{
  "abstract": "Morphogenesis of diatom silica shells involves a sequence of topological transitions: initially separate ribs grow and branch, then merge through bridges, leaving a regular network of pores. Existing models based on diffusion-limited aggregation or reaction-diffusion reproduce either branching or pore formation, but not both within a single framework. Here we propose a two-stage model of diffusion-driven morphogenesis with evolving connectivity. The model is formulated on a fixed finite element mesh with a density field on an active layer. Stage 1 reproduces dendritic growth, where a stimulus based on the local diffusive flux exceeds a threshold. Stage 2 uses an inverted stimulus, where high local flux suppresses precipitation, stabilizing pores between the dendrites. The update rules are analogous to sensitivity in density-based topology optimization and to strain energy density in bone remodeling. The model predicts distinct morphological regimes on each stage, controlled by the respective thresholds. For a reference calculation, the predicted pore network is regular, with approximately uniform spacing, and pores are absent near the domain edges, consistent with observations on diatom valves. The model provides a unified framework for describing both stages of silica morphogenesis and suggests a route for comparing computational predictions with cryo-electron tomography data.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2610.41798",
  "author_total": 1,
  "authors": [
    {
      "name": "Alexander Safonov"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bcmcsd82snxvm.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2610.41798",
  "fulltext_url": null,
  "id": "bcmcsd82snxvm",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2610.41798",
  "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",
      "cs.ET"
    ],
    [
      "arxiv",
      "q-bio.QM"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://arxiv.org/pdf/2610.41798",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-30",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bcmcsd82snxvm.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T12:21:21Z",
      "native_id": "2610.41798",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2610.41798"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.QM",
      "subfield": "bioinformatics"
    }
  ],
  "title": "A two-stage diffusion-driven morphogenesis model with evolving connectivity",
  "title_text": "A two-stage diffusion-driven morphogenesis model with evolving connectivity",
  "type": "preprint",
  "updated_at": "2026-11-04T15:20:53Z",
  "url": "https://research.draconitic.com/paper/bcmcsd82snxvm",
  "venue": "arXiv",
  "versions": []
}