{
  "annotation_id": "eb1839eb-ea38-4b6a-acaa-b8de959663d2",
  "date_created": "2026-03-02T18:00:43.083000Z",
  "date_modified": "2026-03-02T18:00:43.083000Z",
  "file_hash": "fbeb6d7e0c216dec8a77b1a2ad5df2d6ac7d0a341f0e48a1b05456ba728e5ffb",
  "private": false,
  "record": {
    "abstract": "A versatile approach to modeling the conformations and energetics of DNA\nloops is presented. The model is based on the classical theory of elasticity,\nmodified to describe the intrinsic twist and curvature of DNA, the DNA bending\nanisotropy, and electrostatic properties. All the model parameters are\nconsidered to be functions of the loop arclength, so that the DNA\nsequence-specific properties can be modeled. The model is applied to the test\ncase study of a DNA loop clamped by the lac repressor protein. Several\ntopologically different conformations are predicted for various lengths of the\nloop. The dependence of the predicted conformations on the parameters of the\nproblem is systematically investigated. Extensions of the presented model and\nthe scope of the model\u0027s applicability, including multi-scale simulations of\nprotein-DNA complexes and building all-atom structures on the basis of the\nmodel, are discussed.",
    "arxiv_id": "physics/0301006",
    "authors": [
      "Alexander Balaeff",
      "L. Mahadevan",
      "Klaus Schulten"
    ],
    "categories": [
      "physics.bio-ph",
      "q-bio"
    ],
    "title": "Modeling DNA loops using the theory of elasticity",
    "url": "https://arxiv.org/abs/physics/0301006"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "b626051b-0162-4520-ad17-04d3a1abc215",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}