{"id":"https://openalex.org/W4320037739","doi":"https://doi.org/10.1186/s13321-023-00687-y","title":"MDSuite: comprehensive post-processing tool for particle simulations","display_name":"MDSuite: comprehensive post-processing tool for particle simulations","publication_year":2023,"publication_date":"2023-02-11","ids":{"openalex":"https://openalex.org/W4320037739","doi":"https://doi.org/10.1186/s13321-023-00687-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/36774469"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00687-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00687-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00687-y","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/s13321-023-00687-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053400514","display_name":"Samuel Tovey","orcid":"https://orcid.org/0000-0001-9537-8361"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Samuel Tovey","raw_affiliation_strings":["Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034720523","display_name":"Fabian Zills","orcid":"https://orcid.org/0000-0002-6936-4692"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabian Zills","raw_affiliation_strings":["Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039261352","display_name":"Francisco Torres-Herrador","orcid":"https://orcid.org/0000-0002-3901-3461"},"institutions":[{"id":"https://openalex.org/I149208984","display_name":"Von Karman Institute for Fluid Dynamics","ror":"https://ror.org/01r4bn552","country_code":"BE","type":"nonprofit","lineage":["https://openalex.org/I149208984"]},{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Francisco Torres-Herrador","raw_affiliation_strings":["Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Rhode-St-Genese, Belgium","Laboratory for Chemical Technology (LCT), Ghent University, Ghent, Belgium","Thermo and Fluid Dynamics (FLOW), Vrije Universiteit Brussel, Brussels, Belgium"],"affiliations":[{"raw_affiliation_string":"Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Rhode-St-Genese, Belgium","institution_ids":["https://openalex.org/I149208984"]},{"raw_affiliation_string":"Laboratory for Chemical Technology (LCT), Ghent University, Ghent, Belgium","institution_ids":["https://openalex.org/I32597200"]},{"raw_affiliation_string":"Thermo and Fluid Dynamics (FLOW), Vrije Universiteit Brussel, Brussels, Belgium","institution_ids":["https://openalex.org/I13469542"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065081853","display_name":"Christoph Lohrmann","orcid":"https://orcid.org/0000-0002-9011-2975"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph Lohrmann","raw_affiliation_strings":["Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081077098","display_name":"Marco Br\u00fcckner","orcid":null},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marco Br\u00fcckner","raw_affiliation_strings":["Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007676475","display_name":"Christian Holm","orcid":"https://orcid.org/0000-0003-2739-310X"},"institutions":[{"id":"https://openalex.org/I100066346","display_name":"University of Stuttgart","ror":"https://ror.org/04vnq7t77","country_code":"DE","type":"education","lineage":["https://openalex.org/I100066346"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Holm","raw_affiliation_strings":["Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany. holm@icp.uni-stuttgart.de","Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany. holm@icp.uni-stuttgart.de","institution_ids":["https://openalex.org/I100066346"]},{"raw_affiliation_string":"Institute for Computational Physics, Universit\u00e4t Stuttgart, Stuttgart, Germany","institution_ids":["https://openalex.org/I100066346"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5053400514"],"corresponding_institution_ids":["https://openalex.org/I100066346"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1720,"currency":"EUR","value_usd":1855},"fwci":1.1842,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.78774321,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11044","display_name":"Particle Detector Development and Performance","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/3106","display_name":"Nuclear and High Energy Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10527","display_name":"High-Energy Particle Collisions Research","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/3106","display_name":"Nuclear and High Energy Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6498846411705017},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.46406278014183044}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6498846411705017},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.46406278014183044}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00687-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00687-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00687-y","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:36774469","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36774469","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:pubmedcentral.nih.gov:9921696","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9921696","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9921696/pdf/13321_2023_Article_687.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e8087663ecc94a3c8613b47c8c25c955","is_oa":true,"landing_page_url":"https://doaj.org/article/e8087663ecc94a3c8613b47c8c25c955","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-15 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00687-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00687-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00687-y","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":[{"id":"https://openalex.org/G3898666650","display_name":null,"funder_award_id":"1S58718N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G4038838385","display_name":null,"funder_award_id":"EXC 2075-390740016","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320325850","display_name":"Universit\u00e4t Stuttgart","ror":"https://ror.org/04vnq7t77"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4320037739.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1166867742","https://openalex.org/W1560061358","https://openalex.org/W1966326070","https://openalex.org/W2009797711","https://openalex.org/W2018699999","https://openalex.org/W2018763953","https://openalex.org/W2019465613","https://openalex.org/W2019926612","https://openalex.org/W2022306307","https://openalex.org/W2023103876","https://openalex.org/W2029667189","https://openalex.org/W2029973510","https://openalex.org/W2040716987","https://openalex.org/W2061939373","https://openalex.org/W2079153216","https://openalex.org/W2093806300","https://openalex.org/W2109606373","https://openalex.org/W2118233996","https://openalex.org/W2118571345","https://openalex.org/W2147988069","https://openalex.org/W2149073215","https://openalex.org/W2162166182","https://openalex.org/W2170711116","https://openalex.org/W2271736303","https://openalex.org/W2302501749","https://openalex.org/W2332712348","https://openalex.org/W2342249984","https://openalex.org/W2485795334","https://openalex.org/W2511867836","https://openalex.org/W2542617869","https://openalex.org/W2736176297","https://openalex.org/W2772373325","https://openalex.org/W2784644294","https://openalex.org/W2785073945","https://openalex.org/W2887448834","https://openalex.org/W2899070097","https://openalex.org/W2901483778","https://openalex.org/W2921209242","https://openalex.org/W2922050530","https://openalex.org/W2953259383","https://openalex.org/W2963444572","https://openalex.org/W2981603605","https://openalex.org/W3045322909","https://openalex.org/W3075723235","https://openalex.org/W3089827052","https://openalex.org/W3091762523","https://openalex.org/W3097010599","https://openalex.org/W3103785545","https://openalex.org/W3105377648","https://openalex.org/W3106652335","https://openalex.org/W3109054533","https://openalex.org/W3115142961","https://openalex.org/W3138531307","https://openalex.org/W3201073812","https://openalex.org/W3216165377","https://openalex.org/W4200309293","https://openalex.org/W4206712037","https://openalex.org/W6602913128","https://openalex.org/W6893797555","https://openalex.org/W6912443848","https://openalex.org/W6969259846"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Particle-Based":[0],"(PB)":[1],"simulations,":[2],"including":[3,136],"Molecular":[4],"Dynamics":[5],"(MD),":[6],"provide":[7],"access":[8],"to":[9,25,31,207],"system":[10],"observables":[11],"that":[12],"are":[13],"not":[14],"easily":[15],"available":[16],"experimentally.":[17],"However,":[18],"in":[19,40,72,177],"most":[20],"cases,":[21],"PB":[22,42,97],"data":[23,50,83,98],"needs":[24],"be":[26],"processed":[27],"after":[28],"a":[29,92,111,171,182],"simulation":[30,165],"extract":[32],"these":[33],"observables.":[34],"One":[35],"of":[36,49,107,122,134,158,195],"the":[37,46,65,105,120,132,150,155,178,187,193],"main":[38],"challenges":[39],"post-processing":[41,66],"simulations":[43],"is":[44],"managing":[45],"large":[47],"amounts":[48],"typically":[51],"generated":[52],"without":[53],"incurring":[54],"memory":[55,112],"or":[56,161],"computational":[57],"capacity":[58],"limitations.":[59],"In":[60],"this":[61],"work,":[62],"we":[63],"introduce":[64],"tool:":[67],"MDSuite.":[68],"This":[69,101],"software,":[70],"developed":[71],"Python,":[73],"combines":[74],"state-of-the-art":[75],"computing":[76],"technologies":[77],"such":[78,86],"as":[79,87],"TensorFlow,":[80],"with":[81,199],"modern":[82],"management":[84],"tools":[85],"HDF5":[88],"and":[89,95,115,147,181,205],"SQL":[90],"for":[91,119,131,154,163,174,186],"fast,":[93],"scalable,":[94],"accurate":[96],"processing":[99],"engine.":[100],"package,":[102],"built":[103],"around":[104],"principles":[106],"FAIR":[108],"data,":[109],"provides":[110,170],"safe,":[113],"parallelized,":[114],"GPU":[116],"accelerated":[117],"environment":[118],"analysis":[121,197],"particle":[123,203],"simulations.":[124],"The":[125,167],"software":[126],"currently":[127],"offers":[128],"17":[129],"calculators":[130,160],"computation":[133],"properties":[135],"diffusion":[137],"coefficients,":[138],"thermal":[139],"conductivity,":[140],"viscosity,":[141],"radial":[142],"distribution":[143],"functions,":[144],"coordination":[145],"numbers,":[146],"more.":[148],"Further,":[149],"object-oriented":[151],"framework":[152],"allows":[153],"rapid":[156],"implementation":[157],"new":[159],"file-readers":[162],"different":[164],"software.":[166],"Python":[168],"front-end":[169],"familiar":[172],"interface":[173],"many":[175],"users":[176],"scientific":[179],"community":[180],"mild":[183],"learning":[184],"curve":[185],"inexperienced.":[188],"Future":[189],"developments":[190],"will":[191],"include":[192],"introduction":[194],"more":[196],"associated":[198],"ab-initio":[200],"methods,":[201,204],"colloidal/macroscopic":[202],"extension":[206],"experimental":[208],"data.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
