Hidden Heterogeneity in Cross-Platform Josephson-JunctionBenchmarking:A Case Study in Statistical Confounding withArchitecture-Dependent Decoherence Physics

Hidden Heterogeneity in Cross-Platform Josephson-JunctionBenchmarking:A Case Study in Statistical Confounding withArchitecture-Dependent Decoherence Physics | 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 Hidden Heterogeneity in Cross-Platform Josephson-JunctionBenchmarking:A Case Study in Statistical Confounding withArchitecture-Dependent Decoherence Physics Mahgoub A. Salih This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9043332/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 9 You are reading this latest preprint version Abstract Cross-platform comparison of superconducting quantum devices requires statistical care because heterogeneous architectures implement qualitatively different transport mechanisms, couple to distinct microscopic loss channels, and typically operate in different temperature regimes. We present a methodological case study showing how aggregation of data across platforms can mask qualitatively different within-architecture temperature dependencies when platform identity is confounded with operating temperature. To enable controlled comparison, we introduce two scaling parameters: a dimensionless normalized temperature (T^{ } = k_{B}T/(hf)) and a resistance-like decoherence parameter (A = (hf/eI_{c})(\ln Q/2\pi)). We develop a detailed physical argument for why the baseline value of (A) is expected to be architecture-dependent, focusing on the distinct roles of Cooper-pair tunneling in SIS junctions, Andreev bound states in SNS junctions, ferromagnetic layer effects in SIsFS devices, and confinement effects in nanowire junctions. Applying this framework to published data from five distinct junction architectures (Transmon SIS, conventional SIS, SIsFS, planar SNS, and nanowire SNS; (N = 23) points from five independent studies), we find that the pooled dataset exhibits a weak positive correlation between (A) and (T^{ }) ((r = 0.085), (p = 0.70)). However, when stratified by architecture, within-group correlations reveal qualitatively different temperature dependencies: SIsFS shows strong positive dependence ((308.4 \pm 22.6,\Omega), (p = 0.047)), planar SNS shows strong positive dependence ((205.6 \pm 11.6,\Omega), (p = 0.036)), while transmons show near-zero dependence ((-7.2 \pm 17.3,\Omega), (p = 0.688)). Two architectures show positive slopes that reach statistical significance despite small samples ((n=3) each), though these results are sensitive to individual data points (see Appendix C). Analysis of variance confirms that architecture explains the dominant share of variance (ANOVA (F_{4,18} = 670.7), (p < 0.0001); ICC (\approx 0.98)). Decomposition of (A) reveals that the (1/I_c) term accounts for the factor-of-6.6 variation across architectures ((r = -0.94) with (\log I_c)), while the (\ln Q) term varies by only 30%. We argue that these observations are physically expected from architecture-specific transport and loss mechanisms, and we outline experimental designs with overlapping temperature sweeps that could disentangle temperature dependence from platform identity in future benchmarking efforts. All data, extraction uncertainties, and analysis code are provided in the appendices to ensure reproducibility. Physical sciences/Mathematics and computing Physical sciences/Physics Full Text Additional Declarations No competing interests reported. Supplementary Files pyfigures.py Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 14 Apr, 2026 Reviewers agreed at journal 01 Apr, 2026 Reviewers agreed at journal 30 Mar, 2026 Reviewers agreed at journal 30 Mar, 2026 Reviewers invited by journal 23 Mar, 2026 Editor assigned by journal 23 Mar, 2026 Editor invited by journal 18 Mar, 2026 Submission checks completed at journal 10 Mar, 2026 First submitted to journal 10 Mar, 2026 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-9043332","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":611596982,"identity":"52098d1c-d30b-436f-bc65-80e32c0b7a37","order_by":0,"name":"Mahgoub A. 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We present a methodological case study showing how aggregation of data across platforms can mask qualitatively different within-architecture temperature dependencies when platform identity is confounded with operating temperature. To enable controlled comparison, we introduce two scaling parameters: a dimensionless normalized temperature \\(T^{*} = k_{B}T/(hf)\\) and a resistance-like decoherence parameter \\(A = (hf/eI_{c})(\\ln Q/2\\pi)\\). We develop a detailed physical argument for why the baseline value of \\(A\\) is expected to be architecture-dependent, focusing on the distinct roles of Cooper-pair tunneling in SIS junctions, Andreev bound states in SNS junctions, ferromagnetic layer effects in SIsFS devices, and confinement effects in nanowire junctions.\nApplying this framework to published data from five distinct junction architectures (Transmon SIS, conventional SIS, SIsFS, planar SNS, and nanowire SNS; \\(N = 23\\) points from five independent studies), we find that the pooled dataset exhibits a weak positive correlation between \\(A\\) and \\(T^{*}\\) (\\(r = 0.085\\), \\(p = 0.70\\)). However, when stratified by architecture, within-group correlations reveal qualitatively different temperature dependencies: SIsFS shows strong positive dependence (\\(308.4 \\pm 22.6\\,\\Omega\\), \\(p = 0.047\\)), planar SNS shows strong positive dependence (\\(205.6 \\pm 11.6\\,\\Omega\\), \\(p = 0.036\\)), while transmons show near-zero dependence (\\(-7.2 \\pm 17.3\\,\\Omega\\), \\(p = 0.688\\)). Two architectures show positive slopes that reach statistical significance despite small samples (\\(n=3\\) each), though these results are sensitive to individual data points (see Appendix C). Analysis of variance confirms that architecture explains the dominant share of variance (ANOVA \\(F_{4,18} = 670.7\\), \\(p \u003c 0.0001\\); ICC \\(\\approx 0.98\\)). Decomposition of \\(A\\) reveals that the \\(1/I_c\\) term accounts for the factor-of-6.6 variation across architectures (\\(r = -0.94\\) with \\(\\log I_c\\)), while the \\(\\ln Q\\) term varies by only 30\\%.\nWe argue that these observations are physically expected from architecture-specific transport and loss mechanisms, and we outline experimental designs with overlapping temperature sweeps that could disentangle temperature dependence from platform identity in future benchmarking efforts. All data, extraction uncertainties, and analysis code are provided in the appendices to ensure reproducibility.","manuscriptTitle":"Hidden Heterogeneity in Cross-Platform Josephson-JunctionBenchmarking:A Case Study in Statistical Confounding withArchitecture-Dependent Decoherence Physics","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-25 02:40:08","doi":"10.21203/rs.3.rs-9043332/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"editorInvitedReview","content":"","date":"2026-04-14T21:27:35+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"29609330366584348204071426127503137931","date":"2026-04-01T10:52:29+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"232368176560314186982899730849273220462","date":"2026-03-30T14:20:09+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"193037424221575273506691526215586139151","date":"2026-03-30T09:15:01+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-03-23T14:58:56+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-23T14:52:42+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-03-18T04:58:58+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-03-10T19:52:49+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2026-03-10T13:56:08+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"dfa20fbb-dcb9-49f8-9ac5-a48ddbeeab85","owner":[],"postedDate":"March 25th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":65076197,"name":"Physical sciences/Mathematics and computing"},{"id":65076198,"name":"Physical sciences/Physics"}],"tags":[],"updatedAt":"2026-03-25T02:40:08+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-25 02:40:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9043332","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9043332","identity":"rs-9043332","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}