--- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18706' abstract: - lang: eng text: "We prove discrete-to-continuum convergence for dynamical optimal transport on Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of 1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations." acknowledgement: L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65. article_processing_charge: Yes article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 2024:1-29. doi:10.1017/s0956792524000810 apa: Portinale, L., & Quattrocchi, F. (2024). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. Cambridge University Press. https://doi.org/10.1017/s0956792524000810 chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/s0956792524000810. ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” European Journal of Applied Mathematics. Cambridge University Press, pp. 1–29, 2024. ista: Portinale L, Quattrocchi F. 2024. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics., 1–29. mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics, Cambridge University Press, 2024, pp. 1–29, doi:10.1017/s0956792524000810. short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics (2024) 1–29. date_created: 2024-12-23T11:03:59Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-06-25T22:30:43Z day: '20' ddc: - '500' department: - _id: GradSch - _id: JaMa doi: 10.1017/s0956792524000810 external_id: isi: - '001381435800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/S0956792524000810 month: '12' oa: 1 oa_version: Published Version page: 1-29 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: European Journal of Applied Mathematics publication_identifier: eissn: - 1469-4425 issn: - 0956-7925 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '20563' relation: dissertation_contains status: public scopus_import: '1' status: public title: Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20571' abstract: - lang: eng text: "We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum. \ In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. " acknowledgement: "The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n" article_number: '2403.07803' article_processing_charge: No arxiv: 1 author: - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. doi:10.48550/arXiv.2403.07803 apa: Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. https://doi.org/10.48550/arXiv.2403.07803 chicago: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.07803. ieee: F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” arXiv. . ista: Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803. mla: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, 2403.07803, doi:10.48550/arXiv.2403.07803. short: F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:56Z date_published: 2024-04-09T00:00:00Z date_updated: 2026-06-25T22:30:43Z day: '09' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2403.07803 external_id: arxiv: - '2403.07803' keyword: - gradient flows - Jordan–Kinderlehrer–Otto scheme - curves of maximal slope - optimal transport - Dirichlet boundary conditions - Fokker–Planck equation language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2403.07803 month: '04' oa: 1 oa_version: Preprint project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: draft related_material: record: - id: '20865' relation: later_version status: public - id: '20563' relation: dissertation_contains status: public status: public title: Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20570' abstract: - lang: eng text: "We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le parXiv. doi:10.48550/arXiv.2408.12924 apa: Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. arXiv. https://doi.org/10.48550/arXiv.2408.12924 chicago: Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.12924. ieee: F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” arXiv. . ista: Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924. mla: Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, 2408.12924, doi:10.48550/arXiv.2408.12924. short: F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:22Z date_published: 2024-08-23T00:00:00Z date_updated: 2026-06-25T22:30:43Z day: '23' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2408.12924 external_id: arxiv: - '2408.12924' keyword: - optimal empirical quantization - vector quantization - Wasserstein distance - semidiscrete optimal transport - Zador’s Theorem - Pierce’s Lemma language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.12924 month: '08' oa: 1 oa_version: Preprint project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: draft related_material: record: - id: '20563' relation: dissertation_contains status: public status: public title: Asymptotics for optimal empirical quantization of measures type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher _id: '17206' abstract: - lang: eng text: "Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. " acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Raices, Julia id: 3EE67F22-F248-11E8-B48F-1D18A9856A87 last_name: Raices citation: ama: 'Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:10.15479/at:ista:17206' apa: 'Raices, J. (2024). Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17206' chicago: 'Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17206.' ieee: 'J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.' ista: 'Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.' mla: 'Raices, Julia. Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17206.' short: 'J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-07-05T14:15:29Z date_published: 2024-07-05T00:00:00Z date_updated: 2026-04-07T13:03:22Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: BeVi - _id: GradSch doi: 10.15479/at:ista:17206 ec_funded: 1 file: - access_level: closed checksum: d5e9234bde8667b005a8cfe18bb467d3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-07-11T07:18:01Z date_updated: 2025-01-11T23:30:04Z embargo_to: open_access file_id: '17223' file_name: ThesisRaices2024_postDefense.docx file_size: 13788479 relation: source_file - access_level: open_access checksum: f5ed0139aa3e11ce58369f0915647c5c content_type: application/pdf creator: cchlebak date_created: 2024-07-11T07:22:32Z date_updated: 2025-01-11T23:30:04Z embargo: 2025-01-11 file_id: '17224' file_name: ThesisRaices2024_nosignature.pdf file_size: 5580296 relation: main_file file_date_updated: 2025-01-11T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '82' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: 'Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18101' abstract: - lang: eng text: "The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley citation: ama: Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:10.15479/at:ista:18101 apa: Porley Esteves, D. (2024). Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18101 chicago: Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18101. ieee: D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024. ista: Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. mla: Porley Esteves, Darío. Structural Characterization of Spumavirus Capsid Assemblies. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18101. short: D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-20T10:21:03Z date_published: 2024-09-26T00:00:00Z date_updated: 2026-04-07T13:21:01Z day: '26' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:18101 ec_funded: 1 file: - access_level: closed checksum: 3b8b0bacfe61112f3852744f3170e468 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dporley date_created: 2024-09-26T13:40:33Z date_updated: 2025-03-25T23:30:03Z embargo_to: open_access file_id: '18149' file_name: PhD_thesis_DPorley_final_20240919.docx file_size: 14213128 relation: source_file - access_level: open_access checksum: 6c3a652a8eede874118e11d66a63652f content_type: application/pdf creator: dporley date_created: 2024-09-26T13:41:39Z date_updated: 2025-03-25T23:30:03Z embargo: 2025-03-25 file_id: '18150' file_name: PhD_thesis_DPorley_final_20240926_pdfa1.pdf file_size: 18583031 relation: main_file file_date_updated: 2025-03-25T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '131' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication_identifier: isbn: - 978-3-99078-041-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 title: Structural characterization of spumavirus capsid assemblies type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17319' abstract: - lang: eng text: "This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kristina full_name: Lukic, Kristina id: 2B04DB84-F248-11E8-B48F-1D18A9856A87 last_name: Lukic orcid: 0000-0003-1581-881X citation: ama: 'Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:10.15479/at:ista:17319' apa: 'Lukic, K. (2024). Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17319' chicago: 'Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17319.' ieee: 'K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.' ista: 'Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.' mla: 'Lukic, Kristina. Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17319.' short: 'K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-07-26T09:05:55Z date_published: 2024-07-26T00:00:00Z date_updated: 2026-04-07T13:20:44Z day: '26' ddc: - '580' degree_awarded: PhD department: - _id: LeSa - _id: GradSch doi: 10.15479/at:ista:17319 file: - access_level: open_access checksum: 95517e697ea6a87e267e649cad560989 content_type: application/pdf creator: cchlebak date_created: 2024-07-26T13:14:24Z date_updated: 2025-01-26T23:30:04Z embargo: 2025-01-26 file_id: '17320' file_name: Thesis_Kristina_Lukic.pdf file_size: 24639084 relation: main_file - access_level: closed checksum: 74325746a9a05078fb9935dbf2aef752 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-07-26T13:14:50Z date_updated: 2025-01-26T23:30:04Z embargo_to: open_access file_id: '17321' file_name: Thesis_Kristina_Lukic.docx file_size: 96334272 relation: source_file file_date_updated: 2025-01-26T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '224' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: 'Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku''amide B' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17346' abstract: - lang: eng text: "Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lars full_name: Bollmann, Lars id: 47AD3038-F248-11E8-B48F-1D18A9856A87 last_name: Bollmann citation: ama: Bollmann L. Stability and change in the memory system during rest. 2024. doi:10.15479/at:ista:17346 apa: Bollmann, L. (2024). Stability and change in the memory system during rest. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17346 chicago: Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17346. ieee: L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024. ista: Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria. mla: Bollmann, Lars. Stability and Change in the Memory System during Rest. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17346. short: L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-07-29T15:08:42Z date_published: 2024-07-31T00:00:00Z date_updated: 2026-04-07T13:21:20Z day: '31' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:17346 file: - access_level: open_access checksum: 12c76297cc27449da80c60d79127770d content_type: application/pdf creator: lbollman date_created: 2024-07-31T18:37:19Z date_updated: 2025-01-31T23:30:03Z embargo: 2025-01-31 file_id: '17359' file_name: PhD_Thesis_Lars_Bollmann.pdf file_size: 12920169 relation: main_file - access_level: closed checksum: 19a0265079dec8038830ad6e35c5106e content_type: application/zip creator: lbollman date_created: 2024-07-31T18:38:39Z date_updated: 2025-01-31T23:30:03Z embargo_to: open_access file_id: '17360' file_name: Latex_source.zip file_size: 27568807 relation: source_file file_date_updated: 2025-01-31T23:30:03Z has_accepted_license: '1' keyword: - Memory - Hippocampus - Consolidation language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '103' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Stability and change in the memory system during rest type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17368' abstract: - lang: eng text: "Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n" alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Ariadna full_name: Villanueva Marijuan, Ariadna id: e0ae4864-133f-11ed-8f02-adaa8dd27540 last_name: Villanueva Marijuan citation: ama: Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368 apa: Villanueva Marijuan, A. (2024). Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17368 chicago: Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17368. ieee: A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024. ista: Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. mla: Villanueva Marijuan, Ariadna. Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17368. short: A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-08-02T10:52:40Z date_published: 2024-08-13T00:00:00Z date_updated: 2026-04-07T13:03:41Z day: '13' ddc: - '610' degree_awarded: MS department: - _id: GradSch - _id: MaRo doi: 10.15479/at:ista:17368 file: - access_level: open_access checksum: 0c2daa174609f0c00919dccc5701d375 content_type: application/pdf creator: avillanu date_created: 2024-08-14T11:51:24Z date_updated: 2025-02-14T23:30:03Z embargo: 2025-02-14 file_id: '17433' file_name: Masters_thesis_AriadnaVillanueva.pdf file_size: 13052436 relation: main_file - access_level: closed checksum: e9ed4465dfa539ac4c3a8d4d0b6271a1 content_type: application/zip creator: avillanu date_created: 2024-08-14T11:51:57Z date_updated: 2025-02-14T23:30:03Z embargo_to: open_access file_id: '17434' file_name: Masters thesis-AriadnaVillanueva.zip file_size: 45642547 relation: source_file file_date_updated: 2025-02-14T23:30:03Z has_accepted_license: '1' keyword: - Epigenetics - Multi-omics - Bayesian regression language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '60' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 title: Bayesian linear regression for analyzing general omics data with time-to-event phenotypes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '17465' abstract: - lang: eng text: "In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n" acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko citation: ama: Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:10.15479/at:ista:17465 apa: Shevchenko, A. (2024). High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17465 chicago: Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17465. ieee: A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024. ista: Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. mla: Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465. short: A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-08-28T15:14:25Z date_published: 2024-08-29T00:00:00Z date_updated: 2026-06-18T17:55:53Z day: '29' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: MaMo doi: 10.15479/at:ista:17465 file: - access_level: open_access checksum: da6dd3166078934577f6af93d27000e2 content_type: application/pdf creator: ashevche date_created: 2024-09-02T09:23:32Z date_updated: 2024-10-05T22:30:05Z embargo: 2024-10-04 file_id: '17482' file_name: thesis_a2b.pdf file_size: 4468610 relation: main_file - access_level: closed checksum: 76a39ef252239560923cdda4ce0a31a4 content_type: application/zip creator: ashevche date_created: 2024-09-02T09:23:46Z date_updated: 2024-10-05T22:30:05Z embargo_to: open_access file_id: '17483' file_name: Thesis Alex - ISTA.zip file_size: 15930999 relation: source_file file_date_updated: 2024-10-05T22:30:05Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '232' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11420' relation: part_of_dissertation status: public - id: '14459' relation: part_of_dissertation status: public - id: '9198' relation: part_of_dissertation status: public - id: '17469' relation: part_of_dissertation status: public status: public supervisor: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: High-dimensional limits in artificial neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '17881' abstract: - lang: eng text: "This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 citation: ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881 apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881 chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881. ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024. ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881. short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-08T10:23:25Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-06-03T07:16:04Z day: '10' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:17881 file: - access_level: open_access checksum: ed7763c3bbd59e1d7e1b664de3a26f3c content_type: application/pdf creator: smukhopa date_created: 2024-09-12T10:46:04Z date_updated: 2025-03-13T23:30:04Z embargo: 2025-03-13 file_id: '18059' file_name: PhD_Thesis_Soham_Mukhopadhyay.pdf file_size: 10297052 relation: main_file - access_level: closed checksum: e352667482701dd18a9a0e7418aef465 content_type: application/zip creator: smukhopa date_created: 2024-09-12T10:50:58Z date_updated: 2025-03-13T23:30:04Z embargo_to: open_access file_id: '18060' file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip file_size: 29178634 relation: source_file file_date_updated: 2025-03-13T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '82' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication_identifier: isbn: - 978-3-99078-043-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14032' relation: part_of_dissertation status: public - id: '18057' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Thermal effects in one dimensional Josephson chains type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '17469' abstract: - lang: eng text: 'Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.' acknowledgement: "Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE)." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Kevin full_name: Kögler, Kevin id: 94ec913c-dc85-11ea-9058-e5051ab2428b last_name: Kögler - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:24964-25015.' apa: 'Kögler, K., Shevchenko, A., Hassani, H., & Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.' chicago: 'Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In Proceedings of the 41st International Conference on Machine Learning, 235:24964–15. ML Research Press, 2024.' ieee: 'K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 24964–25015.' ista: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.' mla: 'Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 24964–5015.' short: K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' date_created: 2024-08-29T11:47:57Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-06-25T22:30:54Z day: '01' ddc: - '000' department: - _id: DaAl - _id: MaMo external_id: arxiv: - '2402.05013' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.mlr.press/v235/kogler24a.html month: '07' oa: 1 oa_version: Published Version page: 24964-25015 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 41st International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '17465' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2024' ... --- OA_place: repository _id: '18057' abstract: - lang: eng text: "We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations." acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n" article_number: '2408.07829' article_processing_charge: No arxiv: 1 author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 - first_name: Diego A full_name: Lancheros Naranjo, Diego A id: 6c55e976-15b2-11ec-abd3-d790e8937fde last_name: Lancheros Naranjo - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829 apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv. https://doi.org/10.48550/arXiv.2408.07829 chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829. ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” arXiv. . ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829. mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829. short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.). corr_author: '1' date_created: 2024-09-11T09:25:22Z date_published: 2024-08-14T00:00:00Z date_updated: 2026-06-25T22:30:55Z day: '14' department: - _id: AnHi - _id: GradSch doi: 10.48550/arXiv.2408.07829 ec_funded: 1 external_id: arxiv: - '2408.07829' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.07829 month: '08' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: arXiv publication_status: draft related_material: record: - id: '20324' relation: later_version status: public - id: '17881' relation: dissertation_contains status: public status: public title: Dual relaxation oscillations in a Josephson junction array type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher _id: '18129' abstract: - lang: eng text: "State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate\r\nfor qubits due to their long coherence, tunability, control, and readout. However, their natural\r\ncoupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.\r\nLong-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a\r\ncoherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of\r\nhigh-impedance resonators to compensate for this has gained significant attention in the past\r\ndecade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not\r\nexceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The\r\nlarge kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude\r\nenhancement. However, fully exploiting the potential of disordered or granular superconductors\r\nis challenging as their impedances close to the superconductor-to-insulator transition are\r\ndifficult to control reproducibly. We report on the realization of a wireless ohmmeter which\r\nallows in situ resistance measurements during film deposition and, therefore, indirect control\r\nof the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators\r\nwith characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due\r\nto the large sheet kinetic inductance of up to 3 nH □−1\r\n. By integrating an 8 kW resonator\r\nwith a germanium double QD, we demonstrate a strong charge-photon coupling with the\r\nhighest rate reported, 566 MHz. The demonstrated method and grAl properties make these\r\nresonators suitable for boosting the spin-photon coupling strength, a crucial requirement for\r\nfast, high-fidelity, long-distance two-qubit gates.\r\n" acknowledged_ssus: - _id: M-Shop - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 citation: ama: Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:10.15479/at:ista:18129 apa: Janik, M. (2024). Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18129 chicago: Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18129. ieee: M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024. ista: Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria. mla: Janik, Marian. Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18129. short: M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-23T17:25:43Z date_published: 2024-09-24T00:00:00Z date_updated: 2026-06-03T07:16:03Z day: '24' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:18129 file: - access_level: closed checksum: dc15958f6400b5bdaa28bf58fc7a4056 content_type: application/x-zip-compressed creator: mjanik date_created: 2024-09-23T17:15:09Z date_updated: 2025-05-23T22:30:09Z embargo_to: open_access file_id: '18130' file_name: janik_thesis.zip file_size: 156207943 relation: source_file - access_level: open_access checksum: 74737aee285dc1f491643327350efe9c content_type: application/pdf creator: mjanik date_created: 2024-09-23T17:15:30Z date_updated: 2025-05-23T22:30:09Z embargo: 2025-05-23 file_id: '18131' file_name: janik_thesis_pdfa.pdf file_size: 96195684 relation: main_file file_date_updated: 2025-05-23T22:30:09Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '164' project: - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18144' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18104' abstract: - lang: eng text: "We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia orcid: 0000-0003-1144-2763 citation: ama: 'Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:10.15479/at:ista:18104' apa: 'Puglia, D. (2024). Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18104' chicago: 'Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18104.' ieee: 'D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.' ista: 'Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.' mla: 'Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104.' short: 'D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-09-20T12:13:30Z date_published: 2024-09-20T00:00:00Z date_updated: 2026-04-07T13:22:10Z day: '20' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:18104 file: - access_level: open_access checksum: 7969263451b2356bfa0924725aa9de10 content_type: application/pdf creator: cchlebak date_created: 2024-09-20T12:07:48Z date_updated: 2025-05-20T22:30:05Z embargo: 2025-05-20 file_id: '18105' file_name: PhD_DPuglia_Final.pdf file_size: 10778238 relation: main_file - access_level: closed checksum: 98dfe7675775e30efffa03f7ff7c091b content_type: application/x-zip-compressed creator: cchlebak date_created: 2024-09-20T12:13:09Z date_updated: 2025-05-20T22:30:05Z embargo_to: open_access file_id: '18106' file_name: PhD_DPuglia_Thesis.zip file_size: 385419748 relation: source_file file_date_updated: 2025-05-20T22:30:05Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '63' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: 62843413-2b32-11ec-9570-c4ec6eabfae7 grant_number: '26088' name: Surface Charge and Tunneling Multi-Mode Imaging publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18143' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: 'Everyday electromechanics: Capacitive strong coupling to mechanical motion' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '18144' abstract: - lang: eng text: "High kinetic inductance superconductors are gaining increasing interest for\r\nthe realisation of qubits, amplifiers and detectors. Moreover, thanks to their\r\nhigh impedance, quantum buses made of such materials enable large zero-point\r\nfluctuations of the voltage, boosting the coupling rates to spin and charge\r\nqubits. However, fully exploiting the potential of disordered or granular\r\nsuperconductors is challenging, as their inductance and, therefore, impedance\r\nat high values are difficult to control. Here we have integrated a granular\r\naluminium resonator, having a characteristic impedance exceeding the resistance\r\nquantum, with a germanium double quantum dot and demonstrate strong\r\ncharge-photon coupling with a rate of $g_\\text{c}/2\\pi= (566 \\pm 2)$ MHz. This\r\nwas achieved due to the realisation of a wireless ohmmeter, which allows\r\n\\emph{in situ} measurements during film deposition and, therefore, control of\r\nthe kinetic inductance of granular aluminium films. Reproducible fabrication of\r\ncircuits with impedances (inductances) exceeding 13 k$\\Omega$ (1 nH per square)\r\nis now possible. This broadly applicable method opens the path for novel qubits\r\nand high-fidelity, long-distance two-qubit gates." acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "We acknowledge Franco De Palma, Mahya Khorramshahi, Fabian Oppliger, Thomas Reisinger, Pasquale Scarlino and Xiao Xue for helpful discussions. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation, the HORIZON-RIA 101069515 project, the FWF Projects with DOI:10.55776/P32235, DOI:10.55776/I5060 and DOI:10.55776/P36507. IMP acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG – German Research Foundation) under project number 450396347 (GeHoldeQED). ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. We acknowledge support from CSIC Interdisciplinary Thematic Platform (PTI+) on Quantum Technologies (PTI-QTEP+). This research work has been funded by the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC’s\r\nQuantum Technologies Platform (QTEP). ICN2 is supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autònoma de Barcelona Materials Science PhD program. AGM has received funding from Grant RYC2021-033479-I funded by MCIN/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. The authors\r\nacknowledge the use of instrumentation and the technical advice provided by the Joint Electron Microscopy Center at ALBA (JEMCA). ICN2 acknowledges funding from Grant IU16-014206 (METCAM-FIB) funded by the European Union through the European Regional Development\r\nFund (ERDF), with the support of the Ministry of Research and Universities, Generalitat de Catalunya. ICN2 is a founding member of e-DREAM [60]." article_number: '2407.03079' article_processing_charge: No arxiv: 1 author: - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 - first_name: Kevin Etienne Robert full_name: Roux, Kevin Etienne Robert id: 53f93ea2-803f-11ed-ab7e-b283135794ef last_name: Roux - first_name: Carla N full_name: Borja Espinosa, Carla N id: 18777c01-896a-11ed-bdf8-e4851dc07d16 last_name: Borja Espinosa - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Abdulhamid full_name: Baghdadi, Abdulhamid id: 160D87FA-96B5-11E9-BF77-7626E6697425 last_name: Baghdadi - first_name: Thomas full_name: Adletzberger, Thomas id: 38756BB2-F248-11E8-B48F-1D18A9856A87 last_name: Adletzberger - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Marc full_name: Botifoll, Marc last_name: Botifoll - first_name: Alba Garzón full_name: Manjón, Alba Garzón last_name: Manjón - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Ioan M. full_name: Pop, Ioan M. last_name: Pop - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Janik M, Roux KER, Borja Espinosa CN, et al. Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. arXiv. doi:10.48550/arXiv.2407.03079 apa: Janik, M., Roux, K. E. R., Borja Espinosa, C. N., Sagi, O., Baghdadi, A., Adletzberger, T., … Katsaros, G. (n.d.). Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. arXiv. https://doi.org/10.48550/arXiv.2407.03079 chicago: Janik, Marian, Kevin Etienne Robert Roux, Carla N Borja Espinosa, Oliver Sagi, Abdulhamid Baghdadi, Thomas Adletzberger, Stefano Calcaterra, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular  Aluminium Superinductors.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.03079. ieee: M. Janik et al., “Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors,” arXiv. . ista: Janik M, Roux KER, Borja Espinosa CN, Sagi O, Baghdadi A, Adletzberger T, Calcaterra S, Botifoll M, Manjón AG, Arbiol J, Chrastina D, Isella G, Pop IM, Katsaros G. Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors. arXiv, 2407.03079. mla: Janik, Marian, et al. “Strong Charge-Photon Coupling in Planar Germanium Enabled by Granular  Aluminium Superinductors.” ArXiv, 2407.03079, doi:10.48550/arXiv.2407.03079. short: M. Janik, K.E.R. Roux, C.N. Borja Espinosa, O. Sagi, A. Baghdadi, T. Adletzberger, S. Calcaterra, M. Botifoll, A.G. Manjón, J. Arbiol, D. Chrastina, G. Isella, I.M. Pop, G. Katsaros, ArXiv (n.d.). corr_author: '1' date_created: 2024-09-26T09:50:43Z date_published: 2024-07-03T00:00:00Z date_updated: 2026-06-25T22:30:56Z day: '03' department: - _id: GeKa - _id: GradSch - _id: JoFi doi: 10.48550/arXiv.2407.03079 external_id: arxiv: - '2407.03079' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2407.03079 month: '07' oa: 1 oa_version: Preprint project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publication: arXiv publication_status: draft related_material: record: - id: '18886' relation: research_data status: public - id: '19401' relation: later_version status: public - id: '18129' relation: dissertation_contains status: public status: public title: Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository _id: '18143' abstract: - lang: eng text: "Strong optomechanical coupling -- a regime where mechanical motion is damped\r\nby environmental radiation -- has traditionally required demanding experimental\r\ningredients such as superconducting resonators, high-quality optical cavities,\r\nor large magnetic fields. Here we demonstrate a room temperature, cavity-free,\r\nall-electric device reaching this regime at radio frequencies, enabled by a\r\nmechanically compliant parallel-plate capacitor with a nanoscale plate\r\nseparation and an aspect ratio exceeding 1,000. The device has four orders of\r\nmagnitude lower insertion loss than a comparable commercial quartz crystal, and\r\nachieves a position imprecision rivaling an optical interferometer. With the\r\nhelp of a back-action isolation scheme, we observe radiative cooling of\r\nmechanical motion by a remote cryogenic load. This work provides a\r\ntechnologically accessible route to high-precision sensing, transduction, and\r\nsignal processing." article_number: '2407.15314' article_processing_charge: No arxiv: 1 author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia orcid: 0000-0003-1144-2763 - first_name: Rachel H full_name: Odessey, Rachel H id: 9a7a5123-8972-11ed-ae7b-dd1f2af457bd last_name: Odessey - first_name: Peter S. full_name: Burns, Peter S. last_name: Burns - first_name: Niklas full_name: Luhmann, Niklas last_name: Luhmann - first_name: Silvan full_name: Schmid, Silvan last_name: Schmid - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. arXiv. doi:10.48550/arXiv.2407.15314 apa: Puglia, D., Odessey, R. H., Burns, P. S., Luhmann, N., Schmid, S., & Higginbotham, A. P. (n.d.). Room temperature, cavity-free capacitive strong coupling to mechanical  motion. arXiv. https://doi.org/10.48550/arXiv.2407.15314 chicago: Puglia, Denise, Rachel H Odessey, Peter S. Burns, Niklas Luhmann, Silvan Schmid, and Andrew P Higginbotham. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.15314. ieee: D. Puglia, R. H. Odessey, P. S. Burns, N. Luhmann, S. Schmid, and A. P. Higginbotham, “Room temperature, cavity-free capacitive strong coupling to mechanical  motion,” arXiv. . ista: Puglia D, Odessey RH, Burns PS, Luhmann N, Schmid S, Higginbotham AP. Room temperature, cavity-free capacitive strong coupling to mechanical  motion. arXiv, 2407.15314. mla: Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” ArXiv, 2407.15314, doi:10.48550/arXiv.2407.15314. short: D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.). corr_author: '1' date_created: 2024-09-26T06:58:27Z date_published: 2024-08-24T00:00:00Z date_updated: 2026-06-25T22:30:57Z day: '24' department: - _id: AnHi doi: 10.48550/arXiv.2407.15314 external_id: arxiv: - '2407.15314' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2407.15314 month: '08' oa: 1 oa_version: Preprint project: - _id: 62843413-2b32-11ec-9570-c4ec6eabfae7 grant_number: '26088' name: Surface Charge and Tunneling Multi-Mode Imaging - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication: arXiv publication_status: draft related_material: record: - id: '19026' relation: later_version status: public - id: '18104' relation: dissertation_contains status: public status: public title: Room temperature, cavity-free capacitive strong coupling to mechanical motion type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...