{"id":"https://openalex.org/W2974527921","doi":"https://doi.org/10.1021/acs.jcim.9b00324","title":"High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities","display_name":"High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities","publication_year":2019,"publication_date":"2019-09-17","ids":{"openalex":"https://openalex.org/W2974527921","doi":"https://doi.org/10.1021/acs.jcim.9b00324","mag":"2974527921","pmid":"https://pubmed.ncbi.nlm.nih.gov/31525965"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00324","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00324","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":"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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.9b00324","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048765221","display_name":"Alexander J. Bryer","orcid":"https://orcid.org/0000-0002-2039-4778"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander J. Bryer","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056514842","display_name":"Jodi A. Hadden\u2010Perilla","orcid":"https://orcid.org/0000-0003-4685-8291"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jodi A. Hadden-Perilla","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States"],"raw_orcid":"https://orcid.org/0000-0003-4685-8291","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048680880","display_name":"John E. Stone","orcid":"https://orcid.org/0000-0001-7215-762X"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John E. Stone","raw_affiliation_strings":["Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana\u2212Champaign, Urbana, Illinois 61801, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana\u2212Champaign, Urbana, Illinois 61801, United States","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089406511","display_name":"Juan R. Perilla","orcid":"https://orcid.org/0000-0003-1171-6816"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Juan R. Perilla","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States"],"raw_orcid":"https://orcid.org/0000-0003-1171-6816","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089406511"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":null,"apc_paid":null,"fwci":0.9,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.78299908,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"59","issue":"10","first_page":"4328","last_page":"4338"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/container","display_name":"Container (type theory)","score":0.6948707103729248},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5233948826789856},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5033444762229919},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4958864152431488},{"id":"https://openalex.org/keywords/titan","display_name":"Titan (rocket family)","score":0.460529625415802},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.45971041917800903},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.4529203772544861},{"id":"https://openalex.org/keywords/particle","display_name":"Particle (ecology)","score":0.44981151819229126},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.41912057995796204},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34303581714630127},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2968692183494568},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2738523483276367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11547139286994934},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11244788765907288}],"concepts":[{"id":"https://openalex.org/C2781018962","wikidata":"https://www.wikidata.org/wiki/Q5164884","display_name":"Container (type theory)","level":2,"score":0.6948707103729248},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5233948826789856},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5033444762229919},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4958864152431488},{"id":"https://openalex.org/C50805821","wikidata":"https://www.wikidata.org/wiki/Q1136670","display_name":"Titan (rocket family)","level":2,"score":0.460529625415802},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.45971041917800903},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.4529203772544861},{"id":"https://openalex.org/C2778517922","wikidata":"https://www.wikidata.org/wiki/Q7140482","display_name":"Particle (ecology)","level":2,"score":0.44981151819229126},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.41912057995796204},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34303581714630127},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2968692183494568},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2738523483276367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11547139286994934},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11244788765907288},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002236","descriptor_name":"Carbohydrate Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b00324","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00324","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":"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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31525965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31525965","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:pubmedcentral.nih.gov:6817393","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6817393","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.9b00324","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00324","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":"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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[{"id":"https://openalex.org/G1104241873","display_name":null,"funder_award_id":"P41 GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1243934403","display_name":null,"funder_award_id":"P30 GM110758","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2609650503","display_name":null,"funder_award_id":"P50 AI150481","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G394990476","display_name":null,"funder_award_id":"P30GM110758-04","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4578050069","display_name":null,"funder_award_id":"R24 GM145965","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7303780885","display_name":null,"funder_award_id":"P50 GM082251","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7673670378","display_name":null,"funder_award_id":"P50GM082251","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8406324769","display_name":null,"funder_award_id":"P41GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320308928","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1576999979","https://openalex.org/W1875046060","https://openalex.org/W1931164952","https://openalex.org/W1969598347","https://openalex.org/W1976681078","https://openalex.org/W1982104189","https://openalex.org/W1985686491","https://openalex.org/W1987992256","https://openalex.org/W1989144616","https://openalex.org/W1997655258","https://openalex.org/W1998846534","https://openalex.org/W2004383436","https://openalex.org/W2017973821","https://openalex.org/W2020288705","https://openalex.org/W2021064626","https://openalex.org/W2021882008","https://openalex.org/W2025957478","https://openalex.org/W2029667189","https://openalex.org/W2061987443","https://openalex.org/W2062884696","https://openalex.org/W2068578978","https://openalex.org/W2069297570","https://openalex.org/W2072270959","https://openalex.org/W2076127975","https://openalex.org/W2084482408","https://openalex.org/W2088536371","https://openalex.org/W2090571818","https://openalex.org/W2094181979","https://openalex.org/W2098055048","https://openalex.org/W2107278499","https://openalex.org/W2116493166","https://openalex.org/W2124171341","https://openalex.org/W2125872855","https://openalex.org/W2138952800","https://openalex.org/W2158076215","https://openalex.org/W2158667963","https://openalex.org/W2159013299","https://openalex.org/W2159192127","https://openalex.org/W2161002652","https://openalex.org/W2162936939","https://openalex.org/W2164088236","https://openalex.org/W2270926164","https://openalex.org/W2316069655","https://openalex.org/W2317863386","https://openalex.org/W2320259278","https://openalex.org/W2334874683","https://openalex.org/W2464780468","https://openalex.org/W2564351873","https://openalex.org/W2586153982","https://openalex.org/W2605604484","https://openalex.org/W2738606079","https://openalex.org/W2742394249","https://openalex.org/W2786313719","https://openalex.org/W2800650932","https://openalex.org/W2889460279","https://openalex.org/W2914410399","https://openalex.org/W4241614188"],"related_works":["https://openalex.org/W2408545863","https://openalex.org/W643179351","https://openalex.org/W2740469715","https://openalex.org/W2905265805","https://openalex.org/W2162805293","https://openalex.org/W2013629274","https://openalex.org/W2064207836","https://openalex.org/W2025174650","https://openalex.org/W2973472379","https://openalex.org/W2478963093"],"abstract_inverted_index":{"Compartmentalization":[0],"is":[1,89,121,151],"a":[2,35,81,155,204,221,228],"central":[3],"theme":[4],"in":[5,153],"biology.":[6],"Cells":[7],"are":[8],"composed":[9],"of":[10,24,56,99,105,110,127,133,146,190,200,212,218,230],"numerous":[11],"membrane-enclosed":[12],"structures,":[13],"evolved":[14],"to":[15,28,37,124,184,194,203],"facilitate":[16],"specific":[17],"biochemical":[18],"processes;":[19],"viruses":[20],"act":[21],"as":[22,136],"containers":[23,40,98,128,219],"genetic":[25],"material,":[26],"optimized":[27],"drive":[29],"infection.":[30],"Molecular":[31],"dynamics":[32],"simulations":[33],"provide":[34],"mechanism":[36],"study":[38,126],"biomolecular":[39,97,205],"and":[41,108,117,129,144,166,172,174],"the":[42,94,106,125,179,197],"influence":[43],"they":[44],"exert":[45],"on":[46,85,220],"their":[47],"environments;":[48],"however,":[49],"trajectory":[50,209],"analysis":[51,159,217],"software":[52],"generally":[53],"lacks":[54],"knowledge":[55],"container":[57,64,206],"interior":[58],"versus":[59],"exterior.":[60],"Further,":[61],"many":[62,208],"relevant":[63],"analyses":[65],"involve":[66],"large-scale":[67],"particle":[68,214],"tracking":[69],"endeavors,":[70],"which":[71,91],"may":[72],"become":[73],"computationally":[74],"prohibitive":[75],"with":[76],"increasing":[77],"system":[78],"size.":[79],"Here,":[80],"novel":[82],"method":[83,120,150,180],"based":[84],"3-D":[86],"ray":[87],"casting":[88],"presented,":[90],"rapidly":[92,195],"classifies":[93],"space":[95],"surrounding":[96],"arbitrary":[100],"shape,":[101],"enabling":[102],"fast":[103],"determination":[104],"identities":[107],"counts":[109],"particles":[111,201],"(e.g.,":[112],"solvent":[113,137],"molecules)":[114],"found":[115],"inside":[116],"outside.":[118],"The":[119,149,192],"broadly":[122],"applicable":[123],"enables":[130,216],"high-performance":[131],"characterization":[132],"properties":[134],"such":[135],"density,":[138],"small-molecule":[139],"transport,":[140],"transbilayer":[141],"lipid":[142],"diffusion,":[143],"topology":[145],"protein":[147],"cavities.":[148],"implemented":[152],"VMD,":[154],"widely":[156],"used":[157],"simulation":[158],"tool":[160],"that":[161,223,232],"supports":[162],"personal":[163],"computers,":[164],"clouds,":[165],"parallel":[167],"supercomputers,":[168],"including":[169],"ORNL's":[170],"Summit":[171],"Titan":[173],"NCSA's":[175],"Blue":[176],"Waters,":[177],"where":[178],"can":[181],"be":[182],"employed":[183],"efficiently":[185],"analyze":[186],"trajectories":[187],"encompassing":[188],"millions":[189],"particles.":[191],"ability":[193],"characterize":[196],"spatial":[198],"relationships":[199],"relative":[202],"over":[207],"frames,":[210],"irrespective":[211],"large":[213],"counts,":[215],"scale":[222],"was":[224,233],"previously":[225,234],"unfeasible,":[226],"at":[227],"level":[229],"accuracy":[231],"unattainable.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
