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More tuning, changed Ca0 to 2.4. alpha_Ca to 51.8 

Signed-off-by: Schellenberger <schellenberger@inb.uni-luebeck.de>
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1 parent 3495bac commit b9603ae6fa3bf2ba2c923c8cb48bf0f4afb39ea0 @miscco committed Nov 7, 2014
Unified Split
Showing with 55 additions and 50 deletions.
  1. +1 −1 Cortical_Column.h
  2. +30 −28 Plots.m
  3. +1 −1 Stimulation.h
  4. +13 −10 Thalamic_Column.cpp
  5. +10 −10 Thalamic_Column.h
View
2 Cortical_Column.h
@@ -141,7 +141,7 @@ class Cortical_Column {
/* parameters of the firing adaption */
const double alpha_Na = 2; /* Sodium influx per spike in mM ms */
- const double tau_Na = 1.5; /* Sodium time constant in 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 */
View
58 Plots.m
@@ -1,50 +1,50 @@
% mex command is given by:
-% mex CXXFLAGS="\$CXXFLAGS -std=c++11" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp
+% mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp
function Plots(type)
if nargin == 0
- type = 1;
+ type = 2;
end
if type == 1
Param_Cortex = [4.7; % sigma_e
- 1.33; % g_KNa
+ 1.35; % g_KNa
120E-3]; % dphi
- Param_Thalamus = [0.048; % g_h
- 0.0245; % g_LK_t
- 0.0245]; % g_LK_r
+ Param_Thalamus = [0.037; % g_h
+ 0.024; % g_LK_t
+ 0.024]; % g_LK_r
else
- Param_Cortex = [6.05; % sigma_e
+ Param_Cortex = [6.; % sigma_e
2.1; % g_KNa
120E-3]; % dphi
- Param_Thalamus = [0.052; % g_h
- 0.02; % g_LK_t
- 0.02]; % g_LK_r
+ Param_Thalamus = [0.055; % g_h
+ 0.024; % g_LK_t
+ 0.024]; % g_LK_r
end
-Connectivity = [ 3; % N_et
- 3; % N_er
+Connectivity = [ 4; % N_et
+ 4; % N_er
5; % N_te
- 10]; % N_ti
+ 8]; % N_ti
% stimulation parameters
% first number is the mode of stimulation
% 0 == none
% 1 == semi-periodic
% 2 == phase dependend
-var_stim = [ 0; % mode of stimulation
- 50; % strength of the stimulus in Hz (spikes per second)
- 120; % duration of the stimulus in ms
+var_stim = [ 2; % mode of stimulation
+ 80; % strength of the stimulus in Hz (spikes per second)
+ 150; % duration of the stimulus in ms
5; % time between stimulation events in s (ISI)
0; % range of ISI in s [ISI-range,ISI+range]
- 1; % Number of stimuli per event
- 950; % time between stimuli within a event in ms
- 5]; % time until stimuli after minimum in ms
+ 3; % Number of stimuli per event
+ 1050; % time between stimuli within a event in ms
+ 450]; % time until stimuli after minimum in ms
T = 30; % duration of the simulation
@@ -58,28 +58,30 @@ function Plots(type)
title('Pyramidal membrane voltage'),
xlabel('Time in s'),
ylabel('V_{e} in mV')
-ylim([-80, -40])
+xlim([0,30]);
+ylim([-80, -40]);
% vertical line for markers
for i=1:var_stim(6)
- hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'), 'color', 'black', 'LineStyle', ':');
+ hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'),'xdata', get(gca,'xlim'), 'color', 'black', 'LineStyle', ':');
changedependvar(hx,'x');
end
subplot(212), plot(timeaxis,Vt)
title('Thalamic relay membrane voltage'),
xlabel('Time in s'),
ylabel('V_{t} in mV')
+xlim([0,30]);
ylim([-70,-35]);
% vertical line for markers
for i=1:var_stim(6)
- hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'), 'color', 'black', 'LineStyle', ':');
+ hx = graph2d.constantline(Marker_Stim/1E2+(i-1)*var_stim(7)/1E3,'ydata', get(gca,'ylim'),'xdata', get(gca,'xlim'), 'color', 'black', 'LineStyle', ':');
changedependvar(hx,'x');
end
-[Pxx,f] = pwelch(Ve-mean(Ve),hamming(5*L/T), 2*L/T, [], L/T);
-n = find(f<=30, 1, 'last' );
-
-figure(2)
-plot(f(1:n),log(Pxx(1:n)))
-title('Powerspectrum with pwelch'), xlabel('frequency in Hz'), ylabel('Power (log)')
+% [Pxx,f] = pwelch(Ve-mean(Ve),hamming(5*L/T), 2*L/T, [], L/T);
+% n = find(f<=30, 1, 'last' );
+%
+% figure(2)
+% plot(f(1:n),log(Pxx(1:n)))
+% title('Powerspectrum with pwelch'), xlabel('frequency in Hz'), ylabel('Power (log)')
%save('Timeseries', 'Ve', 'Vt');
end
View
2 Stimulation.h
@@ -89,7 +89,7 @@ class Stim {
int time_between_stimuli = 1050E1;
/* Threshold for phase dependent stimulation */
- double threshold = -72;
+ double threshold = -68.5;
/* Internal variables */
/* Simulation on for TRUE and off for FALSE */
View
23 Thalamic_Column.cpp
@@ -160,17 +160,22 @@ double Thalamic_Column::m_inf_h (int N) const{
return h;
}
-/* Activation time for slow components in TC population*/
+/* Activation time for slow components in TC population after Chen2012 */
double Thalamic_Column::tau_m_h (int N) const{
_SWITCH((Vt))
- /* Destexhe 1993 */
- //double tau = 1. / (exp(-14.59 - 0.086 * var_Vt) + exp(-1.87 + 0.07 * var_Vt));
/* Bazhenov1998 */
- double tau = (5.3 + 267/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
+ //double tau = (5.3 + 267/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
/* Chen2012 */
- //double tau = (20 +1000/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
+ double tau = (20 + 1000/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
return tau;
}
+
+/* Instantaneous calcium binding onto messenger protein after Chen2012 */
+double Thalamic_Column::P_h (int N) const{
+ _SWITCH((Ca))
+ double P_h = k1 * pow(var_Ca, n_P)/(k1*pow(var_Ca, n_P)+k2);
+ return P_h;
+}
/****************************************************************************************************/
/* end */
/****************************************************************************************************/
@@ -254,15 +259,14 @@ void Thalamic_Column::set_RK (int N) {
_SWITCH((Ca)
(Phi_tt)(Phi_tr)(Phi_rt)(Phi_rr)(phi)
(x_tt) (x_tr) (x_rt) (x_rr) (y)
- (h_T_t) (h_T_r) (m_h) (m_h2) (P_h))
+ (h_T_t) (h_T_r) (m_h) (m_h2))
Vt [N] = dt*(-(I_L_t(N) + I_et(N) + I_it(N))/tau_t - (I_LK_t(N) + I_T_t(N) + I_h(N)));
Vr [N] = dt*(-(I_L_r(N) + I_er(N) + I_ir(N))/tau_r - (I_LK_r(N) + I_T_r(N)));
Ca [N] = dt*(alpha_Ca * I_T_t(N) - (var_Ca - Ca_0)/tau_Ca);
h_T_t [N] = dt*(h_inf_T_t(N) - var_h_T_t)/tau_h_T_t(N);
h_T_r [N] = dt*(h_inf_T_r(N) - var_h_T_r)/tau_h_T_r(N);
- m_h [N] = dt*((m_inf_h(N) * (1 - var_m_h2) - var_m_h)/tau_m_h(N) - k3 * var_P_h * var_m_h + k4 * var_m_h2);
- m_h2 [N] = dt*(k3 * k1 * pow(var_Ca, n_P)/(k1*pow(var_Ca, n_P)+k2) * var_m_h - k4 * var_m_h2);
- P_h [N] = dt*(k1 * pow(var_Ca, n_P) * (1 - var_P_h) - k2 * var_P_h);
+ m_h [N] = dt*((m_inf_h(N) * (1 - var_m_h2) - var_m_h)/tau_m_h(N) - k3 * P_h(N) * var_m_h + k4 * var_m_h2);
+ m_h2 [N] = dt*(k3 * P_h(N) * var_m_h - k4 * var_m_h2);
Phi_tt [N] = dt*(var_x_tt);
Phi_tr [N] = dt*(var_x_tr);
Phi_rt [N] = dt*(var_x_rt);
@@ -301,7 +305,6 @@ void Thalamic_Column::add_RK(void) {
h_T_r [0] += (h_T_r [1] + h_T_r [2] * 2 + h_T_r [3] * 2 + h_T_r [4])/6;
m_h [0] += (m_h [1] + m_h [2] * 2 + m_h [3] * 2 + m_h [4])/6;
m_h2 [0] += (m_h2 [1] + m_h2 [2] * 2 + m_h2 [3] * 2 + m_h2 [4])/6;
- P_h [0] += (P_h [1] + P_h [2] * 2 + P_h [3] * 2 + P_h [4])/6;
/* Generate noise for the next iteration */
for (unsigned i=0; i<Rand_vars.size(); ++i) {
View
20 Thalamic_Column.h
@@ -57,7 +57,7 @@ class Thalamic_Column {
/* Constructor for simulation */
Thalamic_Column(double* Param, double* Con)
- : g_h (Param[0]), g_LK_t (Param[1]), g_LK_r (Param[2]),
+ : g_LK_t (Param[1]), g_LK_r (Param[2]), g_h (Param[0]),
N_et (Con[0]), N_er (Con[1])
{set_RNG();}
@@ -88,6 +88,7 @@ class Thalamic_Column {
double m_inf_T_r (int) const;
double m_inf_h (int) const;
double tau_m_h (int) const;
+ double P_h (int) const;
/* Deactivation functions */
double h_inf_T_t (int) const;
@@ -132,8 +133,7 @@ class Thalamic_Column {
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 */
- P_h = _INIT(0.0); /* fraction of protein bound with calcium */
+ m_h2 = _INIT(0.0); /* activation of h channel bound with protein */
/* Random number generators */
vector<GEN> MTRands;
@@ -174,15 +174,15 @@ class Thalamic_Column {
const double g_L_r = 1;
/* Potassium leak current */
- const double g_LK_t = 0.024;
- const double g_LK_r = 0.024;
+ const double g_LK_t = 0.02;
+ const double g_LK_r = 0.02;
/* T current */
const double g_T_t = 3;
const double g_T_r = 2.3;
/* h current */
- const double g_h = 0.048;
+ const double g_h = 0.07;
/* Reversal potentials in mV */
/* Synaptic */
@@ -203,9 +203,9 @@ class Thalamic_Column {
const double E_h = -40;
/* Calcium parameters */
- const double alpha_Ca = -50E-6; /* influx per spike in nmol */
+ 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 = 2E-4; /* resting concentration */
+ const double Ca_0 = 2.4E-4; /* resting concentration */
/* I_h activation parameters */
const double k1 = 2.5E7;
@@ -223,8 +223,8 @@ class Thalamic_Column {
/* Connectivities (dimensionless) */
const double N_tr = 3;
- const double N_rt = 4;
- const double N_rr = 22;
+ const double N_rt = 5;
+ const double N_rr = 16;
const double N_et = 5;
const double N_er = 5;

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