title: Computer modeling in biotechnology: a partner in development.
abstract: 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 nano-tube-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.
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
authors.forename: Robert
authors.initials: R
authors.lastname: Brunner
authors.forename: Jordi
authors.initials: J
authors.lastname: Cohen
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Comer
authors.forename: Eduardo
authors.initials: E
authors.lastname: Cruz-Chu
authors.forename: David
authors.initials: D
authors.lastname: Hardy
authors.forename: Aruna
authors.initials: A
authors.lastname: Rajan
authors.forename: Amy
authors.initials: A
authors.lastname: Shih
authors.forename: Grigori
authors.initials: G
authors.lastname: Sigalov
authors.forename: Ying
authors.initials: Y
authors.lastname: Yin
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: D015374:Biosensing Techniques / Q000379:methods*; D001709:Biotechnology / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D008958:Models, Molecular; D049329:Nanostructures