Hauptseminar Multiscale Simulations SS 2016/coupling MD DFT DNA translocation pores

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Coupling MD and DFT: DNA translocation through pores
Maria Fyta


In this topic, the sequential use of density functional theory (DFT) and Molecular Dynamics (MD) simulations in the process of DNA translocation through narrow pores will be discussed. First, some basic details on both methods will be presented. Second, specific examples in the nanopore field which deal with aspects of the DNA translocation through nanopores using both DFT and MD approaches will be presented.


  • E-Book: Kieron Burke et al.,University of California, 2007: E-Book: The ABC of DFT
  • S. Nose, A molecular dynamics method for simulations in the canonical ensemble, Molec. Phys. 52, 255 (1984).
  • S.M. Avdoshenko et al, Dynamic and Electronic Transport Properties of DNA Translocation through Graphene Nanopores, Nano Lett. 13 (5), 1969 (2013).
  • A. Barati Farimani, K. Min, and N.R. Aluru, DNA Base Detection Using a Single-Layer MoS2, ACS Nano 8 (8), 7914 (2014).
  • E. Paulechka, T.A. Wassenaar, K. Kroenlein, A. Kazakova and A. Smolyanitsky, Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing, Nanoscale 8, 1861 (2016).