From 781c2a1c8954d8be42c9f15e1800ac81621df565 Mon Sep 17 00:00:00 2001
From: Schellenberger <schellenberger@inb.uni-luebeck.de>
Date: Thu, 30 Oct 2014 11:06:23 +0100
Subject: [PATCH] More Parameter tuning. Prep work for instant calcium binding
 on P_h

Signed-off-by: Schellenberger <schellenberger@inb.uni-luebeck.de>
---
 .cproject           | 16 +++++++++++++---
 Plots.m             | 15 ++++++++-------
 Thalamic_Column.cpp | 13 +++++++++----
 Thalamic_Column.h   | 26 +++++++++++++-------------
 4 files changed, 43 insertions(+), 27 deletions(-)

diff --git a/.cproject b/.cproject
index 1fee099..dc875a9 100644
--- a/.cproject
+++ b/.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>
diff --git a/Plots.m b/Plots.m
index af7c3b9..12a4711 100644
--- a/Plots.m
+++ b/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
diff --git a/Thalamic_Column.cpp b/Thalamic_Column.cpp
index 1ca2007..7116bc3 100644
--- a/Thalamic_Column.cpp
+++ b/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);
diff --git a/Thalamic_Column.h b/Thalamic_Column.h
index 02b2371..53adebb 100644
--- a/Thalamic_Column.h
+++ b/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;
 };