{
  "annotation_id": "b8f7c19f-d103-42ea-bb72-2653667aefa8",
  "date_created": "2026-03-02T18:01:32.168000Z",
  "date_modified": "2026-03-02T18:01:32.168000Z",
  "file_hash": "5b3e5d4fc478643bbbe975bd34845f860ef3d79bb67819647bba57bf73ba326c",
  "private": false,
  "record": {
    "abstract": "The replica exchange molecular dynamics (REMD) approach is applied to four\noligomeric peptide systems. At physiologically relevant temperature values REMD\nsamples conformation space and aggregation transitions more efficiently than\nconstant temperature molecular dynamics (CTMD). During the aggregation process\nthe energetic and structural properties are essentially the same in REMD and\nCTMD. A condensation stage toward disordered aggregates precedes the\n$\\beta$-sheet formation. Two order parameters, borrowed from anisotropic fluid\nanalysis, are used to monitor the aggregation process. The order parameters do\nnot depend on the peptide sequence and length and therefore allow to compare\nthe amyloidogenic propensity of different peptides.",
    "arxiv_id": "q-bio/0409021",
    "authors": [
      "M. Cecchini",
      "F. Rao",
      "M. Seeber",
      "A. Caflisch"
    ],
    "categories": [
      "q-bio.BM",
      "cond-mat.soft"
    ],
    "doi": "10.1063/1.1809588",
    "title": "Replica exchange molecular dynamics simulations of amyloid peptide   aggregation",
    "url": "https://arxiv.org/abs/q-bio/0409021"
  },
  "schema_id": "dorsal/arxiv",
  "source": {
    "execution_id": "b67deea1-d711-44a2-a82d-68da0b3c2484",
    "id": "arXiv Dataset IDs",
    "type": "Model",
    "variant": "snapshot-2026-03-01",
    "version": "0.1.0"
  },
  "user_id": 1000002
}