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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: 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 thalamic module */ | |
| /******************************************************************************/ | |
| #pragma once | |
| #include <cmath> | |
| #include <vector> | |
| #include "Random_Stream.h" | |
| class Thalamic_Column { | |
| public: | |
| Thalamic_Column(double* Par) | |
| : g_LK (Par[0]), g_h (Par[1]) {set_RNG();} | |
| /* Iterate one time step through SRK4 */ | |
| void iterate_ODE (void); | |
| private: | |
| /* Declaration of private functions */ | |
| /* Initialize the RNGs */ | |
| void set_RNG (void); | |
| /* Firing rates */ | |
| double get_Qt (int) const; | |
| double get_Qr (int) const; | |
| /* Synaptic currents */ | |
| double I_et (int) const; | |
| double I_gt (int) const; | |
| double I_er (int) const; | |
| double I_gr (int) const; | |
| /* Activation functions */ | |
| double m_inf_T_t (int) const; | |
| double m_inf_T_r (int) const; | |
| double m_inf_h (int) const; | |
| double tau_m_h (int) const; | |
| double P_h (int) const; | |
| double act_h (void)const; | |
| /* Deactivation functions */ | |
| double h_inf_T_t (int) const; | |
| double h_inf_T_r (int) const; | |
| double tau_h_T_t (int) const; | |
| double tau_h_T_r (int) const; | |
| /* Currents */ | |
| double I_L_t (int) const; | |
| double I_L_r (int) const; | |
| double I_LK_t (int) const; | |
| double I_LK_r (int) const; | |
| double I_T_t (int) const; | |
| double I_T_r (int) const; | |
| double I_h (int) const; | |
| /* Noise functions */ | |
| double noise_xRK (int,int) const; | |
| double noise_aRK (int) const; | |
| /* ODE functions */ | |
| void set_RK (int); | |
| void add_RK (void); | |
| /* 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_t = 20.; | |
| const double tau_r = 20.; | |
| /* Maximum firing rate in ms^-1 */ | |
| const double Qt_max = 400.E-3; | |
| const double Qr_max = 400.E-3; | |
| /* Sigmoid threshold in mV */ | |
| const double theta_t = -58.5; | |
| const double theta_r = -58.5; | |
| /* Sigmoid gain in mV */ | |
| const double sigma_t = 6.; | |
| const double sigma_r = 6.; | |
| /* Scaling parameter for sigmoidal mapping (dimensionless) */ | |
| const double C1 = (M_PI/sqrt(3)); | |
| /* PSP rise time in ms^-1 */ | |
| const double gamma_e = 70E-3; | |
| const double gamma_g = 100E-3; | |
| /* Membrane capacitance in muF/cm^2 */ | |
| const double C_m = 1.; | |
| /* Weights/ conductivities */ | |
| /* Leak in aU */ | |
| const double g_L = 1.; | |
| /* Synaptic conductivity in ms */ | |
| const double g_AMPA = 1.; | |
| const double g_GABA = 1.; | |
| /* Potassium leak current in mS/m^2 */ | |
| double g_LK = 0.033; | |
| /* T current in mS/m^2 */ | |
| const double g_T_t = 3; | |
| const double g_T_r = 2.3; | |
| /* h current in mS/m^2 */ | |
| double g_h = 0.02; | |
| /* Reversal potentials in mV */ | |
| /* Synaptic */ | |
| const double E_AMPA = 0.; | |
| const double E_GABA = -70.; | |
| /* Leak */ | |
| const double E_L_t = -70.; | |
| const double E_L_r = -70.; | |
| /* Potassium */ | |
| const double E_K = -100.; | |
| /* I_T current */ | |
| const double E_Ca = 120.; | |
| /* I_h current */ | |
| const double E_h = -40.; | |
| /* Calcium parameters */ | |
| const double alpha_Ca = -51.8E-6; /* influx per spike in nmol */ | |
| const double tau_Ca = 10.; /* calcium time constant in ms */ | |
| const double Ca_0 = 2.4E-4; /* resting concentration */ | |
| /* I_h activation parameters */ | |
| const double k1 = 2.5E7; | |
| const double k2 = 4E-4; | |
| const double k3 = 1E-1; | |
| const double k4 = 1E-3; | |
| const double n_P = 4.; | |
| const double g_inc = 2.; | |
| /* Noise parameters in ms^-1 */ | |
| const double mphi = 0E-3; | |
| const double dphi = 0E-3; | |
| double input = 0.0; | |
| /* Connectivities (dimensionless) */ | |
| const double N_tr = 3.; | |
| const double N_rt = 5.; | |
| const double N_rr = 25.; | |
| /* 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> Vt = init(E_L_t), /* TC membrane voltage */ | |
| Vr = init(E_L_r), /* RE membrane voltage */ | |
| Ca = init(Ca_0), /* Calcium concentration of TC population */ | |
| s_et = init(0.0), /* PostSP from TC population to TC population */ | |
| s_er = init(0.0), /* PostSP from TC population to RE population */ | |
| s_gt = init(0.0), /* PostSP from RE population to TC population */ | |
| s_gr = init(0.0), /* PostSP from RE population to RE population */ | |
| x_et = init(0.0), /* derivative of s_et */ | |
| x_er = init(0.0), /* derivative of s_er */ | |
| x_gt = init(0.0), /* derivative of s_gt */ | |
| x_gr = init(0.0), /* derivative of s_gr */ | |
| h_T_t = init(0.0), /* inactivation of T channel */ | |
| h_T_r = init(0.0), /* inactivation of T channel */ | |
| m_h = init(0.0), /* activation of h channel */ | |
| m_h2 = init(0.0); /* activation of h channel bound with protein */ | |
| /* Data storage access */ | |
| friend void get_data (unsigned, Thalamic_Column&, std::vector<double*>&); | |
| }; | |
| /****************************************************************************************************/ | |
| /* end */ | |
| /****************************************************************************************************/ |