Molecular dynamic simulations of biointerfaces

Biointerfaces bridge across inorganic and biological substances within a watercontaining environment. It is related to health care, environmental engineering and bioenergy generation. However, there is a lack of fundamental understanding of bonding and stability of biointerfaces, due to limited capabilities of experimental techniques. The research project employs molecular dynamics (MD) as the basic methodology to study selected biointerfaces, involving five carbon surfaces (amorphous carbon surface, basal graphite surface, basal graphite surface doped with hydrogen and hydroxyl groups, basal graphite surface with Stone-Wales defects, and edge graphite surface). The selected molecules are: a small alpha-helix and a beta-sheet peptide, each with 16 amino acids; and a mid-sized peptide (amyloid peptide). The systematic study of the molecular adsorption on carbon surfaces has shown that it is a very complex process, which depends on several factors such as the molecular structure, the hydropathy of the peptide molecule, the charge and defects of the substrate surface, and the orientation of the molecule upon adsorption. It is clear that the amino acids which face the surface initiate the adsorption process and influence subsequent stages of adsorption. The considered carbon surfaces have different levels of reactivity for the molecule adsorption. The amorphous and charged surfaces tend to stabilise the beta sheet secondary structure. The interaction between the amyloid peptide and the carbon surfaces seems to depend on its molecular orientation, as well as the nature of the carbon surface: it was clearly attracted to the hydrophobic basal surface of graphitic carbon but pushed away from the hydrophilic charge-doped surface in one of the orientations (the second), but the opposite is true for another orientation (the third). Details of the structural change were shown in the Ramachandran plot. The energy change of the system mainly comes from the configurational variation, and electrostatic interactions are more prominent than the others. Water molecules tend to accumulate above a hydrophobic surface, forming a dense water layer, with an estimated distance of 2.9 Å from the carbon surface, whereas they distribute relatively evenly on hydrophilic surfaces.EThOS - Electronic Theses Online ServiceGBUnited Kingdo