{
  "annotation_id": "6cf4878d-110a-4001-a13f-3ab9d168ec5c",
  "date_created": "2026-03-02T18:01:31.921000Z",
  "date_modified": "2026-03-02T18:01:31.921000Z",
  "file_hash": "b02f4f0156576218de7774d8136c1dd4cf3a49b17d86d56c7506b54918c8ba0d",
  "private": false,
  "record": {
    "abstract": "We study the size fluctuations of a local denaturation zone in a DNA molecule\nin the presence of proteins that selectively bind to single-stranded DNA, based\non a (2+1)-dimensional master equation. By tuning the physical parameters we\ncan drive the system from undisturbed bubble fluctuations to full, binding\nprotein-induced denaturation. We determine the effective free energy landscape\nof the DNA-bubble and explore its relaxation modes.",
    "arxiv_id": "q-bio/0411053",
    "authors": [
      "Tobias Ambjornsson",
      "Ralf Metzler"
    ],
    "categories": [
      "q-bio.BM",
      "cond-mat.stat-mech"
    ],
    "title": "Coupled dynamics of DNA-breathing and single-stranded DNA binding   proteins",
    "url": "https://arxiv.org/abs/q-bio/0411053"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "bb99b927-4dda-4c8e-a140-30cddc6f7767",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}