{"id":"https://openalex.org/W4387614347","doi":"https://doi.org/10.1016/j.cpc.2023.108964","title":"Learning coarse-grained force fields for fibrogenesis modeling","display_name":"Learning coarse-grained force fields for fibrogenesis modeling","publication_year":2023,"publication_date":"2023-10-13","ids":{"openalex":"https://openalex.org/W4387614347","doi":"https://doi.org/10.1016/j.cpc.2023.108964"},"language":"en","primary_location":{"id":"doi:10.1016/j.cpc.2023.108964","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cpc.2023.108964","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/A5101808092","display_name":"Ziji Zhang","orcid":"https://orcid.org/0000-0003-3923-6267"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ziji Zhang","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093058821","display_name":"Georgios Kementzidis","orcid":"https://orcid.org/0009-0005-2989-783X"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Georgios Kementzidis","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100364185","display_name":"Peng Zhang","orcid":"https://orcid.org/0000-0002-8403-8289"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Zhang","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075086858","display_name":"Leili Zhang","orcid":"https://orcid.org/0000-0002-2952-4858"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leili Zhang","raw_affiliation_strings":["IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA"],"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091293385","display_name":"James Kozloski","orcid":"https://orcid.org/0000-0003-3420-4688"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Kozloski","raw_affiliation_strings":["IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA"],"affiliations":[{"raw_affiliation_string":"IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027217819","display_name":"Adam Hansen","orcid":"https://orcid.org/0000-0001-8123-2679"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Hansen","raw_affiliation_strings":["Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076863594","display_name":"Miriam Rafailovich","orcid":null},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Miriam Rafailovich","raw_affiliation_strings":["Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024512701","display_name":"Marcia Simon","orcid":null},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcia Simon","raw_affiliation_strings":["Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047165687","display_name":"Yuefan Deng","orcid":"https://orcid.org/0000-0002-5224-3958"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuefan Deng","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5047165687"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":{"value":3670,"currency":"USD","value_usd":3670},"apc_paid":null,"fwci":0.7622,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73377218,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"295","issue":null,"first_page":"108964","last_page":"108964"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.998199999332428,"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":0.998199999332428,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.992900013923645,"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"}},{"id":"https://openalex.org/T11721","display_name":"Blood properties and coagulation","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.7354162335395813},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6347856521606445},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6183335185050964},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5510016679763794},{"id":"https://openalex.org/keywords/operator","display_name":"Operator (biology)","score":0.5092850923538208},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.49439096450805664},{"id":"https://openalex.org/keywords/brownian-dynamics","display_name":"Brownian dynamics","score":0.46919912099838257},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.43751347064971924},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.41075006127357483},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36866581439971924},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32938164472579956},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29049354791641235},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.24468114972114563},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21035003662109375},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16577106714248657},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.13189834356307983},{"id":"https://openalex.org/keywords/brownian-motion","display_name":"Brownian motion","score":0.12090447545051575}],"concepts":[{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.7354162335395813},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6347856521606445},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6183335185050964},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5510016679763794},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.5092850923538208},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.49439096450805664},{"id":"https://openalex.org/C130603088","wikidata":"https://www.wikidata.org/wiki/Q4976526","display_name":"Brownian dynamics","level":3,"score":0.46919912099838257},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.43751347064971924},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.41075006127357483},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36866581439971924},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32938164472579956},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29049354791641235},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.24468114972114563},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21035003662109375},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16577106714248657},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.13189834356307983},{"id":"https://openalex.org/C112401455","wikidata":"https://www.wikidata.org/wiki/Q178036","display_name":"Brownian motion","level":2,"score":0.12090447545051575},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.cpc.2023.108964","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.cpc.2023.108964","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1130685788","display_name":null,"funder_award_id":"FP00004096","funder_id":"https://openalex.org/F4320309644","funder_display_name":"State University of New York"},{"id":"https://openalex.org/G6463238133","display_name":null,"funder_award_id":"FP0002468","funder_id":"https://openalex.org/F4320307762","funder_display_name":"International Business Machines Corporation"}],"funders":[{"id":"https://openalex.org/F4320307762","display_name":"International Business Machines Corporation","ror":"https://ror.org/05hh8d621"},{"id":"https://openalex.org/F4320309500","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94"},{"id":"https://openalex.org/F4320309644","display_name":"State University of New York","ror":"https://ror.org/01q1z8k08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W24013980","https://openalex.org/W379390718","https://openalex.org/W1031578623","https://openalex.org/W1984909504","https://openalex.org/W1986356457","https://openalex.org/W1993765343","https://openalex.org/W1999138060","https://openalex.org/W2026737855","https://openalex.org/W2039680358","https://openalex.org/W2049489032","https://openalex.org/W2049617698","https://openalex.org/W2061308254","https://openalex.org/W2085709924","https://openalex.org/W2159565091","https://openalex.org/W2171695688","https://openalex.org/W2291401466","https://openalex.org/W2326778587","https://openalex.org/W2333894099","https://openalex.org/W2413334978","https://openalex.org/W2498507004","https://openalex.org/W2592033223","https://openalex.org/W2602120015","https://openalex.org/W2761329292","https://openalex.org/W2762806006","https://openalex.org/W2775970449","https://openalex.org/W2778051509","https://openalex.org/W2789106493","https://openalex.org/W2795698891","https://openalex.org/W2901995873","https://openalex.org/W2927687900","https://openalex.org/W2959045520","https://openalex.org/W2969697705","https://openalex.org/W2994626356","https://openalex.org/W3045213745","https://openalex.org/W3046156055","https://openalex.org/W3098370560","https://openalex.org/W3103390675","https://openalex.org/W3104644561","https://openalex.org/W3105774298","https://openalex.org/W3111280780","https://openalex.org/W3113616921","https://openalex.org/W3122535728","https://openalex.org/W3135027603","https://openalex.org/W3162460530","https://openalex.org/W3167312708","https://openalex.org/W4210264818","https://openalex.org/W4211196614","https://openalex.org/W4234552385","https://openalex.org/W4251443534","https://openalex.org/W4283700743","https://openalex.org/W4294891977","https://openalex.org/W4297369678","https://openalex.org/W4319082232","https://openalex.org/W6646753085","https://openalex.org/W6676333094","https://openalex.org/W6687483927","https://openalex.org/W6729210268","https://openalex.org/W6796765926","https://openalex.org/W6903781235"],"related_works":["https://openalex.org/W3127534742","https://openalex.org/W2028501277","https://openalex.org/W2002038078","https://openalex.org/W2022269912","https://openalex.org/W4366465732","https://openalex.org/W2811043963","https://openalex.org/W2161972019","https://openalex.org/W2312858532","https://openalex.org/W1998915375","https://openalex.org/W4321013117"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}