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Queen Mary University of LondonQueen Mary University of London
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School of Engineering and Materials Science
Research Student Awards

PhD Thesis: Molecular dynamic simulations of Biointerfaces

Author: LI, Ruzhen

Year: 2009

Supervisor(s): Xiao Guo

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 absorption. It is clear that the amino acids which face the surface initiate the absorption process and influence subsequent stages of absorption. The considered carbon surfaces have different levels of reactivity for the molecule absorption. 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).