{
  "annotation_id": "2d6673db-62fe-4792-b088-26db157a4308",
  "date_created": "2026-03-02T18:01:31.482000Z",
  "date_modified": "2026-03-02T18:01:31.482000Z",
  "file_hash": "733dbf867a5ef8eeeb7fd34fd111d1af4cbde19976172d5bfafb7206032a6f22",
  "private": false,
  "record": {
    "abstract": "We study the effects of the sequence on the propagation of nonlinear\nexcitations in simple models of DNA in which we incorporate actual DNA\nsequences obtained from human genome data. We show that kink propagation\nrequires forces over a certain threshold, a phenomenon already found for\naperiodic sequences [F. Dom\\\u0027\\i nguez-Adame {\\em et al.}, Phys. Rev. E {\\bf\n52}, 2183 (1995)]. For forces below threshold, the final stop positions are\nhighly dependent on the specific sequence. The results of our model are\nconsistent with the stick-slip dynamics of the unzipping process observed in\nexperiments. We also show that the effective potential, a collective coordinate\nformalism introduced by Salerno and Kivshar [Phys. Lett. A {\\bf 193}, 263\n(1994)] is a useful tool to identify key regions in DNA that control the\ndynamical behavior of large segments. Additionally, our results lead to further\ninsights in the phenomenology observed in aperiodic systems.",
    "arxiv_id": "q-bio/0407002",
    "authors": [
      "Sara Cuenda",
      "Angel Sanchez"
    ],
    "categories": [
      "q-bio.GN",
      "cond-mat.soft",
      "math-ph",
      "math.MP",
      "nlin.PS",
      "q-bio.BM"
    ],
    "doi": "10.1103/PhysRevE.70.051903",
    "title": "Nonlinear excitations in DNA: Aperiodic models vs actual genome   sequences",
    "url": "https://arxiv.org/abs/q-bio/0407002"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "1f0ff123-f253-44f7-853b-114cfdb22d48",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}