{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:00:55Z","timestamp":1791385255005,"version":"4.3.3"},"reference-count":43,"publisher":"American Chemical Society (ACS)","issue":"10","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["566668822"],"award-info":[{"award-number":["566668822"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1021\/jasms.6c00235","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T21:02:43Z","timestamp":1788469363000},"page":"2483-2496","source":"Crossref","is-referenced-by-count":0,"title":["ICARION: A Modular\nFramework for Ion Trajectory Simulation\nin Electric Fields and Neutral Gas Environments"],"prefix":"10.1021","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0687-078X","authenticated-orcid":true,"given":"Christoph","family":"Schaefer","sequence":"first","affiliation":[{"name":"Heyrovsky\u0301 Institute of the Czech Academy of Sciences , Dolejs\u030ckova 3 , ,","place":["Prague 8, Czech Republic, 18223"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juraj","family":"Jas\u030ci\u0301k","sequence":"additional","affiliation":[{"name":"Heyrovsky\u0301 Institute of the Czech Academy of Sciences , Dolejs\u030ckova 3 , ,","place":["Prague 8, Czech Republic, 18223"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrik","family":"S\u030cpane\u030cl","sequence":"additional","affiliation":[{"name":"Heyrovsky\u0301 Institute of the Czech Academy of Sciences , Dolejs\u030ckova 3 , ,","place":["Prague 8, Czech Republic, 18223"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"issue":"3","key":"2026100710065434500_cit1","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1021\/ac504720m","article-title":"Ion mobility-mass spectrometry: time-dispersive instrumentation","volume":"87","author":"May","year":"2015","journal-title":"Anal. Chem."},{"issue":"1","key":"2026100710065434500_cit2","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1002\/mas.21349","article-title":"Ion mobility\nspectrometry-mass spectrometry\n(IMS-MS) of small molecules: separating and assigning structures to\nions","volume":"32","author":"Lapthorn","year":"2013","journal-title":"Mass Spectrom. Rev."},{"key":"2026100710065434500_cit3","doi-asserted-by":"publisher","DOI":"10.1002\/3527602852","volume-title":"Transport Properties\nof Ions in Gases","author":"Mason","year":"1988"},{"issue":"7","key":"2026100710065434500_cit4","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1021\/ac60357a043","article-title":"Theory of plasma chromatography\/gaseous\nelectrophoresis.\nReview","volume":"47","author":"Revercomb","year":"1975","journal-title":"Anal. Chem."},{"issue":"1","key":"2026100710065434500_cit5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijms.2005.03.010","article-title":"SIMION ion optics\nsimulations at atmospheric pressure","volume":"244","author":"Appelhans","year":"2005","journal-title":"Int. J.\nMass Spectrom."},{"issue":"1\u20133","key":"2026100710065434500_cit6","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/S1387-3806(00)00305-5","article-title":"SIMION\nfor the personal computer in reflection","volume":"200","author":"Dahl","year":"2000","journal-title":"Int.\nJ. Mass Spectrom."},{"issue":"7","key":"2026100710065434500_cit7","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1021\/jasms.4c00054","article-title":"IDSimF: An Open-Source\nFramework for the Simulation\nof Molecular Ion Dynamics in Mass Spectrometry and Ion Mobility Spectrometry","volume":"35","author":"Rajkovic","year":"2024","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"24","key":"2026100710065434500_cit8","doi-asserted-by":"publisher","first-page":"9689","DOI":"10.1021\/ac8016295","article-title":"Fundamentals of\ntraveling wave ion mobility spectrometry","volume":"80","author":"Shvartsburg","year":"2008","journal-title":"Anal.\nChem."},{"issue":"20","key":"2026100710065434500_cit9","doi-asserted-by":"publisher","first-page":"2401","DOI":"10.1002\/rcm.1641","article-title":"Applications of a travelling wave-based radio-frequency-only\nstacked ring ion guide","volume":"18","author":"Giles","year":"2004","journal-title":"Rapid Commun. Mass Spectrom."},{"issue":"1","key":"2026100710065434500_cit10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijms.2008.06.011","article-title":"The predictive\npower of SIMION\/SDS simulation software for modeling ion mobility\nspectrometry instruments","volume":"276","author":"Lai","year":"2008","journal-title":"Int. J. Mass Spectrom."},{"issue":"11","key":"2026100710065434500_cit11","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1016\/S1044-0305(02)00622-0","article-title":"Improved ion extraction from a linear\noctopole ion trap: SIMION analysis and experimental demonstration","volume":"13","author":"Wilcox","year":"2002","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"21","key":"2026100710065434500_cit12","doi-asserted-by":"publisher","first-page":"8749","DOI":"10.1021\/ac900880v","article-title":"Simulation of ion motion in FAIMS\nthrough combined\nuse of SIMION and modified SDS","volume":"81","author":"Prasad","year":"2009","journal-title":"Anal. Chem."},{"key":"2026100710065434500_cit13","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S0168-1176(97)00074-8","article-title":"Effect\nof ion-neutral collision mechanism\non the trapped-ion equation of motion: a new mass spectral line shape\nfor high-mass trapped ions","volume":"167\u2013168","author":"Guan","year":"1997","journal-title":"Int. J. Mass Spectrom.\nIon Processes"},{"issue":"17","key":"2026100710065434500_cit14","doi-asserted-by":"publisher","first-page":"11155","DOI":"10.5194\/acp-22-11155-2022","article-title":"Modeling approaches\nfor atmospheric ion\u2013dipole collisions: all-atom trajectory\nsimulations and central field methods","volume":"22","author":"Neefjes","year":"2022","journal-title":"Atmos.\nChem. Phys."},{"issue":"20","key":"2026100710065434500_cit15","doi-asserted-by":"publisher","first-page":"6845","DOI":"10.1039\/C5AN00844A","article-title":"Ion manipulations\nin structures for lossless ion manipulations (SLIM): computational\nevaluation of a 90 degrees turn and a switch","volume":"140","author":"Garimella","year":"2015","journal-title":"Analyst"},{"issue":"3","key":"2026100710065434500_cit16","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1021\/acs.analchem.6b04500","article-title":"Ion Elevators and Escalators in Multilevel Structures\nfor Lossless Ion Manipulations","volume":"89","author":"Ibrahim","year":"2017","journal-title":"Anal. Chem."},{"issue":"8","key":"2026100710065434500_cit17","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1039\/C3AN02174B","article-title":"Ion dynamics in a trapped ion mobility spectrometer","volume":"139","author":"Hernandez","year":"2014","journal-title":"Analyst"},{"issue":"1","key":"2026100710065434500_cit18","doi-asserted-by":"publisher","first-page":"012326","DOI":"10.1103\/PhysRevA.73.012326","article-title":"High-fidelity simulations\nof ion trajectories in miniature ion traps using the boundary-element\nmethod","volume":"73","author":"Brkic\u0301","year":"2006","journal-title":"Phys. Rev. A"},{"issue":"10","key":"2026100710065434500_cit19","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1021\/jasms.3c00139","article-title":"Molecular\nDynamics-Based Modeling\nof Ion-Neutral Collisions in an Open Ion Trajectory Simulation Framework","volume":"34","author":"Rajkovic","year":"2023","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"9","key":"2026100710065434500_cit20","doi-asserted-by":"publisher","first-page":"1216","DOI":"10.1016\/j.jasms.2006.05.004","article-title":"Ion trajectory simulation for electrode\nconfigurations\nwith arbitrary geometries","volume":"17","author":"Wu","year":"2006","journal-title":"J. Am. Soc. Mass\nSpectrom."},{"key":"2026100710065434500_cit21","doi-asserted-by":"publisher","first-page":"15730","DOI":"10.1021\/acs.analchem.6c01278","article-title":"Ion Mobility\nSuite (IMoS) 2: A General Computational Framework for Solving the\nGeneralized Boltzmann Equation with Rotational Transport for Polyatomic\nIons in Arbitrary Fields","volume":"98","author":"Larriba-Andaluz","year":"2026","journal-title":"Anal. Chem."},{"key":"2026100710065434500_cit22","unstructured":"Schaefer, C.\n          \n          ICARION:\nion Collision And Reaction IntegratiON; Zenodo, 2026. 10.5281\/zenodo.20455416."},{"key":"2026100710065434500_cit23","unstructured":"HDF Group.\n          \n          HDF5, version 1.10.10; The HDF\nGroup, 2023."},{"key":"2026100710065434500_cit24","volume-title":"Data for\n\u2018ICARION: a Modular Framework for Ion Trajectory Simulation\nin Electric Fields and Neutral Gas Environments\u2019","author":"Schaefer","year":"2026"},{"issue":"14","key":"2026100710065434500_cit25","doi-asserted-by":"publisher","first-page":"3257","DOI":"10.1039\/D3AN00545C","article-title":"MobCal-MPI 2.0: an accurate and parallelized\npackage for calculating field-dependent collision cross sections and\nion mobilities","volume":"148","author":"Haack","year":"2023","journal-title":"Analyst"},{"issue":"4","key":"2026100710065434500_cit26","doi-asserted-by":"publisher","first-page":"046405","DOI":"10.1103\/PhysRevE.67.046405","article-title":"Monte Carlo\nmodel of ion mobility and diffusion for\nlow and high electric fields","volume":"67","author":"Robertson","year":"2003","journal-title":"Phys. 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Method","volume":"308","author":"Bleiholder","year":"2011","journal-title":"Int. J. Mass Spectrom."},{"issue":"19","key":"2026100710065434500_cit30","doi-asserted-by":"publisher","first-page":"5806","DOI":"10.1021\/jp8111556","article-title":"Consistent\nvan der Waals radii for the whole main group","volume":"113","author":"Mantina","year":"2009","journal-title":"J. Phys. Chem. A"},{"issue":"1\u20132","key":"2026100710065434500_cit31","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/0009-2614(96)00941-4","article-title":"An exact hard-spheres\nscattering model for the mobilities\nof polyatomic ions","volume":"261","author":"Shvartsburg","year":"1996","journal-title":"Chem. Phys. Lett."},{"issue":"19","key":"2026100710065434500_cit32","doi-asserted-by":"publisher","first-page":"3887","DOI":"10.1021\/jp312432z","article-title":"Ion mobilities in diatomic gases:\nmeasurement versus\nprediction with non-specular scattering models","volume":"117","author":"Larriba-Andaluz","year":"2013","journal-title":"J. Phys. Chem. A"},{"key":"2026100710065434500_cit33","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/j.jcp.2013.05.038","article-title":"Free molecular collision cross section calculation\nmethods for nanoparticles and complex ions with energy accommodation","volume":"251","author":"Larriba-Andaluz","year":"2013","journal-title":"J. Comput. Phys."},{"issue":"2","key":"2026100710065434500_cit34","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.70019","article-title":"Software Update:\nThe ORCA Program System\u2500Version 6.0","volume":"15","author":"Neese","year":"2025","journal-title":"Wiley Interdiscip. Rev.: Comput. Mol. Sci."},{"issue":"1","key":"2026100710065434500_cit35","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1021\/ct300715s","article-title":"Long-Range Corrected\nHybrid Density Functionals with Improved Dispersion Corrections","volume":"9","author":"Lin","year":"2013","journal-title":"J. Chem. Theory Comput."},{"issue":"18","key":"2026100710065434500_cit36","doi-asserted-by":"publisher","first-page":"3297","DOI":"10.1039\/b508541a","article-title":"Balanced basis sets\nof split valence, triple zeta valence\nand quadruple zeta valence quality for H to Rn: Design and assessment\nof accuracy","volume":"7","author":"Weigend","year":"2005","journal-title":"Phys. Chem. Chem. Phys."},{"issue":"1\u20133","key":"2026100710065434500_cit37","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.chemphys.2008.10.036","article-title":"Efficient, approximate\nand parallel Hartree-Fo.ck and hybrid DFT calculations. A \u2018chain-of-spheres\u2019\nalgorithm for the Hartree-Fock exchange","volume":"356","author":"Neese","year":"2009","journal-title":"Chem.\nPhys."},{"issue":"3","key":"2026100710065434500_cit38","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1002\/jcc.540110311","article-title":"Determining atom-centered\nmonopoles from molecular\nelectrostatic potentials. The need for high sampling density in formamide\nconformational analysis","volume":"11","author":"Breneman","year":"1990","journal-title":"J. Comput. Chem."},{"issue":"12","key":"2026100710065434500_cit39","doi-asserted-by":"publisher","first-page":"2630","DOI":"10.1021\/jasms.3c00312","article-title":"Robust Automated SIFT-MS\nQuantitation of Volatile Compounds in Air Using a Multicomponent Gas\nStandard","volume":"34","author":"Langford","year":"2023","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2026100710065434500_cit40","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/j.ijms.2017.04.006","article-title":"Calculation of the sensitivity of\nproton-transfer-reaction mass spectrometry (PTR-MS) for organic trace\ngases using molecular properties","volume":"421","author":"Sekimoto","year":"2017","journal-title":"Int. J. Mass\nSpectrom."},{"issue":"30","key":"2026100710065434500_cit41","doi-asserted-by":"publisher","first-page":"12433","DOI":"10.1021\/acs.analchem.4c02010","article-title":"On the Arrival Time Distribution\nof Reacting Systems in Ion Mobility Spectrometry","volume":"96","author":"Haack","year":"2024","journal-title":"Anal. Chem."},{"issue":"8","key":"2026100710065434500_cit42","doi-asserted-by":"publisher","first-page":"1384","DOI":"10.1007\/s13361-014-0909-9","article-title":"Fragmentation and isomerization\ndue\nto field heating in traveling wave ion mobility spectrometry","volume":"25","author":"Morsa","year":"2014","journal-title":"J. Am. Soc. Mass Spectrom."},{"issue":"16","key":"2026100710065434500_cit43","doi-asserted-by":"publisher","first-page":"6450","DOI":"10.1021\/acs.analchem.4c00692","article-title":"Altering Conformational\nStates of Dynamic Ion Populations\nusing Traveling Wave Structures for Lossless Ion Manipulations","volume":"96","author":"Kinlein","year":"2024","journal-title":"Anal. Chem."}],"container-title":["Journal of the American\nSociety for Mass Spectrometry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/jasms.6c00235","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2483\/68293181\/jasms.6c00235.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jamsef\/article-pdf\/37\/10\/2483\/68293181\/jasms.6c00235.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T14:32:17Z","timestamp":1791383537000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jamsef\/article\/37\/10\/2483\/5413964\/ICARION-A-Modular-Framework-for-Ion-Trajectory"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,3]]},"references-count":43,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,9,3]]},"published-print":{"date-parts":[[2026,10,7]]}},"URL":"https:\/\/doi.org\/10.1021\/jasms.6c00235","relation":{},"ISSN":["1044-0305","1879-1123"],"issn-type":[{"value":"1044-0305","type":"print"},{"value":"1879-1123","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,3]]}}}