Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit (Ponzi et al. 2023)

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Accession:267686
Using a data-driven model of a hippocampal microcircuit, we demonstrate that theta-gamma phase amplitude coupling (PAC) can naturally emerge from a single feedback mechanism involving an inhibitory and excitatory neuron population, which interplay to generate theta frequency periodic bursts of higher frequency gamma..
Reference:
1 . Ponzi A, Dura-Bernal S, Migliore M (accepted) Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit PLoS Computational Biology
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 stratum oriens lacunosum-moleculare interneuron ; Hippocampus CA1 basket cell;
Channel(s): I h; I K,Ca; I K; I Calcium; I CAN; I M; I Na,t; Ca pump; I A; I T low threshold; I L high threshold; I_KD;
Gap Junctions:
Receptor(s): Gaba; Glutamate;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NetPyNE;
Model Concept(s): Oscillations; Gamma oscillations; Theta oscillations;
Implementer(s):
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Glutamate; Gaba; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I CAN; I Calcium; I_KD; Ca pump; Gaba; Glutamate; 
Model files in the NetPyNE simulation environment for the paper:

Theta-gamma phase amplitude coupling in a hippocampal CA1 microcircuit

by Adam Ponzi, Salvador Dura-Bernal, and Michele Migliore


Usage:

Download the files. 

Compile the mod files on the command line with 'nrnivmodl mechanisms'.

Install the NetPyNE simulation environment (http://netpyne.org/install.html)

To run the code using mpi-exec: (1) Remove or rename the directory t42_data (which is subsequently recreated when the code is run). (2) Set the numcores parameter in t42_batch.py to the required number of cores. (3) On the command line : 'nrniv -python t42_batch.py' (4) On completion, in the file maketrace.py set asBatch = True. Run maketrace.py.

To run the code directly: (1) On the command line: 'nrniv -python t42_init.py'. In this case no new directories are created. (2) On completion, in the file maketrace.py set asBatch = False. Run maketrace.py.


Questions on how to use this model should be directed to adam.ponzi@ibf.cnr.it

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