{"id":"https://openalex.org/W2914313353","doi":"https://doi.org/10.1109/bibm.2018.8621070","title":"Homopolymer with intrachain reversible bonds as a model of large-scale chromatin organization and dynamics","display_name":"Homopolymer with intrachain reversible bonds as a model of large-scale chromatin organization and dynamics","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2914313353","doi":"https://doi.org/10.1109/bibm.2018.8621070","mag":"2914313353"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621070","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621070","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5079475121","display_name":"Artem Petrov","orcid":"https://orcid.org/0000-0002-1238-3745"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Artem Petrov","raw_affiliation_strings":["Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075705622","display_name":"Pavel Kos","orcid":"https://orcid.org/0000-0002-3625-0939"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Pavel Kos","raw_affiliation_strings":["Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036176580","display_name":"Alexander V. Chertovich","orcid":"https://orcid.org/0000-0001-9772-1573"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander Chertovich","raw_affiliation_strings":["Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia"],"affiliations":[{"raw_affiliation_string":"Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079475121"],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13720893,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"2479","last_page":"2479"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9990000128746033,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9990000128746033,"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":0.9884999990463257,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9783999919891357,"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/chromatin","display_name":"Chromatin","score":0.8396531939506531},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.5624081492424011},{"id":"https://openalex.org/keywords/metastability","display_name":"Metastability","score":0.5403841137886047},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.448326975107193},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.4352598190307617},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.4256861209869385},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.4221777319908142},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3729982078075409},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3711433410644531},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3495136797428131},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2654942274093628},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.20339831709861755},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1995251178741455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.186781108379364},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10319885611534119}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.8396531939506531},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.5624081492424011},{"id":"https://openalex.org/C89464430","wikidata":"https://www.wikidata.org/wiki/Q849516","display_name":"Metastability","level":2,"score":0.5403841137886047},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.448326975107193},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.4352598190307617},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.4256861209869385},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4221777319908142},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3729982078075409},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3711433410644531},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3495136797428131},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2654942274093628},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20339831709861755},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1995251178741455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.186781108379364},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10319885611534119},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621070","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621070","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"display_name":"Life below water","id":"https://metadata.un.org/sdg/14"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4307107610","https://openalex.org/W3213627526","https://openalex.org/W4226159838","https://openalex.org/W98379584","https://openalex.org/W2113253885","https://openalex.org/W2413824894","https://openalex.org/W2020842184","https://openalex.org/W2030159793","https://openalex.org/W1979616193","https://openalex.org/W2082280880"],"abstract_inverted_index":{"Our":[0,160],"aim":[1],"is":[2],"to":[3,122,149],"create":[4],"reliable":[5],"physical":[6],"model":[7],"for":[8,70,172],"large-scale":[9],"chromatin":[10,26,171],"organization":[11],"in":[12,33,155,170],"different":[13,100],"species,":[14],"having":[15],"small":[16,108],"number":[17,93,109],"of":[18,37,94,102,110,137],"non-phenomenological":[19],"variables.":[20],"In":[21],"this":[22,68],"work":[23],"we":[24,98],"study":[25],"as":[27,56,177,179],"a":[28,77,88,117],"coarse-grained":[29],"flexible":[30],"homopolymer":[31],"chain":[32,39,47,115],"athermal":[34],"solvent.":[35],"Beads":[36],"the":[38,92,103,138,156],"can":[40],"form":[41],"reversible":[42,52,96,112],"pairwise":[43],"bonds,":[44,97,113],"which":[45],"induce":[46],"crumpling":[48],"and":[49,116,141,175,182],"collapse.":[50],"The":[51],"bonds":[53],"are":[54,162],"treated":[55],"relatively":[57],"long-living":[58,118],"inter-TAD":[59],"contacts.":[60],"There":[61],"could":[62],"be":[63],"several":[64],"biological":[65],"mechanisms":[66],"underlying":[67],"interactions,":[69],"example":[71],"non-acetylated":[72],"histone":[73,83],"H3":[74],"tail":[75],"forming":[76],"complex":[78],"with":[79,107,126,164,180],"acidic":[80],"patch":[81],"on":[82,167],"H2,":[84],"or":[85],"interactions":[86],"through":[87],"specific":[89],"proteins.":[90],"Varying":[91],"formed":[95,111],"observed":[99],"states":[101],"chain:":[104],"swollen":[105],"state":[106],"Gaussian":[114],"non-equilibrium":[119,158],"state,":[120],"similar":[121],"metastable":[123],"fractal":[124,146],"globule":[125,147],"P(s)":[127],"~":[128],"s":[129],"<sup":[130],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[131],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">-1</sup>":[132],".We":[133],"studied":[134],"dynamic":[135],"behavior":[136],"system":[139],"(MSD)":[140],"showed,":[142],"that":[143],"transition":[144],"from":[145],"dynamics":[148,169],"much":[150],"faster":[151],"anomalous":[152],"subdiffusion":[153],"occurred":[154],"aforementioned":[157],"state.":[159],"results":[161],"consistent":[163],"experimental":[165,184],"data":[166],"loci":[168],"mammals,":[173],"yeast":[174],"Drosophila,":[176],"well":[178],"FISH":[181],"Hi-C":[183],"results.":[185]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
