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Computer Modeling in Biotechnology

A Partner in Development
  • Aleksei Aksimentiev
  • Robert Brunner
  • Jordi Cohen
  • Jeffrey Comer
  • Eduardo Cruz-Chu
  • David Hardy
  • Aruna Rajan
  • Amy Shih
  • Grigori Sigalov
  • Ying Yin
  • Klaus Schulten
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 474)

Summary

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.

Key Words

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 protein engineering tight-binding method 

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Copyright information

© Humana Press, a part of Springer Science + Business Media, LLC 2008

Authors and Affiliations

  • Aleksei Aksimentiev
    • 1
  • Robert Brunner
    • 1
  • Jordi Cohen
    • 1
  • Jeffrey Comer
    • 1
  • Eduardo Cruz-Chu
    • 1
  • David Hardy
    • 1
  • Aruna Rajan
    • 1
  • Amy Shih
    • 1
  • Grigori Sigalov
    • 1
  • Ying Yin
    • 1
  • Klaus Schulten
    • 1
  1. 1.Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-ChampaignUrbana

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