{
  "annotation_id": "ae2b3f5e-ffd1-4235-a614-e84d693d1e3f",
  "date_created": "2026-03-02T18:01:31.941000Z",
  "date_modified": "2026-03-02T18:01:31.941000Z",
  "file_hash": "e6d9085fc5a250aaace2927e5bbf8bd8daffa74fea4f488f710581c3c0303ad2",
  "private": false,
  "record": {
    "abstract": "The kinetic folding of RNA sequences into secondary structures is modeled as\na complex adaptive system, the components of which are possible RNA structural\nrearrangements (SRs) and their associated bases and base pairs. RNA bases and\nbase pairs engage in local stacking interactions that determine the\nprobabilities (or fitnesses) of possible SRs. Meanwhile, selection operates at\nthe level of SRs; an autonomous stochastic process periodically (i.e., from one\ntime step to another) selects a subset of possible SRs for realization based on\nthe fitnesses of the SRs. Using examples based on selected natural and\nsynthetic RNAs, the model is shown to qualitatively reproduce characteristic\n(nonlinear) RNA folding dynamics such as the attainment by RNAs of alternative\nstable states. Possible applications of the model to the analysis of properties\nof fitness landscapes, and of the RNA sequence to structure mapping are\ndiscussed.",
    "arxiv_id": "q-bio/0507039",
    "authors": [
      "Wilfred Ndifon"
    ],
    "categories": [
      "q-bio.BM",
      "nlin.AO"
    ],
    "doi": "10.1016/j.biosystems.2005.08.004",
    "title": "A complex adaptive systems approach to the kinetic folding of RNA",
    "url": "https://arxiv.org/abs/q-bio/0507039"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "be5785c8-f54a-457d-b0b4-ad42e012d12e",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}