The provided code models certain aspects of the basal ganglia, a group of subcortical nuclei in the brain that are involved in various motor and cognitive functions. The basal ganglia are critical for the regulation of voluntary motor movements, procedural learning, and routine behaviors. The specific parts of the basal ganglia modeled in this code include the striatum, subthalamic nucleus (STN), globus pallidus externa (GPe), and globus pallidus interna (GPi). Let’s discuss the biological relevance of the modeled elements: ### Neuronal Populations and Structure - **Nuclei and Neurons**: The model incorporates multiple nuclei and defines neurons within each. These include: - **Striatal D1 (SD1) and D2 (SD2)** neurons, which are associated with dopamine receptor types (D1 and D2, respectively) and are critical for processing motor and reward-related information. - **STN (Subthalamic Nucleus)**: Involved in modulating the output of basal ganglia and plays a role in movement regulation. - **GPe (Globus Pallidus Externa)** and **GPi (Globus Pallidus Interna)**: Involved in the indirect and direct pathways of motor control, respectively. ### Synaptic Dynamics and Network Connectivity - **Connection Proportion**: The connection probability (`p_connect = 0.25`) reflects the sparse connectivity characteristic of neural networks, biologically mimicking the probabilistic synaptic connections in the basal ganglia. - **Synaptic Weights**: The weights of synaptic connections (e.g., `SD1_w`, `STN_GPiw`) influence the strength of interactions among neurons in different nuclei, providing a basis for biological processes like excitation and inhibition. ### Neurotransmission and Currents - **Dopamine Modulation**: Dopaminergic input, modulated via `dop1` and `dop2` parameters, simulates tonic dopamine levels. This is essential for representing the role of dopamine in modulating motor and cognitive functions of the basal ganglia. - **Excitatory and Inhibitory Synapses**: The model includes various synaptic currents such as AMPA, NMDA (excitatory), and GABAa (inhibitory) which are integral to synaptic transmission and plasticity. Time constants provided (`mean_tau_AMPA`, `mean_tau_NMDA`, `mean_tau_GABAa`) reflect their kinetic properties. ### Noise and Spontaneous Activity - **Intrinsic Noise**: The parameter `sigma_bg` introduces randomness to mimic biological neural noise, while `spon` accounts for spontaneous input currents typical of the constant background neural activity observed in vivo. - **Burst-current Parameters**: These reflect biological burst firing modes which are a hallmark of neurons in the STN, involved in high-frequency firing important for normal and abnormal motor behaviors. ### Simulation Conditions - **Urethane Manipulation**: The code includes an option for urethane-based experimental conditions (`do_urethane`). This anesthetic is commonly used in animal studies to simulate slow-wave brain states, impacting synaptic weights (e.g., `glut_scale`, `gaba_scale`). ### Input and Stimulation - **Tonically Active Input**: The `input_method` and `pulse_cells` parameters simulate external inputs to the network representing cortical or thalamic inputs, important for exploring both normal and abnormal neural processing dynamics. In summary, this model code illustrates an effort to simulate the complex dynamics of the basal ganglia, emphasizing the influence of dopaminergic modulation, synaptic transmission, and network architecture on neuronal activity patterns. These aspects are essential for studying motor control and are implicated in disorders such as Parkinson's disease and Huntington's disease.