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More Parameter tuning. Prep work for instant calcium binding on P_h 

Signed-off-by: Schellenberger <schellenberger@inb.uni-luebeck.de>
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1 parent 1ea3c06 commit 781c2a1c8954d8be42c9f15e1800ac81621df565 @miscco committed Oct 30, 2014
Unified Split
Showing with 43 additions and 27 deletions.
  1. +13 −3 .cproject
  2. +8 −7 Plots.m
  3. +9 −4 Thalamic_Column.cpp
  4. +13 −13 Thalamic_Column.h
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16 .cproject
@@ -23,7 +23,7 @@
<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug.2059871958" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.exe.debug">
<option id="gnu.cpp.compiler.exe.debug.option.optimization.level.349862431" name="Optimization Level" superClass="gnu.cpp.compiler.exe.debug.option.optimization.level" value="gnu.cpp.compiler.optimization.level.most" valueType="enumerated"/>
<option id="gnu.cpp.compiler.exe.debug.option.debugging.level.1666482058" name="Debug Level" superClass="gnu.cpp.compiler.exe.debug.option.debugging.level" value="gnu.cpp.compiler.debugging.level.max" valueType="enumerated"/>
- <option id="gnu.cpp.compiler.option.other.other.1199345592" name="Other flags" superClass="gnu.cpp.compiler.option.other.other" value="-std=c++0x -c -fmessage-length=0" valueType="string"/>
+ <option id="gnu.cpp.compiler.option.other.other.1199345592" name="Other flags" superClass="gnu.cpp.compiler.option.other.other" value="-std=c++11 -c -fmessage-length=0" valueType="string"/>
<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.426453201" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
</tool>
<tool id="cdt.managedbuild.tool.gnu.c.compiler.exe.debug.1967098844" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.exe.debug">
@@ -33,7 +33,7 @@
</tool>
<tool id="cdt.managedbuild.tool.gnu.c.linker.exe.debug.1785383603" name="GCC C Linker" superClass="cdt.managedbuild.tool.gnu.c.linker.exe.debug"/>
<tool id="cdt.managedbuild.tool.gnu.cpp.linker.exe.debug.782864723" name="GCC C++ Linker" superClass="cdt.managedbuild.tool.gnu.cpp.linker.exe.debug">
- <option id="gnu.cpp.link.option.flags.712983263" name="Linker flags" superClass="gnu.cpp.link.option.flags" value="-std=c++0x " valueType="string"/>
+ <option id="gnu.cpp.link.option.flags.712983263" name="Linker flags" superClass="gnu.cpp.link.option.flags" value="-std=c++11 " valueType="string"/>
<option id="gnu.cpp.link.option.libs.1849787926" name="Libraries (-l)" superClass="gnu.cpp.link.option.libs"/>
<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.1171029032" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">
<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
@@ -172,6 +172,16 @@
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC"/>
</scannerConfigBuildInfo>
</storageModule>
- <storageModule moduleId="refreshScope"/>
+ <storageModule moduleId="refreshScope" versionNumber="2">
+ <configuration configurationName="Release">
+ <resource resourceType="PROJECT" workspacePath="/T_model"/>
+ </configuration>
+ <configuration configurationName="MATLAB">
+ <resource resourceType="PROJECT" workspacePath="/T_model"/>
+ </configuration>
+ <configuration configurationName="Debug">
+ <resource resourceType="PROJECT" workspacePath="/T_model"/>
+ </configuration>
+ </storageModule>
<storageModule moduleId="org.eclipse.cdt.core.LanguageSettingsProviders"/>
</cproject>
View
15 Plots.m
@@ -4,10 +4,11 @@
function Plots(T)
if nargin == 0
- Con = [ 4; % sigma
- 6; % N_tr
- 5; % N_rt
- 100]; % N_rr
+ Con = [ 0.07; % g_h
+ 0.02; % g_LK_t
+ 3; % N_tr
+ 3; % N_rt
+ 30]; % N_rr
% stimulation parameters
@@ -18,9 +19,9 @@ function Plots(T)
% 3 == phase dependend down state
var_stim = [ 0; % mode of stimulation
- 200; % strength of the stimulus in Hz (spikes per second)
- 100; % duration of the stimulus in ms
- 6; % time between stimuli in s
+ 25; % strength of the stimulus in Hz (spikes per second)
+ 70; % duration of the stimulus in ms
+ 5; % time between stimuli in s
1]; % time until stimuli after min in ms
T = 30; % duration of the simulation
end
View
13 Thalamic_Column.cpp
@@ -160,10 +160,15 @@ double Thalamic_Column::m_inf_h (int N) const{
return h;
}
-/* Activation time for slow components in TC population after Destexhe 1993 */
+/* Activation time for slow components in TC population*/
double Thalamic_Column::tau_m_h (int N) const{
_SWITCH((Vt))
- double tau = 1. / (exp(-14.59 - 0.086 * var_Vt) + exp(-1.87 + 0.07 * var_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)));
+ /* Chen2012 */
+ //double tau = (20 +1000/(exp((var_Vt + 71.5)/14.2) + exp(-(var_Vt + 89)/11.6)));
return tau;
}
/****************************************************************************************************/
@@ -256,8 +261,8 @@ void Thalamic_Column::set_RK (int 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 * var_P_h * var_m_h - k4 * var_m_h2);
+ m_h [N] = dt*((m_inf_h(N) * (1 - var_m_h2) - var_m_h)/tau_m_h(N) - k3 * k1 * pow(var_Ca, n_P)/(k1*pow(var_Ca, n_P)+k2) * 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);
Phi_tt [N] = dt*(var_x_tt);
Phi_tr [N] = dt*(var_x_tr);
View
26 Thalamic_Column.h
@@ -53,9 +53,9 @@ class Thalamic_Column {
{set_RNG();}
/* Constructor for simulation */
- Thalamic_Column(double* Con)
- : sigma_t (Con[0]), sigma_r (Con[0]),
- N_tr (Con[1]), N_rt (Con[2]), N_rr (Con[3])
+ Thalamic_Column(double* Par)
+ : g_h (Par[0]), g_LK_t (Par[1]), g_LK_r (Par[1]),
+ N_tr (Par[2]), N_rt (Par[3]), N_rr (Par[4])
{set_RNG();}
/* Set strength of input */
@@ -145,8 +145,8 @@ class Thalamic_Column {
const double theta_r = -58.6;
/* Sigmoid gain in mV */
- const double sigma_t = 4;
- const double sigma_r = 4;
+ const double sigma_t = 6;
+ const double sigma_r = 6;
/* Scaling parameter for sigmoidal mapping (dimensionless) */
const double C1 = (3.14159265/sqrt(3));
@@ -161,15 +161,15 @@ class Thalamic_Column {
const double g_L_r = 1;
/* Potassium leak current */
- const double g_LK_t = 0.02;
- const double g_LK_r = 0.02;
+ const double g_LK_t = 0.017;
+ const double g_LK_r = 0.01;
/* T current */
const double g_T_t = 3;
- const double g_T_r = 2;
+ const double g_T_r = 2.3;
/* h current */
- const double g_h = 0.08;
+ const double g_h = 0.06;
/* Reversal potentials in mV */
/* Synaptic */
@@ -187,7 +187,7 @@ class Thalamic_Column {
const double E_Ca = 120;
/* I_h current */
- const double E_h = -43;
+ const double E_h = -40;
/* Calcium parameters */
const double alpha_Ca = -50E-6; /* influx per spike in nmol */
@@ -196,7 +196,7 @@ class Thalamic_Column {
/* I_h activation parameters */
const double k1 = 2.5E7;
- const double k2 = 5E-4;
+ const double k2 = 4E-4;
const double k3 = 1E-1;
const double k4 = 1E-3;
const double n_P = 4;
@@ -209,8 +209,8 @@ class Thalamic_Column {
/* Connectivities (dimensionless) */
const double N_tr = 6;
- const double N_rt = 5;
- const double N_rr = 100;
+ const double N_rt = 6;
+ const double N_rr = 20;
friend class Stim;
};

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