Molecular Dynamics Simulations with Multiple ROS Types and Photochemical Effects Refute RNA World Hypothesis, Supporting Synergistic Matter World Model(Estimated Calculation Simulation)

The RNA World Hypothesis (RWH) posits that RNA alone initiated life, serving as both genetic material and catalyst. However, RNA’s susceptibility to reactive oxygen species (ROS) and photochemical damage challenges its viability. The Matter World Hypothesis (MWH) proposes that life emerged from synergistic interactions among RNA, DNA, peptides, lipids, and catalysts in prebiotic environments. We employed molecular dynamics (MD) simulations with the CHARMM36 force field to compare RNA-only systems against MWH-based protocells in hydrothermal vents, ice, tidal pools, and wet-dry cycles. Simulations incorporated multiple ROS types (hydroxyl radicals, superoxide, hydrogen peroxide) and photochemical effects (UV-induced nucleotide damage, relevant for tidal pools and ice). Full ribosome-peptide interactions, vesicle stability, and kinetic modeling of damage rates were included. Results show RNA-only systems degrade rapidly (25–35% RMSD within 100 ns) with negligible catalysis (kcat ~0.003–0.006 min⁻¹), while MWH systems achieve high stability (<10% RMSD) and robust catalysis (kcat ~0.058–0.068 min⁻¹). Statistical analyses (ANOVA, regression) refute RWH, strongly supporting MWH’s synergistic model. These findings guide experimental validation and inform astrobiology and synthetic biology.