Two-compartments Layer 5 Pyramidal Cell Model

The basal-dendritic/somatic compartment includes the classic Hodgkin-Huxley sodium (I_Na) and potassium delayed rectifier (I_Kdr) currents (Hodgkin and Huxley, 1952). The apical-dendrite/trunk compartment includes persistent Na^+ current (I_Nap) (Magistretti and Alonso, 1999), Ca^(2+) L-type current (I_CaL) (Lytton and Sejnowski, 1991), hyperpolarization-activated non-specific cation current (I_h) (Kole et al., 2006), muscarinic K+ current (I_M) (Adams et al., 1982), and the slow-inactivating potassium current (I_Ks) (Korngreen and Sakmann, 2000).

MatLab (release 2018b)

A memory of at least 16 GB is needed to run the trials to create the f-I curves.

For the numerical simulations and data processing the following MatLab toolboxes were used:

• CSDplotter-master
• RasterPlot
• SDETools-master
• EEGLAB, specifically the function eegfilt.m. You can download them from the links or find them in the folder Toolbox.

• InputCurrents: contains the functions used to generate the input currents.
• IonicCurrents: contains the channels kinetics and a test function to visualize the channel kinetics curves: activation/inactivation and time constants.
• SingleNeuron: contains the model codes with Ih blocked and without blocking Ih for a single neuron. Add InputCurrents and IonicCurrents to the MATLAB path before running scripts.
• L5PCs: contains the model codes with Ih blocked and without blocking Ih for a collaction of L5-PCs located randomly in a cortical column. It also contains the codes for the local field potentials (LFPs) and current source density (CSD) estimations. Add InputCurrents and IonicCurrents to the MATLAB path before running scripts.
• GenerateFigures: contains the programs used to create the figures.

Copyright (C) 2020 Beatriz Herrera, Amirsaman Sajad, Geoffrey F. Woodman, Jeffrey D. Schall, Jorge J. Riera.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

GNU GPLv3

Herrera B, Sajad A, Woodman GF, Schall JD, Riera JJ. A minimal biophysical model of neocortical pyramidal cells: implications for frontal cortex microcircuitry and field potential generation. J Neurosci 40, 8513-8529 (2020); DOI: https://doi.org/10.1523/JNEUROSCI.0221-20.2020.