83 lines
2.5 KiB
Python
83 lines
2.5 KiB
Python
# -*- coding: utf-8 -*-
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"""
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Script to run Cb Stellate model
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"""
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__author__ = "Nils A. Koch"
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__copyright__ = "Copyright 2022, Nils A. Koch"
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__license__ = "MIT"
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import numpy as np
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import os
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from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
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from Code.Functions.Cb_stellate_fxns import Cb_stellate_mut
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# model parameters
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dt = 0.01
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sec = 2
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low = 0
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high = 0.0015
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number_steps = 200
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initial_period = 1000
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num_gating = 9
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num_current = 6
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C, surf_area = capacitance(61.4, 1.50148)
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variable = np.array(['m', 'h', 'n', 'n_A', 'h_A', 'n_A_mut', 'h_A_mut', 'm_T', 'h_T'])
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stim_time, I_in, stim_num, V_m = stimulus_init(low, high, number_steps, initial_period, dt, sec)
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shift, scale, slope_shift, E, currents_included, b_param, g = init_dict(np.array(['m', 'h', 'n', 'n_A', 'h_A','n_A_mut', 'h_A_mut', 'm_T', 'h_T']))
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V_init = -70
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# initialize arrays
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current = np.zeros((num_current, stim_num))
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gating = np.zeros((num_gating, stim_num))
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# gating parameters
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b_param['m'][:] = np.array([-37., -3, 1])
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b_param['h'] = np.zeros(4)
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b_param['h'][:] = np.array([-40., 4., 1., 0])
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b_param['n'][:] = np.array([-23, -5, 1])
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b_param['n_A'][:] = np.array([-27, -13.2, 1.])
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b_param['h_A'][:] = np.array([-80., 6.5, 1.])
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b_param['n_A_mut'][:] = np.array([-27, -13.2, 1.])
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b_param['h_A_mut'][:] = np.array([-80., 6.5, 1.])
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b_param['m_T'][:] = np.array([-50., -3, 1.])
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b_param['h_T'][:] = np.array([-68., 3.75, 1.])
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# reversal potentials
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E["Na"] = 55.
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E["K"] = -80.
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E["Ca"] = 22.
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E["Leak"] = -70. # as per Molineux et al 2005 and NOT the -38 in Alexander et al 2019
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# model currents
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currents_included["Na"] = True
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currents_included["Kd"] = True
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currents_included["A_mut"] = True
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currents_included["A"] = True
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currents_included["T"] = True
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currents_included["Leak"] = True
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# model conductances
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g["Na"] = 3.4 * surf_area
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g["Kd"] = 9.0556 * surf_area
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g["A_mut"] = 15.0159 * surf_area * 0.5
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g["A"] = 15.0159 * surf_area* 0.5
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g["T"] = 0.45045 * surf_area
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g["Leak"] = 0.07407 * surf_area
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prominence = 50
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min_spike_height = 0
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desired_AUC_width = high/5
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folder = '../Neuron_models'
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mut = 'Cb_stellate'
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mutations = {mut:{'g_ratio': 1, 'activation_Vhalf_diff': 0, 'activation_k_ratio':0}}
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if not os.path.isdir(folder):
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os.makedirs(folder)
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Cb_stellate_mut(V_init, g, E, I_in, dt, currents_included, stim_time, stim_num, C, shift, scale, b_param, slope_shift,
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gating, current, prominence, desired_AUC_width, mutations, mut, folder, high, low, number_steps,
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initial_period, sec)
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