### Biological Basis of the Code This computational neuroscience model simulates the activity of a small neural network designed to replicate the replay of sequences in the hippocampus during sharp-wave ripples (SWRs). Here is the biological context for the components of the code: #### Hippocampal Structure and Function - **Pyramidal Cells (PCs):** The code models 81 pyramidal cells organized in a 3x3 grid of 9 clusters, with each cluster containing 9 pyramidal cells. Pyramidal cells are fundamental excitatory neurons in the CA1 region of the hippocampus, known for their role in encoding and retrieving spatial memories. - **Basket Cells (Interneurons):** The network includes 9 basket cells, which are inhibitory interneurons. Basket cells provide crucial inhibition to pyramidal cells and help regulate the timing and synchronization of neuronal firing, which is important for generating rhythmic activities in the hippocampus, such as SWRs. #### Temporal Sequence Replay - **Replay Mechanism:** The model emulates the replay of neural sequences, both forward and reverse. This phenomenon is observed in the hippocampus, where sequences of place cell activations that occur during experiences (e.g., traveling through a space) are replayed during rest or sleep. This replay is postulated to contribute to memory consolidation. - **Cue Stimulation:** Two 'cue' stimuli are delivered — one to the first pyramidal cell in the sequence (cell index 0) and another to the last pyramidal cell (cell index 60). These cues initiate the replay sequences, mimicking how particular starting points in physical space or time can trigger memory recall in the hippocampus. #### Synaptic Connections - **Forward and Reverse Synaptic Paths:** The neurons are connected bidirectionally to simulate both forward and reverse replay. This reflects the biological finding that hippocampal circuits can reverse these sequences, a process that's important for understanding temporally ordered information. - **Gap Junctions and Axonal Plexus:** Pyramidal cells are probabilistically connected through an axonal plexus with gap junctions, allowing for direct electrical coupling between neurons. This feature is significant for synchronizing neuronal activity during SWRs, a period characterized by highly coordinated neural firing. #### Neural Dynamics and Synaptic Properties - **Synaptic Weights and Dynamics:** Various synaptic weights (e.g., `wsyn_PC2PC, wsyn_PC2IN, wsyn_IN2PC`) define the strength of synaptic interactions between different neuron types. The excitatory and inhibitory synaptic behaviors (temporal dynamics) are modeled to reflect the actual synaptic conductances found in the hippocampus. - **Stochastic Stimulation of Collaterals:** The model incorporates randomness in the stimulation of axonal collaterals, which introduces variability in the network activity, reflecting the stochastic nature of neurotransmitter release and neuronal firing patterns observed in biological systems. Overall, this model captures key features of hippocampal microcircuitry involved in SWR-associated sequence replay, providing insights into mechanisms of memory recall and consolidation in the brain.