{
  "abstract": "Agent-based models (ABMs) provide a natural framework for representing cell-level rules and spatial heterogeneity in bacterial infections, but their computational cost limits their use for macroscopic tissue-scale simulations and broad parameter exploration. We derive a deterministic coarse-grained description for a class of bacterial-infection ABMs in which immune cells and extracellular bacteria diffuse, immune cells ingest nearby bacteria, and intracellular bacterial loads evolve through prescribed birth and clearance processes. The first coarse-grained model is a semidiscrete reaction--diffusion system that retains a discrete internal state for each immune-cell bacterial load while representing cell and bacterial populations by continuum concentration fields. The key technical step is the derivation of state-dependent effective ingestion rates from the microscopic ABM parameters: these rates are obtained by solving an auxiliary diffusion problem around a single bacterium and computing the flux of immune cells into the interaction region. We then take a continuum limit in the internal state variable, yielding a state-structured reaction--diffusion system in which intracellular dynamics appear as advection and diffusion in state space. Numerical comparisons with ensemble-averaged ABM simulations show close agreement in biologically motivated parameter regimes. The resulting framework preserves the rule-based structure of the ABM while producing PDE models that are substantially more tractable for large-scale simulation and parameter studies.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": "2609.03212",
  "author_total": 2,
  "authors": [
    {
      "name": "Wesley J. M. Ridgway"
    },
    {
      "name": "Raymond J. Spiteri"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ak9mgtvsqyz07.bib",
  "cited_by": 0,
  "doi": "10.48550/arxiv.2609.03212",
  "fulltext_url": null,
  "id": "ak9mgtvsqyz07",
  "issns": [],
  "landing_url": "https://arxiv.org/abs/2609.03212",
  "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",
      "q-bio.CB"
    ],
    [
      "arxiv",
      "q-bio.PE"
    ],
    [
      "openalex",
      "2739|Mathematical and Theoretical Epidemiology and Ecology Models"
    ]
  ],
  "openalex": "W7208767914",
  "pdf_url": "https://arxiv.org/pdf/2609.03212",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-02",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ak9mgtvsqyz07.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:02Z",
      "native_id": "2609.03212",
      "source": "arxiv",
      "url": "https://arxiv.org/abs/2609.03212"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "arxiv:q-bio.CB",
      "subfield": "cell-biology"
    },
    {
      "field": "biology",
      "origin": "arxiv:q-bio.PE",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "Coarse-Graining Agent-Based Models of Bacterial Infections",
  "title_text": "Coarse-Graining Agent-Based Models of Bacterial Infections",
  "type": "preprint",
  "updated_at": "2026-10-30T12:20:02Z",
  "url": "https://research.draconitic.com/paper/ak9mgtvsqyz07",
  "venue": "arXiv",
  "versions": []
}