{
  "abstract": "We present a high-dimensional coarse-grained model of alanine dipeptide that explicitly incorporates global translation and rotation alongside internal conformational dynamics. Using atomistic molecular dynamics trajectories, we construct a 10-bead Markovian Langevin model with a 24-dimensional internal potential of mean force and a full matrix of site-specific friction coefficients. The equilibrium landscape is represented by a Gaussian mixture model, while a rotational-entropy correction accounts for the coupling between internal conformation and global molecular motion. Friction coefficients are obtained using a generalized Einstein relation based on time-correlation functions. We show that the rotational-entropy correction is essential for obtaining a physically admissible friction matrix and significantly affects the inferred dynamics. Without fitting to coarse-grained dynamical observables, the resulting model reproduces a broad range of atomistic auto- and cross-correlation functions. The result is a compact and interpretable dynamical representation of the entire peptide at the chosen CG resolution, which explicitly preserves distinctions between energetic and dissipative coupling over a wide range of motions, including those between conformational fluctuations and global translational and rotational diffusion.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2611.07200",
  "author_total": 2,
  "authors": [
    {
      "name": "Jesse M. Hall"
    },
    {
      "name": "Marina G. Guenza"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b4nazxtnmgj2w.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2611.07200",
  "fulltext_url": null,
  "id": "b4nazxtnmgj2w",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2611.07200",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "http://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": "CC0-1.0",
  "native_subjects": [
    [
      "arxiv",
      "cond-mat.soft"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://arxiv.org/pdf/2611.07200",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-04",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b4nazxtnmgj2w.ris",
  "sources": [
    {
      "first_seen": "2026-11-06T18:21:30Z",
      "native_id": "2611.07200",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2611.07200"
    }
  ],
  "subjects": [
    {
      "field": "physics",
      "origin": "arxiv:cond-mat.soft",
      "subfield": "condensed-matter"
    }
  ],
  "title": "A High-Dimensional Lab-Frame Model of Markovian Dynamics in Alanine Dipeptide",
  "title_text": "A High-Dimensional Lab-Frame Model of Markovian Dynamics in Alanine Dipeptide",
  "type": "preprint",
  "updated_at": "2026-11-09T00:20:40Z",
  "url": "https://research.draconitic.com/paper/b4nazxtnmgj2w",
  "venue": "arXiv",
  "versions": []
}