{"id":"https://openalex.org/W2806830112","doi":"https://doi.org/10.1186/s13321-018-0278-7","title":"Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics","display_name":"Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics","publication_year":2018,"publication_date":"2018-05-21","ids":{"openalex":"https://openalex.org/W2806830112","doi":"https://doi.org/10.1186/s13321-018-0278-7","mag":"2806830112","pmid":"https://pubmed.ncbi.nlm.nih.gov/29785513"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-018-0278-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0278-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-018-0278-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-018-0278-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041754260","display_name":"Karina van den Broek","orcid":"https://orcid.org/0000-0002-9639-7975"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karina van den Broek","raw_affiliation_strings":["Inorganic Chemistry and Center for Nanointegration, University of Duisburg-Essen, Essen, Germany","Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inorganic Chemistry and Center for Nanointegration, University of Duisburg-Essen, Essen, Germany","institution_ids":["https://openalex.org/I62318514"]},{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033169519","display_name":"Hubert Kuhn","orcid":"https://orcid.org/0000-0001-5122-2189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hubert Kuhn","raw_affiliation_strings":["CAM-D Technologies, Essen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAM-D Technologies, Essen, Germany","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089744377","display_name":"Achim Zielesny","orcid":"https://orcid.org/0000-0003-0722-4229"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Achim Zielesny","raw_affiliation_strings":["Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de","Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0722-4229","affiliations":[{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany. achim.zielesny@w-hs.de","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5089744377"],"corresponding_institution_ids":["https://openalex.org/I4210148697"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.495,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.59102341,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"25","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9994000196456909,"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"}},"topics":[{"id":"https://openalex.org/T11471","display_name":"Block Copolymer Self-Assembly","score":0.9994000196456909,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9908999800682068,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9901999831199646,"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/computer-science","display_name":"Computer science","score":0.8113850355148315},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.707497239112854},{"id":"https://openalex.org/keywords/dissipative-particle-dynamics","display_name":"Dissipative particle dynamics","score":0.6925711035728455},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5988983511924744},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.5886058211326599},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.49152836203575134},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4318455457687378},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.41615697741508484},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.40433356165885925},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.39318910241127014},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3696765899658203},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3494369387626648},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.34307989478111267},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09351569414138794}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8113850355148315},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.707497239112854},{"id":"https://openalex.org/C45594756","wikidata":"https://www.wikidata.org/wiki/Q5282784","display_name":"Dissipative particle dynamics","level":3,"score":0.6925711035728455},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5988983511924744},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.5886058211326599},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.49152836203575134},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4318455457687378},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.41615697741508484},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.40433356165885925},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.39318910241127014},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3696765899658203},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3494369387626648},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.34307989478111267},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09351569414138794},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-018-0278-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0278-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-018-0278-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:29785513","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29785513","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:3670f80a69d94c459472dfff3ad33e78","is_oa":true,"landing_page_url":"https://doaj.org/article/3670f80a69d94c459472dfff3ad33e78","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-6 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4983189","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5962482","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-018-0278-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-018-0278-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-018-0278-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2806830112.pdf","grobid_xml":"https://content.openalex.org/works/W2806830112.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1505352099","https://openalex.org/W1969796179","https://openalex.org/W1970585263","https://openalex.org/W1971232585","https://openalex.org/W1971658540","https://openalex.org/W1975353473","https://openalex.org/W1982220212","https://openalex.org/W1988313573","https://openalex.org/W2004812508","https://openalex.org/W2007040080","https://openalex.org/W2011436140","https://openalex.org/W2013979082","https://openalex.org/W2030483511","https://openalex.org/W2030891958","https://openalex.org/W2032655419","https://openalex.org/W2038977497","https://openalex.org/W2041902442","https://openalex.org/W2053343036","https://openalex.org/W2079228930","https://openalex.org/W2093310284","https://openalex.org/W2110447282","https://openalex.org/W2110859765","https://openalex.org/W2121452469","https://openalex.org/W2135631288","https://openalex.org/W2157387245","https://openalex.org/W2171069978","https://openalex.org/W2257796347","https://openalex.org/W2314659927","https://openalex.org/W3102841582","https://openalex.org/W4234347480"],"related_works":["https://openalex.org/W2363861645","https://openalex.org/W2717064866","https://openalex.org/W1973480752","https://openalex.org/W2793851954","https://openalex.org/W2007034665","https://openalex.org/W22410277","https://openalex.org/W2050819322","https://openalex.org/W3035069379","https://openalex.org/W1970971962","https://openalex.org/W2692053082"],"abstract_inverted_index":{"Jdpd":[0],"is":[1,25],"an":[2,28],"open":[3],"Java":[4],"simulation":[5,73,85],"kernel":[6,67],"for":[7,34,60],"Molecular":[8],"Fragment":[9],"Dissipative":[10],"Particle":[11],"Dynamics":[12],"with":[13],"parallelizable":[14],"force":[15],"calculation,":[16],"efficient":[17],"caching":[18],"options":[19],"and":[20,30,38,51],"fast":[21],"property":[22],"calculations.":[23],"It":[24],"characterized":[26],"by":[27],"interface":[29],"factory-pattern":[31],"driven":[32],"design":[33],"simple":[35],"code":[36],"changes":[37],"may":[39,68],"help":[40],"to":[41,81],"avoid":[42],"problems":[43],"of":[44],"polyglot":[45],"programming.":[46],"Detailed":[47],"input/output":[48],"communication,":[49],"parallelization":[50],"process":[52],"control":[53],"as":[54,56],"well":[55],"internal":[57],"logging":[58],"capabilities":[59],"debugging":[61],"purposes":[62],"are":[63],"supported.":[64],"The":[65],"new":[66],"be":[69],"utilized":[70],"in":[71],"different":[72],"environments":[74],"ranging":[75],"from":[76],"flexible":[77],"scripting":[78],"solutions":[79],"up":[80],"fully":[82],"integrated":[83],"\"all-in-one\"":[84],"systems.":[86]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
