• force fields
• molecular dynamics
• plasmonic substrates
• protein-surface interactions
• SARS-CoV-2

Systems composed by a biomolecule, an inorganic substrate and an aqueous solvent are gaining increasing attention due to their potential applications in many areas of nanoscience, e.g. nanomedicine and biosensing. Nevertheless, the design and optimization of nanobiotechnologic applications cannot disregard the importance of understanding the molecular factors that drive the recognition and the binding of the protein on the nanosurface. To better understand the atomistic behaviour of protein-surface interactions, experimental studies can be effectively complemented by computer simulations. The computational strategy proposed in the present thesis provides an effective way to sample the phase-space of the biomolecule in close proximity to the nanosurface by means of classical molecular dynamics (MD) simulations.
As case studies, the pattern of interaction between the receptor binding domain (RBD) of SARS-CoV-2 and three plasmonic surfaces (gold/silver slabs and graphene sheets) is investigated. To exhaustively model the adsorption phenomena, different force fields, able to describe Au/Ag slabs and graphitic surfaces with the direct/indirect inclusion of polarization effect, are tested.
The development of such a computational protocol may help the interpretation of the adsorption process of biological macromolecules (e.g. SARS-CoV-2) on different plasmonic surfaces at a molecular level, leading to the in silico design of biosensors.