rumbell et al. 2016)

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Accession:184497
A stereotypical pyramidal neuron morphology with ion channel parameter combinations that reproduce firing patterns of one young and one aged rhesus monkey L3 PFC pyramidal neurons. Parameters were found through an automated optimization method.
Reference:
1 . Rumbell TH, Draguljic D, Yadav A, Hof PR, Luebke JI, Weaver CM (2016) Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons. J Comput Neurosci 41:65-90 [PubMed]
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): Neocortex L2/3 pyramidal GLU cell;
Channel(s): I Na,p; I Na,t; I A; I K; I M; I h; I K,Ca; I Sodium; I Calcium; I Potassium; I_AHP; I Cl, leak;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Ion Channel Kinetics; Parameter Fitting; Detailed Neuronal Models; Aging/Alzheimer`s;
Implementer(s):
Search NeuronDB for information about:  Neocortex L2/3 pyramidal GLU cell; I Na,p; I Na,t; I A; I K; I M; I h; I K,Ca; I Sodium; I Calcium; I Potassium; I_AHP; I Cl, leak;
/* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib.h"
#undef PI
 
#include "md1redef.h"
#include "section.h"
#include "md2redef.h"

#if METHOD3
extern int _method3;
#endif

#undef exp
#define exp hoc_Exp
extern double hoc_Exp();
 
#define _threadargscomma_ _p, _ppvar, _thread, _nt,
#define _threadargs_ _p, _ppvar, _thread, _nt
 	/*SUPPRESS 761*/
	/*SUPPRESS 762*/
	/*SUPPRESS 763*/
	/*SUPPRESS 765*/
	 extern double *getarg();
 /* Thread safe. No static _p or _ppvar. */
 
#define t _nt->_t
#define dt _nt->_dt
#define gbar _p[0]
#define i _p[1]
#define m _p[2]
#define h _p[3]
#define minf _p[4]
#define hinf _p[5]
#define mtau _p[6]
#define htau _p[7]
#define Dm _p[8]
#define Dh _p[9]
#define v _p[10]
#define _g _p[11]
 
#if MAC
#if !defined(v)
#define v _mlhv
#endif
#if !defined(h)
#define h _mlhh
#endif
#endif
 static int hoc_nrnpointerindex =  -1;
 static Datum* _extcall_thread;
 static Prop* _extcall_prop;
 /* external NEURON variables */
 /* declaration of user functions */
 static int _hoc_settables();
 static int _mechtype;
extern int nrn_get_mechtype();
 extern void _nrn_setdata_reg(int, void(*)(Prop*));
 static void _setdata(Prop* _prop) {
 _extcall_prop = _prop;
 }
 static _hoc_setdata() {
 Prop *_prop, *hoc_getdata_range();
 _prop = hoc_getdata_range(_mechtype);
   _setdata(_prop);
 ret(1.);
}
 /* connect user functions to hoc names */
 static IntFunc hoc_intfunc[] = {
 "setdata_cat", _hoc_setdata,
 "settables_cat", _hoc_settables,
 0, 0
};
 
static void _check_settables(double*, Datum*, Datum*, _NrnThread*); 
static void _check_table_thread(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, int _type) {
   _check_settables(_p, _ppvar, _thread, _nt);
 }
 /* declare global and static user variables */
#define eca eca_cat
 double eca = 0;
#define usetable usetable_cat
 double usetable = 1;
 /* some parameters have upper and lower limits */
 static HocParmLimits _hoc_parm_limits[] = {
 "usetable_cat", 0, 1,
 0,0,0
};
 static HocParmUnits _hoc_parm_units[] = {
 "eca_cat", "mV",
 "gbar_cat", "mho/cm2",
 "i_cat", "mA/cm2",
 0,0
};
 static double delta_t = 1;
 static double h0 = 0;
 static double m0 = 0;
 /* connect global user variables to hoc */
 static DoubScal hoc_scdoub[] = {
 "eca_cat", &eca_cat,
 "usetable_cat", &usetable_cat,
 0,0
};
 static DoubVec hoc_vdoub[] = {
 0,0,0
};
 static double _sav_indep;
 static void nrn_alloc(), nrn_init(), nrn_state();
 static void nrn_cur(), nrn_jacob();
 
static int _ode_count(), _ode_map(), _ode_spec(), _ode_matsol();
 
#define _cvode_ieq _ppvar[0]._i
 /* connect range variables in _p that hoc is supposed to know about */
 static char *_mechanism[] = {
 "6.2.0",
"cat",
 "gbar_cat",
 0,
 "i_cat",
 0,
 "m_cat",
 "h_cat",
 0,
 0};
 
static void nrn_alloc(_prop)
	Prop *_prop;
{
	Prop *prop_ion, *need_memb();
	double *_p; Datum *_ppvar;
 	_p = nrn_prop_data_alloc(_mechtype, 12, _prop);
 	/*initialize range parameters*/
 	gbar = 0;
 	_prop->param = _p;
 	_prop->param_size = 12;
 	_ppvar = nrn_prop_datum_alloc(_mechtype, 1, _prop);
 	_prop->dparam = _ppvar;
 	/*connect ionic variables to this model*/
 
}
 static _initlists();
  /* some states have an absolute tolerance */
 static Symbol** _atollist;
 static HocStateTolerance _hoc_state_tol[] = {
 0,0
};
 _cat_reg() {
	int _vectorized = 1;
  _initlists();
 	register_mech(_mechanism, nrn_alloc,nrn_cur, nrn_jacob, nrn_state, nrn_init, hoc_nrnpointerindex, 1);
 _mechtype = nrn_get_mechtype(_mechanism[1]);
     _nrn_setdata_reg(_mechtype, _setdata);
     _nrn_thread_table_reg(_mechtype, _check_table_thread);
  hoc_register_dparam_size(_mechtype, 1);
 	hoc_register_cvode(_mechtype, _ode_count, _ode_map, _ode_spec, _ode_matsol);
 	hoc_register_tolerance(_mechtype, _hoc_state_tol, &_atollist);
 	hoc_register_var(hoc_scdoub, hoc_vdoub, hoc_intfunc);
 	ivoc_help("help ?1 cat C:/Users/Tim/Dropbox/neuron/optimisetraub/model/cat.mod\n");
 hoc_register_limits(_mechtype, _hoc_parm_limits);
 hoc_register_units(_mechtype, _hoc_parm_units);
 }
 static double *_t_minf;
 static double *_t_mtau;
 static double *_t_hinf;
 static double *_t_htau;
static int _reset;
static char *modelname = "Calcium low threshold T type current for RD Traub, J Neurophysiol 89:909-921, 2003";

static int error;
static int _ninits = 0;
static int _match_recurse=1;
static _modl_cleanup(){ _match_recurse=1;}
static _f_settables();
static settables();
 
static int _ode_spec1(), _ode_matsol1();
 static _n_settables();
 static int _slist1[2], _dlist1[2];
 static int states();
 
/*CVODE*/
 static int _ode_spec1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {int _reset = 0; {
   settables ( _threadargscomma_ v ) ;
   Dm = ( minf - m ) / mtau ;
   Dh = ( hinf - h ) / htau ;
   }
 return _reset;
}
 static int _ode_matsol1 (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
 settables ( _threadargscomma_ v ) ;
 Dm = Dm  / (1. - dt*( ( ( ( - 1.0 ) ) ) / mtau )) ;
 Dh = Dh  / (1. - dt*( ( ( ( - 1.0 ) ) ) / htau )) ;
}
 /*END CVODE*/
 static int states (double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) { {
   settables ( _threadargscomma_ v ) ;
    m = m + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / mtau)))*(- ( ( ( minf ) ) / mtau ) / ( ( ( ( - 1.0) ) ) / mtau ) - m) ;
    h = h + (1. - exp(dt*(( ( ( - 1.0 ) ) ) / htau)))*(- ( ( ( hinf ) ) / htau ) / ( ( ( ( - 1.0) ) ) / htau ) - h) ;
   }
  return 0;
}
 static double _mfac_settables, _tmin_settables;
  static void _check_settables(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
  static int _maktable=1; int _i, _j, _ix = 0;
  double _xi, _tmax;
  if (!usetable) {return;}
  if (_maktable) { double _x, _dx; _maktable=0;
   _tmin_settables =  - 120.0 ;
   _tmax =  40.0 ;
   _dx = (_tmax - _tmin_settables)/641.; _mfac_settables = 1./_dx;
   for (_i=0, _x=_tmin_settables; _i < 642; _x += _dx, _i++) {
    _f_settables(_p, _ppvar, _thread, _nt, _x);
    _t_minf[_i] = minf;
    _t_mtau[_i] = mtau;
    _t_hinf[_i] = hinf;
    _t_htau[_i] = htau;
   }
  }
 }

 static settables(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _lv) { 
#if 0
_check_settables(_p, _ppvar, _thread, _nt);
#endif
 _n_settables(_p, _ppvar, _thread, _nt, _lv);
 return;
 }

 static _n_settables(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _lv){ int _i, _j;
 double _xi, _theta;
 if (!usetable) {
 _f_settables(_p, _ppvar, _thread, _nt, _lv); return; 
}
 _xi = _mfac_settables * (_lv - _tmin_settables);
 _i = (int) _xi;
 if (_xi <= 0.) {
 minf = _t_minf[0];
 mtau = _t_mtau[0];
 hinf = _t_hinf[0];
 htau = _t_htau[0];
 return; }
 if (_i >= 641) {
 minf = _t_minf[641];
 mtau = _t_mtau[641];
 hinf = _t_hinf[641];
 htau = _t_htau[641];
 return; }
 _theta = _xi - (double)_i;
 minf = _t_minf[_i] + _theta*(_t_minf[_i+1] - _t_minf[_i]);
 mtau = _t_mtau[_i] + _theta*(_t_mtau[_i+1] - _t_mtau[_i]);
 hinf = _t_hinf[_i] + _theta*(_t_hinf[_i+1] - _t_hinf[_i]);
 htau = _t_htau[_i] + _theta*(_t_htau[_i+1] - _t_htau[_i]);
 }

 
static int  _f_settables ( _p, _ppvar, _thread, _nt, _lv ) double* _p; Datum* _ppvar; Datum* _thread; _NrnThread* _nt; 
	double _lv ;
 {
   minf = 1.0 / ( 1.0 + exp ( ( - _lv - 56.0 ) / 6.2 ) ) ;
   mtau = 0.204 + 0.333 / ( exp ( ( _lv + 15.8 ) / 18.2 ) + exp ( ( - _lv - 131.0 ) / 16.7 ) ) ;
   hinf = 1.0 / ( 1.0 + exp ( ( _lv + 80.0 ) / 4.0 ) ) ;
   if ( _lv < - 81.0 ) {
     htau = 0.333 * exp ( ( _lv + 466.0 ) / 66.6 ) ;
     }
   else {
     htau = 9.32 + 0.333 * exp ( ( - _lv - 21.0 ) / 10.5 ) ;
     }
    return 0; }
 
static int _hoc_settables() {
  double _r;
   double* _p; Datum* _ppvar; Datum* _thread; _NrnThread* _nt;
   if (_extcall_prop) {_p = _extcall_prop->param; _ppvar = _extcall_prop->dparam;}else{ _p = (double*)0; _ppvar = (Datum*)0; }
  _thread = _extcall_thread;
  _nt = nrn_threads;
 
#if 1
 _check_settables(_p, _ppvar, _thread, _nt);
#endif
 _r = 1.;
 settables ( _p, _ppvar, _thread, _nt, *getarg(1) ) ;
 ret(_r);
}
 
static int _ode_count(_type) int _type;{ return 2;}
 
static int _ode_spec(_NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
     _ode_spec1 (_p, _ppvar, _thread, _nt);
 }}
 
static int _ode_map(_ieq, _pv, _pvdot, _pp, _ppd, _atol, _type) int _ieq, _type; double** _pv, **_pvdot, *_pp, *_atol; Datum* _ppd; { 
	double* _p; Datum* _ppvar;
 	int _i; _p = _pp; _ppvar = _ppd;
	_cvode_ieq = _ieq;
	for (_i=0; _i < 2; ++_i) {
		_pv[_i] = _pp + _slist1[_i];  _pvdot[_i] = _pp + _dlist1[_i];
		_cvode_abstol(_atollist, _atol, _i);
	}
 }
 
static int _ode_matsol(_NrnThread* _nt, _Memb_list* _ml, int _type) {
   double* _p; Datum* _ppvar; Datum* _thread;
   Node* _nd; double _v; int _iml, _cntml;
  _cntml = _ml->_nodecount;
  _thread = _ml->_thread;
  for (_iml = 0; _iml < _cntml; ++_iml) {
    _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
    _nd = _ml->_nodelist[_iml];
    v = NODEV(_nd);
 _ode_matsol1 (_p, _ppvar, _thread, _nt);
 }}

static void initmodel(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt) {
  int _i; double _save;{
  h = h0;
  m = m0;
 {
   settables ( _threadargscomma_ v ) ;
   m = minf ;
   h = hinf ;
   m = 0.0 ;
   }
 
}
}

static void nrn_init(_NrnThread* _nt, _Memb_list* _ml, int _type){
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];

#if 0
 _check_settables(_p, _ppvar, _thread, _nt);
#endif
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 v = _v;
 initmodel(_p, _ppvar, _thread, _nt);
}}

static double _nrn_current(double* _p, Datum* _ppvar, Datum* _thread, _NrnThread* _nt, double _v){double _current=0.;v=_v;{ {
   i = gbar * m * m * h * ( v - 125.0 ) ;
   }
 _current += i;

} return _current;
}

static void nrn_cur(_NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; double _rhs, _v; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 _g = _nrn_current(_p, _ppvar, _thread, _nt, _v + .001);
 	{ _rhs = _nrn_current(_p, _ppvar, _thread, _nt, _v);
 	}
 _g = (_g - _rhs)/.001;
#if CACHEVEC
  if (use_cachevec) {
	VEC_RHS(_ni[_iml]) -= _rhs;
  }else
#endif
  {
	NODERHS(_nd) -= _rhs;
  }
 
}}

static void nrn_jacob(_NrnThread* _nt, _Memb_list* _ml, int _type) {
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml];
#if CACHEVEC
  if (use_cachevec) {
	VEC_D(_ni[_iml]) += _g;
  }else
#endif
  {
     _nd = _ml->_nodelist[_iml];
	NODED(_nd) += _g;
  }
 
}}

static void nrn_state(_NrnThread* _nt, _Memb_list* _ml, int _type) {
 double _break, _save;
double* _p; Datum* _ppvar; Datum* _thread;
Node *_nd; double _v; int* _ni; int _iml, _cntml;
#if CACHEVEC
    _ni = _ml->_nodeindices;
#endif
_cntml = _ml->_nodecount;
_thread = _ml->_thread;
for (_iml = 0; _iml < _cntml; ++_iml) {
 _p = _ml->_data[_iml]; _ppvar = _ml->_pdata[_iml];
 _nd = _ml->_nodelist[_iml];
#if CACHEVEC
  if (use_cachevec) {
    _v = VEC_V(_ni[_iml]);
  }else
#endif
  {
    _nd = _ml->_nodelist[_iml];
    _v = NODEV(_nd);
  }
 _break = t + .5*dt; _save = t;
 v=_v;
{
 { {
 for (; t < _break; t += dt) {
   states(_p, _ppvar, _thread, _nt);
  
}}
 t = _save;
 }}}

}

static terminal(){}

static _initlists(){
 double _x; double* _p = &_x;
 int _i; static int _first = 1;
  if (!_first) return;
 _slist1[0] = &(m) - _p;  _dlist1[0] = &(Dm) - _p;
 _slist1[1] = &(h) - _p;  _dlist1[1] = &(Dh) - _p;
   _t_minf = makevector(642*sizeof(double));
   _t_mtau = makevector(642*sizeof(double));
   _t_hinf = makevector(642*sizeof(double));
   _t_htau = makevector(642*sizeof(double));
_first = 0;
}

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