Atomistic Simulations of Biomolecules at the Water-Amorphous Silica Interface: Application to Peptides and DNA Oligomers

Realistic modeling of the behavior of biomolecules near the materials commonly used for biomedical device fabrication is required for their design and evaluation. Here we report the development of a practical scheme to integrate our previously developed model for the water-amorphous silica interface [Hassanali, Singer, J.Phys.Chem.B, 2007, 111, 11181; Hassanali et al., J. Comput. Theoretical. Chem., 2010, 11, 3456] with common biological force fields to treat biomolecules at this important interface. We then apply the methodology to study binding of the lys-trp-lys and glu-trp-glu tripeptides, and a DNA oligomer, at the water-silica surface. Mechanisms for binding of biomolecules at the water amorphous silica interface are identified.