added GenericSynapse

c++/synapses/nadim98/GenericSynapse.hpp

@@ -0,0 +1,144 @@
+// GENERICSYNAPSE Synapse 
+#ifndef GENERICSYNAPSE
+#define GENERICSYNAPSE
+#include "synapse.hpp"
+
+class GenericSynapse: public synapse {
+
+public:
+
+
+    double k;
+    double Vk;
+    double tau3;
+    double tau4;
+    double lambda;
+    double Vlambda;
+
+
+    // specify parameters + initial conditions 
+    GenericSynapse(double gmax_, double s_, double k_, double Vk_, double tau3_, double tau4_, double lambda_, double Vlambda_)
+    {
+        gmax = gmax_;
+        k = k_;
+        Vk = Vk_;
+        tau3 = tau3_;
+        tau4 = tau4_;
+        lambda = lambda_;
+        Vlambda = Vlambda_;
+
+        // defaults
+        if (isnan (s)) { s = 0; }
+        if (isnan (gmax)) { gmax = 0; }
+        is_electrical = false;
+
+    }
+
+    void integrate(void);
+    void integrateMS(int, double, double);
+    void checkSolvers(int);
+
+    double s_inf(double);
+    double tau_s(double);
+    double sdot(double, double);
+
+    void connect(compartment *pcomp1_, compartment *pcomp2_);
+    int getFullState(double*, int);
+    int getFullStateSize(void);
+};
+
+int GenericSynapse::getFullStateSize() {
+    return 2; 
+}
+
+
+double GenericSynapse::s_inf(double V_pre) {
+    return 1.0/(1.0+exp((V_pre - Vk)*k));
+}
+
+double GenericSynapse::tau_s(double V_pre) {
+    return tau3 + tau4/(1 + exp(lambda*(V_pre - Vlambda)));
+}
+
+double GenericSynapse::sdot(double V_pre, double s_) {
+    return (s_inf(V_pre) - s_)/tau_s(V_pre);
+}
+
+void GenericSynapse::integrate(void) {   
+    // figure out the voltage of the pre-synaptic neuron
+    double V_pre = pre_syn->V;
+    double sinf = s_inf(V_pre);
+
+    // integrate using exponential Euler
+    s = sinf + (s - sinf)*exp(-dt/tau_s(sinf));
+
+    g = gmax*s;
+
+}
+
+void GenericSynapse::integrateMS(int k, double V, double Ca) {
+
+    double V_pre;
+
+    if (k == 0) {
+        V_pre = pre_syn->V_prev;
+        k_s[0] = dt*(sdot(V_pre, s));
+
+    } else if (k == 1) {
+        V_pre = pre_syn->V_prev + pre_syn->k_V[0]/2;
+        k_s[1] = dt*(sdot(V_pre, s + k_s[0]/2));
+
+
+    } else if (k == 2) {
+        V_pre = pre_syn->V_prev + pre_syn->k_V[1]/2;
+        k_s[2] = dt*(sdot(V_pre, s + k_s[1]/2));
+
+
+    } else if (k == 3) {
+        V_pre = pre_syn->V_prev + pre_syn->k_V[2];
+        k_s[3] = dt*(sdot(V_pre, s + k_s[2]));
+
+
+    } else {
+        // last step
+        s = s + (k_s[0] + 2*k_s[1] + 2*k_s[2] + k_s[3])/6;
+
+        if (s < 0) {s = 0;}
+        if (s > 1) {s = 1;}
+    }
+
+}
+
+void GenericSynapse::checkSolvers(int k){
+    if (k == 0) {
+        return;
+    } else if (k == 4) {
+        return;
+    }
+    mexErrMsgTxt("[GenericSynapse] Unsupported solver order\n");
+}
+
+int GenericSynapse::getFullState(double *syn_state, int idx) {
+    // give it the current synapse variable
+    syn_state[idx] = s;
+
+    idx++;
+
+    // also return the current from this synapse
+    syn_state[idx] = gmax*s*(post_syn->V - E);
+    idx++;
+    return idx;
+}
+
+void GenericSynapse::connect(compartment *pcomp1_, compartment *pcomp2_)  {
+    pre_syn = pcomp1_; 
+    post_syn = pcomp2_; 
+
+    // tell the post-synaptic cell that we're connecting to it
+    post_syn->addSynapse(this);
+}
+
+
+
+
+#endif

examples/integer_coupling.m

@@ -1,11 +1,19 @@
 
+close all
+
 x = xolotl;
 
 
 % make Int1
 x.add('compartment','Int1','radius',.025,'len',.05);
 x.add('compartment','Int1Neurite','len',1,'radius',1.25);
 x.add('compartment','Int1Axon','len',1,'radius',1.25);
+x.connect('Int1','Int1Neurite','Axial')
+x.connect('Int1Neurite','Int1','Axial')
+x.connect('Int1Axon','Int1Neurite','Axial')
+x.connect('Int1Neurite','Int1Axon','Axial')
+
+
 
 % add channels to Int1 
 x.Int1Axon.add('nadim98/GenericChannel','NaV','gbar',35,'E',45,'p',3,'km',-.08,'Vkm',-26,'lm',0,'Vlm',0,'tau1m',1,'tau2m',0,'q',1,'kh',.13,'Vkh',-38,'lh',-.12,'Vlh',-67,'tau1h',0,'tau2h',5);
@@ -16,6 +24,25 @@
 x.Int1.add('Leak','gbar',1,'E',-40)
 x.Int1Neurite.add('Leak','gbar',1,'E',-40)
 
+
+
+
+% make LG
+x.add('compartment','LG','radius',.025,'len',.05);
+x.add('compartment','LGNeurite','len',1,'radius',1.25);
+x.add('compartment','LGAxon','len',1,'radius',1.25);
+x.connect('LG','LGNeurite','Axial')
+x.connect('LGNeurite','LG','Axial')
+x.connect('LGAxon','LGNeurite','Axial')
+x.connect('LGNeurite','LGAxon','Axial')
+
+x.LGAxon.add('nadim98/GenericChannel','NaV','gbar',35,'E',45,'p',3,'km',-.08,'Vkm',-21,'lm',0,'Vlm',0,'tau1m',1,'tau2m',0,'q',1,'kh',.13,'Vkh',-33,'lh',-.12,'Vlh',-62,'tau1h',0,'tau2h',5);
+x.LGAxon.add('nadim98/GenericChannel','Kd','gbar',40,'E',-80,'p',4,'km',-.045,'Vkm',-33,'lm',-.065,'Vlm',-5,'tau1m',4,'tau2m',100,'q',0,'kh',0,'Vkh',0,'lh',0,'Vlh',0,'tau1h',0,'tau2h',0);
+
+x.show(x.LGAxon)
+
+x.plot('LGAxon')
+
 return
 
 %Add conductances