{
  "annotation_id": "07960407-e0fc-4075-9a64-560c83c2312e",
  "date_created": "2026-03-02T18:01:35.337000Z",
  "date_modified": "2026-03-02T18:01:35.337000Z",
  "file_hash": "1c6fd9e71419d8134b47e426b5b2ae468437ce3b72af7b1d131fca9c17bad43d",
  "private": false,
  "record": {
    "abstract": "In this work we analyze the possibility that soliton dynamics in a simple\nnonlinear model allows functionally relevant predictions of the behaviour of\nDNA. This suggestion was first put forward by Salerno [Phys. Rev. A, vol. 44,\np. 5292 (1991)] by showing results indicating that sine-Gordon kinks were set\nin motion at certain regions of a DNA sequence that include promoters. We\nrevisit that system and show that the observed behaviour has nothing to do with\npromoters; on the contrary, it originates from the bases at the boundary, which\nare not part of the studied genome. We explain this phenomenology in terms of\nan effective potential for the kink center. This is further extended to\ndisprove recent claims that the dynamics of kinks [Lenholm and H\\\"ornquist,\nPhysica D, vol. 177, p. 233 (2003)] or breathers [Bashford, J. Biol. Phys.,\nvol. 32, p. 27 (2006)] has functional significance. We conclude that no such\ninformation can be extracted from this simple nonlinear model or its associated\neffective potential.",
    "arxiv_id": "q-bio/0606028",
    "authors": [
      "Sara Cuenda",
      "Angel Sanchez",
      "Niurka R. Quintero"
    ],
    "categories": [
      "q-bio.GN",
      "math-ph",
      "math.MP",
      "nlin.PS",
      "q-bio.QM"
    ],
    "doi": "10.1016/j.physd.2006.09.005",
    "title": "Does the dynamics of sine-Gordon solitons predict active regions of DNA?",
    "url": "https://arxiv.org/abs/q-bio/0606028"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "7d5a541a-db6f-4012-9ee2-998a482afab0",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}