Close encounters with DNA

C. Maffeo, J. Yoo, J. Comer, D. B. Wells, B. Luan, A. Aksimentiev

Research output: Contribution to journalReview articlepeer-review

Abstract

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Original languageEnglish (US)
Article number413101
JournalJournal of Physics Condensed Matter
Volume26
Issue number41
DOIs
StatePublished - Oct 15 2014

Keywords

  • charge inversion
  • counterions
  • effective charge
  • electrophoresis
  • molecular dynamics
  • nanopore
  • nucleic acids

ASJC Scopus subject areas

  • Materials Science(all)
  • Condensed Matter Physics

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