{"id":"https://openalex.org/W2008779826","doi":"https://doi.org/10.1007/s11047-004-2639-6","title":"On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing","display_name":"On the model granularity to simulate protein dynamics: A biological physics view on biomolecular computing","publication_year":2004,"publication_date":"2004-12-01","ids":{"openalex":"https://openalex.org/W2008779826","doi":"https://doi.org/10.1007/s11047-004-2639-6","mag":"2008779826"},"language":"en","primary_location":{"id":"doi:10.1007/s11047-004-2639-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s11047-004-2639-6","pdf_url":null,"source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","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/A5052737030","display_name":"Mitsunori Takano","orcid":"https://orcid.org/0000-0001-8855-008X"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Mitsunori Takano","raw_affiliation_strings":["Department of Physics, School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555, Japan","Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan 169-8555"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan 169-8555","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056979882","display_name":"Junichi Higo","orcid":"https://orcid.org/0000-0002-0408-1907"},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Junichi Higo","raw_affiliation_strings":["Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 horinouchi, Hachioji, Tokyo, 192-0392, Japan","Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science, Tokyo, Japan 192-0392"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 horinouchi, Hachioji, Tokyo, 192-0392, Japan","institution_ids":["https://openalex.org/I149964584"]},{"raw_affiliation_string":"Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science, Tokyo, Japan 192-0392","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083584731","display_name":"Hironori Nakamura","orcid":"https://orcid.org/0000-0003-4463-6185"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hironori K. Nakamura","raw_affiliation_strings":["Department of Physics, School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555, Japan","Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan 169-8555"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan 169-8555","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016751632","display_name":"Masaki Sasai","orcid":"https://orcid.org/0000-0002-1028-8242"},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaki Sasai","raw_affiliation_strings":["Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, 464-8601, Japan","Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, Japan 464-8601#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-Ku, Nagoya, 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Nagoya, Japan 464-8601#TAB#","institution_ids":["https://openalex.org/I60134161"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5052737030"],"corresponding_institution_ids":["https://openalex.org/I150744194"],"apc_list":{"value":2290,"currency":"EUR","value_usd":2890},"apc_paid":null,"fwci":0.4823,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.61161425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"3","issue":"4","first_page":"377","last_page":"393"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9909999966621399,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9821000099182129,"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/granularity","display_name":"Granularity","score":0.880547821521759},{"id":"https://openalex.org/keywords/theory-of-computation","display_name":"Theory of computation","score":0.5932682752609253},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5752235651016235},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.48654499650001526},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4860990047454834},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.4146800935268402},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4140869379043579},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.36975300312042236},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3582000136375427},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17853239178657532},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.13060516119003296},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09664103388786316}],"concepts":[{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.880547821521759},{"id":"https://openalex.org/C24858836","wikidata":"https://www.wikidata.org/wiki/Q844718","display_name":"Theory of computation","level":2,"score":0.5932682752609253},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5752235651016235},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.48654499650001526},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4860990047454834},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.4146800935268402},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4140869379043579},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.36975300312042236},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3582000136375427},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17853239178657532},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.13060516119003296},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09664103388786316},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s11047-004-2639-6","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s11047-004-2639-6","pdf_url":null,"source":{"id":"https://openalex.org/S149828480","display_name":"Natural Computing","issn_l":"1567-7818","issn":["1567-7818","1572-9796"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Natural Computing","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1541403646","https://openalex.org/W1554442128","https://openalex.org/W1680174508","https://openalex.org/W1964725350","https://openalex.org/W1971224531","https://openalex.org/W1976499671","https://openalex.org/W1978517242","https://openalex.org/W1985640426","https://openalex.org/W1997310186","https://openalex.org/W2031504050","https://openalex.org/W2032049213","https://openalex.org/W2032341308","https://openalex.org/W2041343732","https://openalex.org/W2044877050","https://openalex.org/W2047580257","https://openalex.org/W2047590512","https://openalex.org/W2063260399","https://openalex.org/W2065864578","https://openalex.org/W2072261891","https://openalex.org/W2075230856","https://openalex.org/W2088957204","https://openalex.org/W2095267650","https://openalex.org/W2108571423","https://openalex.org/W2113994268","https://openalex.org/W2120451413","https://openalex.org/W2125626635","https://openalex.org/W2142883438","https://openalex.org/W2155946997","https://openalex.org/W2159010139","https://openalex.org/W2162817985","https://openalex.org/W2177471540","https://openalex.org/W2579218780","https://openalex.org/W2952226375","https://openalex.org/W4321317585"],"related_works":["https://openalex.org/W2609091291","https://openalex.org/W2146946740","https://openalex.org/W2947762918","https://openalex.org/W1972374761","https://openalex.org/W2159252857","https://openalex.org/W1739118904","https://openalex.org/W2032063490","https://openalex.org/W223567488","https://openalex.org/W3098391775","https://openalex.org/W1539419373"],"abstract_inverted_index":null,"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
