Paper Citing NAMD - Abstract
Aksimentiev, Aleksei; Brunner, Robert; Cohen, Jordi; Comer, Jeffrey; Cruz-Chu, Eduardo; Hardy, David; Rajan, Aruna; Shih, Amy; Sigaloy, Grigori; Yin, Ying; Schulten, Klaus
Computer Modeling in Biotechnology A Partner in Development
Nanostructure Design: Methods and Protocols, 474:181-234, 2008
Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nanotube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.
