{"id":"https://openalex.org/W7221360874","doi":"https://doi.org/10.64898/2026.10.08.757403","title":"AMMPER-2: A spatially explicit agent-based model of microbial radiobiology with redox dye simulation","display_name":"AMMPER-2: A spatially explicit agent-based model of microbial radiobiology with redox dye simulation","publication_year":2026,"publication_date":"2026-10-10","ids":{"openalex":"https://openalex.org/W7221360874","doi":"https://doi.org/10.64898/2026.10.08.757403"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.08.757403","doi":"https://doi.org/10.64898/2026.10.08.757403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.08.757403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.08.757403.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102742819","display_name":"Daniel Palacios","orcid":"https://orcid.org/0000-0001-9608-3311","observed_orcids":["https://orcid.org/0000-0001-9608-3311"]},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210147586","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210147586"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Palacios","raw_affiliation_strings":["Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA","Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, Texas 77030, USA","Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA"],"raw_orcid":"https://orcid.org/0000-0001-9608-3311","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Jan and Dan Duncan Neurological Research Institute, Texas Children\u2019s Hospital, Houston, Texas 77030, USA","institution_ids":["https://openalex.org/I4210147586"]},{"raw_affiliation_string":"Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143403710","display_name":"Pramesh Sharma","orcid":"https://orcid.org/0000-0001-6228-0608","observed_orcids":["https://orcid.org/0000-0001-6228-0608"]},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pramesh Sharma","raw_affiliation_strings":["Department of Computer Science, University of California Davis, Davis, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-6228-0608","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5157888876","display_name":"Madeline Marous","orcid":"https://orcid.org/0009-0004-3670-2546","observed_orcids":["https://orcid.org/0009-0004-3670-2546"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Madeline Marou\u0161","raw_affiliation_strings":["Department of Information Sciences and Technology, Penn State Berks, Reading, PA, USA"],"raw_orcid":"https://orcid.org/0009-0004-3670-2546","affiliations":[{"raw_affiliation_string":"Department of Information Sciences and Technology, Penn State Berks, Reading, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5157943295","display_name":"Danny Mejia","orcid":"https://orcid.org/0009-0000-8351-8398","observed_orcids":["https://orcid.org/0009-0000-8351-8398"]},"institutions":[{"id":"https://openalex.org/I166466826","display_name":"Miami Dade College","ror":"https://ror.org/00rgbr518","country_code":"US","type":"education","lineage":["https://openalex.org/I166466826"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danny Mejia","raw_affiliation_strings":["Miami Dade College, Miami, FL, USA"],"raw_orcid":"https://orcid.org/0009-0000-8351-8398","affiliations":[{"raw_affiliation_string":"Miami Dade College, Miami, FL, USA","institution_ids":["https://openalex.org/I166466826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076633038","display_name":"Lauren C. Liddell","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lauren C. Liddell","raw_affiliation_strings":["Logyx LLC, Mountain View, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Logyx LLC, Mountain View, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000405161","display_name":"Diana M. Gentry","orcid":"https://orcid.org/0000-0002-8009-1816","observed_orcids":["https://orcid.org/0000-0002-8009-1816"]},"institutions":[{"id":"https://openalex.org/I1280536761","display_name":"Ames Research Center","ror":"https://ror.org/02acart68","country_code":"US","type":"facility","lineage":["https://openalex.org/I1280536761","https://openalex.org/I4210124779"]},{"id":"https://openalex.org/I4391768265","display_name":"NASA Earth Science","ror":"https://ror.org/045s99b94","country_code":"US","type":"government","lineage":["https://openalex.org/I4210124779","https://openalex.org/I4391768265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diana M. Gentry","raw_affiliation_strings":["Earth Sciences Division, NASA Ames Research Center, Moffett Field, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-8009-1816","affiliations":[{"raw_affiliation_string":"Earth Sciences Division, NASA Ames Research Center, Moffett Field, CA, USA","institution_ids":["https://openalex.org/I1280536761","https://openalex.org/I4391768265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078390703","display_name":"Sergio R. Santa Maria","orcid":"https://orcid.org/0000-0003-1300-4329","observed_orcids":["https://orcid.org/0000-0003-1300-4329"]},"institutions":[{"id":"https://openalex.org/I1280536761","display_name":"Ames Research Center","ror":"https://ror.org/02acart68","country_code":"US","type":"facility","lineage":["https://openalex.org/I1280536761","https://openalex.org/I4210124779"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergio R. Santa Maria","raw_affiliation_strings":["Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1300-4329","affiliations":[{"raw_affiliation_string":"Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA","institution_ids":["https://openalex.org/I1280536761"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013994582","display_name":"Jessica A. Lee","orcid":"https://orcid.org/0000-0002-0250-4064","observed_orcids":["https://orcid.org/0000-0002-0250-4064"]},"institutions":[{"id":"https://openalex.org/I1280536761","display_name":"Ames Research Center","ror":"https://ror.org/02acart68","country_code":"US","type":"facility","lineage":["https://openalex.org/I1280536761","https://openalex.org/I4210124779"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jessica A. Lee","raw_affiliation_strings":["Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-0250-4064","affiliations":[{"raw_affiliation_string":"Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA","institution_ids":["https://openalex.org/I1280536761"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5013994582"],"corresponding_institution_ids":["https://openalex.org/I1280536761"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11359","display_name":"Effects of Radiation Exposure","score":0.7792999744415283,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11359","display_name":"Effects of Radiation Exposure","score":0.7792999744415283,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12005","display_name":"Spaceflight effects on biology","score":0.19619999825954437,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11176","display_name":"Radiation Therapy and Dosimetry","score":0.006899999920278788,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/agent-based-modeling","display_name":"agent-based modeling","score":0.8799999952316284},{"id":"https://openalex.org/keywords/ionizing-radiation","display_name":"ionizing radiation","score":0.6890000104904175},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.9779999852180481},{"id":"https://openalex.org/keywords/deep-space-radiation","display_name":"deep space radiation","score":0.7950000166893005},{"id":"https://openalex.org/keywords/spaceflight-microbiology","display_name":"spaceflight microbiology","score":0.6859999895095825},{"id":"https://openalex.org/keywords/alamar-blue","display_name":"Alamar Blue","score":0.824999988079071},{"id":"https://openalex.org/keywords/redox-dyes","display_name":"redox dyes","score":0.8270000219345093},{"id":"https://openalex.org/keywords/reactive-oxygen-species","display_name":"reactive oxygen species","score":0.9980000257492065},{"id":"https://openalex.org/keywords/dna-repair-mutants","display_name":"DNA repair mutants","score":0.8069999814033508},{"id":"https://openalex.org/keywords/proton-radiation","display_name":"proton radiation","score":0.9079999923706055},{"id":"https://openalex.org/keywords/simulation-software","display_name":"simulation software","score":0.3569999933242798}],"concepts":[{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.6875},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.5149000287055969},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.4975000023841858},{"id":"https://openalex.org/C153385146","wikidata":"https://www.wikidata.org/wiki/Q18335","display_name":"Radiation","level":2,"score":0.4747999906539917},{"id":"https://openalex.org/C2987978230","wikidata":"https://www.wikidata.org/wiki/Q5691173","display_name":"Space radiation","level":3,"score":0.4733999967575073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46639999747276306},{"id":"https://openalex.org/C125118446","wikidata":"https://www.wikidata.org/wiki/Q690200","display_name":"Radiobiology","level":3,"score":0.4650999903678894},{"id":"https://openalex.org/C2779222958","wikidata":"https://www.wikidata.org/wiki/Q45422","display_name":"Yeast","level":2,"score":0.4496000111103058},{"id":"https://openalex.org/C18231593","wikidata":"https://www.wikidata.org/wiki/Q186161","display_name":"Ionizing radiation","level":3,"score":0.44699999690055847},{"id":"https://openalex.org/C181762993","wikidata":"https://www.wikidata.org/wiki/Q7572581","display_name":"Space environment","level":2,"score":0.3732999861240387},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36489999294281006},{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.36239999532699585},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.35839998722076416},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3522000014781952},{"id":"https://openalex.org/C2992884146","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Budding yeast","level":4,"score":0.349700003862381},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.34860000014305115},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.34790000319480896},{"id":"https://openalex.org/C76969082","wikidata":"https://www.wikidata.org/wiki/Q486902","display_name":"Mathematical model","level":2,"score":0.34470000863075256},{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.335999995470047},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.32670000195503235},{"id":"https://openalex.org/C55904794","wikidata":"https://www.wikidata.org/wiki/Q82682","display_name":"Redox","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.31850001215934753},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.30570000410079956},{"id":"https://openalex.org/C2778447961","wikidata":"https://www.wikidata.org/wiki/Q1146293","display_name":"Saccharomyces","level":4,"score":0.2939000129699707},{"id":"https://openalex.org/C2987992536","wikidata":"https://www.wikidata.org/wiki/Q3026015","display_name":"Radiation tolerance","level":3,"score":0.28700000047683716},{"id":"https://openalex.org/C2987857752","wikidata":"https://www.wikidata.org/wiki/Q12147","display_name":"Human health","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2824000120162964},{"id":"https://openalex.org/C103888896","wikidata":"https://www.wikidata.org/wiki/Q5916","display_name":"Spaceflight","level":2,"score":0.27630001306533813},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C153428861","wikidata":"https://www.wikidata.org/wiki/Q152749","display_name":"Radiation damage","level":3,"score":0.2705000042915344},{"id":"https://openalex.org/C2781298738","wikidata":"https://www.wikidata.org/wiki/Q18041535","display_name":"Sobp","level":4,"score":0.2696000039577484},{"id":"https://openalex.org/C111337013","wikidata":"https://www.wikidata.org/wiki/Q2737837","display_name":"Irradiation","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C104060986","wikidata":"https://www.wikidata.org/wiki/Q180046","display_name":"Space exploration","level":2,"score":0.2556000053882599},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25459998846054077}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.08.757403","doi":"https://doi.org/10.64898/2026.10.08.757403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.08.757403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.08.757403","doi":"https://doi.org/10.64898/2026.10.08.757403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.08.757403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.08.757403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221360874.pdf","grobid_xml":"https://content.openalex.org/works/W7221360874.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W588130648","https://openalex.org/W1967839641","https://openalex.org/W1968435538","https://openalex.org/W1999204358","https://openalex.org/W2004602806","https://openalex.org/W2011301426","https://openalex.org/W2023875464","https://openalex.org/W2040522903","https://openalex.org/W2050183738","https://openalex.org/W2083770395","https://openalex.org/W2097531570","https://openalex.org/W2136351518","https://openalex.org/W2145125216","https://openalex.org/W2150889787","https://openalex.org/W2154385453","https://openalex.org/W2156528247","https://openalex.org/W2180719527","https://openalex.org/W2260781726","https://openalex.org/W2261007487","https://openalex.org/W2295820626","https://openalex.org/W2338506659","https://openalex.org/W2411534500","https://openalex.org/W2528020601","https://openalex.org/W2590809986","https://openalex.org/W2608339826","https://openalex.org/W2965590414","https://openalex.org/W2996518438","https://openalex.org/W2999651325","https://openalex.org/W3003257820","https://openalex.org/W3008261924","https://openalex.org/W3015352831","https://openalex.org/W3037097121","https://openalex.org/W3089803970","https://openalex.org/W3107984511","https://openalex.org/W3119854050","https://openalex.org/W3126268711","https://openalex.org/W3135476342","https://openalex.org/W3135668316","https://openalex.org/W3144671646","https://openalex.org/W3157638995","https://openalex.org/W3185820143","https://openalex.org/W3215426281","https://openalex.org/W4206245272","https://openalex.org/W4210461847","https://openalex.org/W4211191954","https://openalex.org/W4283707804","https://openalex.org/W4285267900","https://openalex.org/W4293030203","https://openalex.org/W4328089227","https://openalex.org/W4365443867","https://openalex.org/W4401544753","https://openalex.org/W4404645210","https://openalex.org/W4407417295","https://openalex.org/W4408039072","https://openalex.org/W4410325360"],"related_works":["https://openalex.org/W4404645210","https://openalex.org/W1989947094","https://openalex.org/W4390882082","https://openalex.org/W3203592153","https://openalex.org/W2611879848","https://openalex.org/W1843675753","https://openalex.org/W649681939","https://openalex.org/W3021443933","https://openalex.org/W4414739907","https://openalex.org/W7005131116"],"abstract_inverted_index":{"ABSTRACT":[0],"To":[1],"reduce":[2],"health":[3],"risks":[4],"for":[5,57,213],"human":[6,216],"space":[7,33,185,200,217],"exploration,":[8],"it":[9],"is":[10,27,37,64,87,211,304],"important":[11],"to":[12,43,61,88,175,189,264],"model":[13,30,69,128,303],"the":[14,48,72,103,109,126,135,138,153,220,226,229,233,282,290,310],"effects":[15,50,73,104,284],"of":[16,74,105,112,125,137,155,228,285,294],"deep-space":[17,206],"radiation":[18,41,76,107,201,207,223,286],"on":[19,77,108,179,287,313],"biological":[20,283],"systems.":[21],"The":[22,54,272],"budding":[23],"yeast":[24],"Saccharomyces":[25],"cerevisiae":[26,79],"a":[28,65,142,180,187,266,305],"common":[29],"organism":[31],"in":[32,147,159,177,240,281,307],"radiobiology,":[34],"but":[35],"little":[36],"known":[38],"about":[39],"how":[40,205],"damage":[42,224],"individual":[44,230],"cells":[45,80],"translates":[46],"into":[47],"population-level":[49,83,234],"that":[51,70,97,248],"experiments":[52,242],"measure.":[53],"Agent-Based":[55],"Model":[56],"Microbial":[58],"Populations":[59],"Exposed":[60],"Radiation":[62],"(AMMPER)":[63],"spatially":[66],"explicit":[67],"agent-based":[68,98],"simulates":[71],"ionizing":[75],"S.":[78],"and":[81,92,114,129,151,169,195,232,236,256,278,289,296,300,309,316],"produces":[82],"results.":[84],"Its":[85],"goal":[86],"improve":[89,253],"experiment":[90,254],"design":[91,255],"data":[93,143,197,257],"interpretation.":[94,258],"AMMPER-1":[95],"demonstrated":[96],"simulations":[99],"can":[100,252],"qualitatively":[101],"reproduce":[102],"proton":[106],"growth":[110,235],"rate":[111],"wild-type":[113],"DNA-repair":[115],"mutant":[116],"yeast.":[117],"Here,":[118],"we":[119],"present":[120],"AMMPER-2,":[121],"which":[122],"addresses":[123],"limitations":[124],"first":[127],"expands":[130],"its":[131],"capabilities.":[132],"AMMPER-2":[133,172],"incorporates":[134],"dynamics":[136],"redox":[139],"dye":[140],"alamarBlue,":[141],"type":[144],"commonly":[145],"generated":[146],"spaceflight":[148,241],"microbiology":[149],"experiments,":[150],"models":[152],"fate":[154],"reactive":[156],"oxygen":[157],"species":[158],"more":[160],"detail.":[161],"It":[162],"also":[163],"adds":[164],"an":[165,262],"improved":[166],"graphical":[167],"interface":[168],"runs":[170],"faster.":[171],"remains":[173,243],"easy":[174],"execute":[176],"Python":[178],"standard":[181],"personal":[182],"laptop,":[183],"providing":[184],"biologists":[186],"tool":[188,291],"explore":[190],"experimental":[191],"conditions,":[192],"generate":[193],"hypotheses,":[194],"interpret":[196],"from":[198],"microbial":[199],"experiments.":[202],"IMPORTANCE":[203],"Understanding":[204],"affects":[208],"living":[209],"systems":[210],"essential":[212],"safe":[214],"long-duration":[215],"exploration.":[218],"However,":[219],"link":[221],"between":[222],"at":[225],"level":[227],"cell":[231],"metabolic":[237],"signals":[238],"measured":[239],"poorly":[244],"understood.":[245],"Computational":[246],"tools":[247],"connect":[249],"these":[250],"scales":[251],"This":[259,302],"manuscript":[260,311],"describes":[261],"update":[263],"AMMPER,":[265],"previously":[267],"published":[268],"computational":[269],"modeling":[270],"tool.":[271],"intended":[273],"users":[274],"are":[275],"scientists,":[276],"educators,":[277],"students":[279],"interested":[280],"organisms,":[288],"prioritizes":[292],"ease":[293],"use":[295],"accessibility":[297],"over":[298],"complexity":[299],"precision.":[301],"work":[306],"progress,":[308],"focuses":[312],"new":[314],"features":[315],"lessons":[317],"learned":[318],"rather":[319],"than":[320],"scientific":[321],"findings.":[322]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-10-11T00:00:00"}
