DCAM_model_sim.py

import math

def simulate_chemically_derived_soil_disk():
    # --- Physical Constants ---
    M_max = 10000.0       # Max electrical surface sites per unit area
    sigma_min = 0.2       # Coiled DNA footprint (Dry/High Salt)
    sigma_max = 2.0       # Extended DNA footprint (Wet/Low Salt)
    kappa = 5.0           # Conformation sensitivity factor
    
    # --- New Chemical Constants (Arrhenius Engine) ---
    R = 8.314             # Universal gas constant (J / mol*K)
    T = 298.15            # Temperature in Kelvin (25°C)
    E_a = 100000.0        # Activation energy for DNA hydrolysis (J / mol)
    A = 1.5e16            # Frequency factor (scaled to per-day basis)
    beta = 3.0            # Steric hindrance exponent for coiled DNA protection
    
    # --- Kinetic Rates ---
    I_in = 500.0          # Constant influx of dying cell DNA per day
    alpha = 0.05          # Adsorption affinity constant
    
    # --- Initial States ---
    D_surf = 1500.0       # Starting amount of bound base pairs
    
    print(f"{'Day':<6}{'Soil State':<12}{'Ionic (I)':<10}{'Footprint (σ)':<15}{'Memory Stored (D)':<20}")
    print("-" * 65)
    
    for day in range(1, 45):
        # Weather profile
        if day <= 30:
            soil_state = "Drying"
            I = 0.1 + (0.9 * (day / 30.0))
            B_live = 1.0 - (0.9 * (day / 30.0)) 
        else:
            soil_state = "Flooded"
            I = 0.05
            B_live = 2.0 
            
        # 1. Calculate the dynamic footprint size of DNA based on Ionic Strength
        sigma = sigma_min + (sigma_max - sigma_min) * math.exp(-kappa * I)
        
        # 2. Calculate available space left on the hard drive (theta)
        theta_clay = max(0.0, 1.0 - (D_surf * sigma / M_max))
        
        # 3. Microbes consuming/retrieving data
        V_max = 0.1
        K_m = 500.0
        phi_microbe = (V_max * B_live) / (K_m + D_surf)
        
        # 4. UPDATE: Chemically derived Arrhenius decay with structural shielding
        base_chemical_rate = A * math.exp(-E_a / (R * T))
        p_exposed = (sigma / sigma_max) ** beta
        protected_decay = base_chemical_rate * p_exposed
        
        decay = (protected_decay + phi_microbe) * D_surf
        
        # 5. Run the differential loop (dD/dt)
        absorption = alpha * I_in * theta_clay
        dD_dt = absorption - decay
        D_surf += dD_dt # Step forward 1 day
        
        # Print matching intervals for exact comparison
        if day in [1, 10, 20, 30, 31, 35, 44]:
            print(f"{day:<6}{soil_state:<12}{I:<10.2f}{sigma:<15.4f}{D_surf:<20.2f}")

simulate_chemically_derived_soil_disk()