{
  "abstract": "Vertex models simulate epithelial mechanics at single-cell resolution but represent cell division as a single in-plane split, agnostic to the differential apicobasal geometry of mitotic cells. Here, we present a protocol that simulates basal mitosis as two sequential changes: basal-cell diminution followed by daughter-cell reinsertion. Apical-side simulations can be performed with minimal code modification. We provide instructions for generating initial configurations, running simulations, and quantifying mechanical and topological rearrangements using command-line operations accessible to experimental biologists.\n\nFor complete details on the use and execution of this protocol, please refer to Ramanathan et al.1",
  "abstract_shown": true,
  "affiliations": [
    "Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.",
    "Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.",
    "Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.",
    "Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA. Electronic address: sramanathan@unmc.edu."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "name": "Tanmoy Sarkar"
    },
    {
      "affs": [
        0
      ],
      "name": "Jeffrey J Lovelace"
    },
    {
      "affs": [
        1
      ],
      "name": "Matej Krajnc"
    },
    {
      "affs": [
        2
      ],
      "name": "Rosemary Mwithiga"
    },
    {
      "affs": [
        3
      ],
      "name": "Subramanian P Ramanathan",
      "orcid": "0000-0002-2876-0322"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9wwzcrk109n6h.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104909",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13698043/",
  "id": "9wwzcrk109n6h",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://doi.org/10.1016/j.xpro.2026.104909",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Protocol"
    ],
    [
      "openalex",
      "1307|Cellular Mechanics and Interactions"
    ]
  ],
  "openalex": "W7222943280",
  "pdf_url": "https://europepmc.org/articles/PMC13698043?pdf=render",
  "pmcid": "PMC13698043",
  "pmid": "42900585",
  "published": "2026-10-19",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/9wwzcrk109n6h.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:00Z",
      "native_id": "PMC13698043",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.xpro.2026.104909"
    },
    {
      "first_seen": "2026-10-30T12:19:33Z",
      "native_id": "MED:42900585",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42900585"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1307|Cellular Mechanics and Interactions",
      "subfield": "cell-biology"
    }
  ],
  "title": "Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model",
  "title_text": "Protocol for simulating cell-contact dynamics of proliferating epithelia using the vertex model",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:34:58Z",
  "url": "https://research.draconitic.com/paper/9wwzcrk109n6h",
  "venue": "STAR Protocols",
  "versions": []
}