{"id":"https://openalex.org/W4416410929","doi":"https://doi.org/10.1016/j.cpc.2025.109949","title":"QUASAR: A flexible QM-MM method for biomolecular systems based on restraining spheres","display_name":"QUASAR: A flexible QM-MM method for biomolecular systems based on restraining spheres","publication_year":2025,"publication_date":"2025-11-20","ids":{"openalex":"https://openalex.org/W4416410929","doi":"https://doi.org/10.1016/j.cpc.2025.109949"},"language":"en","primary_location":{"id":"doi:10.1016/j.cpc.2025.109949","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cpc.2025.109949","pdf_url":null,"source":{"id":"https://openalex.org/S142305363","display_name":"Computer Physics Communications","issn_l":"0010-4655","issn":["0010-4655","1879-2944"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Physics Communications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035220690","display_name":"Christoph Gorgulla","orcid":"https://orcid.org/0000-0001-6986-5270"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Christoph Gorgulla","raw_affiliation_strings":["Department of Physics and Astronomy, University College, London, WC1E 6BT, UK","Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA","Department of Structural Biology, St. Jude Children\u2019s Research Hospital, Memphis, USA"],"raw_orcid":"https://orcid.org/0000-0001-6986-5270","affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, University College, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Structural Biology, St. Jude Children\u2019s Research Hospital, Memphis, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024063229","display_name":"Alejandro J. Garza","orcid":"https://orcid.org/0000-0001-6995-2833"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alejandro J. Garza","raw_affiliation_strings":["Department of Structural Biology, St. Jude Children\u2019s Research Hospital, Memphis, USA"],"raw_orcid":"https://orcid.org/0000-0001-6995-2833","affiliations":[{"raw_affiliation_string":"Department of Structural Biology, St. Jude Children\u2019s Research Hospital, Memphis, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009821984","display_name":"Venkat Kapil","orcid":"https://orcid.org/0000-0003-0324-2198"},"institutions":[{"id":"https://openalex.org/I2801237587","display_name":"London Centre for Nanotechnology","ror":"https://ror.org/04ptp8872","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801237587"]},{"id":"https://openalex.org/I330495657","display_name":"Thomas Young Centre","ror":"https://ror.org/03hdrgy42","country_code":"GB","type":"other","lineage":["https://openalex.org/I330495657"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Venkat Kapil","raw_affiliation_strings":["Department of Physics and Astronomy, University College, London, WC1E 6BT, UK","Thomas Young Centre and London Centre for Nanotechnology, London, WC1E 6BT, UK"],"raw_orcid":"https://orcid.org/0000-0003-0324-2198","affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, University College, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Thomas Young Centre and London Centre for Nanotechnology, London, WC1E 6BT, UK","institution_ids":["https://openalex.org/I330495657","https://openalex.org/I2801237587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040304386","display_name":"Konstantin Fackeldey","orcid":"https://orcid.org/0000-0002-4373-3672"},"institutions":[{"id":"https://openalex.org/I195893171","display_name":"Zuse Institute Berlin","ror":"https://ror.org/02eva5865","country_code":"DE","type":"facility","lineage":["https://openalex.org/I195893171"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Konstantin Fackeldey","raw_affiliation_strings":["Institute of Mathematics, Technical University Berlin, Berlin, Germany","Zuse Institute Berlin, Berlin, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4373-3672","affiliations":[{"raw_affiliation_string":"Institute of Mathematics, Technical University Berlin, Berlin, Germany","institution_ids":[]},{"raw_affiliation_string":"Zuse Institute Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I195893171"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035220690","https://openalex.org/A5040304386"],"corresponding_institution_ids":["https://openalex.org/I1313298211","https://openalex.org/I136199984","https://openalex.org/I195893171","https://openalex.org/I45129253"],"apc_list":{"value":3670,"currency":"USD","value_usd":3670},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26051418,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"320","issue":null,"first_page":"109949","last_page":"109949"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4634999930858612,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4634999930858612,"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/T11965","display_name":"Quantum, superfluid, helium dynamics","score":0.1316000074148178,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.10559999942779541,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.7002999782562256},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.4368000030517578},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.427700012922287},{"id":"https://openalex.org/keywords/open-quantum-system","display_name":"Open quantum system","score":0.42579999566078186},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4212000072002411},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3986999988555908},{"id":"https://openalex.org/keywords/spheres","display_name":"SPHERES","score":0.3896999955177307},{"id":"https://openalex.org/keywords/quantum-system","display_name":"Quantum system","score":0.3871000111103058},{"id":"https://openalex.org/keywords/biomolecular-structure","display_name":"Biomolecular structure","score":0.382099986076355}],"concepts":[{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.7002999782562256},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5472999811172485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5162000060081482},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.4368000030517578},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.427700012922287},{"id":"https://openalex.org/C190474826","wikidata":"https://www.wikidata.org/wiki/Q2495111","display_name":"Open quantum system","level":3,"score":0.42579999566078186},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4212000072002411},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4011000096797943},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3986999988555908},{"id":"https://openalex.org/C72422203","wikidata":"https://www.wikidata.org/wiki/Q7392545","display_name":"SPHERES","level":2,"score":0.3896999955177307},{"id":"https://openalex.org/C2778926657","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum system","level":3,"score":0.3871000111103058},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.382099986076355},{"id":"https://openalex.org/C154018700","wikidata":"https://www.wikidata.org/wiki/Q898323","display_name":"Path integral formulation","level":3,"score":0.36230000853538513},{"id":"https://openalex.org/C11255438","wikidata":"https://www.wikidata.org/wiki/Q7269085","display_name":"Quantum process","level":4,"score":0.34850001335144043},{"id":"https://openalex.org/C15184713","wikidata":"https://www.wikidata.org/wiki/Q7269042","display_name":"Quantum dynamics","level":3,"score":0.33629998564720154},{"id":"https://openalex.org/C161166931","wikidata":"https://www.wikidata.org/wiki/Q7269096","display_name":"Quantum simulator","level":4,"score":0.3287999927997589},{"id":"https://openalex.org/C171912257","wikidata":"https://www.wikidata.org/wiki/Q11019","display_name":"Mechanical system","level":2,"score":0.3231000006198883},{"id":"https://openalex.org/C124657808","wikidata":"https://www.wikidata.org/wiki/Q1133068","display_name":"Quantum dot","level":2,"score":0.3221000134944916},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.31529998779296875},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.31450000405311584},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.31349998712539673},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.313400000333786},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.30559998750686646},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2980000078678131},{"id":"https://openalex.org/C86025842","wikidata":"https://www.wikidata.org/wiki/Q5358432","display_name":"Electronic structure","level":2,"score":0.2913999855518341},{"id":"https://openalex.org/C137019171","wikidata":"https://www.wikidata.org/wiki/Q2623817","display_name":"Quantum algorithm","level":3,"score":0.28540000319480896},{"id":"https://openalex.org/C2776184637","wikidata":"https://www.wikidata.org/wiki/Q6506039","display_name":"Living systems","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.2736000120639801},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.26339998841285706},{"id":"https://openalex.org/C190463098","wikidata":"https://www.wikidata.org/wiki/Q2081419","display_name":"Quantum technology","level":4,"score":0.2621000111103058},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.25209999084472656}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1016/j.cpc.2025.109949","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cpc.2025.109949","pdf_url":null,"source":{"id":"https://openalex.org/S142305363","display_name":"Computer Physics Communications","issn_l":"0010-4655","issn":["0010-4655","1879-2944"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Physics Communications","raw_type":"journal-article"},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:10220265","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/10220265/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Physics Communications , 320     , Article 109949. (2026)","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310040","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967"},{"id":"https://openalex.org/F4320313598","display_name":"American Lebanese Syrian Associated Charities","ror":null},{"id":"https://openalex.org/F4320330291","display_name":"Berlin Mathematics Research Center MATH+","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W106859849","https://openalex.org/W194087576","https://openalex.org/W1564105979","https://openalex.org/W1932588580","https://openalex.org/W1964326958","https://openalex.org/W1965092590","https://openalex.org/W1965378620","https://openalex.org/W1968344479","https://openalex.org/W1969456011","https://openalex.org/W1969524849","https://openalex.org/W1970790514","https://openalex.org/W1971237059","https://openalex.org/W1971617876","https://openalex.org/W1974709252","https://openalex.org/W1976886438","https://openalex.org/W1979313952","https://openalex.org/W1980179156","https://openalex.org/W1981368803","https://openalex.org/W1984686137","https://openalex.org/W1984998783","https://openalex.org/W1986193392","https://openalex.org/W1987274641","https://openalex.org/W1988336950","https://openalex.org/W1990691043","https://openalex.org/W1995808589","https://openalex.org/W1997772366","https://openalex.org/W1998365857","https://openalex.org/W2000411584","https://openalex.org/W2004303971","https://openalex.org/W2019893551","https://openalex.org/W2020544762","https://openalex.org/W2030473080","https://openalex.org/W2035460800","https://openalex.org/W2039216941","https://openalex.org/W2041698026","https://openalex.org/W2047280630","https://openalex.org/W2057502998","https://openalex.org/W2057633968","https://openalex.org/W2060125579","https://openalex.org/W2060433756","https://openalex.org/W2061926875","https://openalex.org/W2062751174","https://openalex.org/W2066438507","https://openalex.org/W2070753604","https://openalex.org/W2072741235","https://openalex.org/W2076678733","https://openalex.org/W2083993424","https://openalex.org/W2089799306","https://openalex.org/W2094279870","https://openalex.org/W2104543060","https://openalex.org/W2108899393","https://openalex.org/W2117649850","https://openalex.org/W2124357718","https://openalex.org/W2125057563","https://openalex.org/W2132262459","https://openalex.org/W2132592887","https://openalex.org/W2138486942","https://openalex.org/W2144526365","https://openalex.org/W2152220941","https://openalex.org/W2153856953","https://openalex.org/W2161545948","https://openalex.org/W2163681071","https://openalex.org/W2168357118","https://openalex.org/W2294031160","https://openalex.org/W2319864391","https://openalex.org/W2322368868","https://openalex.org/W2324727749","https://openalex.org/W2331032519","https://openalex.org/W2345354812","https://openalex.org/W2413829117","https://openalex.org/W2513738974","https://openalex.org/W2554899614","https://openalex.org/W2774933328","https://openalex.org/W2788692372","https://openalex.org/W2886120629","https://openalex.org/W3027308092","https://openalex.org/W3160818551","https://openalex.org/W4283029539","https://openalex.org/W4311506567","https://openalex.org/W4313236419","https://openalex.org/W4401584941"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-01-20T17:24:06.736184","created_date":"2025-11-20T00:00:00"}