The provided code snippet appears to be part of a computational neuroscience model that simulates neuronal networks to study specific brain functions and behaviors. Here’s an overview of the biological basis this code snippet seems to be modeling: ### Biological Basis #### Structures and Cells - **Brain Structures:** The code references "structures" and "cells per structure," which suggests that it models specific brain regions. The mention of STN (Subthalamic Nucleus) and GPe (Globus Pallidus externus) indicates that the model focuses on the basal ganglia, a group of nuclei in the brain associated with various functions, including motor control and cognitive processes. - **Neuronal Cells:** The model appears to simulate individual neurons within these brain structures. The parameter `n_cells_per_structure` suggests detailed modeling of cell populations in each specified brain structure. #### Neuronal Activity and Firing Rates - **Mean Firing Rate:** The variable `extract_thresh` indicates a threshold for mean neuronal firing rates in spikes per second, highlighting a focus on activity levels that may be biologically significant for information processing in neural circuits. - **Spiking Data Extraction:** The function `extract_spikes()` suggests that the code analyzes spiking activity from simulated neurons, which is crucial for understanding neural communication and network dynamics. #### Simulation and Analysis - **Model-As-Animals Protocol:** This term suggests that each simulated model is treated as an individual "animal," potentially capturing variability across simulations analogous to biological variability across individuals. - **Selection and Switching Properties:** The code provides an option for analyzing selection and switching properties, which are critical functions of the basal ganglia involved in decision making and action selection. #### Neurotransmitters and Synaptic Interactions - **AMPA and NMDA Receptors:** The mention of `BATCH_BG_heterogenous_AMPA_NMDA` indicates that the model considers synaptic interactions mediated by AMPA and NMDA receptors. These glutamatergic receptors are crucial for synaptic plasticity and excitatory neurotransmission in the brain, playing key roles in learning and memory. #### Dopaminergic System - **Reference to DA (Dopamine):** The function `batch_selection_grid_DA()` implies involvement of dopamine, a neurotransmitter integral to the function of the basal ganglia, particularly in modulating reward, motivation, and motor behavior. ### Conclusion Overall, the code models the activity and interactions of neurons within the basal ganglia, emphasizing how synaptic and firing properties contribute to cognitive and motor functions. By simulating complex neuronal dynamics and analyzing the resulting activities, the model aims to yield insights into the biological processes underlying action selection, decision-making, and potential disorders involving these systems. This type of modeling is valuable for understanding neural circuit function and dysfunction, relevant to conditions such as Parkinson’s disease, which involves impaired basal ganglia function.