{
  "abstract": "Ion transport in electric fields and neutral gases underlies the operation of ion mobility spectrometers, mass spectrometers, and coupled IMS-MS instruments. Numerical modeling of such systems requires consistent treatment of field-driven motion, stochastic ion-neutral collisions, and reactions across different pressure and field regimes. Many IMS-MS instruments operate in transitional regimes, requiring explicit particle-based treatment of collisions. Here, we present ICARION (Ion Collision And Reaction IntegratiON), an open-source, modular, particle-based simulation framework for reproducible simulations of ion transport, collisions, and reactions. ICARION is intended for mechanistic studies of ion dynamics, exploration of new concepts in IMS, MS, and related techniques, and rapid and reproducible screening of operating parameters and geometries for instrument development and optimization. Its modular architecture combines various selectable field, collision, and reaction models with structured configuration and data processing. Multiple instrument domains with different electric fields, geometries, and environmental conditions can be seamlessly combined in a single simulation of coupled IMS-MS instruments. This work validates ICARION rather than introducing new physical models. Validation includes collisional thermalization, bimolecular reaction kinetics, ion transport in homogeneous electric fields validated with established tools, and coupled multidomain simulations. Across these cases, ICARION reproduces the expected behavior of the selected physical models and enables continuous simulations across domains differing by orders of magnitude in pressure and field time scales. While externally generated field maps can be integrated as needed, a planned internal field solver will enable the calculation of electric fields directly from the user-defined electrode configurations. The modular architecture also facilitates the integration of additional physical models.",
  "abstract_shown": true,
  "affiliations": [
    "Heyrovský Institute of the Czech Academy of Sciences , Dolejškova 3, Prague 818223, Czech Republic."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Christoph Schaefer",
      "orcid": "0000-0003-0687-078X"
    },
    {
      "affs": [
        0
      ],
      "name": "Juraj Jašík"
    },
    {
      "affs": [
        0
      ],
      "name": "Patrik Španěl"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d5dtj9ea8zxfp.bib",
  "cited_by": 0,
  "doi": "10.1021/jasms.6c00235",
  "fulltext_url": "https://europepmc.org/articles/PMC13651595",
  "id": "d5dtj9ea8zxfp",
  "issns": [
    "1044-0305",
    "1879-1123"
  ],
  "landing_url": "https://europepmc.org/article/MED/42916753",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1607|Mass Spectrometry Techniques and Applications"
    ]
  ],
  "openalex": "W7207679686",
  "pdf_url": "https://europepmc.org/articles/PMC13651595?pdf=render",
  "pmcid": "PMC13651595",
  "pmid": "42916753",
  "published": "2026-10-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/d5dtj9ea8zxfp.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:36Z",
      "native_id": "MED:42916753",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42916753"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1607|Mass Spectrometry Techniques and Applications",
      "subfield": "physical"
    }
  ],
  "title": "ICARION: A Modular Framework for Ion Trajectory Simulation in Electric Fields and Neutral Gas Environments.",
  "title_text": "ICARION: A Modular Framework for Ion Trajectory Simulation in Electric Fields and Neutral Gas Environments.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:20:36Z",
  "url": "https://research.draconitic.com/paper/d5dtj9ea8zxfp",
  "venue": "Journal of the American Society for Mass Spectrometry",
  "versions": []
}