[{"keyword":["optimal empirical quantization","vector quantization","Wasserstein distance","semidiscrete optimal transport","Zador’s Theorem","Pierce’s Lemma"],"publication":"arXiv","project":[{"call_identifier":"FWF","grant_number":"F06504","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"type":"preprint","OA_place":"repository","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"corr_author":"1","date_updated":"2026-07-03T22:32:58Z","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.12924"}],"OA_type":"green","month":"08","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"20570","oa_version":"Preprint","article_number":"2408.12924","related_material":{"record":[{"id":"20563","status":"public","relation":"dissertation_contains"}]},"abstract":[{"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, n.d. https://doi.org/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","ista":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924.","ieee":"F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” arXiv. .","ama":"Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv. doi:10.48550/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.)."},"article_processing_charge":"No"},{"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"OA_place":"publisher","type":"dissertation","supervisor":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"ec_funded":1,"project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","_id":"17206","page":"82","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by_sa.png"},"date_updated":"2026-04-07T13:03:22Z","status":"public","publication_status":"published","month":"07","degree_awarded":"PhD","doi":"10.15479/at:ista:17206","day":"05","abstract":[{"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. ","lang":"eng"}],"oa":1,"author":[{"last_name":"Raices","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Raices, Julia"}],"date_published":"2024-07-05T00:00:00Z","ddc":["570"],"file_date_updated":"2025-01-11T23:30:04Z","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file":[{"file_size":13788479,"date_updated":"2025-01-11T23:30:04Z","file_name":"ThesisRaices2024_postDefense.docx","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-07-11T07:18:01Z","embargo_to":"open_access","file_id":"17223","relation":"source_file","access_level":"closed","checksum":"d5e9234bde8667b005a8cfe18bb467d3"},{"date_created":"2024-07-11T07:22:32Z","creator":"cchlebak","file_name":"ThesisRaices2024_nosignature.pdf","content_type":"application/pdf","embargo":"2025-01-11","date_updated":"2025-01-11T23:30:04Z","file_size":5580296,"relation":"main_file","checksum":"f5ed0139aa3e11ce58369f0915647c5c","access_level":"open_access","file_id":"17224"}],"citation":{"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.","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.","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.","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","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."},"has_accepted_license":"1","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","publication_identifier":{"issn":["2663-337X"]},"date_created":"2024-07-05T14:15:29Z","year":"2024"},{"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"type":"dissertation","OA_place":"publisher","corr_author":"1","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078"}],"ec_funded":1,"alternative_title":["ISTA Thesis"],"status":"public","date_updated":"2026-04-07T13:21:01Z","publication_status":"published","month":"09","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Published Version","_id":"18101","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"131","day":"26","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."}],"author":[{"full_name":"Porley, Dario J","first_name":"Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","last_name":"Porley"}],"oa":1,"date_published":"2024-09-26T00:00:00Z","doi":"10.15479/at:ista:18101","has_accepted_license":"1","title":"Structural characterization of spumavirus capsid assemblies","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"date_created":"2024-09-20T10:21:03Z","year":"2024","ddc":["570"],"file_date_updated":"2025-03-25T23:30:03Z","publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","checksum":"3b8b0bacfe61112f3852744f3170e468","relation":"source_file","file_id":"18149","embargo_to":"open_access","date_created":"2024-09-26T13:40:33Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_thesis_DPorley_final_20240919.docx","creator":"dporley","file_size":14213128,"date_updated":"2025-03-25T23:30:03Z"},{"access_level":"open_access","checksum":"6c3a652a8eede874118e11d66a63652f","relation":"main_file","file_id":"18150","date_created":"2024-09-26T13:41:39Z","date_updated":"2025-03-25T23:30:03Z","file_size":18583031,"embargo":"2025-03-25","content_type":"application/pdf","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","creator":"dporley"}],"article_processing_charge":"No","citation":{"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.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:10.15479/at:ista:18101","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024."}},{"_id":"17319","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","page":"224","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_updated":"2026-04-07T13:20:44Z","status":"public","degree_awarded":"PhD","month":"07","publication_status":"published","type":"dissertation","OA_place":"publisher","department":[{"_id":"LeSa"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2025-01-26T23:30:04Z","ddc":["580"],"citation":{"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.","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.","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.","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.","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"},"article_processing_charge":"No","file":[{"file_size":24639084,"date_updated":"2025-01-26T23:30:04Z","embargo":"2025-01-26","content_type":"application/pdf","file_name":"Thesis_Kristina_Lukic.pdf","creator":"cchlebak","date_created":"2024-07-26T13:14:24Z","file_id":"17320","checksum":"95517e697ea6a87e267e649cad560989","access_level":"open_access","relation":"main_file"},{"date_created":"2024-07-26T13:14:50Z","embargo_to":"open_access","date_updated":"2025-01-26T23:30:04Z","file_size":96334272,"file_name":"Thesis_Kristina_Lukic.docx","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"74325746a9a05078fb9935dbf2aef752","access_level":"closed","file_id":"17321"}],"publisher":"Institute of Science and Technology Austria","title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","has_accepted_license":"1","year":"2024","date_created":"2024-07-26T09:05:55Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:17319","abstract":[{"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.","lang":"eng"}],"day":"26","date_published":"2024-07-26T00:00:00Z","oa":1,"author":[{"orcid":"0000-0003-1581-881X","first_name":"Kristina","full_name":"Lukic, Kristina","last_name":"Lukic","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87"}]},{"day":"31","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."}],"oa":1,"author":[{"full_name":"Bollmann, Lars","first_name":"Lars","last_name":"Bollmann","id":"47AD3038-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2024-07-31T00:00:00Z","doi":"10.15479/at:ista:17346","has_accepted_license":"1","title":"Stability and change in the memory system during rest","publication_identifier":{"issn":["2663-337X"]},"year":"2024","date_created":"2024-07-29T15:08:42Z","file_date_updated":"2025-01-31T23:30:03Z","ddc":["573"],"file":[{"relation":"main_file","checksum":"12c76297cc27449da80c60d79127770d","access_level":"open_access","file_id":"17359","date_created":"2024-07-31T18:37:19Z","embargo":"2025-01-31","file_size":12920169,"date_updated":"2025-01-31T23:30:03Z","creator":"lbollman","file_name":"PhD_Thesis_Lars_Bollmann.pdf","content_type":"application/pdf"},{"embargo_to":"open_access","date_created":"2024-07-31T18:38:39Z","file_name":"Latex_source.zip","creator":"lbollman","content_type":"application/zip","file_size":27568807,"date_updated":"2025-01-31T23:30:03Z","relation":"source_file","checksum":"19a0265079dec8038830ad6e35c5106e","access_level":"closed","file_id":"17360"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"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.","ama":"Bollmann L. Stability and change in the memory system during rest. 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.","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.","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","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."},"keyword":["Memory","Hippocampus","Consolidation"],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"type":"dissertation","OA_place":"publisher","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"status":"public","date_updated":"2026-04-07T13:21:20Z","publication_status":"published","month":"07","degree_awarded":"PhD","_id":"17346","oa_version":"Published Version","page":"103","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"doi":"10.15479/at:ista:17368","day":"13","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"}],"oa":1,"author":[{"last_name":"Villanueva Marijuan","id":"e0ae4864-133f-11ed-8f02-adaa8dd27540","first_name":"Ariadna","full_name":"Villanueva Marijuan, Ariadna"}],"date_published":"2024-08-13T00:00:00Z","file_date_updated":"2025-02-14T23:30:03Z","ddc":["610"],"file":[{"relation":"main_file","checksum":"0c2daa174609f0c00919dccc5701d375","access_level":"open_access","file_id":"17433","date_created":"2024-08-14T11:51:24Z","embargo":"2025-02-14","date_updated":"2025-02-14T23:30:03Z","file_size":13052436,"creator":"avillanu","file_name":"Masters_thesis_AriadnaVillanueva.pdf","content_type":"application/pdf"},{"date_updated":"2025-02-14T23:30:03Z","file_size":45642547,"file_name":"Masters thesis-AriadnaVillanueva.zip","creator":"avillanu","content_type":"application/zip","date_created":"2024-08-14T11:51:57Z","embargo_to":"open_access","file_id":"17434","relation":"source_file","access_level":"closed","checksum":"e9ed4465dfa539ac4c3a8d4d0b6271a1"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"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.","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","ista":"Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria.","ieee":"A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024.","ama":"Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368","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."},"has_accepted_license":"1","title":"Bayesian linear regression for analyzing general omics data with time-to-event phenotypes","publication_identifier":{"issn":["2791-4585"]},"year":"2024","date_created":"2024-08-02T10:52:40Z","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"type":"dissertation","OA_place":"publisher","supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"}],"corr_author":"1","alternative_title":["ISTA Master's Thesis"],"keyword":["Epigenetics","Multi-omics","Bayesian regression"],"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","_id":"17368","page":"60","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"status":"public","date_updated":"2026-04-07T13:03:41Z","publication_status":"published","month":"08","degree_awarded":"MS"},{"status":"public","date_updated":"2026-06-18T17:55:53Z","month":"08","publication_status":"published","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"page":"232","_id":"17465","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"11420","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14459"},{"id":"9198","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"17469"}]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35"}],"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"type":"dissertation","OA_place":"repository","supervisor":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco"},{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","title":"High-dimensional limits in artificial neural networks","publication_identifier":{"issn":["2663-337X"]},"date_created":"2024-08-28T15:14:25Z","year":"2024","file_date_updated":"2024-10-05T22:30:05Z","ddc":["519"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"relation":"main_file","checksum":"da6dd3166078934577f6af93d27000e2","access_level":"open_access","file_id":"17482","date_created":"2024-09-02T09:23:32Z","creator":"ashevche","file_name":"thesis_a2b.pdf","content_type":"application/pdf","embargo":"2024-10-04","file_size":4468610,"date_updated":"2024-10-05T22:30:05Z"},{"date_created":"2024-09-02T09:23:46Z","embargo_to":"open_access","file_size":15930999,"date_updated":"2024-10-05T22:30:05Z","content_type":"application/zip","file_name":"Thesis Alex - ISTA.zip","creator":"ashevche","access_level":"closed","checksum":"76a39ef252239560923cdda4ce0a31a4","relation":"source_file","file_id":"17483"}],"citation":{"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.","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.","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","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:10.15479/at:ista:17465","mla":"Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465."},"day":"29","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"}],"oa":1,"author":[{"first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko"}],"date_published":"2024-08-29T00:00:00Z","doi":"10.15479/at:ista:17465"},{"doi":"10.15479/at:ista:17881","day":"10","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."}],"oa":1,"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559"}],"date_published":"2024-09-10T00:00:00Z","ddc":["539"],"file_date_updated":"2025-03-13T23:30:04Z","article_processing_charge":"No","file":[{"content_type":"application/pdf","creator":"smukhopa","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","date_updated":"2025-03-13T23:30:04Z","file_size":10297052,"embargo":"2025-03-13","date_created":"2024-09-12T10:46:04Z","file_id":"18059","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","access_level":"open_access","relation":"main_file"},{"content_type":"application/zip","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","creator":"smukhopa","date_updated":"2025-03-13T23:30:04Z","file_size":29178634,"embargo_to":"open_access","date_created":"2024-09-12T10:50:58Z","file_id":"18060","checksum":"e352667482701dd18a9a0e7418aef465","access_level":"closed","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","citation":{"short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881","mla":"Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi: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.","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.","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"},"has_accepted_license":"1","title":"Thermal effects in one dimensional Josephson chains","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"year":"2024","date_created":"2024-09-08T10:23:25Z","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"type":"dissertation","OA_place":"publisher","supervisor":[{"first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","_id":"17881","page":"82","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"status":"public","id":"14032","relation":"part_of_dissertation"},{"status":"public","id":"18057","relation":"part_of_dissertation"}]},"status":"public","date_updated":"2026-06-03T07:16:04Z","month":"09","publication_status":"published","degree_awarded":"PhD"},{"author":[{"id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler","first_name":"Kevin","full_name":"Kögler, Kevin"},{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco"}],"arxiv":1,"oa":1,"date_published":"2024-07-01T00:00:00Z","day":"01","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."}],"conference":{"start_date":"2024-07-21","location":"Vienna, Austria","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27"},"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).","external_id":{"arxiv":["2402.05013"]},"date_created":"2024-08-29T11:47:57Z","year":"2024","intvolume":" 235","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","article_processing_charge":"No","publisher":"ML Research Press","citation":{"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.","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.","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.","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.","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.","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.","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."},"ddc":["000"],"language":[{"iso":"eng"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","corr_author":"1","scopus_import":"1","alternative_title":["PMLR"],"department":[{"_id":"DaAl"},{"_id":"MaMo"}],"type":"conference","publication_status":"published","volume":235,"month":"07","main_file_link":[{"url":"https://proceedings.mlr.press/v235/kogler24a.html","open_access":"1"}],"status":"public","date_updated":"2026-07-03T22:33:59Z","related_material":{"record":[{"status":"public","id":"17465","relation":"dissertation_contains"}]},"quality_controlled":"1","page":"24964-25015","_id":"17469","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"external_id":{"arxiv":["2408.07829"]},"year":"2024","date_created":"2024-09-11T09:25:22Z","title":"Dual relaxation oscillations in a Josephson junction array","article_processing_charge":"No","citation":{"short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.).","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829.","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","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. 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. .","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."},"oa":1,"arxiv":1,"author":[{"first_name":"Soham","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay"},{"last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde","full_name":"Lancheros Naranjo, Diego A","first_name":"Diego A"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","first_name":"Jorden L","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2024-08-14T00:00:00Z","day":"14","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."}],"doi":"10.48550/arXiv.2408.07829","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","month":"08","publication_status":"draft","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"status":"public","date_updated":"2026-07-03T22:34:02Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"20324"},{"status":"public","id":"17881","relation":"dissertation_contains"}]},"article_number":"2408.07829","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18057","oa_version":"Preprint","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"publication":"arXiv","corr_author":"1","ec_funded":1,"department":[{"_id":"AnHi"},{"_id":"GradSch"}],"type":"preprint","OA_place":"repository"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"18129","oa_version":"Published Version","page":"164","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"license":"https://creativecommons.org/licenses/by/4.0/","related_material":{"record":[{"status":"public","id":"18144","relation":"part_of_dissertation"}]},"status":"public","date_updated":"2026-06-03T07:16:03Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","publication_status":"published","month":"09","OA_place":"publisher","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","project":[{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"language":[{"iso":"eng"}],"file_date_updated":"2025-05-23T22:30:09Z","ddc":["539"],"citation":{"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.","ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 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.","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.","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","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."},"file":[{"file_id":"18130","access_level":"closed","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","relation":"source_file","content_type":"application/x-zip-compressed","creator":"mjanik","file_name":"janik_thesis.zip","date_updated":"2025-05-23T22:30:09Z","file_size":156207943,"embargo_to":"open_access","date_created":"2024-09-23T17:15:09Z"},{"file_name":"janik_thesis_pdfa.pdf","creator":"mjanik","content_type":"application/pdf","embargo":"2025-05-23","date_updated":"2025-05-23T22:30:09Z","file_size":96195684,"date_created":"2024-09-23T17:15:30Z","file_id":"18131","relation":"main_file","checksum":"74737aee285dc1f491643327350efe9c","access_level":"open_access"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","has_accepted_license":"1","date_created":"2024-09-23T17:25:43Z","year":"2024","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:18129","abstract":[{"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","lang":"eng"}],"day":"24","date_published":"2024-09-24T00:00:00Z","oa":1,"author":[{"last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian","first_name":"Marian"}]},{"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].","doi":"10.48550/arXiv.2407.03079","day":"03","abstract":[{"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.","lang":"eng"}],"arxiv":1,"author":[{"orcid":"0009-0003-9037-8831","first_name":"Marian","full_name":"Janik, Marian","last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roux, Kevin Etienne Robert","first_name":"Kevin Etienne Robert","last_name":"Roux","id":"53f93ea2-803f-11ed-ab7e-b283135794ef"},{"full_name":"Borja Espinosa, Carla N","first_name":"Carla N","id":"18777c01-896a-11ed-bdf8-e4851dc07d16","last_name":"Borja Espinosa"},{"full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Baghdadi","id":"160D87FA-96B5-11E9-BF77-7626E6697425","first_name":"Abdulhamid","full_name":"Baghdadi, Abdulhamid"},{"last_name":"Adletzberger","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Adletzberger, Thomas"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"full_name":"Botifoll, Marc","first_name":"Marc","last_name":"Botifoll"},{"last_name":"Manjón","first_name":"Alba Garzón","full_name":"Manjón, Alba Garzón"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","full_name":"Isella, Giovanni","last_name":"Isella"},{"last_name":"Pop","first_name":"Ioan M.","full_name":"Pop, Ioan M."},{"full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"oa":1,"date_published":"2024-07-03T00:00:00Z","article_processing_charge":"No","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","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.).","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."},"title":"Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors","external_id":{"arxiv":["2407.03079"]},"date_created":"2024-09-26T09:50:43Z","year":"2024","department":[{"_id":"GeKa"},{"_id":"GradSch"},{"_id":"JoFi"}],"OA_place":"repository","type":"preprint","corr_author":"1","project":[{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"},{"grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins","grant_number":"I05060"}],"publication":"arXiv","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"_id":"18144","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","related_material":{"record":[{"id":"18886","status":"public","relation":"research_data"},{"status":"public","id":"19401","relation":"later_version"},{"relation":"dissertation_contains","id":"18129","status":"public"}]},"article_number":"2407.03079","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2407.03079","open_access":"1"}],"status":"public","date_updated":"2026-07-03T22:34:07Z","publication_status":"draft","month":"07"},{"status":"public","date_updated":"2026-04-07T13:22:10Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"degree_awarded":"PhD","month":"09","publication_status":"published","_id":"18104","oa_version":"Published Version","page":"63","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"related_material":{"record":[{"status":"public","id":"18143","relation":"part_of_dissertation"}]},"project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"},{"name":"Surface Charge and Tunneling Multi-Mode Imaging","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","grant_number":"26088"}],"language":[{"iso":"eng"}],"OA_place":"publisher","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","supervisor":[{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","has_accepted_license":"1","year":"2024","date_created":"2024-09-20T12:13:30Z","publication_identifier":{"issn":["2663-337X"]},"ddc":["530"],"file_date_updated":"2025-05-20T22:30:05Z","citation":{"ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","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.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:10.15479/at:ista:18104","mla":"Puglia, Denise. Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18104."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"relation":"main_file","access_level":"open_access","checksum":"7969263451b2356bfa0924725aa9de10","file_id":"18105","date_created":"2024-09-20T12:07:48Z","embargo":"2025-05-20","date_updated":"2025-05-20T22:30:05Z","file_size":10778238,"creator":"cchlebak","file_name":"PhD_DPuglia_Final.pdf","content_type":"application/pdf"},{"relation":"source_file","access_level":"closed","checksum":"98dfe7675775e30efffa03f7ff7c091b","file_id":"18106","embargo_to":"open_access","date_created":"2024-09-20T12:13:09Z","file_name":"PhD_DPuglia_Thesis.zip","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":385419748,"date_updated":"2025-05-20T22:30:05Z"}],"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"}],"day":"20","date_published":"2024-09-20T00:00:00Z","author":[{"orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","first_name":"Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425"}],"oa":1,"doi":"10.15479/at:ista:18104"},{"external_id":{"arxiv":["2407.15314"]},"publication_status":"draft","month":"08","date_created":"2024-09-26T06:58:27Z","year":"2024","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.15314"}],"status":"public","date_updated":"2026-07-03T22:34:10Z","title":"Room temperature, cavity-free capacitive strong coupling to mechanical motion","related_material":{"record":[{"id":"19026","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"18104","status":"public"}]},"article_processing_charge":"No","article_number":"2407.15314","citation":{"mla":"Puglia, Denise, et al. “Room Temperature, Cavity-Free Capacitive Strong Coupling to Mechanical  Motion.” ArXiv, 2407.15314, doi:10.48550/arXiv.2407.15314.","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","short":"D. Puglia, R.H. Odessey, P.S. Burns, N. Luhmann, S. Schmid, A.P. Higginbotham, ArXiv (n.d.).","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.","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","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.","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. ."},"_id":"18143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","author":[{"orcid":"0000-0003-1144-2763","first_name":"Denise","full_name":"Puglia, Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425"},{"full_name":"Odessey, Rachel H","first_name":"Rachel H","id":"9a7a5123-8972-11ed-ae7b-dd1f2af457bd","last_name":"Odessey"},{"last_name":"Burns","first_name":"Peter S.","full_name":"Burns, Peter S."},{"first_name":"Niklas","full_name":"Luhmann, Niklas","last_name":"Luhmann"},{"first_name":"Silvan","full_name":"Schmid, Silvan","last_name":"Schmid"},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"arxiv":1,"oa":1,"date_published":"2024-08-24T00:00:00Z","project":[{"grant_number":"26088","name":"Surface Charge and Tunneling Multi-Mode Imaging","_id":"62843413-2b32-11ec-9570-c4ec6eabfae7"},{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692"}],"day":"24","publication":"arXiv","abstract":[{"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.","lang":"eng"}],"corr_author":"1","doi":"10.48550/arXiv.2407.15314","department":[{"_id":"AnHi"}],"type":"preprint","OA_place":"repository"},{"citation":{"apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442."},"publisher":"Springer Nature","article_processing_charge":"No","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","intvolume":" 60","year":"2023","date_created":"2022-06-05T22:01:50Z","publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"external_id":{"isi":["000803119400002"]},"article_type":"original","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","doi":"10.1007/s00382-022-06337-7","abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"day":"01","date_published":"2023-01-01T00:00:00Z","author":[{"orcid":"0000-0001-8602-3083","full_name":"Goswami, Bidyut B","first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11434","page":"427-442","oa_version":"None","quality_controlled":"1","related_material":{"link":[{"url":" https://doi.org/10.1007/s00382-022-06401-2","relation":"erratum"}]},"status":"public","date_updated":"2024-10-09T20:53:52Z","month":"01","volume":60,"publication_status":"published","isi":1,"type":"journal_article","department":[{"_id":"CaMu"}],"scopus_import":"1","corr_author":"1","publication":"Climate Dynamics","language":[{"iso":"eng"}]},{"citation":{"chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559."},"publisher":"Wiley","file":[{"date_created":"2023-02-27T07:10:17Z","date_updated":"2023-02-27T07:10:17Z","file_size":2269822,"creator":"dernst","file_name":"2023_EvolutionaryApplications_DeJode.pdf","success":1,"content_type":"application/pdf","relation":"main_file","checksum":"d4d6fa9ddf36643af994a6a757919afb","access_level":"open_access","file_id":"12685"}],"article_processing_charge":"No","file_date_updated":"2023-02-27T07:10:17Z","ddc":["576"],"intvolume":" 16","date_created":"2022-07-03T22:01:33Z","year":"2023","publication_identifier":{"eissn":["1752-4571"]},"external_id":{"isi":["000815663700001"],"pmid":["36793688"]},"title":"Ten years of demographic modelling of divergence and speciation in the sea","pmid":1,"has_accepted_license":"1","doi":"10.1111/eva.13428","article_type":"original","issue":"2","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","date_published":"2023-02-01T00:00:00Z","oa":1,"author":[{"first_name":"Aurélien","full_name":"De Jode, Aurélien","last_name":"De Jode"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean"},{"full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"day":"01","quality_controlled":"1","_id":"11479","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"542-559","publication_status":"published","month":"02","volume":16,"isi":1,"date_updated":"2025-04-23T08:49:14Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","type":"journal_article","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"language":[{"iso":"eng"}],"publication":"Evolutionary Applications"},{"abstract":[{"lang":"eng","text":"We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques. "}],"day":"01","date_published":"2023-07-01T00:00:00Z","author":[{"last_name":"Liebenau","full_name":"Liebenau, Anita","first_name":"Anita"},{"last_name":"Mattos","full_name":"Mattos, Letícia","first_name":"Letícia"},{"last_name":"Mendonca Dos Santos","id":"12c6bd4d-2cd0-11ec-a0da-e28f42f65ebd","full_name":"Mendonca Dos Santos, Walner","first_name":"Walner"},{"last_name":"Skokan","full_name":"Skokan, Jozef","first_name":"Jozef"}],"oa":1,"article_type":"original","acknowledgement":"This work was started at the thematic program GRAPHS@IMPA (January–March 2018), in Rio de Janeiro. We thank IMPA and the organisers for the hospitality and for providing a pleasant research environment. We thank Rob Morris for helpful discussions, and the anonymous referees for their careful reading and many helpful suggestions. Open Access funding enabled and organized by Projekt DEAL.\r\nA. Liebenau was supported by an ARC DECRA Fellowship Grant DE170100789. L. Mattos was supported by CAPES and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – The Berlin Mathematics Research Center MATH+ (EXC-2046/1, project ID: 390685689). W. Mendonça was supported by CAPES project 88882.332408/2010-01.","issue":"4","doi":"10.1002/rsa.21106","title":"Asymmetric Ramsey properties of random graphs involving cliques and cycles","has_accepted_license":"1","date_created":"2022-07-31T22:01:49Z","year":"2023","intvolume":" 62","external_id":{"isi":["000828530400001"]},"publication_identifier":{"eissn":["1098-2418"],"issn":["1042-9832"]},"ddc":["510"],"file_date_updated":"2023-10-04T09:37:26Z","citation":{"chicago":"Liebenau, Anita, Letícia Mattos, Walner Mendonca dos Santos, and Jozef Skokan. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms. Wiley, 2023. https://doi.org/10.1002/rsa.21106.","apa":"Liebenau, A., Mattos, L., Mendonca dos Santos, W., & Skokan, J. (2023). Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. Wiley. https://doi.org/10.1002/rsa.21106","ista":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. 2023. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 62(4), 1035–1055.","ieee":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, and J. Skokan, “Asymmetric Ramsey properties of random graphs involving cliques and cycles,” Random Structures and Algorithms, vol. 62, no. 4. Wiley, pp. 1035–1055, 2023.","ama":"Liebenau A, Mattos L, Mendonca dos Santos W, Skokan J. Asymmetric Ramsey properties of random graphs involving cliques and cycles. Random Structures and Algorithms. 2023;62(4):1035-1055. doi:10.1002/rsa.21106","mla":"Liebenau, Anita, et al. “Asymmetric Ramsey Properties of Random Graphs Involving Cliques and Cycles.” Random Structures and Algorithms, vol. 62, no. 4, Wiley, 2023, pp. 1035–55, doi:10.1002/rsa.21106.","short":"A. Liebenau, L. Mattos, W. Mendonca dos Santos, J. Skokan, Random Structures and Algorithms 62 (2023) 1035–1055."},"article_processing_charge":"Yes (in subscription journal)","file":[{"checksum":"3a5969d0c512aef01c30f3dc81c6d59b","access_level":"open_access","relation":"main_file","file_id":"14389","date_created":"2023-10-04T09:37:26Z","file_size":1362334,"date_updated":"2023-10-04T09:37:26Z","content_type":"application/pdf","creator":"dernst","success":1,"file_name":"2023_RandomStructureAlgorithms_Liebenau.pdf"}],"publisher":"Wiley","publication":"Random Structures and Algorithms","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"MaKw"}],"scopus_import":"1","date_updated":"2023-10-04T09:38:45Z","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"isi":1,"publication_status":"published","month":"07","volume":62,"page":"1035-1055","_id":"11706","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1"},{"scopus_import":"1","corr_author":"1","type":"journal_article","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"publication":"Probability Theory and Related Fields","quality_controlled":"1","page":"1183–1218","_id":"11741","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication_status":"published","volume":185,"month":"04","date_updated":"2024-10-09T21:03:02Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00440-022-01156-7","article_type":"original","acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","date_published":"2023-04-01T00:00:00Z","arxiv":1,"author":[{"id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992"},{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"},{"last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"oa":1,"abstract":[{"text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.","lang":"eng"}],"day":"01","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218."},"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","file":[{"access_level":"open_access","checksum":"b9247827dae5544d1d19c37abe547abc","relation":"main_file","file_id":"14054","date_created":"2023-08-14T12:47:32Z","file_size":782278,"date_updated":"2023-08-14T12:47:32Z","content_type":"application/pdf","creator":"dernst","success":1,"file_name":"2023_ProbabilityTheory_Cipolloni.pdf"}],"file_date_updated":"2023-08-14T12:47:32Z","ddc":["510"],"year":"2023","date_created":"2022-08-07T22:02:00Z","intvolume":" 185","external_id":{"arxiv":["2106.10200"],"isi":["000830344500001"]},"publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"title":"Quenched universality for deformed Wigner matrices","has_accepted_license":"1"},{"status":"public","date_updated":"2025-04-14T07:43:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"04","volume":69,"publication_status":"published","isi":1,"oa_version":"Published Version","_id":"11999","page":"745–770","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Discrete and Computational Geometry","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"UlWa"}],"ec_funded":1,"scopus_import":"1","title":"Inserting one edge into a simple drawing is hard","has_accepted_license":"1","intvolume":" 69","date_created":"2022-08-28T22:02:01Z","year":"2023","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"external_id":{"arxiv":["1909.07347"],"isi":["000840292800001"]},"ddc":["510"],"file_date_updated":"2022-08-29T11:23:15Z","citation":{"chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023.","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770."},"file":[{"date_created":"2022-08-29T11:23:15Z","file_size":1002218,"date_updated":"2022-08-29T11:23:15Z","content_type":"application/pdf","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","creator":"alisjak","success":1,"access_level":"open_access","checksum":"def7ae3b28d9fd6aec16450e40090302","relation":"main_file","file_id":"12006"}],"publisher":"Springer Nature","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"day":"01","date_published":"2023-04-01T00:00:00Z","oa":1,"arxiv":1,"author":[{"orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fabian","full_name":"Klute, Fabian","last_name":"Klute"},{"first_name":"Irene","full_name":"Parada, Irene","last_name":"Parada"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"last_name":"Wiedera","first_name":"Tilo","full_name":"Wiedera, Tilo"}],"article_type":"original","acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","doi":"10.1007/s00454-022-00394-9"},{"type":"journal_article","department":[{"_id":"HeEd"}],"ec_funded":1,"scopus_import":"1","corr_author":"1","publication":"Algorithmica","project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12086","oa_version":"Published Version","page":"277-295","quality_controlled":"1","date_updated":"2025-04-23T08:46:48Z","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"month":"01","publication_status":"published","volume":85,"article_type":"original","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","doi":"10.1007/s00453-022-01027-6","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"day":"01","date_published":"2023-01-01T00:00:00Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Georg F","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang"}],"oa":1,"file_date_updated":"2023-01-20T10:02:48Z","ddc":["510"],"citation":{"mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."},"file":[{"relation":"main_file","access_level":"open_access","checksum":"71685ca5121f4c837f40c3f8eb50c915","file_id":"12322","date_created":"2023-01-20T10:02:48Z","date_updated":"2023-01-20T10:02:48Z","file_size":911017,"success":1,"creator":"dernst","file_name":"2023_Algorithmica_Edelsbrunner.pdf","content_type":"application/pdf"}],"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","pmid":1,"has_accepted_license":"1","year":"2023","date_created":"2022-09-11T22:01:57Z","intvolume":" 85","external_id":{"pmid":["36687803"],"isi":["000846967100001"]},"publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]}}]