Novel Approaches to DNA Sequencing

Europe/Stockholm
122:026

122:026

Alexander Balatsky (Nordita), Dmitry A. Yarotski (Los Alamos National Laboratory), Ralph Scheicher (Uppsala University), Rodrigo G. Amorim (Uppsala University)
Description

Venue

Nordita, Stockholm, Sweden

Scope

This workshop will be centered on the physical principles behind novel approaches to electronic DNA sequencing and shall provide a forum to review the state of the field and to discuss venues for future methodology development. It will bring together leading researchers who work on experimental, theoretical and computational studies of DNA sequencing with nano-sized electrical probes, in particular on the promising recent development regarding graphene-based architectures. The workshop will foster close collaboration between theorists and researchers who are experts either in the fabrication of nano-structures or in the field of experimental genome sequencing.

Timetable

Invited Participants

  • Towfiq Ahmed (U Washington)
  • Aleksei Aksimentiev (Urbana, Illinois)
  • Tim Albrecht (Imperial College London)
  • Cees Dekker (TU Delft)
  • Massimiliano Di Ventra (UCSD)
  • Marija Drndic (U Penn)
  • Ralf Eichhorn (Nordita)
  • Gustavo Feliciano (UNESP and UFABC, São Paulo)
  • Maria Fyta (U Stuttgart)
  • Anton Grigoriev (Uppsala U)
  • Yuhui He (Osaka University)
  • Stephanie Heerema (TU Delft)
  • Tomoji Kawai (Osaka University)
  • Ulrich Keyser (University of Cambridge)
  • Yong-Hoon Kim (KAIST, Korea)
  • Kwang Soo Kim (POSTECH, Korea)
  • Predrag Krstic (University of Tennessee)
  • Joakim Lundeberg (SciLifeLab Stockholm)
  • Branislav Nikolic (U Delaware)
  • Jariyanee Prasongkit (Nakhon Phanom University, Thailand)
  • Oleg Prezhdo (U Rochester)
  • Alexandre Reily Rocha (Universidade Estadual Paulista, São Paulo)
  • Ivan Rungger (Trinity College Dublin)
  • Dmitry Ryndyk (TU Dresden)
  • Konstantin Zakharchenko (Nordita)
  • Michael Zwolak (Oregon State)
Other speakers:
  • Clive Brown (Oxford Nanopore Technologies)
  • Lorenz Steinbock (ETHL STI-IBI)
Organizers that gave talks:
  • Rodrigo Amorim (Uppsala University)
  • Dmitry Yarotski (LANL)

Application

If you want to apply for participation in the program, please fill in the application form. You will be informed by the organizers shortly after the application deadline whether your application has been approved. Due to space restrictions, the total number of participants is strictly limited. (Invited speakers are of course automatically approved, but need to register anyway.)

Application deadline: 1 May 2013

There is no registration fee.

Travel Reimbursement

There is a limited number of travel grants available for PhD students and young Postdoc fellows from the Nordic countries. If you are interested in such a grant, please contact the organizers via email.

Accommodation

Nordita provides a limited number of rooms in the Stockholm apartment hotel BizApartments free of charge for accepted program participants.

Sponsored by:

Nordita STINT

    • 1
      Registration
    • 10:30
      welcome coffee
    • 2
      Cranking up the signal-to-noise ratio at MHz bandwidth
      Speaker: Marija Drndic
    • 3
      Using heat, charge and electric field to control DNA translocation through nanopores
      Speaker: Aleksei Aksimentiev
    • 12:30
      lunch
    • 4
      Massively parallel sequencing used for single cells at SciLifeLab
      Speaker: Joakim Lundeberg
    • 5
      DNA sequencing device from molecular sensor perspective
      Speaker: Anton Grigoriev
    • 6
      Theoretical Study of Electronic Transport through DNA Nucleotides in a Graphene Nanogap
      Speaker: Jariyanee Prasongkit
    • 15:00
      coffee
    • 7
      Scanning Tunneling Microscopy of DNA Molecules Adsorbed on Carbon
      Speaker: Dmitry A. Yarotski
    • 8
      Functionalized carbon nanoelectrodes as tunneling DNA sensors: A multiscale computational study
      Speaker: Yong-Hoon Kim
    • 9
      Single Molecule DNA and RNA Sequencing by Gating Nanopore systems
      Speaker: Tomoji Kawai
    • 10
      Electrical means to sequence DNA
      Speaker: Massimiliano Di Ventra
    • 10:30
      coffee
    • 11
      Using tunnelling current for sensing - an assessment
      Speaker: Tim Albrecht
      slides
    • 12
      A first-principles approach to DNA fingerprinting on Graphene
      Speaker: Towfiq Ahmed
      slides
    • 12:30
      lunch
    • 13
      Probing DNA via thermal transport
      Speaker: Michael Zwolak
    • 14
      Statistical sampling of conductance through molecules and water
      Speaker: Ivan Rungger
    • 15:00
      coffee
    • 15
      From statistics and dynamics of DNA translocation towards functionalized nanopores
      Speaker: Maria Fyta
      slides
    • 16
      Control of the DNA Translocation Through the Various Types of Synthetic Nanopores
      Speaker: Predrag S. Krstic
    • 17:00
      BBQ dinner
    • 17
      Devices and Methods for Nucleic Acid Sequencing Using Nanopores
      Speaker: Clive G. Brown (C.T.O. Oxford Nanopore Technologies)
    • 18
      Label-free separation of DNA fragments in microfluidic devices
      Speaker: Ralf Eichhorn
    • 10:30
      coffee
    • 19
      Graphene nanopores for DNA sensing
      Speaker: Stephanie Heerema
    • 20
      Controlled healing of graphene nanopore
      Speaker: Konstantin Zakharchenko
    • 12:30
      lunch
    • 21
      Glass Nanopores as Single Molecule Detectors
      Speaker: Lorenz J. Steinbock
    • 22
      discussion time / free time
    • 23
      DNA origami nanopores for controlling DNA translocation
      Speaker: Ulrich Keyser
    • 24
      Graphene/h-BN/Graphene nanopore for single-molecule detection
      Speaker: Yuhui He
    • 10:30
      coffee
    • 25
      Nanoscale Carbon for DNA Sequencing and Drug Delivery
      Speaker: Oleg Prezhdo
      notype
    • 26
      Four-terminal graphene nanoribbon crossbars with a nanopore for DNA sequencing via multiple transverse currents measurement
      Speaker: Branislav K. Nikolic
    • 12:30
      lunch
    • 27
      Fano Resonance Driven Molecular Electronics Spectroscopy and Fast DNA Sequencing
      Speaker: Kwang S. Kim
    • 28
      New alternatives to improve biomolecule-sensing using 2D nanodevices
      Speaker: Rodrigo G. Amorim
    • 15:00
      coffee
    • 29
      AlbaNova/Nordita Colloquium
    • 17:00
      BBQ dinner
    • 30
      A variety of solid-state nanopores for single-molecule analysis
      Speaker: Cees Dekker
    • 31
      DNA Translocation through Graphene Nanopores and the Sequencing Problem: A Theoretical Study
      Speaker: Dmitry A. Ryndyk
    • 10:30
      coffee
    • 32
      QM/MM Nonequilibrium Green's function approach to simulating DNA sequencing using graphene nanopores
      Speaker: Alexandre Reily Rocha
    • 33
      Graphene-based DNA sequencing devices and the effect of the environment: A NEGF/QMMM hybrid study
      Speaker: Gustavo Troiano Feliciano
    • 34
      concluding remarks
    • 12:30
      lunch
    • 35
      departure