void Conductance::update(DefaultGUIModel::update_flags_t flag) {
switch(flag) {
case MODIFY:
Cm = getParameter("Cm").toDouble();
G_Na_max = getParameter("G_Na_max").toDouble();
E_Na = getParameter("E_Na").toDouble();
G_K_max = getParameter("G_K_max").toDouble();
E_K = getParameter("E_K").toDouble();
G_L = getParameter("G_L").toDouble();
E_L = getParameter("E_L").toDouble();
R_L_MC = getParameter("R_L_MC").toDouble();
Iapp_offset = getParameter("Iapp_offset").toDouble();
rate = getParameter("rate").toDouble();
steps = static_cast<int>(ceil(period*rate));
m = m_inf(Vm);
h = h_inf(Vm);
n = n_inf(Vm);
break;
case PERIOD:
period = RT::System::getInstance()->getPeriod()*1e-9; // ms
steps = static_cast<int>(ceil(period*rate));
break;
case PAUSE:
output(0) = 0.0;
break;
case UNPAUSE:
break;
default:
break;
}
}
void
Neuron::update(DefaultGUIModel::update_flags_t flag)
{
if (flag == MODIFY)
{
V0 = getParameter("V0").toDouble();
Cm = getParameter("Cm").toDouble();
G_Na_max = getParameter("G_Na_max").toDouble();
E_Na = getParameter("E_Na").toDouble();
G_K_max = getParameter("G_K_max").toDouble();
E_K = getParameter("E_K").toDouble();
G_L = getParameter("G_L").toDouble();
E_L = getParameter("E_L").toDouble();
Iapp_offset = getParameter("Iapp_offset").toDouble();
rate = getParameter("rate").toDouble();
steps = static_cast<int> (ceil(period * rate / 1000.0));
V = V0;
m = m_inf(V0);
h = h_inf(V0);
n = n_inf(V0);
}
else if (flag == PERIOD)
{
period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
steps = static_cast<int> (ceil(period * rate / 1000.0));
}
}
void
Neuron::derivs(double *y, double *dydt)
{
dV = (Iapp - G_Na * (V - E_Na) - G_K * (V - E_K) - G_L * (V - E_L)) / Cm;
dm = (m_inf(V) - m) / tau_m(V);
dh = (h_inf(V) - h) / tau_h(V);
dn = (n_inf(V) - n) / tau_n(V);
}
void ConnorStevens::derivs(double *y, double *dydt) {
dV = (Iapp - input(0) * 1e6 - G_Na * (V - E_Na) - G_K * (V - E_K) - G_L * (V - E_L) - G_A * (V - E_A)) * 1000 / Cm;
dm = (m_inf(V) - m) / tau_m(V);
dh = (h_inf(V) - h) / tau_h(V);
dn = (n_inf(V) - n) / tau_n(V);
da = (a_inf(V) - a) / tau_a(V);
db = (b_inf(V) - b) / tau_b(V);
IKA = G_A * (V - E_A) * 1e-6 ; // A
}
void ConnorStevens::update(DefaultGUIModel::update_flags_t flag) {
switch (flag) {
case INIT:
setParameter("V0 (mV)", QString::number(V0)); // initialized in mV, display in mV
setParameter("Cm (uF/cm^2)", QString::number(Cm * 100)); // initialized in uF/mm^2, display in uF/cm^2
setParameter("G_Na_max (mS/cm^2)", QString::number(G_Na_max * 100)); // initialized in mS/mm^2, display in mS/cm^2
setParameter("E_Na (mV)", QString::number(E_Na)); // initialized in mV, display in mV
setParameter("G_K_max (mS/cm^2)", QString::number(G_K_max * 100)); // initialized in mS/mm^2, display in mS/cm^2
setParameter("E_K (mV)", QString::number(E_K)); // initialized in mV, display in mV
setParameter("G_A_max (mS/cm^2)", QString::number(G_A_max * 100)); // initialized in mS/mm^2, display in mS/cm^2
setParameter("E_A (mV)", QString::number(E_A)); // initialized in mV, display in mV
setParameter("G_L (mS/cm^2)", QString::number(G_L * 100)); // initialized in mS/mm^2, display in mS/cm^2
setParameter("E_L (mV)", QString::number(E_L)); // initialized in mV, display in mV
setParameter("Iapp (uA/cm^2)", QString::number(Iapp * 100)); // initialized in uA/mm^2, display in uA/cm^2
setParameter("Rate (Hz)", rate);
setState("m", m);
setState("h", h);
setState("n", n);
setState("a", a);
setState("b", b);
setState("IKA",IKA);
setState("Time (s)", systime);
break;
case MODIFY:
V0 = getParameter("V0 (mV)").toDouble();
Cm = getParameter("Cm (uF/cm^2)").toDouble() / 100;
G_Na_max = getParameter("G_Na_max (mS/cm^2)").toDouble() / 100;
E_Na = getParameter("E_Na (mV)").toDouble();
G_K_max = getParameter("G_K_max (mS/cm^2)").toDouble() / 100;
E_K = getParameter("E_K (mV)").toDouble();
G_A_max = getParameter("G_A_max (mS/cm^2)").toDouble() / 100;
E_A = getParameter("E_A (mV)").toDouble();
G_L = getParameter("G_L (mS/cm^2)").toDouble() / 100;
E_L = getParameter("E_L (mV)").toDouble();
Iapp = getParameter("Iapp (uA/cm^2)").toDouble() / 100; // displayed in uA/cm^2, calculated in uA/mm^2
rate = getParameter("Rate (Hz)").toDouble();
steps = static_cast<int> (ceil(period * rate));
V = V0;
m = m_inf(V0);
h = h_inf(V0);
n = n_inf(V0);
a = a_inf(V0);
b = b_inf(V0);
break;
case PERIOD:
period = RT::System::getInstance()->getPeriod() * 1e-9; // time in seconds
steps = static_cast<int> (ceil(period * rate));
break;
default:
break;
}
}
void derivs_one(const double* y, double* dydt, const double* p)
{
double V=y[0], h=y[1], n=y[2], x=y[3], Ca=y[4];
double V_tilde = C_1*V+C_2, V_Ca=p[0];
dydt[0] = -g_Na*powf(m_inf(V_tilde), 3)*h*(V-V_Na) - g_Ca*x*(V-V_Ca) - (g_K*powf(n, 4)+g_K_Ca*Ca/(0.5+Ca))*(V-V_K) - g_L*(V-V_L); // dV/dt
dydt[1] = lambda*(h_inf(V_tilde)-h)/tau_h(V_tilde); // dh/dt
dydt[2] = lambda*(n_inf(V_tilde)-n)/tau_n(V_tilde); // dn/dt
dydt[3] = (x_inf(V)-x)/tau_x; // dx/dt
dydt[4] = rho * (K_c * x * (V_Ca - V) - Ca); // d[Ca2+]/dt
}
Neuron::Neuron(void) : DefaultGUIModel("Neuron", ::vars, ::num_vars) {
setWhatsThis("<p><b>Hodgkin-Huxley Neuron:</b><br>This module simulates a Hodgkin-Huxley neuron "
"in real-time. It can be used in place of a biological cell to test algorithms.</p>");
createGUI(vars, num_vars);
/*
* Initialize Parameters
*/
V0 = -65.0;
Cm = 1.0;
G_Na_max = 120.0;
E_Na = 50.0;
G_K_max = 36.0;
E_K = -77.0;
G_L = 0.3;
E_L = -54.4;
Iapp_offset = 0.0;
rate = 40000;
/*
* Initialize Variables
*/
V = V0;
m = m_inf(V0);
h = h_inf(V0);
n = n_inf(V0);
period = RT::System::getInstance()->getPeriod() * 1e-6;
steps = static_cast<int> (ceil(period / rate / 1000.0));
/*
* Initialize States
*/
setState("m", m);
setState("h", h);
setState("n", n);
/*
* Initialize GUI
*/
setParameter("V0", V0);
setParameter("Cm", Cm);
setParameter("G_Na_max", G_Na_max);
setParameter("E_Na", E_Na);
setParameter("G_K_max", G_K_max);
setParameter("E_K", E_K);
setParameter("G_L", G_L);
setParameter("E_L", E_L);
setParameter("Iapp_offset", Iapp_offset);
setParameter("rate", rate);
refresh();
// QTimer::singleShot(0, this, SLOT(resizeMe()));
resizeMe();
}
Conductance::Conductance(void)
: DefaultGUIModel("HH neuron ICs",::vars,::num_vars) {
createGUI(vars, num_vars);
/*
* Initialize Parameters
*/
Cm = 22.0;
G_Na_max = 1.0;
E_Na = 50.0;
G_K_max = 0.4;
E_K = -79.0;
G_L = 0.005;
E_L = -54.4;
R_L_MC = 0.5181;
Iapp_offset = 0.0;
rate = 40000;
/*
* Initialize Variables
*/
m = m_inf(Vm);
h = h_inf(Vm);
n = n_inf(Vm);
period = RT::System::getInstance()->getPeriod()*1e-9;
steps = static_cast<int>(ceil(period*rate));
/*
* Initialize States
*/
setState("m",m);
setState("h",h);
setState("n",n);
/*
* Initialize GUI
*/
setParameter("Cm",Cm);
setParameter("G_Na_max",G_Na_max);
setParameter("E_Na",E_Na);
setParameter("G_K_max",G_K_max);
setParameter("E_K",E_K);
setParameter("G_L",G_L);
setParameter("E_L",E_L);
setParameter("R_L_MC",R_L_MC);
setParameter("Iapp_offset",Iapp_offset);
setParameter("rate",rate);
refresh();
}
void ConnorStevens::initParameters() {
V0 = -65; // mV
Cm = 1e-2; // uF/mm^2
G_Na_max = 1.2; // mS/mm^2
G_K_max = 0.2;
G_L = 0.003;
G_A_max = 0.477;
E_Na = 55.0; // mV
E_K = -72.0;
E_L = -70.0;
E_A = -75.0;
Iapp = .2404; // 1 Hz spiking
rate = 40000;
V = V0;
m = m_inf(V0);
h = h_inf(V0);
n = n_inf(V0);
a = a_inf(V0);
b = b_inf(V0);
count = 0;
systime = 0;
period = RT::System::getInstance()->getPeriod() * 1e-9; // s
steps = static_cast<int> (ceil(period * rate)); // calculate how many integrations to perform per execution step
}
void Conductance::derivs(double *y,double *dydt) {
dm = (m_inf(Vm)-m)/tau_m(Vm);
dh = (h_inf(Vm)-h)/tau_h(Vm);
dn = (n_inf(Vm)-n)/tau_n(Vm);
}
