{"id":"https://openalex.org/W7138912131","doi":"https://doi.org/10.48550/arxiv.2603.17633","title":"Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics","display_name":"Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics","publication_year":2026,"publication_date":"2026-03-18","ids":{"openalex":"https://openalex.org/W7138912131","doi":"https://doi.org/10.48550/arxiv.2603.17633"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.17633","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.17633","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2603.17633","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5130209680","display_name":"Liang Shi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shi, Liang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129980113","display_name":"Jiarui Lu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lu, Jiarui","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129864482","display_name":"Junqi Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Junqi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130101496","display_name":"Chence Shi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shi, Chence","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129975980","display_name":"Zhi Qi Yang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yang, Zhi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5129963128","display_name":"Tang, Jian, 1968-","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tang, Jian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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/T11948","display_name":"Machine Learning in Materials Science","score":0.6930000185966492,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.6930000185966492,"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":0.18070000410079956,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.061900001019239426,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.7419000267982483},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4796999990940094},{"id":"https://openalex.org/keywords/state-space","display_name":"State space","score":0.4138000011444092},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.3991999924182892},{"id":"https://openalex.org/keywords/basis","display_name":"Basis (linear algebra)","score":0.38989999890327454},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.3889999985694885},{"id":"https://openalex.org/keywords/biomolecular-structure","display_name":"Biomolecular structure","score":0.374099999666214},{"id":"https://openalex.org/keywords/autoregressive-model","display_name":"Autoregressive model","score":0.3666999936103821},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.3549000024795532}],"concepts":[{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.7419000267982483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5949000120162964},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4796999990940094},{"id":"https://openalex.org/C72434380","wikidata":"https://www.wikidata.org/wiki/Q230930","display_name":"State space","level":2,"score":0.4138000011444092},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3991999924182892},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.38989999890327454},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.3889999985694885},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3882000148296356},{"id":"https://openalex.org/C38111792","wikidata":"https://www.wikidata.org/wiki/Q15712714","display_name":"Biomolecular structure","level":3,"score":0.374099999666214},{"id":"https://openalex.org/C159877910","wikidata":"https://www.wikidata.org/wiki/Q2202883","display_name":"Autoregressive model","level":2,"score":0.3666999936103821},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.3549000024795532},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35280001163482666},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.3499000072479248},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.34950000047683716},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.33980000019073486},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.3206999897956848},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.3199999928474426},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.31150001287460327},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.30880001187324524},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.30630001425743103},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.299699991941452},{"id":"https://openalex.org/C126701199","wikidata":"https://www.wikidata.org/wiki/Q264224","display_name":"Complex dynamics","level":2,"score":0.28690001368522644},{"id":"https://openalex.org/C77405623","wikidata":"https://www.wikidata.org/wiki/Q598451","display_name":"System dynamics","level":2,"score":0.2775000035762787},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2694999873638153},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.26910001039505005},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.2619999945163727},{"id":"https://openalex.org/C32230216","wikidata":"https://www.wikidata.org/wiki/Q7882499","display_name":"Uncertainty quantification","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C20702342","wikidata":"https://www.wikidata.org/wiki/Q5190506","display_name":"Cryo-electron microscopy","level":2,"score":0.2612999975681305},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2603999972343445},{"id":"https://openalex.org/C5917680","wikidata":"https://www.wikidata.org/wiki/Q2621825","display_name":"Basis function","level":2,"score":0.2535000145435333}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.17633","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.17633","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.17633","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.17633","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1],"dynamic":[2],"behavior":[3],"of":[4,153,156],"biomolecules":[5],"is":[6,111],"fundamental":[7],"to":[8,50,78,93,102],"elucidating":[9],"biological":[10],"function":[11],"and":[12,118,128,145],"facilitating":[13],"drug":[14],"discovery.":[15],"While":[16],"Molecular":[17],"Dynamics":[18],"(MD)":[19],"simulations":[20],"provide":[21],"a":[22,67,88,99,161],"rigorous":[23],"physical":[24],"basis":[25],"for":[26,34,57,83,141,164],"studying":[27],"these":[28],"dynamics,":[29],"they":[30],"remain":[31],"computationally":[32],"expensive":[33],"long":[35],"timescales.":[36],"Conversely,":[37],"recent":[38],"deep":[39],"generative":[40,69],"models":[41],"accelerate":[42],"conformation":[43,119,139],"generation":[44],"but":[45],"are":[46],"typically":[47],"either":[48],"failing":[49],"model":[51],"temporal":[52,96],"relationship":[53],"or":[54],"built":[55],"only":[56],"monomeric":[58],"proteins.":[59],"To":[60],"bridge":[61],"this":[62,158],"gap,":[63],"we":[64],"introduce":[65],"ATMOS,":[66],"novel":[68],"framework":[70],"based":[71],"on":[72],"State":[73],"Space":[74],"Models":[75],"(SSM)":[76],"designed":[77],"generate":[79],"atom-level":[80],"MD":[81,123],"trajectories":[82,140],"biomolecular":[84,166],"systems.":[85,148],"ATMOS":[86,110,133],"integrates":[87],"Pairformer-based":[89],"state":[90],"transition":[91],"mechanism":[92],"capture":[94],"long-range":[95],"dependencies,":[97],"with":[98],"diffusion-based":[100],"module":[101],"decode":[103],"trajectory":[104,120,155],"frames":[105],"in":[106,137],"an":[107],"autoregressive":[108],"manner.":[109],"trained":[112],"across":[113],"crystal":[114],"structures":[115],"from":[116,121],"PDB":[117],"large-scale":[122],"simulation":[124],"datasets":[125],"including":[126],"mdCATH":[127],"MISATO.":[129],"We":[130],"demonstrate":[131],"that":[132],"achieves":[134],"state-of-the-art":[135],"performance":[136],"generating":[138],"both":[142],"protein":[143],"monomers":[144],"complex":[146],"protein-ligand":[147],"By":[149],"enabling":[150],"efficient":[151],"inference":[152],"atomic":[154],"motions,":[157],"work":[159],"establishes":[160],"promising":[162],"foundation":[163],"modeling":[165],"dynamics.":[167]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-03-20T00:00:00"}