A comprehensive framework to simulate real-time chemical dynamics on a fault-tolerant quantum computer

A comprehensive framework to simulate real-time chemical dynamics on a fault-tolerant quantum computer | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article A comprehensive framework to simulate real-time chemical dynamics on a fault-tolerant quantum computer Karthik Seetharam, Burak Sahinoglu, Matteo Lostaglio, Sam Pallister, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7411164/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract We present a comprehensive end-to-end framework for simulating the real-time dynamics of chemical systems on a fault-tolerant quantum computer, incorporating both electronic and nuclear quantum degrees of freedom. An all-particle simulation is nominally efficient on a quantum computer, but practically infeasible. Hence, central to our approach is the construction of a first-quantized plane-wave algorithm making use of pseudoions. The latter consolidate chemically inactive electrons and the nucleus into a single effective dynamical ionic entity, extending the well-established concept of pseudopotentials in quantum chemistry to a two-body interaction. We explicitly describe efficient quantum circuits for initial state preparation across all degrees of freedom, as well as for block-encoding the Hamiltonian describing interacting pseudoions and chemically active electrons, by leveraging recent advances in quantum rejection sampling to optimize the implementations. To extract useful chemical information, we first design molecular fingerprints by combining density-functional calculations with machine learning techniques, and subsequently validate them through surrogate classical molecular dynamics simulations. These fingerprints are then coherently encoded on a quantum computer for efficient molecular identification via amplitude estimation. We provide an extensive analysis of the cost of running the algorithm on a fault-tolerant quantum computer for several chemically interesting systems. As an illustration, simulating the interaction between NH3 and BF3 (a 40-particle system) requires 808 logical qubits to encode the problem, and approximately 10^11 Toffoli gates per femtosecond of time evolution. Our results establish a foundation for further quantum algorithm development targeting chemical and material dynamics. Physical sciences/Chemistry/Theoretical chemistry/Method development Physical sciences/Mathematics and computing/Computational science Physical sciences/Chemistry/Theoretical chemistry/Quantum chemistry Physical sciences/Physics/Condensed-matter physics Full Text Additional Declarations There is NO Competing Interest. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7411164","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":516450876,"identity":"e496a2bd-a4f2-4a72-99e1-3ae3cbc9f2c1","order_by":0,"name":"Karthik Seetharam","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA1ElEQVRIiWNgGAWjYBACCRDB2MDAwA9iJBQQq+UgUItkA0iLASlaDA6AWMRokew/fPDxxx12+cbnVyd+eGDAIM8vdgC/FmmJtGSDg2eSLbfdeLtZAugww5mzE/BrkZPgMZM42MZsYHbj7AaQlgSD24S08J///uNgW72B8Yyzm38QpUWaIYeN4WDbYQMD/t5txNkiOSPNWOJs23EDiRu82ywSDCQI+0Xi/OGHHyrbqg34+89uvvmjwkaeX5qAFiTNYJUSxCoHAf4DpKgeBaNgFIyCkQQATTNF8sKmV2wAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0003-1928-8019","institution":"PsiQuantum Corporation","correspondingAuthor":true,"prefix":"","firstName":"Karthik","middleName":"","lastName":"Seetharam","suffix":""},{"id":516450877,"identity":"94431886-19f2-48af-8de9-d7739640a141","order_by":1,"name":"Burak Sahinoglu","email":"","orcid":"https://orcid.org/0000-0003-4488-2300","institution":"PsiQuantum Corporation","correspondingAuthor":false,"prefix":"","firstName":"Burak","middleName":"","lastName":"Sahinoglu","suffix":""},{"id":516450878,"identity":"461208c7-832d-4c8c-b454-6dab592c0919","order_by":2,"name":"Matteo Lostaglio","email":"","orcid":"","institution":"PsiQuantum Corporation","correspondingAuthor":false,"prefix":"","firstName":"Matteo","middleName":"","lastName":"Lostaglio","suffix":""},{"id":516450879,"identity":"c617fbd3-b6fd-44e7-a234-2d1cb8c2b136","order_by":3,"name":"Sam Pallister","email":"","orcid":"","institution":"PsiQuantum Corporation","correspondingAuthor":false,"prefix":"","firstName":"Sam","middleName":"","lastName":"Pallister","suffix":""},{"id":516450880,"identity":"6ab3a07f-0e5a-4a89-b606-15cab1bfb3d0","order_by":4,"name":"Felipe Jornada","email":"","orcid":"https://orcid.org/0000-0001-6712-7151","institution":"Stanford University","correspondingAuthor":false,"prefix":"","firstName":"Felipe","middleName":"","lastName":"Jornada","suffix":""}],"badges":[],"createdAt":"2025-08-19 18:35:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7411164/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7411164/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":95526680,"identity":"3d9fe2c2-b54d-4f7a-9ad0-b6d83cab3a1a","added_by":"auto","created_at":"2025-11-10 10:07:34","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2760122,"visible":true,"origin":"","legend":"Article File","description":"","filename":"SeetharampreprintAcompreshensiveframeworktosimulaterealtimechemicaldynamicsonafaulttolerantquantumcomputer.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7411164/v1_covered_00766d3e-3f58-4c14-9ac4-22044a0b4aab.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"A comprehensive framework to simulate real-time chemical dynamics on a fault-tolerant quantum computer","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7411164/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7411164/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"We present a comprehensive end-to-end framework for simulating the real-time dynamics of chemical systems on a fault-tolerant quantum computer, incorporating both electronic and nuclear quantum degrees of freedom. An all-particle simulation is nominally efficient on a quantum computer, but practically infeasible. Hence, central to our approach is the construction of a first-quantized plane-wave algorithm making use of pseudoions. The latter consolidate chemically inactive electrons and the nucleus into a single effective dynamical ionic entity, extending the well-established concept of pseudopotentials in quantum chemistry to a two-body interaction. We explicitly describe efficient quantum circuits for initial state preparation across all degrees of freedom, as well as for block-encoding the Hamiltonian describing interacting pseudoions and chemically active electrons, by leveraging recent advances in quantum rejection sampling to optimize the implementations. 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