{"id":"https://openalex.org/W2765483224","doi":"https://doi.org/10.1145/3295740","title":"Runtime Fault Detection in Programmed Molecular Systems","display_name":"Runtime Fault Detection in Programmed Molecular Systems","publication_year":2019,"publication_date":"2019-03-13","ids":{"openalex":"https://openalex.org/W2765483224","doi":"https://doi.org/10.1145/3295740","mag":"2765483224"},"language":"en","primary_location":{"id":"doi:10.1145/3295740","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3295740","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3295740","source":{"id":"https://openalex.org/S142627899","display_name":"ACM Transactions on Software Engineering and Methodology","issn_l":"1049-331X","issn":["1049-331X","1557-7392"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Software Engineering and Methodology","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3295740","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084617443","display_name":"Samuel Ellis","orcid":"https://orcid.org/0000-0002-5012-4277"},"institutions":[{"id":"https://openalex.org/I4210137786","display_name":"Molecular Sciences Software Institute","ror":"https://ror.org/03x8p5f11","country_code":"US","type":"other","lineage":["https://openalex.org/I4210137786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel J. Ellis","raw_affiliation_strings":["Molecular Sciences Software Institute, Blacksburg, VA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Sciences Software Institute, Blacksburg, VA","institution_ids":["https://openalex.org/I4210137786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043303629","display_name":"Titus H. Klinge","orcid":"https://orcid.org/0000-0002-2297-6712"},"institutions":[{"id":"https://openalex.org/I188497080","display_name":"Carleton College","ror":"https://ror.org/03jep7677","country_code":"US","type":"education","lineage":["https://openalex.org/I188497080"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Titus H. Klinge","raw_affiliation_strings":["Carleton College, Des Moines, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carleton College, Des Moines, IA","institution_ids":["https://openalex.org/I188497080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001352332","display_name":"James I. Lathrop","orcid":"https://orcid.org/0000-0002-5467-5818"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James I. Lathrop","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064796448","display_name":"Jack H. Lutz","orcid":"https://orcid.org/0000-0003-1004-3891"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack H. Lutz","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013390075","display_name":"Robyn R. Lutz","orcid":"https://orcid.org/0000-0001-5390-7982"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robyn R. Lutz","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":"https://orcid.org/0000-0001-5390-7982","affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037662686","display_name":"Andrew S. Miner","orcid":"https://orcid.org/0000-0002-7737-6888"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew S. Miner","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hugh D. Potter","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugh D. Potter","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1211,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43340731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"28","issue":"2","first_page":"1","last_page":"20"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11005","display_name":"Radiation Effects in Electronics","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11005","display_name":"Radiation Effects in Electronics","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10913","display_name":"Molecular Junctions and Nanostructures","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/timer","display_name":"Timer","score":0.8987804055213928},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6897594332695007},{"id":"https://openalex.org/keywords/fault-detection-and-isolation","display_name":"Fault detection and isolation","score":0.5253198146820068},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.52512127161026},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5025570392608643},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4873722195625305},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.48146024346351624},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4541073441505432},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.447022944688797},{"id":"https://openalex.org/keywords/real-time-computing","display_name":"Real-time computing","score":0.35001862049102783},{"id":"https://openalex.org/keywords/microcontroller","display_name":"Microcontroller","score":0.20366919040679932},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12673252820968628},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08373081684112549}],"concepts":[{"id":"https://openalex.org/C2776633867","wikidata":"https://www.wikidata.org/wiki/Q186612","display_name":"Timer","level":3,"score":0.8987804055213928},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6897594332695007},{"id":"https://openalex.org/C152745839","wikidata":"https://www.wikidata.org/wiki/Q5438153","display_name":"Fault detection and isolation","level":3,"score":0.5253198146820068},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.52512127161026},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5025570392608643},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4873722195625305},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.48146024346351624},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4541073441505432},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.447022944688797},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.35001862049102783},{"id":"https://openalex.org/C173018170","wikidata":"https://www.wikidata.org/wiki/Q165678","display_name":"Microcontroller","level":2,"score":0.20366919040679932},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12673252820968628},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08373081684112549},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C172707124","wikidata":"https://www.wikidata.org/wiki/Q423488","display_name":"Actuator","level":2,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/3295740","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3295740","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3295740","source":{"id":"https://openalex.org/S142627899","display_name":"ACM Transactions on Software Engineering and Methodology","issn_l":"1049-331X","issn":["1049-331X","1557-7392"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Software Engineering and Methodology","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1710.09494","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1710.09494","pdf_url":"https://arxiv.org/pdf/1710.09494","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2765483224","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1710.09494.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1710.09494","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1710.09494","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1145/3295740","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3295740","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3295740","source":{"id":"https://openalex.org/S142627899","display_name":"ACM Transactions on Software Engineering and Methodology","issn_l":"1049-331X","issn":["1049-331X","1557-7392"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Software Engineering and Methodology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1510989973","display_name":null,"funder_award_id":"1247051 and 1545028","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5237333017","display_name":null,"funder_award_id":"1247051","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2765483224.pdf","grobid_xml":"https://content.openalex.org/works/W2765483224.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W136607018","https://openalex.org/W172803389","https://openalex.org/W227597898","https://openalex.org/W1512198009","https://openalex.org/W1548362700","https://openalex.org/W1976815031","https://openalex.org/W1987535580","https://openalex.org/W1990476699","https://openalex.org/W1992710424","https://openalex.org/W1996074994","https://openalex.org/W1997088148","https://openalex.org/W2000804241","https://openalex.org/W2001429914","https://openalex.org/W2005615084","https://openalex.org/W2008591003","https://openalex.org/W2017989625","https://openalex.org/W2041226400","https://openalex.org/W2053378109","https://openalex.org/W2056134008","https://openalex.org/W2069431083","https://openalex.org/W2075031385","https://openalex.org/W2084815973","https://openalex.org/W2088398545","https://openalex.org/W2104525378","https://openalex.org/W2106267572","https://openalex.org/W2113750341","https://openalex.org/W2115179079","https://openalex.org/W2117818414","https://openalex.org/W2120158030","https://openalex.org/W2129096474","https://openalex.org/W2129289644","https://openalex.org/W2133035852","https://openalex.org/W2134929758","https://openalex.org/W2135648313","https://openalex.org/W2140372466","https://openalex.org/W2141478443","https://openalex.org/W2142364125","https://openalex.org/W2145071552","https://openalex.org/W2145609304","https://openalex.org/W2150985916","https://openalex.org/W2153965331","https://openalex.org/W2158313010","https://openalex.org/W2222782578","https://openalex.org/W2285729654","https://openalex.org/W2327602015","https://openalex.org/W2538438209","https://openalex.org/W2620092116","https://openalex.org/W2747253451","https://openalex.org/W2962738471","https://openalex.org/W6712267375"],"related_works":["https://openalex.org/W1511934478","https://openalex.org/W1999041183","https://openalex.org/W2480957914","https://openalex.org/W3050381783","https://openalex.org/W2039069941","https://openalex.org/W1492366453","https://openalex.org/W2275241203","https://openalex.org/W2273763794","https://openalex.org/W2213664160","https://openalex.org/W2293216165","https://openalex.org/W2065752991","https://openalex.org/W2037794309","https://openalex.org/W3166388217","https://openalex.org/W3022459224","https://openalex.org/W3022933992","https://openalex.org/W2461431977","https://openalex.org/W1191863128","https://openalex.org/W2286042729","https://openalex.org/W2972765956","https://openalex.org/W2548032328"],"abstract_inverted_index":{"Watchdog":[0],"timers":[1],"are":[2,5,85,146,153],"devices":[3],"that":[4,35,70,113],"commonly":[6],"used":[7],"to":[8,22,31,87,94],"monitor":[9,134],"the":[10,27,52,68,76,96,106,127,139,144,154],"health":[11,53],"of":[12,54,79,98,108,158],"safety-critical":[13],"hardware":[14],"and":[15,44,67,89,121,143],"software":[16,122],"systems.":[17],"Their":[18],"primary":[19],"function":[20],"is":[21,91,105],"raise":[23],"an":[24,109],"alarm":[25],"if":[26],"monitored":[28],"systems":[29],"fail":[30],"emit":[32],"periodic":[33],"\u201cheartbeats\u201d":[34],"signal":[36],"their":[37],"well-being.":[38],"In":[39],"this":[40],"article,":[41],"we":[42],"design":[43,111],"verify":[45],"a":[46,99,135],"molecular":[47,56,64,102,128,136,140,162],"watchdog":[48,65,103,141],"timer":[49,66,104,142],"for":[50,160],"monitoring":[51],"programmed":[55],"nanosystems.":[57],"This":[58],"raises":[59],"new":[60],"challenges,":[61],"because":[62],"our":[63],"system":[69],"it":[71,90,133],"monitors":[72],"both":[73],"operate":[74],"in":[75],"probabilistic":[77],"environment":[78],"chemical":[80,149],"kinetics,":[81],"where":[82],"many":[83,161],"failures":[84],"certain":[86],"occur":[88],"especially":[92],"hard":[93],"detect":[95],"absence":[97],"signal.":[100],"Our":[101],"result":[107],"incremental":[110],"process":[112],"uses":[114],"goal-oriented":[115],"requirements":[116],"engineering,":[117],"simulation,":[118],"stochastic":[119],"analysis,":[120],"verification":[123],"tools.":[124],"We":[125],"demonstrate":[126],"watchdog\u2019s":[129],"functionality":[130],"by":[131],"having":[132],"oscillator.":[137],"Both":[138],"oscillator":[145],"implemented":[147],"as":[148],"reaction":[150],"networks,":[151],"which":[152],"current":[155],"programming":[156,163],"language":[157],"choice":[159],"applications.":[164]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
