# Biological Basis of the Code The code models the **sodium-potassium pump** (Na⁺/K⁺-ATPase) in neural membranes, a crucial enzyme that maintains the electrochemical gradients of sodium (Na⁺) and potassium (K⁺) ions across the cell membrane. These gradients are essential for various physiological functions, including nerve impulse transmission and muscle contraction. ## Key Biological Features ### Sodium (Na⁺) and Potassium (K⁺) Ions - **Na⁺ Concentration**: The code uses typical intracellular (nain) and extracellular (naout) concentrations of Na⁺. The intracellular Na⁺ concentration is set to 9.6 mmol/l, and the extracellular Na⁺ is 140 mmol/l. - **K⁺ Concentration**: The intracellular (kin) and extracellular (kout) K⁺ concentrations are set to 150.4 mmol/l and 5.4 mmol/l, respectively. ### ATP and Phosphorylation - **ATP and ADP**: ATP (adenosine triphosphate) is used in the code to model the energy source of the pump, while ADP (adenosine diphosphate) is produced as a result of ATP hydrolysis. These are modeled with concentrations of 4.99 mmol/l for ATP and 0.06 mmol/l for ADP, reflecting the energy dynamics in cells. ### Pump Cycle Components - **Enzyme States**: The code models various enzyme states (`eatp`, `na3eatp`, `na3ep`, `ep`, `k2e`, `k2eatp`) that reflect stages in the pumping cycle, simulating the binding and release of ions and ATP, which facilitates conformational changes needed for ion transport. - **Binding and Transport Reactions**: The pump's function is expressed through a series of reversible binding reactions and ion transfer steps. These reactions involve transitions between different states (e.g., Na⁺ and K⁺ binding/release and ATP hydrolysis). ### Temperature and Voltage Dependence - **Temperature (T)**: The temperature is set to 310 K (approximately 37°C), reflecting the typical physiological temperature for mammals, including humans. - **Voltage Dependence**: Voltage sensitivity is incorporated through the parameters `a3`, `a5`, and `beta`, indicating how membrane potential influences the Na⁺/K⁺-pump's transitional states. ## Functionality and Ion Transport The Na⁺/K⁺-ATPase pump actively transports 3 Na⁺ ions out of the cell and 2 K⁺ ions into the cell against their concentration gradients. This active transport is fueled by ATP hydrolysis, a key biochemical aspect captured in the code. The pump's activity is quantified via the `atpact` variable, which captures its electrical current contribution in microamperes per square centimeter. ### Molecular and Electrical Balance - **Compartmentalization**: The compartmental model utilizes intracellular and extracellular environments to reflect real cellular conditions. - **Electrical Flux Calculations**: The electrical flux is determined by the reaction rates and ion transfers, which are further expressed in terms of electrical current (uA), showcasing how the pump maintains membrane potential and cellular electrochemical stability. Overall, this model encapsulates the complex interplay of biochemical and biophysical aspects of the Na⁺/K⁺-ATPase, highlighting its vital role in maintaining the resting membrane potential and the overall homeostasis in neural cells.