{
  "id": "0801.3947",
  "version": "v2",
  "published": "2008-01-25T19:46:11.000Z",
  "updated": "2009-08-03T19:25:06.000Z",
  "title": "Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule",
  "authors": [
    "Henk Vocks",
    "Debabrata Panja",
    "Gerard T. Barkema"
  ],
  "comment": "Significantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matter",
  "journal": "J. Phys.: Condens. Matter 21, 375105 (2009)",
  "doi": "10.1088/0953-8984/21/37/375105",
  "categories": [
    "cond-mat.stat-mech",
    "cond-mat.soft",
    "physics.bio-ph",
    "q-bio.BM"
  ],
  "abstract": "Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed study of these thermal fluctuations, including the frequency spectrum, and show that these rule out single-nucleotide resolution under the experimental conditions which we simulated. Two possible ways to improve this resolution are strong stretching of the RNA with a back-pulling voltage across the membrane, and stiffening of the translocated part of the RNA by biochemical means.",
  "revisions": [
    {
      "version": "v2",
      "updated": "2009-08-03T19:25:06.000Z"
    }
  ],
  "analyses": {
    "keywords": [
      "thermal fluctuations",
      "translocating rna molecule",
      "frequency spectrum",
      "secondary structure",
      "solid-state nanopore"
    ],
    "tags": [
      "journal article"
    ],
    "publication": {
      "journal": "Journal of Physics Condensed Matter",
      "year": 2009,
      "month": "Sep",
      "volume": 21,
      "number": 37,
      "pages": 375105
    },
    "note": {
      "typesetting": "TeX",
      "pages": 13,
      "language": "en",
      "license": "arXiv",
      "status": "editable",
      "adsabs": "2009JPCM...21.5105V"
    }
  }
}