{"id":"https://openalex.org/W4410130771","doi":"https://doi.org/10.1021/acs.jcim.5c00409","title":"Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More","display_name":"Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More","publication_year":2025,"publication_date":"2025-05-06","ids":{"openalex":"https://openalex.org/W4410130771","doi":"https://doi.org/10.1021/acs.jcim.5c00409","pmid":"https://pubmed.ncbi.nlm.nih.gov/40325552"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00409","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00409","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2502.16253","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008159641","display_name":"Andrej Antal\u00edk","orcid":"https://orcid.org/0000-0002-8422-8410"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Andrej Antal\u00edk","raw_affiliation_strings":["Laboratory of Computational Chemistry and Biochemistry","\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056015104","display_name":"Andrea Levy","orcid":"https://orcid.org/0000-0003-1255-859X"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andrea Levy","raw_affiliation_strings":["Laboratory of Computational Chemistry and Biochemistry","\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053139524","display_name":"Sophia K. Johnson","orcid":"https://orcid.org/0000-0003-4207-4350"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sophia K. Johnson","raw_affiliation_strings":["Laboratory of Computational Chemistry and Biochemistry","\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005096983","display_name":"J\u00f3gvan Magnus Haugaard Olsen","orcid":"https://orcid.org/0000-0001-7487-944X"},"institutions":[{"id":"https://openalex.org/I4210117424","display_name":"Debre Tabor University","ror":"https://ror.org/02bzfxf13","country_code":"ET","type":"education","lineage":["https://openalex.org/I4210117424"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","ET"],"is_corresponding":false,"raw_author_name":"J\u00f3gvan Magnus Haugaard Olsen","raw_affiliation_strings":["DTU Chemistry","Technical University of Denmark (DTU)"],"affiliations":[{"raw_affiliation_string":"DTU Chemistry","institution_ids":["https://openalex.org/I4210117424"]},{"raw_affiliation_string":"Technical University of Denmark (DTU)","institution_ids":["https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087482363","display_name":"Ursula R\u00f6thlisberger","orcid":"https://orcid.org/0000-0002-1704-8591"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Ursula Rothlisberger","raw_affiliation_strings":["Laboratory of Computational Chemistry and Biochemistry","\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Chemistry and Biochemistry","institution_ids":[]},{"raw_affiliation_string":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008159641","https://openalex.org/A5087482363"],"corresponding_institution_ids":["https://openalex.org/I5124864"],"apc_list":null,"apc_paid":null,"fwci":2.0746,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.86472147,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"65","issue":"10","first_page":"4994","last_page":"5005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9745000004768372,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10591","display_name":"Theoretical and Computational Physics","score":0.9718999862670898,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4271664023399353},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3694372773170471}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4271664023399353},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3694372773170471}],"mesh":[{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.5c00409","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00409","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40325552","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40325552","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:arXiv.org:2502.16253","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2502.16253","pdf_url":"https://arxiv.org/pdf/2502.16253","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:infoscience.epfl.ch:20.500.14299/250027","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/250027","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"research article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2502.16253","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2502.16253","pdf_url":"https://arxiv.org/pdf/2502.16253","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4399001274","display_name":null,"funder_award_id":"200020-185092","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7083506496","display_name":null,"funder_award_id":"VIL29478","funder_id":"https://openalex.org/F4320310490","funder_display_name":"Villum Fonden"},{"id":"https://openalex.org/G8929188989","display_name":null,"funder_award_id":"200020-219440","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320310490","display_name":"Villum Fonden","ror":"https://ror.org/007ww2d15"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1968755006","https://openalex.org/W1972157628","https://openalex.org/W1976499671","https://openalex.org/W1977482735","https://openalex.org/W1980179156","https://openalex.org/W1981021420","https://openalex.org/W1981164194","https://openalex.org/W1989060947","https://openalex.org/W1989716167","https://openalex.org/W1998524463","https://openalex.org/W2000770615","https://openalex.org/W2004303971","https://openalex.org/W2014166972","https://openalex.org/W2019321155","https://openalex.org/W2023271753","https://openalex.org/W2027815611","https://openalex.org/W2030695915","https://openalex.org/W2031597111","https://openalex.org/W2038533471","https://openalex.org/W2043668344","https://openalex.org/W2045596260","https://openalex.org/W2058247180","https://openalex.org/W2062852634","https://openalex.org/W2069123478","https://openalex.org/W2078413200","https://openalex.org/W2086957099","https://openalex.org/W2090549322","https://openalex.org/W2106566162","https://openalex.org/W2110872379","https://openalex.org/W2148284063","https://openalex.org/W2154181301","https://openalex.org/W2171268876","https://openalex.org/W2318948631","https://openalex.org/W2325975598","https://openalex.org/W2789277401","https://openalex.org/W2936390190","https://openalex.org/W2972712857","https://openalex.org/W2994756795","https://openalex.org/W3027308092","https://openalex.org/W3210029782","https://openalex.org/W4251723943","https://openalex.org/W4388870365","https://openalex.org/W4393335315","https://openalex.org/W4400422268","https://openalex.org/W4407359110","https://openalex.org/W6738960860"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"MiMiC":[0,57,95,103,152],"is":[1],"a":[2,71,77,88,110,133,159,184],"framework":[3],"for":[4,128],"modeling":[5],"large-scale":[6],"chemical":[7],"processes":[8],"that":[9,142,165],"require":[10],"treatment":[11],"at":[12],"multiple":[13,67],"resolutions.":[14],"It":[15],"does":[16],"not":[17,147],"aim":[18],"to":[19,25,35,93,98,132,169],"implement":[20],"single-handedly":[21],"all":[22],"methods":[23],"required":[24],"treat":[26],"individual":[27],"subsystems,":[28],"but":[29],"instead,":[30],"it":[31,41],"relegates":[32],"this":[33,81],"task":[34],"specialized":[36],"computational":[37,163],"chemistry":[38],"software":[39],"while":[40],"serves":[42],"as":[43],"an":[44],"intermediary":[45],"between":[46,54],"these":[47],"external":[48],"programs":[49,68,131],"and":[50,123,155],"computes":[51],"the":[52,55,85,94,100,114,143,149,175,178],"interactions":[53],"subsystems.":[56],"minimizes":[58],"issues":[59],"typically":[60],"associated":[61],"with":[62,66,76,104,190,194],"molecular":[63],"dynamics":[64],"performed":[65,109],"by":[69,136,182],"adopting":[70],"multiple-program":[72],"multiple-data":[73],"paradigm":[74],"combined":[75],"loose-coupling":[78],"model.":[79],"In":[80],"work,":[82],"we":[83,108,140,173],"present":[84],"addition":[86],"of":[87,102,113,151,161,177],"new":[89,130],"client":[90],"program,":[91],"CP2K,":[92,154],"ecosystem.":[96],"Moreover,":[97],"align":[99],"implementation":[101,197],"its":[105,120],"modular":[106,180],"philosophy,":[107],"major":[111],"refactoring":[112],"entire":[115],"framework.":[116],"This":[117],"endeavor":[118],"unlocks":[119],"full":[121],"flexibility":[122],"reduces":[124],"any":[125],"future":[126],"efforts":[127],"introducing":[129],"minimum.":[134],"Furthermore,":[135],"thorough":[137],"timing":[138],"analysis,":[139],"verify":[141],"introduced":[144],"changes":[145],"do":[146],"affect":[148],"performance":[150],"or":[153],"neither":[156],"are":[157],"they":[158],"source":[160],"significant":[162],"overheads":[164],"would":[166],"be":[167],"detrimental":[168],"simulation":[170,187],"efficiency.":[171],"Finally,":[172],"demonstrate":[174],"benefits":[176],"framework's":[179],"design,":[181],"performing":[183],"QM/MM":[185],"MD":[186],"combining":[188],"CP2K":[189],"previously":[191],"interfaced":[192],"OpenMM,":[193],"no":[195],"additional":[196],"effort":[198],"required.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
