{
  "abstract": "To reduce health risks for human space exploration, it is important to model the effects of deep-space radiation on biological systems. The budding yeast Saccharomyces cerevisiae is a common model organism in space radiobiology, but little is known about how radiation damage to individual cells translates into the population-level effects that experiments measure. The Agent-Based Model for Microbial Populations Exposed to Radiation (AMMPER) is a spatially explicit agent-based model that simulates the effects of ionizing radiation on S. cerevisiae cells and produces population-level results. Its goal is to improve experiment design and data interpretation. AMMPER-1 demonstrated that agent-based simulations can qualitatively reproduce the effects of proton radiation on the growth rate of wild-type and DNA-repair mutant yeast. Here, we present AMMPER-2, which addresses limitations of the first model and expands its capabilities. AMMPER-2 incorporates the dynamics of the redox dye alamarBlue, a data type commonly generated in spaceflight microbiology experiments, and models the fate of reactive oxygen species in more detail. It also adds an improved graphical interface and runs faster. AMMPER-2 remains easy to execute in Python on a standard personal laptop, providing space biologists a tool to explore experimental conditions, generate hypotheses, and interpret data from microbial space radiation experiments.",
  "abstract_shown": true,
  "affiliations": [
    "NASA Ames Research Center"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "name": "D. Palacios"
    },
    {
      "affs": [
        0
      ],
      "name": "J. Lee"
    },
    {
      "name": "P. Sharma"
    },
    {
      "name": "M. Marous"
    },
    {
      "name": "D. Mejia"
    },
    {
      "name": "L. Liddell"
    },
    {
      "name": "D. Gentry"
    },
    {
      "name": "S. Santa Maria"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bcjbk389spafa.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.08.757403",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.08.757403v1.full",
  "id": "bcjbk389spafa",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.08.757403v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "openalex",
      "2741|Effects of Radiation Exposure"
    ]
  ],
  "openalex": "W7221360874",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.08.757403v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-08",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bcjbk389spafa.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:58Z",
      "native_id": "10.64898/2026.10.08.757403",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.08.757403v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "AMMPER-2: A spatially explicit agent-based model of microbial radiobiology with redox dye simulation",
  "title_text": "AMMPER-2: A spatially explicit agent-based model of microbial radiobiology with redox dye simulation",
  "type": "preprint",
  "updated_at": "2026-10-30T12:28:17Z",
  "url": "https://research.draconitic.com/paper/bcjbk389spafa",
  "venue": "bioRxiv",
  "versions": []
}