/****************************************************************************
Copyright (c) California Institute of Technology, 2006 -- All Rights Reserved
Royalty free license granted for non-profit research and educational purposes.
******************************************************************************/
/*
This file defines all the parameters that are held constant across
simulations described in Gold, Henze, Koch & Buzsaki (2006) and Gold,
Henze and Koch (2006). The approach is that absolutely all parameters
of the simulation must be defined in either this file or the file
containing cell specific conductance density parameters. No
parameters should appear in any code files. All parameters are
defined through define_param() or define_ratio_param() procedure calls
so that they are all saved to the data files produced for the trials.
All of this is intended to create a simulation with no "magic"
(hidden) numbers.
The parameters are categorized as follows:
Simulation Time Parameters
Ionic Reversal Potentials (etc.)
Dendrite Classification
Compartment Size
Spines
Passive Parameters
Ionic Current Density Paremeters
Ionic Current Kinetics
Note: this must be loaded AFTER the cell specific conductance
densities have been loaded because some of the ionic current densities
defined here are ratios of the cell specific conductances.
*/
//-------------------------------------------------------------------------------
// a little message to standard output when the file is loaded
print "LOADING STANDARD PARAMS for CA1 pyramidal cells..."
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// SIMULATION TIME PARAMETERS
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* stop time, the minum step length between currents output. Also set
the integration method */
define_param("tstop","25")
define_param("min_tstep","0.045") // minimum step for printing variable step currents
// must be >= fprint(...%06.3f...) roundoff in making filenames!
// 0 = backwards Euler, 2=crank-nicholson
define_param("secondorder","2")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// REVERSAL POTENTIALS, ETC.
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* Resting potential and ionic reversal potentials. Note that Gold,
Henze, Koch & Buzsaki (2006) used E_k=-140 while Gold, Henze and Koch
(2006) used the more standard E_k=-100. Also a few miscellaneous
parameters are set for the benefit of NEURON NMODL mechanisms. */
define_param("V_rest","-65") // rest potential
define_param("E_na" ,"71") // sodium reversal potential
define_param("E_ca", "140") // calcium reversal potential
define_param("E_k" ,"-100") // potassium reversal potential
define_param("celsius","37.5") // temperature
// this sets it to be the same as in the mod database
// see file:/usr/local/nrn/nrnhelp/help/neuron/general/predec.html#Constants
define_param("FARADAY","96520")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// DENDRITE CLASSIFICATION PARAMETER
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* params determing trunk vs. non-trunk in apical tree. A smaller
diameter than the trunk_min and greater thant tuft_max defines
oblique. See cell_util.hoc (make lists). Used in channel model
initialization */
define_param("trunk_min_diam","1.25")
define_param("tuft_max_diam","0.5")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// COMPARTMENT SIZE PARAMETERS
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* The parameter 'my_dlambda' defines the fraction of lamda_f100 to
use in determing the number of compartments. See cell_util.hoc
(Defining the number of compartments.) The max_seg_length parameters
are used to force exceptions to the dlambda rule - only in the apical
trunk (at the moment). the n_axon_seg parameter is the number of
compartments to use for the axon hillock and initial segment - this is
many more than would be assigned by the dlambda approach (follows the
approach of Mainen & Sejnowski 1995 and Holt & Koch 1999). */
define_param("my_dlambda",".1")
// force more compartments in wide sections...
define_param("trunk_max_seg_length","15")
define_param("oblique_max_seg_length", "0")
define_param("tuft_max_seg_length","0")
define_param("basal_max_seg_length","0")
define_param("n_axon_seg","5")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// SPINES
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* These parameters define the spine densities described in the
appendix of Gold et. al (2006). They are used in the
membrane_init.hoc (spines & passive setup & dendrite setup sections)
The "is_spiny" area turns on/off the entire spine correction system. So for
a non-spiny cell simply set this parameter to zero. */
define_param("is_spiny", "1")
define_param("spine_area","0.83") // um^2 -- KM Harris & JK Stevens, (1989) J. Neursoci 9:2982-2997
define_param("trunk_prox_spine_dens","0.03") // megias "radiatum thick proximal"
define_param("trunk_med_spine_dens","2.3") // megias "radiatum thick medial"
define_param("trunk_dist_spine_dens","6.9") // megias "radiatum thick distal"
define_param("trunk_lm_spine_dens", "1.72") // megias "l-m/thick"
define_param("trunk_med_min_dist","100")
define_param("trunk_med_max_dist","175")
define_param("lm_min_dist","250")
define_param("oblique_prox_spine_dens","3.5") // megias "radiatum/thin"
define_param("oblique_dist_spine_dens","1.7") // megias "l-m/thin"
define_param("tuft_prox_spine_dens","3.5") // megias "radiatum/thin"
define_param("tuft_dist_spine_dens","0.8") // megias avg of l-m medium
define_param("tuft_prox_max_dist","300")
define_param("basal_prox_spine_dens","0.64") // megias "radiatum/thin"
define_param("basal_dist_spine_dens","3.4") // megias "l-m/thin"
define_param("basal_prox_max_dist","50")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// PASSIVE
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/* Parameters for passive mechanism conductance (i.e. 1/r_m), cm and
Ra.(They are defined here and saved to the parameter file and actual
NEURON variables by the same name are defined in membrane_init.hoc) */
define_param("r_m", "1.5e4")
define_param("r_m_my", "4e4")
define_param("r_m_node", "1e3")
define_param("c_m", "1.0")
define_param("c_m_my","0.05")
define_param("r_a", "70")
define_param("r_a_ax" , "50")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// ION CHANNEL DENSITIES
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/*
These are parameters controlling ionic current densities that are held
constant for all cells in Gold, Henze, Koch & Buzsaki. (2006) and
Gold, Henze and Koch (2006). These include distance parameters for
non-uniform conductance densities and some densities which are simply
constant for all cells (i.e. calcium and H type currents). Also in
this file are a number of parameters allowing different densities in
apical and basal dendrites - these parameters are all currently set to
1.0 (identical basal/apical density.) These were never used in the
final simulation versions described in the papers, but the parameters
were left intact to make further experimentation convenient
(membrane_init.hoc already has separate apical/basal initiation
functions, so why not?)
If you want to vary any of these parameters on a cell by cell basis,
simply cut it from this file and paste it into all of the cell
specific density files (i.e d151_params.hoc)
*/
//----------------------------------------------------
// NAF
define_param("gna_apical_min_dist","300")
define_param("gna_basal_min_dist","300")
define_ratio_param("gna_node", "gna_default", "gna_default_node_ratio", "3")
//-----------------------------------------------------
// KK
define_ratio_param("gkk_basal", "gkk", "gkk_basal_ratio", "1.0")
define_ratio_param("gkd_basal", "gkd", "gkd_basal_ratio", "1.0")
//-----------------------------------------------
// KA PROX
define_ratio_param("gka_prox_basal", "gka_prox_apical", "gka_prox_apical_basal_ratio", "1.0")
define_param("kaprox_max_dist_apical" ,"100")
define_param("kaprox_max_dist_basal" ,"100")
//-----------------------------------------------
// KA DIST
define_param("kadist_peak_dist_apical","350")
define_param("kadist_peak_dist_basal" ,"350")
define_ratio_param("gka_dist_max_basal", "gka_dist_min_basal", "gka_dist_prox_ratio_basal", "6")
define_ratio_param("gka_dist_max_apical", "gka_dist_min_apical", "gka_dist_prox_ratio_apical", "6")
//----------------------------------------------
// KC
define_param("kc_max_distance_apical","50")
define_param("kc_max_distance_basal","50")
//----------------------------------------------
// KM
define_ratio_param("gkm_basal", "gkm", "gkm_basal_ratio", "1.0")
//----------------------------------------------
// KAHP
define_param("gkahp_hi_apical" ,"5e-4")
define_param("gkahp_lo_apical" , "2.5e-4")
define_ratio_param("gkahp_hi_basal", "gkahp_hi_apical", "gkahp_hi_basal_apical_ratio", "1.0")
define_ratio_param("gkahp_lo_basal", "gkahp_lo_apical", "gkahp_lo_basal_apical_ratio", "1.0")
define_param("kahp_max_hi_distance_apical","100")
define_param("kahp_max_hi_distance_basal","100")
//----------------------------------------------
// CAT
define_param("gcat_apical" ,".0001")
define_ratio_param("gcat_basal", "gcat_apical", "gcat_basal_apical_ratio", "1.0")
define_param("cat_max_distance_apical","150")
define_param("cat_max_distance_basal" ,"150")
// -----------------------------------------
// CAR
define_param("gcar_dend" ,".0002")
define_ratio_param("gcar_soma", "gcar_dend", "car_soma_apical_ratio", "0.1")
define_ratio_param("gcar_basal","gcar_dend", "car_apical_basal_ratio", "1.0")
// -----------------------------------------
// CAN
define_param("gcan_soma" ,".0002")
// -----------------------------------------
// CAL (HVAl)
define_param("gcal_soma" ,".0002")
define_ratio_param("gcal_apical_hi", "gcal_soma", "gcal_apical_hi_soma_ratio", "1.0")
define_ratio_param("gcal_apical_lo", "gcal_soma", "gcal_apical_lo_soma_ratio", "0.02")
define_ratio_param("gcal_basal_hi", "gcal_soma", "gcal_basal_hi_soma_ratio", "1.0")
define_ratio_param("gcal_basal_lo", "gcal_soma", "gcal_basal_lo_soma_ratio", "0.02")
define_param("cal_max_hi_distance_apical","50")
define_param("cal_max_hi_distance_basal" ,"50")
//------------------------------------
// H SOMA
define_param("gh_soma" ,"0.0005")
//------------------------------------
// H DEND
define_ratio_param("gh_apical_min", "gh_soma", "gh_apical_min_soma_ratio", "1.0")
define_ratio_param("gh_apical_max", "gh_soma", "gh_apical_max_soma_ratio", "6.0")
define_ratio_param("gh_basal_min", "gh_soma", "gh_basal_min_soma_ratio", "1.0")
define_ratio_param("gh_basal_max", "gh_soma", "gh_basal_max_soma_ratio", "6.0")
define_param("h_max_distance_apical", "300")
define_param("h_max_distance_basal", "300")
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
// ION CHANNEL KINETICS
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
/*
In contrast to the usual NEURON practice of setting all mechanism
kinetics parameters in the mod file the approach here is to leave all
mod files blank and set the parameters from the hoc code (below.)
This was particularly useful during tuning of the kinetics for two
reasons: 1) no recompilation of the mod files when the parameters
are changed; 2) the parameters used on every trial are saved via
the define_param mechanism.
In the paper Gold et al. (2006) it said that the Hodgkin-Huxley style
mechanisms use the formulation of Borg-Graham (1999): this is in fact
not quite true as the formulation is _equivalent_ to that of
Borg-Graham but not exactly the same. In particular, rather than
formulating the kinetics using forward and backward Boltzman rates
(alpha & beta) that explicitly include the temperature and Faradays
constant and then caculating the x_inf(V) and tau_x(V) from the rates
(x_inf=a/[a+b] x_tau=1/[a+b]) the mechanisms here simply calculate
equivalent x_inf(V) and tau_x(V) directly with a slightly more
intuitive set of parameters.
The equations are:
------------------
x_inf(V) = 1 / (1 + exp((V - vhalf_x)/(vsteep_x)))
tau_x(V) = var_tau = toffset_x + (tscale_x / ( exp(-tskew_x*(V-vhalf_x)/vsteep_x) * (1+exp((V-vhalf_x)/vsteep_x))) )
The parameters are:
-------------------
Vhalf - the potential at which a single gate variable (i.e. with
exponent=1)is 50% likely to be open
Vsteep - controls the steepness of the sigmoidal slope of x_inf(V)
and the tightness of the tau_x(V) curve.
Tskew - the skewness of the the tau_x(V) curves (0 < tskew < 1, 0 and
correspond to step functions)
TScale - scaling of the tau_x(V) curve
TOffset - offset of the tau_x(V) curve
Exp - the power to which the gate variable is raised in calculating
the conductance (i.e m^3h has m_exp=3, h_exp=1)
The parameters vhalf, tskew and toff are identical to the parameters
vhalf, gamma, and tau_0 in Borg_graham (1999). The parameter tscale
is equivalent to 1/K in Borg-Graham, and the parameter vsteep is
equivalent to 1000/([F/RT]*z) in Borg-Grahm. Consequently these
mechanisms do not actually incorporate temperature.
The formulation for the Calcium dependent potassium channels (kahp and
kc) are in fact exactly the same as the Borg-Graham (1999) versions.
Several parameters for the non-uniform distribution are also set
below, mainly distances and some ratios that are not allowed to vary
from cell to cell.
*/
//----------------------------------------------------
// NAF
define_param( "exp_m_naf","3")
define_param( "vhalf_m_naf","-46")
define_param( "vsteep_m_naf", "-6")
define_param( "tskew_m_naf", "0.05")
define_param( "tscale_m_naf", "0.01")
define_param("toffset_m_naf", "0.04")
define_param( "exp_h_naf","1")
define_param( "vhalf_h_naf","-50")
define_param( "vsteep_h_naf", "2")
define_param( "tskew_h_naf", "0.2")
define_param( "tscale_h_naf", "0.5")
define_param("toffset_h_naf", "0.25")
//----------------------------------------------------
// NAX
define_param( "exp_m_nax","3")
define_param( "vhalf_m_nax","-51")
define_param( "vsteep_m_nax", "-5.5")
define_param( "tskew_m_nax", "0.05")
define_param( "tscale_m_nax", "0.01")
define_param("toffset_m_nax", "0.04")
define_param( "exp_h_nax","1")
define_param( "vhalf_h_nax","-50")
define_param( "vsteep_h_nax", "2")
define_param( "tskew_h_nax", "0.2")
define_param( "tscale_h_nax", "0.75")
define_param("toffset_h_nax", "0.35")
//-----------------------------------------------------
// KK
define_param( "exp_m_kk","1")
define_param( "vhalf_m_kk","-5")
define_param( "vsteep_m_kk","-5")
define_param( "tskew_m_kk", "0.5")
define_param( "tscale_m_kk", "4")
define_param("toffset_m_kk", "0.25")
define_param( "exp_h_kk","1")
define_param( "vhalf_h_kk","-65")
define_param( "vsteep_h_kk","15")
define_param( "tskew_h_kk", "0.5")
define_param( "tscale_h_kk", "1")
define_param("toffset_h_kk", "100")
//-----------------------------------------------
// KD
define_param( "exp_m_kd","4")
define_param( "vhalf_m_kd","-60")
define_param( "vsteep_m_kd","-8.4")
define_param( "tskew_m_kd", "0.5")
define_param( "tscale_m_kd", "1")
define_param("toffset_m_kd", ".25")
define_param( "exp_h_kd","2")
define_param( "vhalf_h_kd","-73")
define_param( "vsteep_h_kd","10")
define_param( "tskew_h_kd", "0.5")
define_param( "tscale_h_kd", "0")
define_param("toffset_h_kd", "1e3")
//-----------------------------------------------
// KA PROX
define_param( "exp_m_kaprox","4")
define_param( "vhalf_m_kaprox","-40")
define_param( "vsteep_m_kaprox","-8")
define_param( "tskew_m_kaprox", "0.85")
define_param( "tscale_m_kaprox", "0")
define_param("toffset_m_kaprox", "0.2")
define_param( "exp_h_kaprox","2")
define_param( "vhalf_h_kaprox","-50")
define_param( "vsteep_h_kaprox","8")
define_param( "tskew_h_kaprox", "0.5")
define_param( "tscale_h_kaprox", "1.5")
define_param("toffset_h_kaprox", "0.3")
//-----------------------------------------------
// KA DIST
define_param( "exp_m_kadist","4")
define_param( "vhalf_m_kadist","-50")
define_param( "vsteep_m_kadist","-8")
define_param( "tskew_m_kadist", "0.85")
define_param( "tscale_m_kadist", "0")
define_param("toffset_m_kadist", "0.2")
define_param( "exp_h_kadist","2")
define_param( "vhalf_h_kadist","-60")
define_param( "vsteep_h_kadist","8")
define_param( "tskew_h_kadist", "0.5")
define_param( "tscale_h_kadist", "1.5")
define_param("toffset_h_kadist", "0.3")
//-----------------------------------------------
// KC
define_param("k_oi_kc","12")
define_param("k_ic_kc","-10")
define_param("k_co_kc","6")
define_param("k_oc_kc","-3")
define_param("vhalf_oi_kc","-30")
define_param("vhalf_ic_kc","-120")
define_param("vhalf_co_kc","-45")
define_param("vhalf_oc_kc","-40")
define_param("tmin_oi_kc","1.5e0")
define_param("tmin_ic_kc","1e-1")
define_param("tmin_co_kc","2e-2")
define_param("tmin_oc_kc","1.5e0")
/* only the co transition has a tmax - this is hard coded into the mod
file kc.mod*/
define_param("tmax_co_kc","50")
define_param("alpha_co_kc","2.5e10")
//----------------------------------------------
// KM
define_param( "exp_n_km","2")
define_param( "vhalf_n_km","-45")
define_param( "vsteep_n_km","-4")
define_param( "tskew_n_km", "0.5")
define_param( "tscale_n_km", "2.0")
define_param("toffset_n_km", "2.0")
//----------------------------------------------
// KAHP
define_param("alpha_n_kahp", "1e31")
define_param("beta_n_kahp", "2e-1")
define_param("toffset_n_kahp", "5")
define_param("exp_n_kahp", "2")
define_param("exp_ca_kahp", "8")
//----------------------------------------------
// CAT
define_param( "exp_m_cat","2")
define_param( "vhalf_m_cat","-30")
define_param( "vsteep_m_cat","-7")
define_param( "tskew_m_cat","0.1")
define_param( "tscale_m_cat","5.0")
define_param("toffset_m_cat","2.0")
define_param( "exp_h_cat","1")
define_param( "vhalf_h_cat","-60")
define_param( "vsteep_h_cat","5.0")
define_param( "tskew_h_cat","0.5")
define_param( "tscale_h_cat","1")
define_param("toffset_h_cat","25")
// -----------------------------------------
// CAR
define_param( "exp_m_car","2")
define_param( "vhalf_m_car","0")
define_param( "vsteep_m_car","-8")
define_param( "tskew_m_car","0.5")
define_param( "tscale_m_car","3")
define_param("toffset_m_car","2.0")
define_param( "exp_h_car","1")
define_param( "vhalf_h_car","-40")
define_param( "vsteep_h_car","9")
define_param( "tskew_h_car","0.5")
define_param( "tscale_h_car","1")
define_param("toffset_h_car","50")
// -----------------------------------------
// CAN
define_param( "exp_m_can","2")
define_param( "vhalf_m_can","-14")
define_param( "vsteep_m_can","-6.5")
define_param( "tskew_m_can","0.2")
define_param( "tscale_m_can","5")
define_param("toffset_m_can","1")
define_param( "exp_h_can","1")
define_param( "vhalf_h_can","-40")
define_param( "vsteep_h_can","10")
define_param( "tskew_h_can","0.5")
define_param( "tscale_h_can","1")
define_param("toffset_h_can","50")
// -----------------------------------------
// CAL (HVAl)
define_param( "exp_n_cal","2")
define_param( "vhalf_n_cal","5")
define_param( "vsteep_n_cal","-8")
define_param( "tskew_n_cal","0.5")
define_param( "tscale_n_cal","2.0")
define_param("toffset_n_cal","2.0")
//------------------------------------
// H SOMA
define_param( "exp_n_hsoma","1")
define_param( "vhalf_n_hsoma","-82")
define_param( "vsteep_n_hsoma","4")
define_param( "tskew_n_hsoma","0.005")
define_param( "tscale_n_hsoma","0")
define_param("toffset_n_hsoma","10")
//------------------------------------
// H DEND
define_param( "exp_n_hdend","1")
define_param( "vhalf_n_hdend","-90")
define_param( "vsteep_n_hdend","4")
define_param( "tskew_n_hdend","0.005")
define_param( "tscale_n_hdend","0")
define_param("toffset_n_hdend","10")
//----------------------------------------------
// CADIFUS
define_param("cai_init","75e-6")
define_param( "DCa_cadifus","0.6")
define_param( "TotalBuffer_cadifus","0.005")
define_param( "k1buf_cadifus","250")
define_param( "k2buf_cadifus","0.1")