Journal of Materials Science

, Volume 47, Issue 21, pp 7439–7446 | Cite as

DNA sequencing with nanopores from an ab initio perspective

  • Ralph H. Scheicher
  • Anton Grigoriev
  • Rajeev Ahuja
First Principles Computations


Advances in materials research means that we find ourselves at the verge of constructing nano-scale devices capable of electrically addressing individual molecules in order to identify or utilize their electrical or electromechanical properties. An important application in life sciences would be electromechanical translocation of a DNA molecule through a nanopore, between nano-scale electrodes, allowing to electrically read out the base sequence (genome). This approach promises to drastically lower the cost per genome, allowing for extensive application in medical diagnostics. Owing to the involved extremely small dimensions which require nanometer-resolution in the fabrication, atomistic modeling plays a crucial role in testing hypothetical device architectures for their performance in nucleobase distinction. First-principles simulations are ideally suited to explore the interactions involved in such scenarios and lay the foundation for electronic transport calculations. This role of computations is even more important here, since it is experimentally not possible to observe directly the kinetics occurring during translocation of a DNA molecule through a nanopore. Here, we provide a brief review of the state of the field, focusing on ab initio studies of nanopore-based DNA sequencing, in particular on the promising recent development regarding graphene nanopores and nanogaps.


Graphene Nanoribbon Voltage Window Graphene Electrode Graphene Membrane Graphene Nanopores 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The success of any large science endeavor these days depends on team work and we would like to acknowledge our direct collaborators here, as well as the fast-growing group of scientists with whom we had the pleasure to discuss about nanopore-based DNA sequencing. Thanks go to, in alphabetical order: Tobias Blom, Gustavo Troiano Feliciano, Roman Gorbachev, Haiying He, Yuhui He, S. Hassan M. Jafri, Shashi P. Karna, Kwang Soo Kim, Klaus Leifer, Ming Liu, Henrik Löfås, Henrik Ottosson, Manuel Melle-Franco, Ravi Pandey, Biswarup Pathak, Henk W. Ch. Postma, Jariyanee Prasongkit, Alexandre Reily Rocha, Stefano Sanvito, and Gregory Schneider. Furthermore, the possibility to carry out research on this fascinating topic was enabled through the generous financial support from various Swedish sources, in particular the Wenner-Gren Foundations, the Swedish Research Council (VR, Grant No. 621-2009-3628), the Swedish Foundation for International Cooperation in Research and Higher Education (STINT), the Carl Tryggers Foundation, and the Uppsala University UniMolecular Electronics Center (U3MEC). Finally, since the calculations and simulations discussed in this article heavily depend on the availability of sufficient computational power, we would also like to thank the Swedish National Infrastructure for Computing (SNIC) and the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) for providing the necessary CPU hours.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Ralph H. Scheicher
    • 1
  • Anton Grigoriev
    • 1
  • Rajeev Ahuja
    • 1
  1. 1.Department of Physics and AstronomyCondensed Matter Theory GroupUppsalaSweden

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