Atomistic simulations of biomolecules at the water-amorphous silica interface: Application to peptides and DNA oligomers

Bobo Shi, Yun Kyung Shin, Ali Hassanali, Sherwin J. Singer

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish (US)
Title of host publicationNanotechnology 2012
Subtitle of host publicationElectronics, Devices, Fabrication, MEMS, Fluidics and Computational - 2012 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2012
Pages341-344
Number of pages4
StatePublished - Aug 17 2012
EventNanotechnology 2012: Electronics, Devices, Fabrication, MEMS, Fluidics and Computational - 2012 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2012 - Santa Clara, CA, United States
Duration: Jun 18 2012Jun 21 2012

Publication series

NameTechnical Proceedings of the 2012 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2012

Conference

ConferenceNanotechnology 2012: Electronics, Devices, Fabrication, MEMS, Fluidics and Computational - 2012 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2012
CountryUnited States
CitySanta Clara, CA
Period6/18/126/21/12

All Science Journal Classification (ASJC) codes

  • Ceramics and Composites
  • Surfaces, Coatings and Films

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