{"id":"https://openalex.org/W3202259692","doi":"https://doi.org/10.1016/j.cpc.2021.108176","title":"Efficient generation of self-avoiding, semiflexible rotational isomeric chain ensembles in bulk, in confined geometries, and on surfaces","display_name":"Efficient generation of self-avoiding, semiflexible rotational isomeric chain ensembles in bulk, in confined geometries, and on surfaces","publication_year":2021,"publication_date":"2021-09-27","ids":{"openalex":"https://openalex.org/W3202259692","doi":"https://doi.org/10.1016/j.cpc.2021.108176","mag":"3202259692"},"language":"en","primary_location":{"id":"doi:10.1016/j.cpc.2021.108176","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cpc.2021.108176","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Physics Communications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/j.cpc.2021.108176","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078023428","display_name":"Oliver Weismantel","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Oliver Weismantel","raw_affiliation_strings":["Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077679067","display_name":"Aikaterini A. Galata","orcid":"https://orcid.org/0000-0003-3133-9704"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Aikaterini A. Galata","raw_affiliation_strings":["Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102967059","display_name":"Morteza Sadeghi","orcid":"https://orcid.org/0000-0003-4164-2539"},"institutions":[{"id":"https://openalex.org/I133529467","display_name":"Sharif University of Technology","ror":"https://ror.org/024c2fq17","country_code":"IR","type":"education","lineage":["https://openalex.org/I133529467"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Morteza Sadeghi","raw_affiliation_strings":["Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Tehran 11155-9567, Iran"],"affiliations":[{"raw_affiliation_string":"Center of Excellence in Energy Conversion (CEEC), School of Mechanical Engineering, Sharif University of Technology, Tehran 11155-9567, Iran","institution_ids":["https://openalex.org/I133529467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042371041","display_name":"Achim Kr\u00f6ger","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Achim Kr\u00f6ger","raw_affiliation_strings":["a.kroger software development studio, Rothehausstr. 9, D-50823 Cologne, Germany"],"affiliations":[{"raw_affiliation_string":"a.kroger software development studio, Rothehausstr. 9, D-50823 Cologne, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042161653","display_name":"Martin Kr\u00f6ger","orcid":"https://orcid.org/0000-0003-1402-6714"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Martin Kr\u00f6ger","raw_affiliation_strings":["Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5042161653"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":3670,"currency":"USD","value_usd":3670},"apc_paid":{"value":3670,"currency":"USD","value_usd":3670},"fwci":0.8132,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71464543,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"270","issue":null,"first_page":"108176","last_page":"108176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9983000159263611,"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/T10923","display_name":"Force Microscopy Techniques and Applications","score":0.9968000054359436,"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/T11162","display_name":"Enzyme Structure and Function","score":0.993399977684021,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.593890368938446},{"id":"https://openalex.org/keywords/fortran","display_name":"Fortran","score":0.447430819272995},{"id":"https://openalex.org/keywords/radius-of-gyration","display_name":"Radius of gyration","score":0.4421248435974121},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.4293592572212219},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3686695694923401},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2761554718017578},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12801241874694824}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.593890368938446},{"id":"https://openalex.org/C2778241615","wikidata":"https://www.wikidata.org/wiki/Q83303","display_name":"Fortran","level":2,"score":0.447430819272995},{"id":"https://openalex.org/C168568712","wikidata":"https://www.wikidata.org/wiki/Q909999","display_name":"Radius of gyration","level":3,"score":0.4421248435974121},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.4293592572212219},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3686695694923401},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2761554718017578},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12801241874694824},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1016/j.cpc.2021.108176","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cpc.2021.108176","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Physics Communications","raw_type":"journal-article"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/507953","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/507953","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Physics Communications, 270","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000507953","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000507953","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1016/j.cpc.2021.108176","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cpc.2021.108176","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computer Physics Communications","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8299999833106995,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G4836148144","display_name":null,"funder_award_id":"20002","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G4868840158","display_name":null,"funder_award_id":"200021L_185052","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5433795946","display_name":"VISIONNANO - Viscoelastic properties, entanglements, and polymer dynamics in ionic nanocomposites","funder_award_id":"185052","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5799696092","display_name":null,"funder_award_id":"200021L","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G993971353","display_name":null,"funder_award_id":"200021","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320331518","display_name":"Centro Svizzero di Calcolo Scientifico","ror":null},{"id":"https://openalex.org/F4320331617","display_name":"National Supercomputing Centre Singapore","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W227143473","https://openalex.org/W1518747218","https://openalex.org/W1672997411","https://openalex.org/W1762183920","https://openalex.org/W1964571290","https://openalex.org/W1966597912","https://openalex.org/W1966879608","https://openalex.org/W1967461608","https://openalex.org/W1970484081","https://openalex.org/W1972514606","https://openalex.org/W1974704755","https://openalex.org/W1978950676","https://openalex.org/W1980428120","https://openalex.org/W1981498694","https://openalex.org/W1982150094","https://openalex.org/W1987464018","https://openalex.org/W1992058458","https://openalex.org/W1993438819","https://openalex.org/W1993574168","https://openalex.org/W2001851051","https://openalex.org/W2005942984","https://openalex.org/W2011005325","https://openalex.org/W2019465613","https://openalex.org/W2020094987","https://openalex.org/W2021747642","https://openalex.org/W2022183655","https://openalex.org/W2025776405","https://openalex.org/W2026466407","https://openalex.org/W2030827454","https://openalex.org/W2031961095","https://openalex.org/W2037339664","https://openalex.org/W2044263284","https://openalex.org/W2046634290","https://openalex.org/W2047065033","https://openalex.org/W2054496592","https://openalex.org/W2059991053","https://openalex.org/W2061768183","https://openalex.org/W2062110460","https://openalex.org/W2062291586","https://openalex.org/W2063006435","https://openalex.org/W2066851117","https://openalex.org/W2070044040","https://openalex.org/W2071164800","https://openalex.org/W2081134479","https://openalex.org/W2082791536","https://openalex.org/W2082950643","https://openalex.org/W2085001624","https://openalex.org/W2087216138","https://openalex.org/W2091351360","https://openalex.org/W2093548231","https://openalex.org/W2095363174","https://openalex.org/W2104081251","https://openalex.org/W2108710510","https://openalex.org/W2121273485","https://openalex.org/W2130383718","https://openalex.org/W2337066637","https://openalex.org/W2483006069","https://openalex.org/W2801179766","https://openalex.org/W2885436955","https://openalex.org/W2969576843","https://openalex.org/W3020831226","https://openalex.org/W3022683284","https://openalex.org/W3057964128","https://openalex.org/W3095282800","https://openalex.org/W3178205541","https://openalex.org/W4245290239","https://openalex.org/W4254831362","https://openalex.org/W4255959743","https://openalex.org/W4300223101","https://openalex.org/W6767027819"],"related_works":["https://openalex.org/W4242381503","https://openalex.org/W1513967072","https://openalex.org/W2107057257","https://openalex.org/W2803775568","https://openalex.org/W108818988","https://openalex.org/W2103189458","https://openalex.org/W2108255180","https://openalex.org/W2357128959","https://openalex.org/W2886331427","https://openalex.org/W2153913439"],"abstract_inverted_index":{"We":[0,66,276],"provide":[1,140],"an":[2,141,245,278],"efficient":[3],"ready-to-run":[4],"code":[5,106,242,265],"gensaw":[6,124,161,165,310],"that":[7,125,146,232,282],"generates":[8],"single":[9],"or":[10,19,25,63,184,193],"large":[11],"ensembles":[12],"of":[13,80,93,104,111,207,211,216,235,247,259],"self-avoiding,":[14,212],"flexible,":[15],"semiflexible,":[16,82],"rotationally":[17],"isometric":[18],"helical":[20,83],"chains":[21,260,296],"in":[22,50,107],"the":[23,72,81,105,108,118,136,155,256,264,271,287,306,318,335],"bulk":[24],"subject":[26,220],"to":[27,59,117,169,221,331],"arbitrary":[28,37,96,222,236,298],"confinement":[29,223],"and":[30,40,54,77,84,95,102,128,153,224,238,289,300,313,329,333],"tethering":[31,225],"conditions,":[32,226],"where":[33],"we":[34,139],"allow":[35],"for":[36,71,99,131,270,294,303],"intramolecular":[38],"bending":[39,237,299],"dihedral":[41],"energy":[42,231],"functions.":[43],"The":[44,241],"resulting":[45,156],"configuration":[46,127,312],"files":[47,130,316],"are":[48],"provided":[49],"various":[51],"common":[52],"formats":[53],"can":[55],"be":[56],"immediately":[57],"used":[58],"do":[60],"molecular":[61],"simulations":[62],"statistical":[64],"analysis.":[65],"work":[67],"out":[68],"analytic":[69,268,292],"expressions":[70],"mean":[73],"squared":[74],"end-to-end":[75],"distance":[76],"gyration":[78],"radius":[79],"rotational":[85],"isomeric":[86],"state":[87],"models":[88],"with":[89,261,297,305],"a":[90,159,229,251,324],"finite":[91],"number":[92],"bonds":[94],"interaction":[97],"potentials":[98,302],"direct":[100],"comparison":[101,304],"testing":[103],"limiting":[109,257],"case":[110,258],"unconfined":[112],"phantom":[113],"chains.":[114,273],"In":[115],"addition":[116],"graphics-free":[119],"linux":[120],"standalone":[121],"batch":[122,182,199],"version":[123,144],"creates":[126,311],"other":[129,315],"high":[132],"throughput":[133],"applications":[134],"from":[135,317],"command":[137,319],"line,":[138,320],"interactive":[142],"online":[143,187,204],"gensaw-visualization":[145,321],"serves":[147,322],"as":[148,323],"platform-independent":[149,325],"graphical":[150,326],"user":[151,327],"interface,":[152],"animates":[154],"conformations":[157],"using":[158,250],"remote":[160],"server.":[162],"Program":[163],"title:":[164],"CPC":[166],"Library":[167],"link":[168],"program":[170],"files:":[171],"https://doi.org/10.17632/8xfgf88f3w.1":[172],"Licensing":[173],"provisions:":[174],"MIT":[175],"Programming":[176],"languages:":[177],"fortran":[178],"90,":[179],"perl":[180,196],"(standalone":[181,198],"version)":[183,188,205],"java":[185],"(interactive":[186,203],"Required":[189],"software:":[190],"ifort":[191],"16+":[192],"gfortran":[194],"4+,":[195],"5+":[197],"version),":[200],"jre":[201],"1.8.0+":[202],"Nature":[206],"problem:":[208],"Efficient":[209],"creation":[210],"semiflexible":[213,295],"multibead":[214],"walks/chains":[215],"variable":[217],"contour":[218],"length,":[219],"characterized":[227],"by":[228],"conformational":[230],"is":[233],"composed":[234],"torsion":[239,301],"contributions.":[240],"must":[243],"produce":[244],"ensemble":[246],"such":[248],"chains,":[249],"flexible":[252],"output":[253],"format.":[254],"For":[255],"zero":[262],"thickness,":[263],"should":[266],"reproduce":[267],"results":[269,293],"ideal":[272],"Solution":[274],"method:":[275],"use":[277],"adapted":[279],"enrichment":[280],"procedure":[281],"optimizes":[283],"its":[284],"parameters":[285],"on":[286],"fly":[288],"derive":[290],"all":[291],"created":[307],"ensembles.":[308],"While":[309],"optionally":[314],"interface":[328],"allows":[330],"visualize":[332],"animate":[334],"conformations.":[336]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
