{"id":"https://openalex.org/W7214952949","doi":"https://doi.org/10.64898/2026.09.28.754770","title":"PySTARC : GPU-accelerated Brownian dynamics for bimolecular association rate constants","display_name":"PySTARC : GPU-accelerated Brownian dynamics for bimolecular association rate constants","publication_year":2026,"publication_date":"2026-09-29","ids":{"openalex":"https://openalex.org/W7214952949","doi":"https://doi.org/10.64898/2026.09.28.754770"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.28.754770","doi":"https://doi.org/10.64898/2026.09.28.754770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.28.754770","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.09.28.754770","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077404629","display_name":"Anupam Anand Ojha","orcid":"https://orcid.org/0000-0001-6588-3092","observed_orcids":["https://orcid.org/0000-0001-6588-3092"]},"institutions":[{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Anupam Anand Ojha","raw_affiliation_strings":["Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA"],"raw_orcid":"https://orcid.org/0000-0001-6588-3092","affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA","institution_ids":["https://openalex.org/I4387153999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071701467","display_name":"Gary Huber","orcid":"https://orcid.org/0000-0002-5936-6184","observed_orcids":["https://orcid.org/0000-0002-5936-6184"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary Huber","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA"],"raw_orcid":"https://orcid.org/0000-0002-5936-6184","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138501069","display_name":"Shiksha Dutta","orcid":"https://orcid.org/0009-0002-8419-6436","observed_orcids":["https://orcid.org/0009-0002-8419-6436"]},"institutions":[{"id":"https://openalex.org/I4210142730","display_name":"Centre Hospitalier de l\u2019Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0410a8y51","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801902503","https://openalex.org/I4210139015","https://openalex.org/I4210142730","https://openalex.org/I4405279980"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shiksha Dutta","raw_affiliation_strings":["Department of Molecular Biology, Centre de recherche du Centre hospitalier de l\u2019Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H2X 0A9, Canada"],"raw_orcid":"https://orcid.org/0009-0002-8419-6436","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Centre de recherche du Centre hospitalier de l\u2019Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, QC H2X 0A9, Canada","institution_ids":["https://openalex.org/I4210142730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041965787","display_name":"Sonya M. Hanson","orcid":"https://orcid.org/0000-0001-8960-5353","observed_orcids":["https://orcid.org/0000-0001-8960-5353"]},"institutions":[{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sonya M. Hanson","raw_affiliation_strings":["Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA"],"raw_orcid":"https://orcid.org/0000-0001-8960-5353","affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA","institution_ids":["https://openalex.org/I4387153999"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5077404629"],"corresponding_institution_ids":["https://openalex.org/I4387153999"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3237000107765198,"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":0.3237000107765198,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.2371000051498413,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.21850000321865082,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/brownian-dynamics","display_name":"Brownian dynamics","score":0.921999990940094},{"id":"https://openalex.org/keywords/gpu-acceleration","display_name":"GPU acceleration","score":0.9010000228881836},{"id":"https://openalex.org/keywords/brownian-bridge","display_name":"Brownian bridge","score":0.9670000076293945},{"id":"https://openalex.org/keywords/protein-ligand-complex","display_name":"protein-ligand complex","score":0.7990000247955322},{"id":"https://openalex.org/keywords/protein-protein-complex","display_name":"protein-protein complex","score":0.9940000176429749},{"id":"https://openalex.org/keywords/reaction-probability","display_name":"reaction probability","score":0.4180000126361847}],"concepts":[{"id":"https://openalex.org/C130603088","wikidata":"https://www.wikidata.org/wiki/Q4976526","display_name":"Brownian dynamics","level":3,"score":0.6668999791145325},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5753999948501587},{"id":"https://openalex.org/C112401455","wikidata":"https://www.wikidata.org/wiki/Q178036","display_name":"Brownian motion","level":2,"score":0.517799973487854},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5109999775886536},{"id":"https://openalex.org/C2983325608","wikidata":"https://www.wikidata.org/wiki/Q17084606","display_name":"Data association","level":3,"score":0.48910000920295715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4634000062942505},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.39739999175071716},{"id":"https://openalex.org/C102931765","wikidata":"https://www.wikidata.org/wiki/Q189673","display_name":"Dissociation (chemistry)","level":2,"score":0.3817000091075897},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.3752000033855438},{"id":"https://openalex.org/C2779712033","wikidata":"https://www.wikidata.org/wiki/Q28208841","display_name":"Dissociation rate","level":3,"score":0.3555000126361847},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35370001196861267},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.3522999882698059},{"id":"https://openalex.org/C93391505","wikidata":"https://www.wikidata.org/wiki/Q658700","display_name":"Reaction rate constant","level":3,"score":0.3497999906539917},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3479999899864197},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34310001134872437},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30219998955726624},{"id":"https://openalex.org/C2987642246","wikidata":"https://www.wikidata.org/wiki/Q5452196","display_name":"First order","level":2,"score":0.27149999141693115},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.26919999718666077},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2648000121116638},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2644999921321869},{"id":"https://openalex.org/C149792144","wikidata":"https://www.wikidata.org/wiki/Q2071902","display_name":"Coalescence (physics)","level":2,"score":0.2623000144958496},{"id":"https://openalex.org/C8272713","wikidata":"https://www.wikidata.org/wiki/Q176737","display_name":"Stochastic process","level":2,"score":0.2605000138282776}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.28.754770","doi":"https://doi.org/10.64898/2026.09.28.754770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.28.754770","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.28.754770","doi":"https://doi.org/10.64898/2026.09.28.754770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.28.754770","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":140,"referenced_works":["https://openalex.org/W176484652","https://openalex.org/W1552029653","https://openalex.org/W1587498640","https://openalex.org/W1964672693","https://openalex.org/W1969723894","https://openalex.org/W1970111528","https://openalex.org/W1970973025","https://openalex.org/W1977949865","https://openalex.org/W1980055293","https://openalex.org/W1988287340","https://openalex.org/W1989732138","https://openalex.org/W1989814214","https://openalex.org/W1989925383","https://openalex.org/W1991130269","https://openalex.org/W1995387731","https://openalex.org/W2000523053","https://openalex.org/W2001398410","https://openalex.org/W2003128923","https://openalex.org/W2003288227","https://openalex.org/W2008605008","https://openalex.org/W2011738663","https://openalex.org/W2014387919","https://openalex.org/W2015039690","https://openalex.org/W2016408686","https://openalex.org/W2017829285","https://openalex.org/W2021988453","https://openalex.org/W2022178479","https://openalex.org/W2022473533","https://openalex.org/W2023269994","https://openalex.org/W2023387870","https://openalex.org/W2029582401","https://openalex.org/W2031260419","https://openalex.org/W2032543787","https://openalex.org/W2032937791","https://openalex.org/W2033163073","https://openalex.org/W2034257801","https://openalex.org/W2038408373","https://openalex.org/W2040370739","https://openalex.org/W2047723546","https://openalex.org/W2053246876","https://openalex.org/W2053475844","https://openalex.org/W2057109095","https://openalex.org/W2061724671","https://openalex.org/W2063945425","https://openalex.org/W2064759971","https://openalex.org/W2076054862","https://openalex.org/W2077393211","https://openalex.org/W2078391824","https://openalex.org/W2078818508","https://openalex.org/W2079122045","https://openalex.org/W2085617912","https://openalex.org/W2085934556","https://openalex.org/W2095719702","https://openalex.org/W2098076038","https://openalex.org/W2105406875","https://openalex.org/W2106447917","https://openalex.org/W2106768806","https://openalex.org/W2108715896","https://openalex.org/W2133620840","https://openalex.org/W2139820020","https://openalex.org/W2142868265","https://openalex.org/W2144020793","https://openalex.org/W2144667632","https://openalex.org/W2146031422","https://openalex.org/W2149655632","https://openalex.org/W2151970891","https://openalex.org/W2154670681","https://openalex.org/W2171356751","https://openalex.org/W2182983741","https://openalex.org/W2207535250","https://openalex.org/W2265661434","https://openalex.org/W2313116527","https://openalex.org/W2319735119","https://openalex.org/W2322812643","https://openalex.org/W2328508377","https://openalex.org/W2343097429","https://openalex.org/W2464012090","https://openalex.org/W2516856487","https://openalex.org/W2549178826","https://openalex.org/W2556565974","https://openalex.org/W2593981338","https://openalex.org/W2606751507","https://openalex.org/W2607348308","https://openalex.org/W2616655501","https://openalex.org/W2664285537","https://openalex.org/W2760367307","https://openalex.org/W2772606519","https://openalex.org/W2779060209","https://openalex.org/W2781821160","https://openalex.org/W2783073729","https://openalex.org/W2784213390","https://openalex.org/W2787959647","https://openalex.org/W2801926893","https://openalex.org/W2804603144","https://openalex.org/W2868115494","https://openalex.org/W2888553603","https://openalex.org/W2898094195","https://openalex.org/W2912171584","https://openalex.org/W2914236451","https://openalex.org/W2917833092","https://openalex.org/W2947171186","https://openalex.org/W2949223833","https://openalex.org/W2971028405","https://openalex.org/W2974531988","https://openalex.org/W3035762603","https://openalex.org/W3035815479","https://openalex.org/W3037317174","https://openalex.org/W3080588469","https://openalex.org/W3082176322","https://openalex.org/W3093450407","https://openalex.org/W3105010031","https://openalex.org/W3121524252","https://openalex.org/W3130554079","https://openalex.org/W3156286114","https://openalex.org/W3168430821","https://openalex.org/W3207186070","https://openalex.org/W3211306614","https://openalex.org/W4211160326","https://openalex.org/W4214936800","https://openalex.org/W4226013321","https://openalex.org/W4280531501","https://openalex.org/W4281558021","https://openalex.org/W4283584533","https://openalex.org/W4285744850","https://openalex.org/W4285744851","https://openalex.org/W4311393387","https://openalex.org/W4318671359","https://openalex.org/W4321004126","https://openalex.org/W4353109120","https://openalex.org/W4361295032","https://openalex.org/W4362677414","https://openalex.org/W4386624589","https://openalex.org/W4387918243","https://openalex.org/W4389730558","https://openalex.org/W4403334720","https://openalex.org/W4404142486","https://openalex.org/W4408355335","https://openalex.org/W4411463597","https://openalex.org/W4414821922","https://openalex.org/W7164542099"],"related_works":["https://openalex.org/W4414821922","https://openalex.org/W6903510585","https://openalex.org/W2791769108","https://openalex.org/W2915065624","https://openalex.org/W2794206956","https://openalex.org/W2028656965","https://openalex.org/W1574201790","https://openalex.org/W2417649934","https://openalex.org/W2994745860","https://openalex.org/W6906548160"],"abstract_inverted_index":{"Abstract":[0,183],"Drug-target":[1],"association":[2,16,77],"and":[3,39,145,161],"dissociation":[4],"rates":[5],"often":[6],"determine":[7],"in":[8,35,169],"vivo":[9],"efficacy":[10],"more":[11],"than":[12],"affinity":[13],"alone.":[14],"The":[15,110],"rate":[17,78,154],"k":[18,170],"on":[19,95,171],",":[20,172],"however,":[21],"is":[22,31,81,157],"computationally":[23],"challenging":[24],"to":[25,153],"predict":[26],"since":[27],"the":[28,46,86,124,128,147],"productive":[29],"encounter":[30],"a":[32,36,69,82,96,100,106,119,131],"rare":[33],"event":[34],"large":[37,107],"translational":[38],"orientational":[40],"search":[41],"space,":[42],"which":[43],"lies":[44],"beyond":[45],"reach":[47],"of":[48,85,127,167,179,181],"conventional":[49],"atomistic":[50],"simulations.":[51],"We":[52],"present":[53],"PySTARC":[54,80,156],"(":[55],"Py":[56],"thon":[57],"S":[58],"imulation":[59],"T":[60],"oolkit":[61],"for":[62,74],"A":[63],"ssociation":[64],"R":[65],"ate":[66],"C":[67],"onstants),":[68],"GPU-accelerated":[70],"Brownian":[71,121],"dynamics":[72],"engine":[73,88],"estimating":[75],"bimolecular":[76],"constants.":[79],"Python":[83],"reimplementation":[84],"BrownDye":[87],"that":[89,102],"converges":[90],"even":[91],"small":[92],"reaction":[93],"probabilities":[94],"single":[97],"GPU,":[98],"at":[99],"throughput":[101],"would":[103],"otherwise":[104],"require":[105],"CPU":[108],"cluster.":[109],"current":[111],"framework":[112],"resolves":[113],"reactions":[114],"between":[115],"integration":[116],"steps":[117],"with":[118,173],"closed-form":[120],"bridge,":[122],"models":[123],"internal":[125],"flexibility":[126],"solute":[129],"through":[130],"coarse-grained":[132],"bead":[133],"chain,":[134],"distributes":[135],"trajectories":[136],"across":[137],"multiple":[138],"GPUs,":[139],"checkpoints":[140],"long":[141],"runs,":[142],"monitors":[143],"convergence,":[144],"automates":[146],"entire":[148],"workflow":[149],"from":[150],"input":[151],"structures":[152],"estimates.":[155],"validated":[158],"against":[159],"protein-ligand":[160],"protein-protein":[162],"complexes":[163],"spanning":[164],"five":[165],"orders":[166],"magnitude":[168,180],"most":[174],"estimates":[175],"within":[176],"one":[177],"order":[178],"experiment.":[182],"Figure":[184]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-01T00:00:00"}