{
  "abstract": "DNA often functions in heterogeneous molecular systems containing proteins, lipids, polymers, and other materials. All-atom molecular dynamics simulations can be used to study DNA in these multicomponent systems, but computational cost limits the accessible system sizes and time scales. Coarse-grained models extend these scales, but existing DNA models are generally not designed for interactions with a broad range of other molecular species. To fill this gap, we develop a coarse-grained model of DNA designed for use with the Martini 3 force field. The model was parameterized through an iterative Bayesian optimization workflow, which used a scaled Wasserstein metric to compare distributions of local geometrical features and global structure from coarse-grained simulations against all-atom reference simulations. The optimized model captures key structural and mechanical properties of single- and double-stranded DNA across varying strand lengths and ionic conditions, while retaining compatibility with the broader Martini 3 ecosystem. This compatibility enables DNA to be integrated with a broad range of molecular systems, as we illustrate through simulations of double-stranded DNA bound to a transcription factor, cholesterol-tagged DNA duplex interacting with a lipid bilayer, a crossover-containing DNA nanostructure, and single-stranded DNA adsorbing onto graphene. Together, these results establish a transferable coarse-grained model of DNA for simulations of heterogeneous biomolecular and engineered systems.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Mechanical Engineering and Materials Science, Duke University, Durham"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "R. Dargis"
    },
    {
      "affs": [
        0
      ],
      "name": "G. Arya"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b865r6y9vkj7b.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.14.751576",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1.full",
  "id": "b865r6y9vkj7b",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "1312|Protein Structure and Dynamics"
    ]
  ],
  "openalex": "W7213465044",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-14",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b865r6y9vkj7b.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:44Z",
      "native_id": "10.64898/2026.09.14.751576",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.14.751576v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems",
  "title_text": "Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems",
  "type": "preprint",
  "updated_at": "2026-10-30T12:22:44Z",
  "url": "https://research.draconitic.com/paper/b865r6y9vkj7b",
  "venue": "bioRxiv",
  "versions": []
}