Emergent Molecular Complexity in Prebiotic Chemistry Simulations: A Physics-Based Approach

Background: The emergence of complex organic molecules from simple precursors remains a fundamental question in the origin of life. While experimental prebiotic chemistry has identified key reaction pathways, computational approaches capable of discovering novel reactions and autocatalytic networks are limited by either excessive computational cost (ab initio methods) or oversimplification (abstract reaction networks). Methods: We present a physics-based particle simulation framework that models prebiotic chemistry through continuous molecular dynamics with validated thermodynamic properties. The simulation employs literature-derived bond parameters, adaptive timestep integration, and real-time chemical novelty detection. We conducted 30 independent simulations across three prebiotic scenarios: Miller-Urey reducing atmosphere, alkaline hydrothermal vents, and formamide-rich environments, each running for 500,000 simulation steps (~140 hours of simulated time). Results: Our simulations generated 2,315 unique molecular species across all scenarios, with significant diversity differences between conditions. We detected 769,315 autocatalytic cycles, including both direct autocatalysis (1,199 instances) and indirect hypercycles (732,021 instances). The Miller-Urey scenario showed the highest autocatalytic cycle frequency (20,555 ± 84,750 cycles/run), followed by hydrothermal vents (11,403 ± 47,014) and formamide environments (10,782 ± 44,457). Network analysis revealed distinct hub molecules serving as key intermediates in each scenario. Amplification factors ranged from 1.11 to 6.0 (median 1.43), demonstrating significant autocatalytic enhancement of molecular abundances. Significance: This work demonstrates that physics-based simulations can discover emergent chemical complexity without pre-defined reaction rules, providing testable predictions for experimental validation. The detection of scenario-specific autocatalytic networks suggests multiple plausible pathways toward chemical evolution, supporting the idea of inevitable emergence of complexity in diverse prebiotic conditions.