Figure 3.28: Response of a neuron to a current input

Chapter	System Modeling
Figure number	3.28
Figure title	Response of a neuron to a current input
GitHub URL	https://github.com/murrayrm/fbs2e-python/blob/main/example-3.19-fitzhugh nagumo.py
Requires	python-control

Figure 3.28: Response of a neuron to a current input. The current input is shown in (a) and the neuron voltage V in (b). The simulation was done using the FitzHugh–Nagumo model (Exercise 3.11).

# example-3.19-fitzhugh_nagumo.py - nerve cell dynamics
# RMM, 30 Aug 2021
#
# Figure 3.28: Response of a neuron to a current input. The current
# input is shown in (a) and the neuron voltage V in (b). The
# simulation was done using the FitzHugh–Nagumo model (Exercise 3.11).

import control as ct
import numpy as np
import matplotlib.pyplot as plt
ct.use_fbs_defaults()

#
# System dynamics
#

# FitzHugh-Nagumo dynamics (from KJA)
def fitzhugh_nagumo_dynamics(t, x, u, params):
    dx = np.zeros(3)

    # Get the system state
    V = x[0]
    R = x[1]

    # Compute the dim derivative
    dx[0] = 10 * (V - (V**3) / 3 - R + u)
    dx[1] = 0.8 * (-R + 1.25 * V + 1.5)
    dx[2] = 1

    return dx

# Set up an input/output system
sys = ct.NonlinearIOSystem(
    updfcn=fitzhugh_nagumo_dynamics, states=3, inputs=1, outputs=3)

# Set up the plotting grid to match the layout in the book
fig = plt.figure(constrained_layout=True)
gs = fig.add_gridspec(3, 2)

#
# (a) Current input
#

fig.add_subplot(gs[0, 0])       # first row, first column

# Set up input stimulation
t = np.linspace(0, 50, 500)
u = np.zeros_like(t)
u[t >= 5] = 1.5                 # start of short input pulse
u[t >= 6] = 0                   # end of short input pulse
u[t >= 30] = 1.5                # longer input pulse

# Initial state
x0 = [-1.5, -3/8, 0]

response = ct.input_output_response(sys, t, u, x0)

plt.plot(response.time, response.inputs[0])
plt.xlabel("Time $t$ [ms]")
plt.ylabel("Current $I$ [mA]")
plt.title("Input stimulation")

#
# (b) Neuron response
#

fig.add_subplot(gs[0, 1])       # first row, second column

plt.plot(response.time, response.states[0])
plt.xlabel("Time $t$ [ms]")
plt.ylabel("Voltage $V$ [mV]")
plt.title("Neuron response")

# Save the figure
plt.savefig("figure-3.19-fitzhugh_nagumo.png", bbox_inches='tight')