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Optimization of the Molecular Dynamics Method for Simulations of DNA and Ion Transport Through Biological Nanopores

  • David B. Wells
  • Swati Bhattacharya
  • Rogan Carr
  • Christopher Maffeo
  • Anthony Ho
  • Jeffrey Comer
  • Aleksei Aksimentiev
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 870)

Abstract

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA–ion interactions, and the ionic current through a nanopore.

Key words

Molecular dynamics Transmembrane transport Nucleic acids Membrane proteins Bionanotechnology Computer simulations 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • David B. Wells
    • 1
  • Swati Bhattacharya
    • 1
  • Rogan Carr
    • 1
  • Christopher Maffeo
    • 1
  • Anthony Ho
    • 1
  • Jeffrey Comer
    • 1
  • Aleksei Aksimentiev
    • 2
  1. 1.Department of PhysicsUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of Physics and Beckman InstituteUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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