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NM_TC/Cortical_Column.h
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/*
* Copyright (c) 2015 University of Lübeck
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*
* AUTHORS: Michael Schellenberger Costa: mschellenbergercosta@gmail.com
*
* Based on: Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
* A Weigenand, M Schellenberger Costa, H-VV Ngo, JC Claussen, T Martinetz
* PLoS Computational Biology. 2014;10:e1003923
*
* A thalamocortical neural mass model of the EEG during NREM sleep and its response
* to auditory stimulation.
* M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
* JC Claussen.
* PLoS Computational Biology http://dx.doi.org/10.1371/journal.pcbi.1005022
*/
/******************************************************************************/
/* Implementation of a cortical module */
/******************************************************************************/
#pragma once
#include <cmath>
#include <vector>
#include "Random_Stream.h"
#include "Thalamic_Column.h"
class Thalamic_Column;
class Cortical_Column {
public:
Cortical_Column(double* Param, double* Con)
:sigma_p (Param[0]), g_KNa (Param[1]), dphi (Param[2]),
N_pt (Con[2]), N_it (Con[3])
{set_RNG();}
/* Connect to the thalamic module */
void get_Thalamus(Thalamic_Column& T) {Thalamus = &T;}
/* ODE functions */
void set_RK (int);
void add_RK (void);
private:
/* Declaration of private functions */
/* Initialize the RNGs */
void set_RNG (void);
/* Firing rates */
double get_Qp (int) const;
double get_Qi (int) const;
/* Currents */
double I_ep (int) const;
double I_ei (int) const;
double I_gp (int) const;
double I_gi (int) const;
double I_L_p (int) const;
double I_L_i (int) const;
double I_KNa (int) const;
/* Potassium pump */
double Na_pump (int) const;
/* Noise functions */
double noise_xRK (int,int) const;
double noise_aRK (int) const;
/* Helper functions */
inline std::vector<double> init (double value)
{return {value, 0.0, 0.0, 0.0, 0.0};}
inline void add_RK (std::vector<double>& var)
{var[0] = (-3*var[0] + 2*var[1] + 4*var[2] + 2*var[3] + var[4])/6;}
inline void add_RK_noise (std::vector<double>& var, unsigned noise)
{var[0] = (-3*var[0] + 2*var[1] + 4*var[2] + 2*var[3] + var[4])/6 + noise_aRK(noise);}
/* Declaration and Initialization of parameters */
/* Membrane time in ms */
const double tau_p = 30;
const double tau_i = 30;
/* Maximum firing rate in ms^-1 */
const double Qp_max = 30.E-3;
const double Qi_max = 60.E-3;
/* Sigmoid threshold in mV */
const double theta_p = -58.5;
const double theta_i = -58.5;
/* Sigmoid gain in mV */
const double sigma_p = 4;
const double sigma_i = 6;
/* Scaling parameter for sigmoidal mapping (dimensionless) */
const double C1 = (M_PI/sqrt(3));
/* parameters of the firing adaption */
const double alpha_Na = 2; /* Sodium influx per spike in mM ms */
const double tau_Na = 1.7; /* Sodium time constant in ms */
const double R_pump = 0.09; /* Na-K pump constant in mM/ms */
const double Na_eq = 9.5; /* Na-eq concentration in mM */
/* PSP rise time in ms^-1 */
const double gamma_e = 70E-3;
const double gamma_g = 58.6E-3;
/* Axonal flux time constant */
const double nu = 120E-3;
/* Leak weight in aU*/
const double g_L = 1.;
/* Synaptic weight in ms */
const double g_AMPA = 1.;
const double g_GABA = 1.;
/* Conductivity */
/* KNa in mS/cm^2 */
const double g_KNa = 1.33;
/* Reversal potentials in mV */
/* Synaptic */
const double E_AMPA = 0;
const double E_GABA = -70;
/* Leak */
const double E_L_p = -64;
const double E_L_i = -64;
/* Potassium */
const double E_K = -100;
/* Noise parameters in ms^-1 */
const double mphi = 0E-3;
const double dphi = 20E-1;
double input = 0.0;
/* Connectivities (dimensionless) */
const double N_pp = 115;
const double N_ip = 72;
const double N_pi = 90;
const double N_ii = 90;
const double N_pt = 2.5;
const double N_it = 2.5;
/* Pointer to thalamic column */
Thalamic_Column* Thalamus;
/* Parameters for SRK4 iteration */
const std::vector<double> A = {0.5, 0.5, 1.0, 1.0};
const std::vector<double> B = {0.75, 0.75, 0.0, 0.0};
/* Random number generators */
std::vector<randomStreamNormal> MTRands;
/* Container for noise */
std::vector<double> Rand_vars;
/* Population variables */
std::vector<double> Vp = init(E_L_p), /* excitatory membrane voltage */
Vi = init(E_L_i), /* inhibitory membrane voltage */
Na = init(Na_eq), /* Na concentration */
s_ep= init(0.0), /* PostSP from excitatory to excitatory population */
s_ei= init(0.0), /* PostSP from excitatory to inhibitory population */
s_gp= init(0.0), /* PostSP from inhibitory to excitatory population */
s_gi= init(0.0), /* PostSP from inhibitory to inhibitory population */
y = init(0.0), /* axonal flux */
x_ep= init(0.0), /* derivative of s_ep */
x_ei= init(0.0), /* derivative of s_ei */
x_gp= init(0.0), /* derivative of s_gp */
x_gi= init(0.0), /* derivative of s_gi */
x = init(0.0); /* derivative of y */
/* Data storage access */
friend void get_data (int, Cortical_Column&, Thalamic_Column&, std::vector<double*>&);
/* Stimulation protocol access */
friend class Stim;
friend class Thalamic_Column;
};