{
  "annotation_id": "65f72243-0dd6-440c-97f4-284f8ea5d910",
  "date_created": "2026-03-02T18:01:35.490000Z",
  "date_modified": "2026-03-02T18:01:35.490000Z",
  "file_hash": "09dd9bbe3d2ecfac8689ad77938b61f605fa36c5fe26bcb6dcda52a424b9af82",
  "private": false,
  "record": {
    "abstract": "The Yakushevich (Y) model provides a very simple pictures of DNA torsion\ndynamics, yet yields remarkably correct predictions on certain physical\ncharacteristics of the dynamics. In the standard Y model, the interaction\nbetween bases of a pair is modelled by a harmonic potential, which becomes\nanharmonic when described in terms of the rotation angles; here we substitute\nto this different types of improved potentials, providing a more physical\ndescription of the H-bond mediated interactions between the bases. We focus in\nparticular on soliton solutions; the Y model predicts the correct size of the\nnonlinear excitations supposed to model the ``transcription bubbles\u0027\u0027, and this\nis essentially unchanged with the improved potential. Other features of soliton\ndynamics, in particular curvature of soliton field configurations and the\nPeierls-Nabarro barrier, are instead significantly changed.",
    "arxiv_id": "q-bio/0604004",
    "authors": [
      "G. Gaeta"
    ],
    "categories": [
      "q-bio.BM"
    ],
    "doi": "10.2991/jnmp.2007.14.1.6",
    "journal_ref": "J. Nonlin. Math. Phys. 14 (2007), 57-81",
    "title": "Solitons in Yakushevich-like models of DNA dynamics with improved   intrapair potential",
    "url": "https://arxiv.org/abs/q-bio/0604004"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "7c9b7cf6-baab-414e-8b93-637fe1ea5da5",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}