NEURON files & Python code from paper:

Rachel Humphries, Jack R. Mellor, Cian O'Donnell, Acetylcholine Boosts Dendritic NMDA Spikes in a CA3 Pyramidal Neuron Model, Neuroscience, 2021,ISSN 0306-4522 https://doi.org/10.1016/j.neuroscience.2021.11.014

In this paper, this model was used to compare the nonlinearity of NMDA inputs between dendritic sections in a CA3 pyramidal neuron as well as investigate the effect of cholinergic modulation/potassium channel inhibition on this dendritic NMDA-mediated nonlinearity.

NEURON and Python 3.8 were used to run the simulations.

In the folder provided here are the mod files for each of the conductances/synaptic mechanisms and the main hoc file (ca3b-cell1zr-fig9b.hoc - adapted from Hemond et al. 2008 model (accession no.:101629)).

The mod files will need to be compiled using the "mknrndll" command (on Windows).

**Hoc files**
(adapted from Hemond et al. 2008 (accession no.:101629))
ca3b-cell1zr-fig9b.hoc - main hoc file to set up model and insert conductances
geo-cell1zr.hoc - sets up neuron morphology
fixnseg.hoc - sets number of segments for each section

Python was used to run simulations, analyse and plot the data.

**Python files**
measure_dend_Rin_rest.py - Measures dendritic input resistance at rest.
nonlinearity_all_dends.py - Produces data used in Figures 3 and 4 of the paper.
ach_exp.py - Produces data used in Figures 5 and 6 of the paper.
ca3_synapse_functions.py - additional functions required for running the simulations
Fig5_example_dend_traces.py - Runs the simulation for 6 example dendrites and plots neuron morphology and example voltages traces from Figure 5A,B+C of the paper.
add_scalebar_func.py & scalebars.py - scalebar functions for plotting

Simulation outputs are saved in pickle files.

**PNG files**
Output from running Fig5_example_dend_traces.py - this will take a couple of hours to run.
Representative of Figure 5A,B+C from paper - from running the simulation with the 6 highlighted dendrites.

**Note**
On a standard PC, ach_exp.py with the default parameters (20 inputs on all dendritic sections + all conditions) may take >24 hours to run.