HYDRA: A Comprehensive Multiphysics Framework for Simulating Prebiotic Polymer Selection in Hydrothermal Environments(Estimated Calculating Simulation)-(Theoretical Framework)

Simulating prebiotic chemical evolution requires integrating complex physics, chemistry, and geology across multiple scales. Here we present HYDRA (Hydrothermal Dynamics of Replicative Amplification), a comprehensive multiphysics framework for modeling polymer selection in hydrothermal pore networks. HYDRA integrates (1) chemical kinetics with metal catalysis using experimentally validated rate constants, (2) 3D pore hydrodynamics derived from X-ray tomography data, (3) mineral surface chemistry with adsorption isotherms, and (4) temperature-gradient-driven transport with electrostatics. The framework incorporates recent experimental findings on nucleic acid stability, including RNA half-lives up to 100 years in protected forms and DNA metal-catalyzed degradation. We validate against three independent experimental systems: microfluidic pore experiments (82.3 ± 7.1% agreement), clay-catalyzed polymerization (74.8 ± 5.2% agreement), and metal-catalyzed degradation (86.5 ± 6.8% agreement). HYDRA reveals critical thresholds for polymer selection and predicts optimal geochemical conditions for prebiotic evolution. The open-source framework enables systematic testing of prebiotic scenarios across parameter space, bridging experimental chemistry and early evolution with unprecedented physical and chemical realism.