UNDERSTANDING BACTERICIDAL MECHANISMS USING MOLECULAR DYNAMICS SIMULATIONS

Molecular dynamics (MD) simulations were conducted to investigate the bactericidal and bacteriostatic effects of copper (Cu) and carbon (C) substrates with different crystallinity. Five materials were modelled: nanocrystalline (NC) and polycrystalline (PC) copper and carbon, and amorphous carbon (aC). The study examined how grain boundaries, crystallinity, and chemistry influence charge transfer and structural stability at both BamABCDE protein–substrate interface and in a bacterial outer membrane model; both vital for the survival of Gram-negative bacteria. Analyses included charge distribution, potential energy, root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), dihedral angles, residue displacement, lipid bilayer diffusion, membrane thickness profiling and twodimensional lipid density mapping. In protein–substrate models, a dual mechanism was observed for the copper substrates: NC-Cu caused rapid, localised backbone deformation through torsional strain, while PC-Cu produced broader residue-level disruption associated with grain boundary–driven electrostatics. Carbon substrates, especially aC, maintained secondary structure and stable electrostatics. In membrane–substrate models, PC-Cu showed the highest charge transfer (0.17 C), followed by NC-Cu (0.14 C), both linked to large potential energy reductions, increased lipid mobility, lipid-bilayer expansion and lateral packing disruption. NC-C and PC-C induced moderate perturbations, such as localised channel formation, while aC remained stable and slightly compressed the bilayer. Membrane thickness analysis confirmed the greatest expansion for NC-Cu and PC-Cu, whereas twodimensional density mapping revealed distinct substrate-dependent clustering and depletion patterns. Experimental antibacterial assays on polycrystalline (PC) pure (99%) copper thin block supported simulation findings, showing >99% Escherichia (E.) coli reduction within 4 h assessed by colony counting. This integrated computational–experimental study links substrate microstructure to specific atomic-scale destabilisation pathways in both protein and membrane. By resolving distinct electrostatic and structural mechanisms for copper and carbon substrates, the work advances understanding of early-stage bacterial inactivation and provides a mechanistic foundation for the design of application-specific antibacterial coatings.