Computer modeling in biotechnology: A partner in development

Aleksei Aksimentiev, Robert Kraemer Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, Klaus Schulten

Research output: Contribution to journalArticle

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.

Original languageEnglish
Pages (from-to)181-234
Number of pages54
JournalMethods in Molecular Biology
Volume474
DOIs
StatePublished - Dec 1 2008

Keywords

  • Biosensors
  • Carbon nanotubes
  • Coarse-grained modeling
  • DNA sequencing
  • Empirical force field
  • High-density lipoprotein
  • High-throughput simulations
  • Hydrogenase
  • Molecular dynamics
  • Multiscale modeling
  • Nanodisc
  • Nanopore
  • Oxygen migration pathways
  • Polarization

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Aksimentiev, A., Brunner, R. K., Cohen, J., Comer, J., Cruz-Chu, E., Hardy, D., Rajan, A., Shih, A., Sigalov, G., Yin, Y., & Schulten, K. (2008). Computer modeling in biotechnology: A partner in development. Methods in Molecular Biology, 474, 181-234. https://doi.org/10.1007/978-1-59745-480-3_11