How the Translocation Dynamics of DNA in an Oscillating Electric Field change with Frequency

POSTER

Abstract

To make DNA sequencing more efficient and economical one proposed method has been to use nanopores. In nature, nanopores are the gateways that exist on a cell’s membrane, and are used by proteins which pass through them. By artificially creating these nanopores in a salt solution we can measure the current flow of the salt ions that pass through the nanopore, and if there is a strand of ssDNA in the nanopore, the current measured will change in accordance with the type of base that is in the constriction point, or the narrowest point, of the nanopore. In doing this, theoretically, we can completely sequence any strand of DNA that goes through the nanopore. However, there are two main problems with this method; the DNA translocates too quickly to measure accurately and nearby bases inside the constriction point influence the output current. My project seeks to better understand this process through molecular dynamics simulations. In my simulations, I will be testing whether applying an alternating current to the system will slow the translocation time of the ssDNA, and thereby, increase the accuracy of the sequencing process. In addition, I will be looking for the optimal frequency of the alternating current to maximize the length of the translocation time.

Authors

  • Thomas Longo

    Villanova Univ

  • Debbie Andres

    Department of Applied Physics and Department of Physics, Columbia University, Istituto Italiano di Tecnologia, Graphene Labs, Italy, Department of Physics and Astronomy, Purdue University, Department of Electrical Engineering, Princeton University, Department of Applied Physics and Applied Mathematics, Columbia University, NJIT, New Jersey Inst of Technology, New Jersey Inst of Tech, New Jersey Institute of Technology, Center for Advanced Radiation Sources, University of Chicago, High Pressure Science and Technology Advanced Research, State University of New York at Stony Brook, Rutgers University, NIST, Brookhaven National Laboratory, University of Chicago, University of South Florida, ETH Zurich, Max Planck POSTECH/Korea Research Initiative, University of Virginia, Rutgers University - Camden, New Jersey Institute of technology, Shaanxi Normal University, Pohang Science and Technology University, Sungkyunkwan University, Northern Illinois University and Argonne National Laboratory, Beijing National Laboratory for Condensed Matter Physics , and Institute of Physics, Chinese Academy of Sciences, Rutgers U., Orsova Engineers, U.S. Naval Research Laboratory, Center for Space Science and Engineering Research, Virginia Tech, Virginia., Princeton University, NASA Goddard Space Flight Center, Villanova University, SOFIA/USRA, Jet Propulsion Laboratory, Hudson Regional Health Commision, Rutgers University, College of William & Mary, Department of Physics, Drexel University, Drexel University, Drexel Universty, University of Massachusetts Amherst, Pohang Institue of Science and Technology, Indiana University - Purdue University Indianapolis, Department of Physics, University of Maryland, Naval Research Laboratory, Towson Univ, Rice University, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, Department of Physics, Temple University, PulseTorr LLC, Department of Chemistry, West Chester University, Department of Physics, West Chester University, College of William and Mary Dept. of Physics, University of Virginia Dept. of Materials Science and Engineering, United States Naval Academy, Rutgers The State University of New Jersey, Univ of Maryland-College Park, Los Alamos National Laboratory, POSTECH, New Jersey Institute of Technology, Department of Electrical and Computer Engineering, HamSCI/ARRL, Virginia Tech, Rutgers University-Camden, University of Washington, Rutgers, The State University of New Jersey

  • Debbie Andres

    Department of Applied Physics and Department of Physics, Columbia University, Istituto Italiano di Tecnologia, Graphene Labs, Italy, Department of Physics and Astronomy, Purdue University, Department of Electrical Engineering, Princeton University, Department of Applied Physics and Applied Mathematics, Columbia University, NJIT, New Jersey Inst of Technology, New Jersey Inst of Tech, New Jersey Institute of Technology, Center for Advanced Radiation Sources, University of Chicago, High Pressure Science and Technology Advanced Research, State University of New York at Stony Brook, Rutgers University, NIST, Brookhaven National Laboratory, University of Chicago, University of South Florida, ETH Zurich, Max Planck POSTECH/Korea Research Initiative, University of Virginia, Rutgers University - Camden, New Jersey Institute of technology, Shaanxi Normal University, Pohang Science and Technology University, Sungkyunkwan University, Northern Illinois University and Argonne National Laboratory, Beijing National Laboratory for Condensed Matter Physics , and Institute of Physics, Chinese Academy of Sciences, Rutgers U., Orsova Engineers, U.S. Naval Research Laboratory, Center for Space Science and Engineering Research, Virginia Tech, Virginia., Princeton University, NASA Goddard Space Flight Center, Villanova University, SOFIA/USRA, Jet Propulsion Laboratory, Hudson Regional Health Commision, Rutgers University, College of William & Mary, Department of Physics, Drexel University, Drexel University, Drexel Universty, University of Massachusetts Amherst, Pohang Institue of Science and Technology, Indiana University - Purdue University Indianapolis, Department of Physics, University of Maryland, Naval Research Laboratory, Towson Univ, Rice University, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, Department of Physics, Temple University, PulseTorr LLC, Department of Chemistry, West Chester University, Department of Physics, West Chester University, College of William and Mary Dept. of Physics, University of Virginia Dept. of Materials Science and Engineering, United States Naval Academy, Rutgers The State University of New Jersey, Univ of Maryland-College Park, Los Alamos National Laboratory, POSTECH, New Jersey Institute of Technology, Department of Electrical and Computer Engineering, HamSCI/ARRL, Virginia Tech, Rutgers University-Camden, University of Washington, Rutgers, The State University of New Jersey

  • Debbie Andres

    Department of Applied Physics and Department of Physics, Columbia University, Istituto Italiano di Tecnologia, Graphene Labs, Italy, Department of Physics and Astronomy, Purdue University, Department of Electrical Engineering, Princeton University, Department of Applied Physics and Applied Mathematics, Columbia University, NJIT, New Jersey Inst of Technology, New Jersey Inst of Tech, New Jersey Institute of Technology, Center for Advanced Radiation Sources, University of Chicago, High Pressure Science and Technology Advanced Research, State University of New York at Stony Brook, Rutgers University, NIST, Brookhaven National Laboratory, University of Chicago, University of South Florida, ETH Zurich, Max Planck POSTECH/Korea Research Initiative, University of Virginia, Rutgers University - Camden, New Jersey Institute of technology, Shaanxi Normal University, Pohang Science and Technology University, Sungkyunkwan University, Northern Illinois University and Argonne National Laboratory, Beijing National Laboratory for Condensed Matter Physics , and Institute of Physics, Chinese Academy of Sciences, Rutgers U., Orsova Engineers, U.S. Naval Research Laboratory, Center for Space Science and Engineering Research, Virginia Tech, Virginia., Princeton University, NASA Goddard Space Flight Center, Villanova University, SOFIA/USRA, Jet Propulsion Laboratory, Hudson Regional Health Commision, Rutgers University, College of William & Mary, Department of Physics, Drexel University, Drexel University, Drexel Universty, University of Massachusetts Amherst, Pohang Institue of Science and Technology, Indiana University - Purdue University Indianapolis, Department of Physics, University of Maryland, Naval Research Laboratory, Towson Univ, Rice University, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, Department of Physics, Temple University, PulseTorr LLC, Department of Chemistry, West Chester University, Department of Physics, West Chester University, College of William and Mary Dept. of Physics, University of Virginia Dept. of Materials Science and Engineering, United States Naval Academy, Rutgers The State University of New Jersey, Univ of Maryland-College Park, Los Alamos National Laboratory, POSTECH, New Jersey Institute of Technology, Department of Electrical and Computer Engineering, HamSCI/ARRL, Virginia Tech, Rutgers University-Camden, University of Washington, Rutgers, The State University of New Jersey

  • Debbie Andres

    Department of Applied Physics and Department of Physics, Columbia University, Istituto Italiano di Tecnologia, Graphene Labs, Italy, Department of Physics and Astronomy, Purdue University, Department of Electrical Engineering, Princeton University, Department of Applied Physics and Applied Mathematics, Columbia University, NJIT, New Jersey Inst of Technology, New Jersey Inst of Tech, New Jersey Institute of Technology, Center for Advanced Radiation Sources, University of Chicago, High Pressure Science and Technology Advanced Research, State University of New York at Stony Brook, Rutgers University, NIST, Brookhaven National Laboratory, University of Chicago, University of South Florida, ETH Zurich, Max Planck POSTECH/Korea Research Initiative, University of Virginia, Rutgers University - Camden, New Jersey Institute of technology, Shaanxi Normal University, Pohang Science and Technology University, Sungkyunkwan University, Northern Illinois University and Argonne National Laboratory, Beijing National Laboratory for Condensed Matter Physics , and Institute of Physics, Chinese Academy of Sciences, Rutgers U., Orsova Engineers, U.S. Naval Research Laboratory, Center for Space Science and Engineering Research, Virginia Tech, Virginia., Princeton University, NASA Goddard Space Flight Center, Villanova University, SOFIA/USRA, Jet Propulsion Laboratory, Hudson Regional Health Commision, Rutgers University, College of William & Mary, Department of Physics, Drexel University, Drexel University, Drexel Universty, University of Massachusetts Amherst, Pohang Institue of Science and Technology, Indiana University - Purdue University Indianapolis, Department of Physics, University of Maryland, Naval Research Laboratory, Towson Univ, Rice University, Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, Department of Physics, Temple University, PulseTorr LLC, Department of Chemistry, West Chester University, Department of Physics, West Chester University, College of William and Mary Dept. of Physics, University of Virginia Dept. of Materials Science and Engineering, United States Naval Academy, Rutgers The State University of New Jersey, Univ of Maryland-College Park, Los Alamos National Laboratory, POSTECH, New Jersey Institute of Technology, Department of Electrical and Computer Engineering, HamSCI/ARRL, Virginia Tech, Rutgers University-Camden, University of Washington, Rutgers, The State University of New Jersey