[{"corr_author":"1","has_accepted_license":"1","acknowledgement":"The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65.","keyword":["optimal transport","kinetic equations","boundary value problems","quantization","gradient flows","homogenization"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"doi":"10.15479/AT-ISTA-20563","file_date_updated":"2026-01-01T23:30:03Z","type":"dissertation","date_published":"2025-11-03T00:00:00Z","OA_place":"publisher","day":"03","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","first_name":"Jan","orcid":"0000-0002-0845-1338"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"mla":"Quattrocchi, Filippo. <i>Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>.","chicago":"Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>.","apa":"Quattrocchi, F. (2025). <i>Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20563\">https://doi.org/10.15479/AT-ISTA-20563</a>","ieee":"F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025.","ista":"Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria.","ama":"Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20563\">10.15479/AT-ISTA-20563</a>","short":"F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025."},"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","oa_version":"Published Version","date_created":"2025-10-28T13:10:49Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18706","status":"public"},{"relation":"part_of_dissertation","id":"20569","status":"public"},{"relation":"part_of_dissertation","id":"20571","status":"public"},{"id":"20570","relation":"part_of_dissertation","status":"public"}]},"project":[{"_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems","grant_number":"F06504"}],"year":"2025","abstract":[{"lang":"eng","text":"The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n"}],"page":"240","author":[{"last_name":"Quattrocchi","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","full_name":"Quattrocchi, Filippo","orcid":"0009-0000-9773-1931","first_name":"Filippo"}],"month":"11","ddc":["515","519"],"date_updated":"2026-04-07T12:39:35Z","publication_status":"published","title":"Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures","file":[{"date_updated":"2026-01-01T23:30:03Z","date_created":"2025-11-17T21:04:15Z","checksum":"6f55275bdf99992be3a6457d949dd664","file_size":4326411,"file_name":"2025_quattrocchi_filippo_thesis.pdf","relation":"main_file","embargo":"2026-01-01","content_type":"application/pdf","access_level":"open_access","file_id":"20653","creator":"fquattro"},{"embargo_to":"open_access","date_created":"2025-11-17T21:05:43Z","date_updated":"2026-01-01T23:30:03Z","checksum":"707e580f5d993a214c0dba456b75837b","file_size":11726509,"relation":"source_file","content_type":"application/zip","access_level":"closed","file_name":"2025_quattrocchi_thesis.zip","file_id":"20654","creator":"fquattro"}],"status":"public","_id":"20563","language":[{"iso":"eng"}]},{"oa_version":"Published Version","date_created":"2025-03-25T11:22:38Z","year":"2025","page":"96","abstract":[{"lang":"eng","text":"Making decisions requires flexibly adapting to changing environments, a process that\r\ndepends on accurately interpreting current contingencies and integrating them with\r\npast experience. Two brain regions are particularly critical for this process, the medial\r\nprefrontal cortex (mPFC) and the hippocampus. Using contextual information from the\r\nhippocampus, the mPFC selects relevant cognitive frameworks and suppresses\r\nirrelevant ones to guide appropriate actions. Several studies have shown that some\r\nmPFC pyramidal neurons become spatially tuned when spatial information is required\r\nto guide goal-directed behavior. However, the role of prefrontal spatial representations\r\nin learning and decision making is not well understood. This work aims to characterize\r\nthe role of mPFC spatial tuning in supporting a contextual association task. Rats were\r\ntrained to learn two cue–location associations on a radial arm maze over multiple days,\r\nwhile we simultaneously recorded from dorsal CA1 of the hippocampus and the\r\nprelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and\r\nprefrontal pyramidal neurons that “flicker” between multiple spatial representations on\r\ndifferent trials, suggesting dynamic, context-dependent coding. This flickering may\r\nprovide a substrate for how the network reorganizes in response to task demands,\r\nlikely by enabling the flexible evaluation of competing representations. "}],"author":[{"id":"3F158B32-F248-11E8-B48F-1D18A9856A87","last_name":"Cumpelik","first_name":"Andrea D","orcid":"0000-0003-1727-6612","full_name":"Cumpelik, Andrea D"}],"month":"02","publication_status":"published","date_updated":"2026-04-07T12:37:58Z","ddc":["612"],"status":"public","file":[{"checksum":"1c7573303d8e5f6da3eb03d59055390f","file_size":11869040,"date_updated":"2025-09-30T22:30:02Z","date_created":"2025-03-25T11:07:55Z","file_id":"19457","creator":"acumpeli","file_name":"2025_Thesis_Cumpelik_corrections_PDFA.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2025-09-30"},{"file_size":20436467,"checksum":"b93265ebd9a53f7a14100d0d48b4ff5b","date_updated":"2025-09-30T22:30:02Z","embargo_to":"open_access","date_created":"2025-03-25T11:08:05Z","creator":"acumpeli","file_id":"19458","file_name":"2025_Thesis_Cumpelik_corrections.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"}],"title":"The role of prefrontal spatial coding in supporting a contextual association task","OA_embargo":"6 months","language":[{"iso":"eng"}],"_id":"19456","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"corr_author":"1","keyword":["neuroscience","decision making","learning","cognitive flexibility","medial prefrontal cortex","hippocampus","electrophysiology"],"has_accepted_license":"1","doi":"10.15479/AT-ISTA-19456","oa":1,"type":"dissertation","file_date_updated":"2025-09-30T22:30:02Z","OA_place":"publisher","date_published":"2025-02-18T00:00:00Z","day":"18","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-056-5"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"alternative_title":["ISTA Thesis"],"citation":{"mla":"Cumpelik, Andrea D. <i>The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>.","chicago":"Cumpelik, Andrea D. “The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>.","apa":"Cumpelik, A. D. (2025). <i>The role of prefrontal spatial coding in supporting a contextual association task</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19456\">https://doi.org/10.15479/AT-ISTA-19456</a>","ieee":"A. D. Cumpelik, “The role of prefrontal spatial coding in supporting a contextual association task,” Institute of Science and Technology Austria, 2025.","ista":"Cumpelik AD. 2025. The role of prefrontal spatial coding in supporting a contextual association task. Institute of Science and Technology Austria.","ama":"Cumpelik AD. The role of prefrontal spatial coding in supporting a contextual association task. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19456\">10.15479/AT-ISTA-19456</a>","short":"A.D. Cumpelik, The Role of Prefrontal Spatial Coding in Supporting a Contextual Association Task, Institute of Science and Technology Austria, 2025."}},{"day":"11","OA_place":"publisher","date_published":"2025-07-11T00:00:00Z","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"SyCr"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Strahodinsky, Florian. <i>Social Immunity in a Tri-Partite Host-Pathogen Relationship</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>.","chicago":"Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>.","ieee":"F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025.","apa":"Strahodinsky, F. (2025). <i>Social immunity in a tri-partite host-pathogen relationship</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19993\">https://doi.org/10.15479/AT-ISTA-19993</a>","ista":"Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria.","ama":"Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19993\">10.15479/AT-ISTA-19993</a>","short":"F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025."},"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"corr_author":"1","file_date_updated":"2026-01-15T23:30:03Z","type":"dissertation","doi":"10.15479/AT-ISTA-19993","oa":1,"date_updated":"2026-04-07T12:39:58Z","publication_status":"published","ddc":["570"],"month":"07","author":[{"full_name":"Strahodinsky, Florian","first_name":"Florian","last_name":"Strahodinsky","id":"979E35EE-C996-11E9-8C7C-CF13E6697425"}],"language":[{"iso":"eng"}],"_id":"19993","title":"Social immunity in a tri-partite host-pathogen relationship","status":"public","file":[{"creator":"fstrahod","file_id":"20021","file_name":"Thesis_Florian_Strahodinsky_DOCX.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"df3a02f0d937ea9a3d79d5fb94fff097","file_size":9857392,"date_updated":"2026-01-15T23:30:03Z","date_created":"2025-07-14T13:18:37Z","embargo_to":"open_access"},{"date_created":"2025-07-14T13:18:38Z","date_updated":"2026-01-15T23:30:03Z","file_size":6439602,"checksum":"7164c21fe1946e839f7b8acd255ce803","embargo":"2026-01-15","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"Thesis_Florian_Strahodinsky_PDF.pdf","creator":"fstrahod","file_id":"20022"}],"date_created":"2025-07-10T14:12:20Z","oa_version":"Published Version","page":"138","abstract":[{"lang":"eng","text":"Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense."}],"year":"2025"},{"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Suresh, Sarath S. <i>Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>.","chicago":"Suresh, Sarath S. “Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>.","ieee":"S. S. Suresh, “Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote,” Institute of Science and Technology Austria, 2025.","apa":"Suresh, S. S. (2025). <i>Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19906\">https://doi.org/10.15479/AT-ISTA-19906</a>","ista":"Suresh SS. 2025. Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria.","ama":"Suresh SS. Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19906\">10.15479/AT-ISTA-19906</a>","short":"S.S. Suresh, Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and Technology Austria, 2025."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2025-06-26T00:00:00Z","OA_place":"publisher","day":"26","oa":1,"doi":"10.15479/AT-ISTA-19906","file_date_updated":"2025-12-27T23:30:02Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","acknowledgement":"This work was partially funded by the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo. 665385.","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"title":"Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote","file":[{"file_id":"19907","creator":"cchlebak","file_name":"Thesis_v9_PDFA2b.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-12-27","checksum":"302a07605a9e64ac247c2036d5f5b1cd","file_size":6504571,"date_updated":"2025-12-27T23:30:02Z","date_created":"2025-06-26T08:40:53Z"},{"date_updated":"2025-12-27T23:30:02Z","embargo_to":"open_access","date_created":"2025-06-26T08:41:24Z","file_size":59092991,"checksum":"5d69d10bdacc24c27f02924379405bd9","file_name":"Thesis Template - ISTA [istaustriathesis].zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","creator":"cchlebak","file_id":"19908"}],"status":"public","_id":"19906","language":[{"iso":"eng"}],"month":"06","author":[{"full_name":"Suresh, Sarath S","first_name":"Sarath S","id":"3D126CC4-F248-11E8-B48F-1D18A9856A87","last_name":"Suresh"}],"ddc":["530"],"date_updated":"2026-04-07T12:39:19Z","publication_status":"published","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"year":"2025","ec_funded":1,"abstract":[{"text":"Flows of ordinary fluids such as water or air transition from laminar to turbulent\r\nmotion as the velocity increases. This simple dependence of the flow state\r\nsolely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here\r\nvarious different instabilities and turbulent states can arise at low and even\r\nvanishing inertia, while high inertia turbulence counterintuitively is suppressed\r\nand its drag strongly reduced. We here show in experiments of a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia, all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases of flow at high polymer concentrations, exploring the\r\nrelationship between flow at these wide range of control parameters.\r\n","lang":"eng"}],"page":"82","oa_version":"Published Version","date_created":"2025-06-26T08:39:08Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"10299","status":"public"}]}},{"OA_place":"publisher","date_published":"2025-05-29T00:00:00Z","day":"29","supervisor":[{"first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"AnKi"},{"_id":"GradSch"}],"citation":{"short":"S. Rus, Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube, Institute of Science and Technology Austria, 2025.","ama":"Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>","ieee":"S. Rus, “Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube,” Institute of Science and Technology Austria, 2025.","chicago":"Rus, Stefanie. “Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>.","apa":"Rus, S. (2025). <i>Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19763\">https://doi.org/10.15479/AT-ISTA-19763</a>","ista":"Rus S. 2025. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. Institute of Science and Technology Austria.","mla":"Rus, Stefanie. <i>Dynamics of Morphogen Signalling and Cell Fate Decisions in the Dorsal Neural Tube</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19763\">10.15479/AT-ISTA-19763</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","acknowledgement":"My work would also not have been possible without the Imaging and Optics, the Life Science\r\nand the Preclinical Facility of ISTA. Your support has facilitated my research substantially. I\r\nalso want to thank the Graduate School Office for their never-ending support and their sincere\r\neffort to improve the PhD programme of the ISTA even further.\r\nThis work was supported by the Gesellschaft für Forschungsförderung Niederösterreich\r\nm.b.H. fellowship (SC19-011). Thank you for recognizing the importance of this project.","doi":"10.15479/AT-ISTA-19763","oa":1,"file_date_updated":"2025-11-30T23:30:02Z","type":"dissertation","author":[{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","last_name":"Rus","first_name":"Stefanie","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie"}],"month":"05","date_updated":"2026-04-14T09:50:53Z","publication_status":"published","ddc":["570"],"title":"Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube","status":"public","file":[{"file_name":"Thesis_Lehr_PDFA.pdf","relation":"main_file","embargo":"2025-11-30","access_level":"open_access","content_type":"application/pdf","file_id":"19764","creator":"cchlebak","date_updated":"2025-11-30T23:30:02Z","date_created":"2025-05-30T09:10:22Z","file_size":42879974,"checksum":"8cd7fe3ca990adbcafdece119aa0973d"},{"file_size":18731094,"checksum":"0c87dd5fc803450a47b20736b5f86a2f","date_updated":"2025-11-30T23:30:02Z","date_created":"2025-05-30T09:31:15Z","embargo_to":"open_access","file_id":"19765","creator":"cchlebak","file_name":"Thesis_Lehr_emptyPages.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"language":[{"iso":"eng"}],"_id":"19763","oa_version":"Published Version","date_created":"2025-05-30T09:14:58Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18601"},{"id":"17148","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18807","relation":"part_of_dissertation"},{"status":"public","id":"13136","relation":"part_of_dissertation"}]},"project":[{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"year":"2025","page":"129","abstract":[{"lang":"eng","text":"Pattern formation in developing organs is controlled by morphogens. These signalling\r\nmolecules form concentration gradients across tissues, thereby providing positional\r\ninformation that instructs the pattern of cell differentiation. Morphogen gradients are highly\r\ndynamic in space and time. Many factors such as morphogen production, spreading,\r\ndegradation, cellular rearrangements and others could contribute to changes in the gradient\r\nshape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear.\r\nWe studied the dynamics of morphogen signalling and tissue patterning in the developing\r\nvertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor\r\nsubtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are\r\nestablished and interpreted to ensure ordered cell specification is poorly understood.\r\nTo address this question, we developed a 2D embryonic stem cell differentiation system that\r\ncaptures key features of dorsal neural tube development. In this system, differentiated\r\ncolonies display remarkable self-organised pattern formation in response to uniformly\r\napplied BMP ligand. We established a method of differentiating the colonies using\r\nmicrofabricated stencils, which allowed us to control the initial size and shape of colonies\r\nwithout confining cell migration and colony growth. This led to highly reproducible pattern\r\nformation that facilitates quantification.\r\nUsing this approach, we observed striking two-phase temporal dynamics of BMP signalling in\r\nour colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies,\r\nsubsequently disappears and is re-established again in the second phase. By combining our\r\nquantitative data with a data-driven theoretical model, we uncovered a temporal relay\r\nmechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is\r\ncontrolled by fast tissue-autonomous negative feedback that restricts the duration of the\r\ninitial response to BMP. The early BMP activity gradient moreover controls the spatial\r\norganisation of the cell type pattern: the absence of a first phase results in disordered cell\r\ntype pattern. The second phase is controlled by slow positive regulation of BMP signalling by\r\nthe transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the\r\nsecond phase of BMP signalling via positive feedback on LMX1A.\r\nAltogether, the mechanism that we uncovered ensures the coupling of sequential\r\ndevelopmental events, making pattern formation spatially and temporally organised.\r\nFurthermore, this mechanism allows the BMP signalling pathway to be reused in different\r\ncontexts – first for the establishment of the neural plate border, and subsequently for dorsal\r\nneural progenitor patterning. Our study supports a general developmental principle in which\r\nmultiple morphogens interact with transcriptional networks resulting in complex\r\nspatiotemporal signalling dynamics that ultimately drive organised pattern formation."}]},{"day":"24","OA_place":"publisher","date_published":"2025-01-24T00:00:00Z","degree_awarded":"PhD","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"citation":{"mla":"Arnold, Georg M. <i>Microwave-Optic Interconnects for Superconducting Circuits</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>.","ista":"Arnold GM. 2025. Microwave-optic interconnects for superconducting circuits. Institute of Science and Technology Austria.","apa":"Arnold, G. M. (2025). <i>Microwave-optic interconnects for superconducting circuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>","chicago":"Arnold, Georg M. “Microwave-Optic Interconnects for Superconducting Circuits.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/at:ista:18871\">https://doi.org/10.15479/at:ista:18871</a>.","ieee":"G. M. Arnold, “Microwave-optic interconnects for superconducting circuits,” Institute of Science and Technology Austria, 2025.","ama":"Arnold GM. Microwave-optic interconnects for superconducting circuits. 2025. doi:<a href=\"https://doi.org/10.15479/at:ista:18871\">10.15479/at:ista:18871</a>","short":"G.M. Arnold, Microwave-Optic Interconnects for Superconducting Circuits, Institute of Science and Technology Austria, 2025."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053\r\n(ERC StG QUNNECT) and the European Union’s Horizon 2020 research, innovation program\r\nunder grant agreement no. 899354 (FETopen SuperQuLAN) and the Austrian Science Fund\r\n(FWF) through BeyondC (F7105). I want to acknowledge generous support from the Austrian\r\nAcademy of Sciences from a DOC [Doctoral program of the Austrian Academy of Sciences]\r\nfellowship (no. 25129).\r\n","corr_author":"1","acknowledged_ssus":[{"_id":"SSU"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"file_date_updated":"2026-01-29T23:30:03Z","type":"dissertation","doi":"10.15479/at:ista:18871","oa":1,"date_updated":"2026-04-16T12:20:43Z","publication_status":"published","ddc":["530"],"month":"01","author":[{"first_name":"Georg M","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","last_name":"Arnold"}],"language":[{"iso":"eng"}],"_id":"18871","title":"Microwave-optic interconnects for superconducting circuits","file":[{"file_size":18856130,"checksum":"71872702e8f46c275eaea44efc4d304f","date_created":"2025-01-29T08:38:08Z","embargo_to":"open_access","date_updated":"2026-01-29T23:30:03Z","file_id":"18946","creator":"cchlebak","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"tex for upload.zip"},{"date_created":"2025-01-29T08:38:34Z","date_updated":"2026-01-29T23:30:03Z","checksum":"dfaa06591970f4bff163705802fad56d","file_size":17344760,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2026-01-29","file_name":"ISTThesisGA2022_final.pdf","file_id":"18947","creator":"cchlebak"}],"status":"public","date_created":"2025-01-24T10:28:39Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6609"},{"id":"8529","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18953"},{"status":"public","relation":"part_of_dissertation","id":"10924"},{"id":"9114","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13200"}]},"oa_version":"Published Version","page":"135","ec_funded":1,"abstract":[{"lang":"eng","text":"\"Can we do this with a new type of computer - a quantum computer?\". This famous\r\nquotation of the brilliant Richard Feynman within a conference talk on \"Simulating physics\r\nwith computers.” is often reverently praised as the origin of the field of quantum computing.\r\nThe idea was to use quantum mechanical systems itself to simulate \"Nature\", which is\r\ninherently quantum mechanical. Now, 43 years later, the theoretical framework of how such\r\na computer can operate has been developed. Two main important concepts for a potential\r\nquantum supremacy, superposition and entanglement, have been exploited to design quantum\r\nalgorithms to significantly speed up certain tasks. Yet, the specific hardware implementation\r\nis still far from being certain, in fact the race between the most promising platforms such as\r\nsuperconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well\r\nas spin qubits has recently intensified. If one also includes the most mature applications of\r\nquantum communication technologies, secure quantum key distribution and quantum random\r\nnumber generators, as part of a quantum information technology ecosystem, we are confronted\r\nwith a plethora of different materials, concepts, and also operation frequencies. While\r\nsuperconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5\r\nGHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum\r\ncomputing operate with light in the infrared or visible range.\r\nConsequently, a quantum frequency converter or microwave-optic transducer is required\r\nto interface the different frequency domains or establish a long-range network connection\r\nwith suitable telecom fibers. In fact, the combination of different frequency regimes is also\r\nan essential part in our classical modern communication network, where computations are\r\nperformed in electrical circuits and the information exchange over longer distances happens\r\nvia optical fibers. However, the specific challenges specific to building a quantum computer,\r\nalso apply to the development of such a quantum frequency transducer: 1) As we deal with\r\nsingle excitations as the carrier of information, i.e. the smallest possible quantity, the signal\r\ncan easily be corrupted by other noise sources which needs to be avoided by all means. This\r\nis also the reason why microwave quantum computers operate at temperature environments\r\nclose to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The\r\nfrequency interface generally needs to preserve the phase of the signal as an essential part\r\nof the quantum state. And 3) Quantum signals cannot be copied which would be a typical\r\nstrategy to account for errors in classical computers. And finally, there is a challenge specific to\r\nmicrowave-optic transducers: While quantum computers are operating in one specific frequency\r\ndomain, microwave-optic transducers combine microwave and optical fields in one device.\r\nThis results in the particular challenge that high-energy optical radiation, which is usually\r\nwell-shielded from superconducting microwave quantum processors, are now an essential part\r\nof the device. The concomitant optical radiation in the operating transducer will inevitably\r\nhave a detrimental effect on the superconducting microwave components. Together with the\r\nrequirement of minimal background noise for quantum-limited operation as described above,\r\nv\r\nheating from the absorption of optical photons within the same device where single microwave\r\nexcitations are processed forms a formidable challenge.\r\nThis thesis aims to address this challenge by developing microwave-optic transducers where\r\nthe impact of optical absorption on superconducting circuits in general and superconducting\r\nqubits specifically can be mitigated. In our first approach, we developed a compact device\r\nwith optimized interaction strengths between the different frequency domains. This minimizes\r\nthe optical powers used for transducer operation and thus the optical absorption heating. This\r\nwork was - to the best of our knowledge - the first comprehensive noise study, in an integrated\r\nmicrowave-optic transducer. Unfortunately, we saw that the optical absorption heating added\r\nnoise way above a single excitation. Consequently, a potential quantum signal would have\r\nbeen buried in the noise, added by the transduction.\r\nBuilding on this insight, we utilized a three-dimensional microwave-optic transducer instead\r\nof an integrated device. The larger heat capacity of the macroscopic device with a size\r\nof a few millimeters can absorb a larger fraction of the optical heating before it increases\r\nthe temperature of the device. This allowed us to interface the transducer directly with a\r\nsuperconducting qubit to readout the qubit state in a novel all-optical manner. We showed\r\nthat the microwave-optic transducer can be operated in a regime in which optical fields don’t\r\nharm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic\r\ntransducers in conjunction with microwave quantum processors and brings the integration and\r\nseamless orchestration of different frequency components in a quantum network a step closer.\r\n"}],"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"year":"2025"},{"date_created":"2025-11-25T13:19:11Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"12159","status":"public"},{"relation":"part_of_dissertation","id":"14796","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"20190"}]},"oa_version":"Published Version","page":"268","abstract":[{"text":"Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us.","lang":"eng"}],"year":"2025","project":[{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"},{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"publication_status":"published","date_updated":"2026-04-28T13:20:36Z","ddc":["576","578"],"month":"11","author":[{"full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"}],"language":[{"iso":"eng"}],"_id":"20694","file":[{"date_updated":"2026-03-01T23:30:03Z","date_created":"2025-12-01T13:53:36Z","file_size":42723135,"checksum":"7a10a738d58524aebb5dcbd9b34c21c5","file_name":"2025_Pal_Arka_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2026-03-01","relation":"main_file","creator":"apal","file_id":"20721"},{"checksum":"166d832b08d0434ce407f8f3cb930fe5","file_size":60632116,"embargo_to":"open_access","date_created":"2025-12-01T13:53:39Z","date_updated":"2026-03-01T23:30:03Z","file_id":"20722","creator":"apal","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2025_Pal_Arka_Thesis.docx"}],"status":"public","title":"Using genealogies to study the genomic basis of species divergence","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","type":"dissertation","file_date_updated":"2026-03-01T23:30:03Z","doi":"10.15479/AT-ISTA-20694","oa":1,"day":"25","OA_place":"publisher","date_published":"2025-11-25T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"mla":"Pal, Arka. <i>Using Genealogies to Study the Genomic Basis of Species Divergence</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>.","ieee":"A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025.","apa":"Pal, A. (2025). <i>Using genealogies to study the genomic basis of species divergence</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>","chicago":"Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20694\">https://doi.org/10.15479/AT-ISTA-20694</a>.","ista":"Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria.","ama":"Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20694\">10.15479/AT-ISTA-20694</a>","short":"A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025."},"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]}},{"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Sett, Riya. “ Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>.","ieee":"R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025.","apa":"Sett, R. (2025). <i> Quantum remote sensing and non-equilibrium phase transitions in the microwave regime</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19533\">https://doi.org/10.15479/AT-ISTA-19533</a>","ista":"Sett R. 2025.  Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria.","mla":"Sett, Riya. <i> Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>.","short":"R. Sett,  Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025.","ama":"Sett R.  Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19533\">10.15479/AT-ISTA-19533</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","date_published":"2025-04-01T00:00:00Z","OA_place":"publisher","day":"1","oa":1,"doi":"10.15479/AT-ISTA-19533","type":"dissertation","file_date_updated":"2025-10-11T22:30:02Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"corr_author":"1","acknowledgement":"I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"keyword":["phase transition","open quantum system","phase diagram","cavity quantum electrodynamics","superconducting qubits","semiclassical physics","quantum optics","josephson junction","parametric converter","phase conjugation","quantum radar","quantum entanglement","correlation","quantum sensing"],"status":"public","file":[{"file_id":"19538","creator":"rsett","file_name":"PhD_Thesis_Riya_Sett_pdfa.pdf","relation":"main_file","embargo":"2025-10-11","content_type":"application/pdf","access_level":"open_access","file_size":4129208,"checksum":"ba6cd2289d0141a160a14fc97df1632f","date_updated":"2025-10-11T22:30:02Z","date_created":"2025-04-10T11:33:22Z"},{"embargo_to":"open_access","date_created":"2025-04-10T11:34:08Z","date_updated":"2025-10-11T22:30:02Z","file_size":6646110,"checksum":"ee63a94cb8f7adf5e766903028b81ed6","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"PhD Thesis Riya Sett.zip","file_id":"19539","creator":"rsett"}],"title":" Quantum remote sensing and non-equilibrium phase transitions in the microwave regime","_id":"19533","language":[{"iso":"eng"}],"month":"04","author":[{"full_name":"Sett, Riya","first_name":"Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett"}],"ddc":["530"],"publication_status":"published","date_updated":"2026-04-16T12:20:42Z","year":"2025","project":[{"grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Quantum readout techniques and technologies"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"abstract":[{"lang":"eng","text":"This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n"}],"ec_funded":1,"page":"109","oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"18978","status":"public"},{"relation":"part_of_dissertation","id":"19280","status":"public"},{"relation":"part_of_dissertation","id":"13117","status":"public"},{"status":"public","id":"17183","relation":"part_of_dissertation"}]},"date_created":"2025-04-09T16:44:26Z"},{"_id":"19836","language":[{"iso":"eng"}],"title":"Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ","status":"public","file":[{"date_updated":"2026-04-01T22:30:07Z","embargo_to":"open_access","date_created":"2025-06-16T09:38:49Z","checksum":"643bfddead59857536cce4d57c775b32","file_size":59892829,"file_name":"istaustriathesis-master - Copy.zip","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"19849","creator":"jsaezmol"},{"creator":"jsaezmol","file_id":"19851","embargo":"2026-04-01","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"SaezMollejo_PhDFinal_pdfa-1b.pdf","file_size":22382376,"checksum":"e3dcb767fcc2b1787a455fdda991cefb","date_created":"2025-06-18T08:50:16Z","date_updated":"2026-04-01T22:30:07Z"}],"ddc":["530","539"],"date_updated":"2026-04-28T13:29:28Z","publication_status":"published","author":[{"first_name":"Jaime","full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo"}],"month":"06","abstract":[{"text":"Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n","lang":"eng"}],"page":"175","project":[{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"},{"grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"}],"year":"2025","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"19424"}]},"date_created":"2025-06-13T09:01:50Z","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Saez Mollejo J. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>","short":"J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.","mla":"Saez Mollejo, Jaime. <i>Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning </i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19836\">10.15479/AT-ISTA-19836</a>.","ieee":"J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.","chicago":"Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>.","apa":"Saez Mollejo, J. (2025). <i>Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19836\">https://doi.org/10.15479/AT-ISTA-19836</a>","ista":"Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"day":"13","date_published":"2025-06-13T00:00:00Z","OA_place":"publisher","file_date_updated":"2026-04-01T22:30:07Z","type":"dissertation","oa":1,"doi":"10.15479/AT-ISTA-19836","has_accepted_license":"1","acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaGu"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>.","apa":"Wu, B. (2025). <i>An examination on phages as a naturally composable system</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20470\">https://doi.org/10.15479/AT-ISTA-20470</a>","ieee":"B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025.","ista":"Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria.","mla":"Wu, Bryan. <i>An Examination on Phages as a Naturally Composable System</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>.","short":"B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025.","ama":"Wu B. An examination on phages as a naturally composable system. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20470\">10.15479/AT-ISTA-20470</a>"},"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"day":"30","date_published":"2025-10-30T00:00:00Z","OA_place":"publisher","type":"dissertation","file_date_updated":"2026-04-30T22:30:02Z","oa":1,"doi":"10.15479/AT-ISTA-20470","has_accepted_license":"1","corr_author":"1","_id":"20470","language":[{"iso":"eng"}],"file":[{"file_name":"2025_Wu_Bryan_Thesis.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"brwu","file_id":"20516","date_updated":"2026-04-30T22:30:02Z","embargo_to":"open_access","date_created":"2025-10-21T17:33:27Z","file_size":10603235,"checksum":"d32ea83f259f6b0506325cd57b1d44c3"},{"file_name":"2025_Wu_Bryan_Thesis.pdf","embargo":"2026-04-30","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"brwu","file_id":"20517","date_updated":"2026-04-30T22:30:02Z","date_created":"2025-10-21T17:33:26Z","file_size":6251936,"checksum":"53590046fd3244c5550b4022282449d2"}],"status":"public","title":"An examination on phages as a naturally composable system","ddc":["579"],"publication_status":"published","date_updated":"2026-05-06T08:01:28Z","author":[{"first_name":"Bryan","full_name":"Wu, Bryan","id":"3C521EBA-F248-11E8-B48F-1D18A9856A87","last_name":"Wu"}],"month":"10","abstract":[{"lang":"eng","text":"Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems."}],"page":"102","year":"2025","date_created":"2025-10-15T13:30:21Z","oa_version":"Published Version"},{"author":[{"full_name":"Li, Vyacheslav","first_name":"Vyacheslav","last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"}],"month":"07","publication_status":"published","date_updated":"2026-04-07T12:42:28Z","ddc":["530"],"status":"public","file":[{"creator":"vli","file_id":"17228","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","checksum":"15b2dbe8d2c9ed7ca5dd413827928077","file_size":6729761,"date_created":"2024-07-11T10:26:22Z","success":1,"date_updated":"2024-07-11T10:26:22Z"},{"file_id":"17229","creator":"vli","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"PhD Thesis Vyacheslav Li.zip","file_size":9542859,"checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","date_created":"2024-07-11T10:26:22Z","date_updated":"2024-07-11T10:26:22Z"}],"title":"Towards a quantum entanglement enhanced atom interferomter","language":[{"iso":"eng"}],"_id":"17225","oa_version":"Published Version","date_created":"2024-07-11T09:46:48Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"11438","status":"public"}]},"year":"2024","project":[{"grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"page":"79","abstract":[{"text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence.","lang":"eng"}],"OA_place":"publisher","date_published":"2024-07-11T00:00:00Z","day":"11","supervisor":[{"last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024.","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>","apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>."},"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","doi":"10.15479/at:ista:17225","oa":1,"type":"dissertation","file_date_updated":"2024-07-11T10:26:22Z"},{"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"citation":{"short":"M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024.","ama":"Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>","ista":"Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria.","chicago":"Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>.","apa":"Sisak, M. A. (2024). <i>T-dual branes on hyperkähler manifolds</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>","ieee":"M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024.","mla":"Sisak, Maria A. <i>T-Dual Branes on Hyperkähler Manifolds</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Hausel, Tamás","first_name":"Tamás","orcid":"0000-0002-9582-2634","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel"}],"day":"24","date_published":"2024-10-24T00:00:00Z","OA_place":"publisher","file_date_updated":"2024-10-24T08:09:13Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:18443","has_accepted_license":"1","keyword":["hyperkaehler geometry","branes","mirror symmetry","T-duality"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","_id":"18443","language":[{"iso":"eng"}],"title":"T-dual branes on hyperkähler manifolds","file":[{"file_size":1672547,"checksum":"8c4893e726aaa4b3efb82758da9b6851","date_updated":"2024-10-23T14:42:45Z","date_created":"2024-10-23T14:42:45Z","success":1,"file_id":"18467","creator":"msisak","file_name":"MASisak_dissertation.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"1831b072e861a1e5481024ca9d02b036","file_size":617913,"date_created":"2024-10-23T14:43:56Z","date_updated":"2024-10-24T08:09:13Z","creator":"msisak","file_id":"18468","access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"MASisak_source.zip"}],"status":"public","ddc":["516"],"OA_type":"free access","date_updated":"2026-04-07T12:42:44Z","publication_status":"published","month":"10","author":[{"full_name":"Sisak, Maria A","first_name":"Maria A","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","last_name":"Sisak"}],"abstract":[{"lang":"eng","text":"In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n"}],"page":"178","project":[{"name":"Branes on hyperkähler manifolds","_id":"6286e8c4-2b32-11ec-9570-f5297902f67f","grant_number":"26069"}],"year":"2024","date_created":"2024-10-19T12:00:37Z","oa_version":"Published Version"},{"project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"year":"2024","ec_funded":1,"abstract":[{"lang":"eng","text":"Large language models (LLMs) have made tremendous progress in the past few years, from being able to generate coherent text to matching or surpassing humans in a wide variety of creative, knowledge or reasoning tasks. Much of this can be attributed to massively increased scale, both in the size of the model as well as the amount of training data, from 100s of millions to 100s of billions, or even trillions. This trend is expected to continue, which, although exciting, also raises major practical concerns. Already today's 100+ billion parameter LLMs require top-of-the-line hardware just to run. Hence, it is clear that sustaining these developments will require significant efficiency advances.\r\n\r\nHistorically, one of the most practical ways of improving model efficiency has been compression, especially in the form of sparsity or quantization. While this has been studied extensively in the past, existing accurate methods are all designed for models around 100 million parameters; scaling them up to ones literally 1000x larger is highly challenging. In this thesis, we introduce a new unified sparsification and quantization approach OBC, which through additional algorithmic enhancements leads to GPTQ and SparseGPT, the first techniques fast and accurate enough to compress 100+ billion parameter models to 4- or even 3-bit precision and 50% weight-sparsity, respectively. Additionally, we show how weight-only quantizion does not just bring space savings but also up to 4.5x faster generation speed, via custom GPU kernels.\r\n\r\nIn fact, we show for the first time that it is possible to develop an FP16 times INT4 mixed-precision matrix multiplication kernel, called Marlin, which comes close to simultaneously maximizing both memory and compute utilization, making weight-only quantization highly practical even for multi-user serving. Further, we demonstrate that GPTQ can be scaled to widely overparametrized trillion-parameter models, where extreme sub-1-bit compression rates can be achieved without any inference slow-down, by co-designing a bespoke entropy coding scheme together with an efficient kernel.\r\n\r\nFinally, we also study compression from the perspective of someone with access to massive amounts of compute resources for training large models completely from scratch. Here the key questions evolve around the joint scaling behavior between compression, model size, and amount of training data used. Based on extensive experimental results for both vision and text models, we introduce the first scaling law which accurately captures the relationship between weight-sparsity, number of non-zero weights and data. This further allows us to characterize the optimal sparsity, which we find to increase the longer a fixed cost model is being trained.\r\n\r\nOverall, this thesis presents contributions to three different angles of large model efficiency: affordable but accurate algorithms, highly efficient systems implementations, and fundamental scaling laws for compressed training."}],"page":"129","oa_version":"Published Version","related_material":{"record":[{"id":"18062","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18061"},{"status":"public","relation":"part_of_dissertation","id":"17378"},{"relation":"part_of_dissertation","id":"17087","status":"public"},{"id":"14458","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-09-02T11:01:48Z","title":"Compressing large neural networks : Algorithms, systems and scaling laws","file":[{"checksum":"5d785645805a78c5b4ce7cc3df557b09","file_size":1615167,"date_updated":"2024-09-05T12:04:11Z","date_created":"2024-09-05T12:04:11Z","creator":"efrantar","file_id":"17570","file_name":"thesis-final.zip","content_type":"application/zip","access_level":"closed","relation":"source_file"},{"creator":"efrantar","file_id":"17880","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"frantar_thesis_final.pdf","checksum":"a9dd1c2d23734986924eb44ebb55fd8f","file_size":2376611,"date_created":"2024-09-06T16:24:59Z","success":1,"date_updated":"2024-09-06T16:24:59Z"}],"status":"public","_id":"17485","language":[{"iso":"eng"}],"month":"09","author":[{"id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","first_name":"Elias","full_name":"Frantar, Elias"}],"ddc":["000"],"date_updated":"2026-04-07T12:43:04Z","publication_status":"published","oa":1,"doi":"10.15479/at:ista:17485","file_date_updated":"2024-09-06T16:24:59Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"E. Frantar, Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws, Institute of Science and Technology Austria, 2024.","ama":"Frantar E. Compressing large neural networks : Algorithms, systems and scaling laws. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>","chicago":"Frantar, Elias. “Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>.","ieee":"E. Frantar, “Compressing large neural networks : Algorithms, systems and scaling laws,” Institute of Science and Technology Austria, 2024.","apa":"Frantar, E. (2024). <i>Compressing large neural networks : Algorithms, systems and scaling laws</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17485\">https://doi.org/10.15479/at:ista:17485</a>","ista":"Frantar E. 2024. Compressing large neural networks : Algorithms, systems and scaling laws. Institute of Science and Technology Austria.","mla":"Frantar, Elias. <i>Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17485\">10.15479/at:ista:17485</a>."},"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2024-09-05T00:00:00Z","OA_place":"publisher","day":"05"},{"date_published":"2024-07-09T00:00:00Z","OA_place":"publisher","day":"09","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>."},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"oa":1,"doi":"10.15479/at:ista:17208","type":"dissertation","file_date_updated":"2024-07-17T09:23:24Z","month":"07","author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","orcid":"0000-0002-5383-2869"}],"ddc":["539"],"publication_status":"published","date_updated":"2026-04-07T12:43:22Z","file":[{"date_created":"2024-07-09T09:21:44Z","date_updated":"2024-07-10T11:34:09Z","checksum":"6f45273d04f4418bc2adc018baed0525","file_size":"14218691","content_type":"application/zip","access_level":"closed","relation":"source_file","file_name":"Raimel_Thesis-Final.zip","creator":"rmedinar","file_id":"17212"},{"date_created":"2024-07-17T09:23:24Z","success":1,"date_updated":"2024-07-17T09:23:24Z","file_size":11253627,"checksum":"6724a95bec772dbabc0111b9f08a805e","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Raimel_Thesis-20_pdfa.pdf","creator":"rmedinar","file_id":"17275"}],"status":"public","title":"Exploring the optimization landscape of variational quantum algorithms","_id":"17208","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10545"},{"status":"public","relation":"part_of_dissertation","id":"10067"},{"relation":"part_of_dissertation","id":"17222","status":"public"},{"id":"13125","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"11471","status":"public"}]},"date_created":"2024-07-09T09:14:24Z","year":"2024","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"abstract":[{"text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration.","lang":"eng"}],"ec_funded":1,"page":"133"},{"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Glas J. Counting rational points over function fields. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>","short":"J. Glas, Counting Rational Points over Function Fields, Institute of Science and Technology Austria, 2024.","mla":"Glas, Jakob. <i>Counting Rational Points over Function Fields</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18132\">10.15479/at:ista:18132</a>.","ieee":"J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024.","apa":"Glas, J. (2024). <i>Counting rational points over function fields</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>","chicago":"Glas, Jakob. “Counting Rational Points over Function Fields.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18132\">https://doi.org/10.15479/at:ista:18132</a>.","ista":"Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"TiBr"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"23","OA_place":"publisher","date_published":"2024-09-23T00:00:00Z","file_date_updated":"2024-09-25T14:08:57Z","type":"dissertation","doi":"10.15479/at:ista:18132","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"_id":"18132","title":"Counting rational points over function fields","file":[{"date_created":"2024-09-23T18:49:22Z","date_updated":"2024-09-23T18:49:22Z","checksum":"2f8cf5cefdab108b1979caa8146cae9a","file_size":5382106,"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_name":"PhDthesis (3).zip","creator":"jglas","file_id":"18133"},{"date_updated":"2024-09-25T14:08:57Z","date_created":"2024-09-25T14:08:57Z","success":1,"file_size":2380127,"checksum":"08bb6f14c42b47ff25882a2ce3ea0d8a","file_name":"example-phd.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"jglas","file_id":"18140"}],"status":"public","date_updated":"2026-04-07T12:53:54Z","publication_status":"published","ddc":["512"],"month":"09","author":[{"id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","last_name":"Glas","full_name":"Glas, Jakob","first_name":"Jakob"}],"page":"195","abstract":[{"text":"In this thesis, we are dealing with both arithmetic and geometric problems coming from the\r\nstudy of rational points with a particular focus on function fields over finite fields:\r\n(1) Using the circle method we produce upper bounds for the number of rational points of\r\nbounded height on diagonal cubic surfaces and fourfolds over Fq(t). This is based on\r\njoint work with Leonhard Hochfilzer.\r\n(2) We study rational points on smooth complete intersections X defined by cubic and\r\nquadratic hypersurfaces over Fq(t). We refine the Farey dissection of the “unit square”\r\ndeveloped by Vishe [202] and use the circle method with a Kloosterman refinement to\r\nestablish an asymptotic formula for the number of rational points of bounded height on\r\nX when dim(X) ≥ 23. Under the same hypotheses, we also verify weak approximation.\r\n(3) In joint work with Hochfilzer, we obtain upper bounds for the number of rational points of\r\nbounded height on del Pezzo surfaces of low degree over any global field. Our approach\r\nis to take hyperplane sections, which reduces the problem to uniform estimates for the\r\nnumber of rational points on curves.\r\n(4) We develop a version of the circle method capable of counting Fq-points on jet schemes\r\nof moduli spaces of rational curves on hypersurfaces. Combining this with a spreading\r\nout argument and a result of Mustaţă [150], this allows us to show that these moduli\r\nspaces only have canonical singularities under suitable assumptions on the degree and the\r\ndimension.\r\nIn addition, we give an overview of guiding questions and conjectures in the field of rational\r\npoints and explain the basic mechanism underlying the circle method.\r\n","lang":"eng"}],"project":[{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"year":"2024","date_created":"2024-09-23T18:58:08Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"18293","status":"public"},{"status":"public","id":"18294","relation":"part_of_dissertation"},{"status":"public","id":"18295","relation":"part_of_dissertation"},{"id":"18173","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version"},{"oa":1,"doi":"10.15479/at:ista:18667","type":"dissertation","file_date_updated":"2024-12-19T10:24:50Z","corr_author":"1","acknowledgement":"I was supported by the European Research Council (ERC) Horizon 2020 project\r\n“Alpha Shape Theory Extended” No. 788183 and by the Pöttinger Scholarship. In addition,\r\nI am very thankful for having been able to attend the second Workshop for Women in\r\nComputational Topology in July 2019, funded by the Mathematical Sciences Institute at\r\nANU, the US National Science Foundation through the award CCF-1841455, the Australian\r\nMathematical Sciences Institute and the Association for Women in Mathematics. Two of the\r\nprojects presented in this thesis started there. One of them reached completion thanks to\r\nfunding from the MSRI Summer Research in Mathematics program awarded to me and my\r\ncollaborators in 2020.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"keyword":["persistent homology","topological data analysis","periodic","crystalline materials","images","fingerprint"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-052-7"]},"supervisor":[{"first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"citation":{"short":"T. Heiss, New Methods for Applying Topological Data Analysis to Materials Science, Institute of Science and Technology Austria, 2024.","ama":"Heiss T. New methods for applying topological data analysis to materials science. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>","apa":"Heiss, T. (2024). <i>New methods for applying topological data analysis to materials science</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>","chicago":"Heiss, Teresa. “New Methods for Applying Topological Data Analysis to Materials Science.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>.","ieee":"T. Heiss, “New methods for applying topological data analysis to materials science,” Institute of Science and Technology Austria, 2024.","ista":"Heiss T. 2024. New methods for applying topological data analysis to materials science. Institute of Science and Technology Austria.","mla":"Heiss, Teresa. <i>New Methods for Applying Topological Data Analysis to Materials Science</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>."},"degree_awarded":"PhD","date_published":"2024-12-17T00:00:00Z","OA_place":"publisher","day":"17","year":"2024","project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Many chemical and physical properties of materials are determined by the material’s shape,\r\nfor example the size of its pores and the width of its tunnels. This makes materials science\r\na prime application area for geometrical and topological methods. Nevertheless many\r\nmethods in topological data analysis have not been satisfyingly extended to the needs of\r\nmaterials science. This thesis provides new methods and new mathematical theorems\r\ntargeted at those specific needs by answering four different research questions. While the\r\nmotivation for each of the research questions arises from materials science, the methods\r\nare versatile and can be applied in different areas as well. \r\n\r\nThe first research question is concerned with image data, for example a three-dimensional\r\ncomputed tomography (CT) scan of a material, like sand or stone. There are two commonly\r\nused topologies for digital images and depending on the application either of them might be\r\nrequired. However, software for computing the topological data analysis method persistence\r\nhomology, usually supports only one of the two topologies. We answer the question how to\r\ncompute persistent homology of an image with respect to one of the two topologies using\r\nsoftware that is intended for the other topology. \r\n\r\nThe second research question is concerned with image data as well, and asks how much\r\nof the topological information of an image is lost when the resolution is coarsened. As\r\ncomputer tomography scanners are more expensive the higher the resolution, it is an\r\nimportant question in materials science to know which resolution is enough to get satisfying\r\npersistent homology. We give theoretical bounds on the information loss based on different\r\ngeometrical properties of the object to be scanned. In addition, we conduct experiments on\r\nsand and stone CT image data. \r\n\r\nThe third research question is motivated by comparing crystalline materials efficiently. As\r\nthe atoms within a crystal repeat periodically, crystalline materials are either modeled by\r\nunmanageable infinite periodic point sets, or by one of their fundamental domains, which is\r\nunstable under perturbation. Therefore a fingerprint of crystalline materials is needed, with\r\nappropriate properties such that comparing the crystals can be eased by comparing the\r\nfingerprints instead. We define the density fingerprint and prove the necessary properties. \r\n\r\nThe fourth research question is motivated by studying the hole-structure or connectedness,\r\ni.e. persistent homology or merge trees, of crystalline materials. A common way to deal\r\nwith periodicity is to take a fundamental domain and identify opposite boundaries to form a\r\ntorus. However, computing persistent homology or merge trees on that torus loses some\r\nof the information materials scientists are interested in and is additionally not stable under\r\ncertain noise. We therefore decorate the merge tree stemming from the torus with additional\r\ninformation describing the density and growth rate of the periodic copies of a component\r\nwithin a growing spherical window. We prove all desired properties, like stability and efficient\r\ncomputability."}],"page":"111","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"10828","status":"public"},{"id":"11440","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18673","status":"public"},{"relation":"part_of_dissertation","id":"9345","status":"public"}]},"date_created":"2024-12-17T16:17:55Z","status":"public","file":[{"checksum":"247bb057aed2fba1cd4711917aaa2d77","file_size":7752253,"success":1,"date_created":"2024-12-19T10:24:46Z","date_updated":"2024-12-19T10:24:46Z","creator":"theiss","file_id":"18686","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Teresa_Heiss_PhD_Thesis_final.pdf"},{"file_size":17197731,"checksum":"9648b45c07a008ee11a07f99856a139d","date_updated":"2024-12-19T10:24:50Z","date_created":"2024-12-19T10:24:50Z","file_id":"18687","creator":"theiss","file_name":"PhD_Thesis.zip","relation":"source_file","access_level":"closed","content_type":"application/zip"}],"title":"New methods for applying topological data analysis to materials science","_id":"18667","language":[{"iso":"eng"}],"author":[{"full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689","first_name":"Teresa","last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87"}],"month":"12","ddc":["514","516","004"],"publication_status":"published","date_updated":"2026-04-07T12:54:10Z"},{"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). <i>Local adaptation, genetic load and extinction in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14711\">https://doi.org/10.15479/at:ista:14711</a>.","mla":"Olusanya, Oluwafunmilola O. <i>Local Adaptation, Genetic Load and Extinction in Metapopulations</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14711\">10.15479/at:ista:14711</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"article_processing_charge":"No","day":"19","date_published":"2024-01-19T00:00:00Z","OA_place":"publisher","type":"dissertation","file_date_updated":"2024-01-03T18:31:34Z","oa":1,"doi":"10.15479/at:ista:14711","has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"corr_author":"1","acknowledged_ssus":[{"_id":"SSU"}],"_id":"14711","language":[{"iso":"eng"}],"status":"public","file":[{"relation":"source_file","content_type":"application/zip","access_level":"closed","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","file_id":"14730","creator":"oolusany","date_created":"2024-01-03T18:30:13Z","date_updated":"2024-01-03T18:30:13Z","file_size":16986244,"checksum":"de179b1c6758f182ff0c70d8b38c1501"},{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","creator":"oolusany","file_id":"14731","success":1,"date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_size":6460403}],"title":"Local adaptation, genetic load and extinction in metapopulations","ddc":["576"],"publication_status":"published","date_updated":"2026-04-07T12:54:29Z","month":"01","author":[{"orcid":"0000-0003-1971-8314","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"page":"183","year":"2024","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation"}],"related_material":{"record":[{"id":"10787","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10658"},{"id":"14732","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-12-26T22:49:53Z","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"_id":"17156","title":"Equivariant cohomology and rings of functions","file":[{"date_updated":"2024-06-26T21:00:14Z","date_created":"2024-06-26T20:56:27Z","checksum":"1610063569f5452f8a5acef728c2fc26","file_size":2761814,"file_name":"thesis.zip","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"17179","creator":"krychlew"},{"date_updated":"2024-06-26T20:58:24Z","date_created":"2024-06-26T20:58:24Z","checksum":"7bbadb1fbc9ed2a1ecf54597f88af99c","file_size":3695952,"file_name":"thesis.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"krychlew","file_id":"17180"}],"status":"public","date_updated":"2026-04-07T12:55:46Z","publication_status":"published","ddc":["516"],"author":[{"full_name":"Rychlewicz, Kamil P","first_name":"Kamil P","last_name":"Rychlewicz","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"month":"06","page":"117","abstract":[{"text":"This dissertation is the summary of the author’s work, concerning the relations between\r\ncohomology rings of algebraic varieties and rings of functions on zero schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth complex varieties with\r\nan action of a principally paired group, e.g. a parabolic subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored article [66] says that if the principal\r\nnilpotent has a unique zero, then the zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant cohomology ring, remembering the grading in terms of\r\na C^* action. A similar statement is proved also for the G-invariant functions on the total\r\nzero scheme over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult for the GKM spaces, which poses the question on a joint generalisation.\r\nWe also tackle the situation of a singular variety. As long as it is embedded in a smooth\r\nvariety with regular action, we are able to study its cohomology as well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines the cohomology ring\r\ncompletely. In largest generality, this allows us to see a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1) that the cohomology ring of spherical varieties appears as\r\nthe ring of functions on the zero scheme. The computational aspect is not easy, but one\r\ncan hope that this can bring some concrete information about such cohomology rings.\r\nLastly, the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe thesis includes also an introduction to group actions on algebraic varieties. In\r\nparticular, the vector fields associated to the actions are extensively studied. We also\r\nprovide a version of the Kostant section for arbitrary principally paired group, which\r\nparametrises the regular orbits in the Lie algebra of an algebraic group. Before proving\r\nthe main theorem, we also include a historical overview of the field. In particular we bring\r\ntogether the results of Akyildiz, Carrell and Lieberman on non-equivariant cohomology\r\nrings.","lang":"eng"}],"project":[{"grant_number":"26525","_id":"34cd0f74-11ca-11ed-8bc3-bf0492a14a24","name":"Topology of open smooth varieties with a torus action"}],"year":"2024","date_created":"2024-06-23T15:07:06Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17157"}]},"oa_version":"Published Version","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"TaHa"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"citation":{"ama":"Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17156\">10.15479/at:ista:17156</a>","short":"K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute of Science and Technology Austria, 2024.","mla":"Rychlewicz, Kamil P. <i>Equivariant Cohomology and Rings of Functions</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17156\">10.15479/at:ista:17156</a>.","apa":"Rychlewicz, K. P. (2024). <i>Equivariant cohomology and rings of functions</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17156\">https://doi.org/10.15479/at:ista:17156</a>","ieee":"K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute of Science and Technology Austria, 2024.","chicago":"Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17156\">https://doi.org/10.15479/at:ista:17156</a>.","ista":"Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamás","orcid":"0000-0002-9582-2634","full_name":"Hausel, Tamás"}],"publication_identifier":{"issn":["2663-337X"]},"day":"25","OA_place":"publisher","date_published":"2024-06-25T00:00:00Z","file_date_updated":"2024-06-26T21:00:14Z","type":"dissertation","doi":"10.15479/at:ista:17156","oa":1,"keyword":["equivariant cohomology","zero schemes","algebraic groups","Lie algebras"],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","corr_author":"1"},{"author":[{"first_name":"Parvathy","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"}],"month":"11","publication_status":"published","date_updated":"2026-04-07T12:56:52Z","OA_type":"gold","ddc":["576"],"status":"public","file":[{"date_updated":"2024-11-07T10:59:29Z","success":1,"date_created":"2024-11-07T10:59:29Z","file_size":37019760,"checksum":"c32cf7bc75748d9c551d8eb70178bbec","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18519","creator":"psurendr"},{"file_size":41198857,"checksum":"4417e02d54084d89e75734e18caaa96d","date_created":"2024-11-07T10:59:42Z","date_updated":"2024-11-07T10:59:42Z","file_id":"18520","creator":"psurendr","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"PhD Thesis- Parvathy_071124.zip"}],"title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","language":[{"iso":"eng"}],"_id":"18515","oa_version":"Published Version","date_created":"2024-11-06T21:25:37Z","year":"2024","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"page":"219","abstract":[{"text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations.","lang":"eng"}],"OA_place":"publisher","date_published":"2024-11-07T00:00:00Z","day":"07","article_processing_charge":"No","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria.","mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>"},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","has_accepted_license":"1","doi":"10.15479/at:ista:18515","oa":1,"type":"dissertation","file_date_updated":"2024-11-07T10:59:42Z"},{"related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"18688"},{"relation":"part_of_dissertation","id":"18677","status":"public"},{"status":"public","id":"18689","relation":"part_of_dissertation"}]},"date_created":"2024-12-19T02:30:39Z","oa_version":"Published Version","page":"230","year":"2024","project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"ddc":["600","570"],"publication_status":"published","date_updated":"2026-04-07T12:56:37Z","month":"12","author":[{"orcid":"0000-0002-7667-6854","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"}],"_id":"18681","OA_embargo":"20","language":[{"iso":"eng"}],"status":"public","file":[{"checksum":"b61651d417cafddd740a8528f46068c5","file_size":118593521,"date_updated":"2024-12-20T10:31:37Z","date_created":"2024-12-20T10:23:17Z","file_id":"18699","creator":"mtavakol","file_name":"Thesis_Mojtaba Tavakoli_.docx","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"18700","creator":"mtavakol","relation":"main_file","content_type":"application/pdf","embargo":"2026-08-01","access_level":"closed","file_name":"Thesis_Mojtaba Tavakoli_.pdf","checksum":"c80bcfd1a34c23afc3538052325283e5","file_size":63885521,"embargo_to":"open_access","date_created":"2024-12-20T10:25:12Z","date_updated":"2024-12-20T10:25:12Z"}],"title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"type":"dissertation","file_date_updated":"2024-12-20T10:31:37Z","doi":"10.15479/at:ista:18681","day":"20","date_published":"2024-12-20T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>"},"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-048-0"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"article_processing_charge":"No"}]