The provided code is a segment from a computational model that simulates the accumulation and diffusion of calcium ions (Ca²⁺) within the subcellular space, with particular emphasis on the spatial and temporal dynamics influenced by various biological factors. The model also incorporates calcium buffering by mobile buffers and the activity of calcium pumps, which are biological processes essential for maintaining calcium homeostasis. ### Key Biological Components and Processes: 1. **Calcium Ions (Ca²⁺)**: - Calcium is a vital second messenger in numerous cellular processes, including muscle contraction, neurotransmitter release, and enzymatic activity. - The code models both the radial (across the cell radius) and longitudinal (along the cell length) diffusion of calcium ions. This models how Ca²⁺ spreads throughout the cell in response to concentration gradients. 2. **Buffered Calcium**: - **Calbindin and Parvalbumin**: These are calcium-binding proteins acting as mobile buffers. They play crucial roles in modulating intracellular calcium dynamics by transiently binding free Ca²⁺ ions, thereby reducing peak calcium levels and influencing the spatial spread of calcium signals. - The model includes multiple binding sites and states for calbindin and parvalbumin, simulating their interaction with Ca²⁺ and incorporating both high and low-affinity binding sites. 3. **Magnesium Ions (Mg²⁺)**: - Magnesium, another important cation, competes with Ca²⁺ for binding sites on proteins like parvalbumin. This competition modulates the availability and buffering capacity for Ca²⁺ within the cell. 4. **Calcium Pump**: - **Plasma Membrane Calcium ATPase (PMCA)**: This pump actively expels Ca²⁺ from the cytoplasm to the extracellular space, using ATP hydrolysis for energy. It is a vital mechanism for restoring resting calcium levels after cellular activities that evoke Ca²⁺ influx. - The `TotalPump` parameter and its associated reactions simulate the pump dynamics, which are critical for calcium clearance. 5. **Diffusion Coefficients**: - The code specifies diffusion coefficients (`DCa`, `Dbtc`, etc.) for calcium and the various buffers. These parameters are essential for defining how fast these ions and molecules can move within the cellular matrix. 6. **Radial Geometry and Compartmentalization**: - The model divides the cellular space into concentric annuli (`Nannuli`), representing layer-by-layer diffusion and buffering. This accounts for the nonuniform distribution of ions and buffers across the radial depth of the modeled area, which can mimic the calcium microdomains observed experimentally. 7. **Temperature**: - The model runs simulations at a physiological temperature (`celsius = 34°C`), which impacts reaction kinetics and diffusion properties. In summary, the code models the complex interplay between calcium dynamics, buffer interactions, and active transport processes, which collectively govern the cellular calcium homeostasis crucial for neuronal function and signaling. These processes are representative of the fine-tuned mechanisms that cells employ to process and respond to calcium-mediated signals.