SLEEPY: Simple simulation of relaxation and dynamics in nuclear magnetic resonance

SLEEPY: Simple simulation of relaxation and dynamics in nuclear magnetic resonance | 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 SLEEPY: Simple simulation of relaxation and dynamics in nuclear magnetic resonance Albert Smith, Kai Zumpfe This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6253171/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 20 Oct, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Nuclear magnetic resonance is a powerful method for characterizing dynamics of biological systems in a native-like environment. Accurate dynamics characterization, however, often requires simulations of complex NMR experiments. The SLEEPY Python module makes it straightforward to simulate arbitrary pulse sequences while including both relaxation and exchange processes. SLEEPY furthermore allows simulation of solid-state (static and spinning) and solution NMR experiments, in both the rotating and lab frames. We demonstrate its application to a wide variety of experiments, including T1ρ, T1, nuclear Overhauser effect, REDOR, and paramagnetic effects. We also provide an extensive tutorial that explains how to use the various capabilities of SLEEPY. This tool can then be used for both better understanding of the impact of dynamics on NMR and in reproduction of experimental results. Physical sciences/Mathematics and computing/Software Biological sciences/Biophysics/Computational biophysics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files nrsoftwarepolicy.pdf Software Policy Checklist Cite Share Download PDF Status: Published Journal Publication published 20 Oct, 2025 Read the published version in Nature Communications → 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-6253171","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":436235365,"identity":"1d3bb26a-2a8e-4928-a01c-1a860cf81c1b","order_by":0,"name":"Albert Smith","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0002-9372-7297","institution":"Leipzig University","correspondingAuthor":true,"prefix":"","firstName":"Albert","middleName":"","lastName":"Smith","suffix":""},{"id":436235366,"identity":"09117705-1eab-43b0-914f-f4d07bf52407","order_by":1,"name":"Kai Zumpfe","email":"","orcid":"","institution":"Leipzig University","correspondingAuthor":false,"prefix":"","firstName":"Kai","middleName":"","lastName":"Zumpfe","suffix":""}],"badges":[],"createdAt":"2025-03-18 12:35:09","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6253171/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6253171/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41467-025-65091-6","type":"published","date":"2025-10-20T04:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":93996296,"identity":"2f42834e-76f4-4e04-af7d-7c24251714cd","added_by":"auto","created_at":"2025-10-21 07:08:23","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1004931,"visible":true,"origin":"","legend":"Article File","description":"","filename":"SLEEPY250310.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6253171/v1_covered_4d1eba31-f052-43e5-aa3d-fb79a27697c9.pdf"},{"id":79895637,"identity":"76e0e3e2-4b4c-4124-86a2-688200e6be2b","added_by":"auto","created_at":"2025-04-04 08:56:41","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1316981,"visible":true,"origin":"","legend":"Software Policy Checklist","description":"","filename":"nrsoftwarepolicy.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6253171/v1/2256140d9cca552a6f512746.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"SLEEPY: Simple simulation of relaxation and dynamics in nuclear magnetic resonance","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-6253171/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6253171/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Nuclear magnetic resonance is a powerful method for characterizing dynamics of biological systems in a native-like environment. 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