[{"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","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","type":"dissertation","file_date_updated":"2024-03-14T14:14:35Z","oa":1,"doi":"10.15479/at:ista:15094","day":"08","date_published":"2024-03-08T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"citation":{"ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15094\">10.15479/at:ista:15094</a>.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","apa":"Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete geometric structures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15094\">https://doi.org/10.15479/at:ista:15094</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"15091","status":"public"},{"relation":"part_of_dissertation","id":"11660","status":"public"},{"id":"15090","relation":"part_of_dissertation","status":"public"},{"id":"15093","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"13182","status":"public"},{"status":"public","id":"11658","relation":"part_of_dissertation"}]},"date_created":"2024-03-08T15:28:10Z","oa_version":"Published Version","ec_funded":1,"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"page":"108","year":"2024","project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"ddc":["514","500","516"],"publication_status":"published","date_updated":"2026-04-07T12:58:48Z","month":"03","author":[{"full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"}],"_id":"15094","language":[{"iso":"eng"}],"status":"public","file":[{"date_updated":"2024-03-14T08:55:07Z","success":1,"date_created":"2024-03-14T08:55:07Z","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_size":4106872,"file_name":"Thesis Sebastiano.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"scultrer","file_id":"15112"},{"file_id":"15113","creator":"scultrer","relation":"source_file","content_type":"application/zip","access_level":"closed","file_name":"Thesis (1).zip","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_size":4746234,"date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z"}],"title":"Persistence and Morse theory for discrete geometric structures"},{"related_material":{"record":[{"id":"12334","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14979","relation":"part_of_dissertation"}]},"date_created":"2025-01-07T10:23:12Z","oa_version":"Published Version","page":"106","abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445"}],"year":"2024","date_updated":"2026-04-07T12:59:44Z","publication_status":"published","ddc":["570"],"month":"12","author":[{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"_id":"18766","title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","status":"public","file":[{"file_name":"PhD_thesis_Julia_Datler.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"jstanger","file_id":"18769","date_updated":"2025-01-07T12:15:11Z","date_created":"2025-01-07T12:15:11Z","file_size":38814932,"checksum":"3e51cab327c754045c3d29c1a50cc9a9"},{"creator":"jstanger","file_id":"18770","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"PhD_thesis_Julia_Datler.pdf","checksum":"22fabe5b97950bf852212f6edb555173","file_size":12044865,"success":1,"date_created":"2025-01-07T12:15:14Z","date_updated":"2025-01-07T12:15:14Z"}],"keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"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)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","has_accepted_license":"1","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"file_date_updated":"2025-01-07T12:15:14Z","type":"dissertation","doi":"10.15479/at:ista:18766","oa":1,"day":"30","OA_place":"publisher","date_published":"2024-12-30T00:00:00Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA thesis"],"citation":{"ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","mla":"Datler, Julia. <i>Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18766\">10.15479/at:ista:18766</a>.","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria.","apa":"Datler, J. (2024). <i>Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18766\">https://doi.org/10.15479/at:ista:18766</a>."},"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"publication_identifier":{"isbn":["978-3-99078-049-7"],"issn":["2663-337X"]}},{"article_processing_charge":"No","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"citation":{"mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2024-02-23T00:00:00Z","day":"23","doi":"10.15479/at:ista:15020","oa":1,"file_date_updated":"2024-02-23T14:20:16Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"],"has_accepted_license":"1","title":"Genetic information and biological optimization","file":[{"date_created":"2024-02-23T13:50:53Z","success":1,"date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"checksum":"b2d3da47c98d481577a4baf68944fe41","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"hledik thesis pdfa 2b.pdf","file_id":"15021","creator":"mhledik"},{"date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_size":14014790,"relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"hledik thesis source.zip","file_id":"15022","creator":"mhledik"}],"status":"public","language":[{"iso":"eng"}],"_id":"15020","month":"02","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"}],"date_updated":"2026-04-07T12:59:25Z","publication_status":"published","ddc":["576","519"],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"year":"2024","page":"158","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7606","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12081","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7553"}]},"date_created":"2024-02-23T14:02:04Z"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"18444"}]},"date_created":"2024-11-19T12:34:30Z","oa_version":"Published Version","abstract":[{"text":"Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the  optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males\r\nengaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion.","lang":"eng"}],"ec_funded":1,"page":"114","year":"2024","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"ddc":["573"],"publication_status":"published","date_updated":"2026-04-07T13:00:36Z","author":[{"full_name":"Satapathy, Roshan K","orcid":"0009-0006-2974-5075","first_name":"Roshan K","last_name":"Satapathy","id":"46046B7A-F248-11E8-B48F-1D18A9856A87"}],"month":"11","_id":"18568","language":[{"iso":"eng"}],"status":"public","file":[{"date_updated":"2024-11-19T12:39:55Z","date_created":"2024-11-19T12:39:55Z","success":1,"checksum":"340f2bfe882c8a85e11ec0687ca15f5e","file_size":10960975,"file_name":"Roshan PhD thesis-Final.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18570","creator":"rsatapat"},{"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Roshan PhD thesis-Final.docx","file_id":"18571","creator":"rsatapat","date_created":"2024-11-19T12:46:47Z","date_updated":"2024-12-13T10:27:25Z","checksum":"0f846fce60d6ea511e07f77eff59a6a1","file_size":36695917}],"title":"Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster","acknowledgement":"I am incredibly thankful for the outstanding support provided by ISTA, especially the Machine Shop team, who made conducting research much easier and more efficient. I am also grateful for the funding provided by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization of neuronal processing”.","has_accepted_license":"1","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-sa/4.0/","acknowledged_ssus":[{"_id":"M-Shop"}],"corr_author":"1","type":"dissertation","file_date_updated":"2024-12-13T10:27:25Z","oa":1,"doi":"10.15479/at:ista:18568","day":"20","date_published":"2024-11-20T00:00:00Z","OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>.","ieee":"R. K. Satapathy, “Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria, 2024.","apa":"Satapathy, R. K. (2024). <i>Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18568\">https://doi.org/10.15479/at:ista:18568</a>","ista":"Satapathy RK. 2024. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria.","mla":"Satapathy, Roshan K. <i>Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>.","short":"R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria, 2024.","ama":"Satapathy RK. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18568\">10.15479/at:ista:18568</a>"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-047-3"]},"supervisor":[{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"file_date_updated":"2024-08-02T09:27:15Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:17336","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","citation":{"ama":"Pedrotti F. Functional inequalities and convergence of stochastic processes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>","short":"F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes, Institute of Science and Technology Austria, 2024.","mla":"Pedrotti, Francesco. <i>Functional Inequalities and Convergence of Stochastic Processes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17336\">10.15479/at:ista:17336</a>.","apa":"Pedrotti, F. (2024). <i>Functional inequalities and convergence of stochastic processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>","ieee":"F. Pedrotti, “Functional inequalities and convergence of stochastic processes,” Institute of Science and Technology Austria, 2024.","chicago":"Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic Processes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17336\">https://doi.org/10.15479/at:ista:17336</a>.","ista":"Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JaMa"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-0845-1338","first_name":"Jan","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"day":"31","date_published":"2024-07-31T00:00:00Z","OA_place":"publisher","ec_funded":1,"abstract":[{"lang":"eng","text":"This thesis deals with the study of stochastic processes and their ergodicity properties. The\r\nvariety of problems encountered calls for a set of different approaches, ranging from classical to\r\nmodern ones: a special place is held by probabilistic methods based on couplings, by functional\r\ninequalities, and by the theory of gradient flows in the space of measures.\r\n\r\nThe material is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith a general presentation of some of the relevant topics. Section 1.1 is dedicated to the\r\ntheory of gradient flows in metric spaces, and introduces the first contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding with a brief description of our second contribution\r\n[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome related problems, concerning the regularization properties of the heat flow. It serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular stochastic model from quantitative genetics:\r\nthis is established via some functional inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n"}],"page":"183","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"year":"2024","related_material":{"record":[{"id":"17351","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"17353","status":"public"},{"relation":"part_of_dissertation","id":"17350","status":"public"},{"relation":"part_of_dissertation","id":"17352","status":"public"},{"relation":"part_of_dissertation","id":"17143","status":"public"}]},"date_created":"2024-07-29T09:14:14Z","oa_version":"Published Version","_id":"17336","language":[{"iso":"eng"}],"title":"Functional inequalities and convergence of stochastic processes","status":"public","file":[{"file_id":"17366","creator":"fpedrott","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_final.pdf","checksum":"11650bab714ef85ad43a287060850523","file_size":2941599,"success":1,"date_created":"2024-08-02T09:23:26Z","date_updated":"2024-08-02T09:23:26Z"},{"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"thesis_final_source.zip","creator":"fpedrott","file_id":"17367","date_created":"2024-08-02T09:27:15Z","date_updated":"2024-08-02T09:27:15Z","checksum":"c30ba5611941226cf1bfc867c25b1e80","file_size":6293375}],"ddc":["500","510","515","519"],"date_updated":"2026-04-07T13:00:03Z","publication_status":"published","month":"07","author":[{"id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","last_name":"Pedrotti","first_name":"Francesco","full_name":"Pedrotti, Francesco"}]},{"date_published":"2024-09-18T00:00:00Z","OA_place":"publisher","day":"18","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"article_processing_charge":"No","citation":{"ama":"Pascual Perez G. On the efficiency and security of secure group messaging. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18088\">10.15479/at:ista:18088</a>","short":"G. Pascual Perez, On the Efficiency and Security of Secure Group Messaging, Institute of Science and Technology Austria, 2024.","mla":"Pascual Perez, Guillermo. <i>On the Efficiency and Security of Secure Group Messaging</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18088\">10.15479/at:ista:18088</a>.","ieee":"G. Pascual Perez, “On the efficiency and security of secure group messaging,” Institute of Science and Technology Austria, 2024.","chicago":"Pascual Perez, Guillermo. “On the Efficiency and Security of Secure Group Messaging.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18088\">https://doi.org/10.15479/at:ista:18088</a>.","apa":"Pascual Perez, G. (2024). <i>On the efficiency and security of secure group messaging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18088\">https://doi.org/10.15479/at:ista:18088</a>","ista":"Pascual Perez G. 2024. On the efficiency and security of secure group messaging. Institute of Science and Technology Austria."},"department":[{"_id":"KrPi"},{"_id":"GradSch"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","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"},"oa":1,"doi":"10.15479/at:ista:18088","file_date_updated":"2024-09-19T12:36:08Z","type":"dissertation","month":"09","author":[{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez","first_name":"Guillermo","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo"}],"ddc":["000"],"date_updated":"2026-04-07T13:01:26Z","publication_status":"published","title":"On the efficiency and security of secure group messaging","file":[{"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"thesis_bundle.zip","creator":"gpascual","file_id":"18099","date_created":"2024-09-19T12:35:38Z","date_updated":"2024-09-19T12:35:38Z","checksum":"ce0dca715b3df48e52e2e891b6ac1bc5","file_size":11917734},{"date_updated":"2024-09-19T12:36:08Z","date_created":"2024-09-19T12:36:08Z","file_size":2729427,"checksum":"4a2c72e90f1a0ef2a13cff800f8d1265","file_name":"thesis_gpasper.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"gpascual","file_id":"18100"}],"status":"public","_id":"18088","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2024-09-18T12:59:49Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10408"},{"relation":"part_of_dissertation","id":"11476","status":"public"},{"status":"public","id":"18086","relation":"part_of_dissertation"},{"id":"10049","relation":"part_of_dissertation","status":"public"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2024","ec_funded":1,"abstract":[{"text":"Instant messaging applications like Whatsapp, Signal or Telegram have become ubiquitous in today's society.\r\nMany of them provide not only end-to-end encryption, but also security guarantees even when the key material gets compromised.\r\nThese are achieved through frequent key update performed by users.\r\nIn particular, the compromise of a group key should preserve confidentiality of previously exchanged messages (forward secrecy), and a subsequent key update will ensure security for future ones (post-compromise security).\r\nThough great protocols for one-on-one communication have been known for some time, the design of ones that scale efficiently for larger groups while achieving akin security guarantees is a hard problem.\r\nA great deal of research has been aimed at this topic, much of it under the umbrella of the Messaging Layer Security (MLS) working group at the IETF. \r\nStarted in 2018, this joint effort by academics and industry culminated in 2023 with the publication of the first standard for secure group messaging [IETF, RFC9420].\r\n\r\nAt the core of secure group messaging is a cryptographic primitive termed Continuous Group Key Agreement, or CGKA [Alwen et al. 2021], that essentially allows a changing group of users to agree on a common key with the added functionality security against compromises is achieved by users asynchronously issuing a key update. In this thesis we contribute to the understanding of CGKA across different angles.\r\nFirst, we present a new technique to effect dynamic operations in groups, i.e., add or remove members, that can be more efficient that the one employed by MLS in certain settings.\r\nConsidering the setting of users belonging to multiple overlapping groups, we then show lowerbounds on the communication cost of constructions that leverage said overlap, at the same time showing protocols that are asymptotically optimal and efficient for practical settings, respectively. Along the way, we show that the communication cost of key updates in MLS is average-cost optimal.\r\nAn important feature in CGKA protocols, particularly for big groups, is the possibility of executing several group operations concurrently. While later versions of MLS support this, they do at the cost of worsening the communication efficiency of future group operations.\r\nIn this thesis we introduce two new protocols that permit concurrency without any negative effect on efficiency. Our protocols circumvent previously existing lower bounds by satisfying a new notion of post-compromise security that only asks for security to be re-established after a certain number of key updates have taken place. While this can be slower than MLS in terms of rounds of communication, we show that it leads to more efficient overall communication. \r\nAdditionally, we introduce a new technique that allows group members to decrease the information they need to store and download, which makes one of our protocols enjoy much lower download cost than any other existing CGKA constructions. ","lang":"eng"}],"page":"239"},{"type":"dissertation","file_date_updated":"2024-09-04T08:36:06Z","doi":"10.15479/at:ista:17490","oa":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","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Markov I. 2024. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. Institute of Science and Technology Austria.","ieee":"I. Markov, “Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective,” Institute of Science and Technology Austria, 2024.","chicago":"Markov, Ilia. “Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>.","apa":"Markov, I. (2024). <i>Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>","mla":"Markov, Ilia. <i>Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>.","short":"I. Markov, Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective, Institute of Science and Technology Austria, 2024.","ama":"Markov I. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"04","OA_place":"publisher","date_published":"2024-09-04T00:00:00Z","page":"102","ec_funded":1,"abstract":[{"text":"Deep learning is essential in numerous applications nowadays, with many recent advancements made possible by training very large models. Despite their broad applicability, training neural networks is often time-intensive, and it is usually impractical to manage large models and datasets on a single machine. To address these issues, distributed deep learning training has become increasingly important. However, distributed training requires synchronization among nodes, and the mini-batch stochastic gradient descent algorithm places a significant load on network connections. A possible solution to tackle the synchronization bottleneck is to reduce a message size by lossy compression.\r\n\r\nIn this thesis, we investigate systems and algorithmic approaches to communication compression during training. From the systems perspective, we demonstrate that a common approach of expensive hardware overprovisioning can be replaced through a thorough system design. We introduce a framework that introduces efficient software support for compressed communication in machine learning applications, applicable to both multi-GPU single-node training and larger-scale multi-node training. Our framework integrates with popular ML frameworks, providing up to 3x speedups for multi-GPU nodes based on commodity hardware and order-of-magnitude improvements in the multi-node setting, with negligible impact on accuracy.\r\n\r\nAlso, we consider an application of our framework to different communication schemes, such as Fully Sharded Data Parallel. We provide strong convergence guarantees for the compression in such a setup. Empirical validation shows that our method preserves model accuracy for GPT-family models with up to 1.3 billion parameters, while completely removing the communication bottlenecks of non-compressed alternatives, providing up to 2.2x speedups end-to-end.\r\n\r\nFrom the algorithmic side, we propose a general framework that dynamically adjusts the degree of compression across a model's layers during training. This approach enhances overall compression and results in significant speedups without compromising accuracy. Our algorithm utilizes an adaptive algorithm that automatically selects the optimal compression parameters for model layers, ensuring the best compression ratio while adhering to an error constraint. Our method is effective across all existing families of compression methods. It achieves up to 2.5x faster training and up to a 5x improvement in compression compared to efficient implementations of current approaches. Additionally, LGreCo can complement existing adaptive algorithms.\r\n","lang":"eng"}],"year":"2024","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"}],"related_material":{"record":[{"status":"public","id":"17456","relation":"part_of_dissertation"},{"status":"public","id":"14461","relation":"part_of_dissertation"},{"id":"12780","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-09-04T08:51:11Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17490","status":"public","file":[{"date_updated":"2024-09-04T08:35:35Z","date_created":"2024-09-04T08:35:35Z","file_size":43327753,"checksum":"77609f4835d2730e46fa0d42d9134ed9","file_name":"Thesis.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"17491","creator":"imarkov"},{"file_name":"Thesis_final_version_pdfa2.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17492","creator":"imarkov","date_updated":"2024-09-04T08:36:06Z","success":1,"date_created":"2024-09-04T08:36:06Z","checksum":"9e68f7217570f756ceb8f70b980938cd","file_size":2756082}],"title":"Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective","publication_status":"published","date_updated":"2026-04-07T13:00:54Z","ddc":["000"],"month":"09","author":[{"first_name":"Ilia","full_name":"Markov, Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","last_name":"Markov"}]},{"type":"dissertation","file_date_updated":"2024-06-26T12:44:53Z","doi":"10.15479/at:ista:17164","oa":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"},"keyword":["Random Matrices","Spectrum","Central Limit Theorem","Resolvent","Free Probability"],"has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"citation":{"ama":"Reker J. Central limit theorems for random matrices: From resolvents to free probability. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17164\">10.15479/at:ista:17164</a>","short":"J. Reker, Central Limit Theorems for Random Matrices: From Resolvents to Free Probability, Institute of Science and Technology Austria, 2024.","mla":"Reker, Jana. <i>Central Limit Theorems for Random Matrices: From Resolvents to Free Probability</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17164\">10.15479/at:ista:17164</a>.","ista":"Reker J. 2024. Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria.","apa":"Reker, J. (2024). <i>Central limit theorems for random matrices: From resolvents to free probability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17164\">https://doi.org/10.15479/at:ista:17164</a>","chicago":"Reker, Jana. “Central Limit Theorems for Random Matrices: From Resolvents to Free Probability.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17164\">https://doi.org/10.15479/at:ista:17164</a>.","ieee":"J. Reker, “Central limit theorems for random matrices: From resolvents to free probability,” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603"}],"publication_identifier":{"issn":["2663-337X"]},"day":"26","OA_place":"publisher","date_published":"2024-06-26T00:00:00Z","page":"206","abstract":[{"lang":"eng","text":"This thesis is structured into two parts. In the first part, we consider the random\r\nvariable X := Tr(f1(W)A1 . . . fk(W)Ak) where W is an N × N Hermitian Wigner matrix, k ∈ N, and we choose (possibly N-dependent) regular functions f1, . . . , fk as well as\r\nbounded deterministic matrices A1, . . . , Ak. In this context, we prove a functional central\r\nlimit theorem on macroscopic and mesoscopic scales, showing that the fluctuations of X\r\naround its expectation are Gaussian and that the limiting covariance structure is given\r\nby a deterministic recursion. We further give explicit error bounds in terms of the scaling\r\nof f1, . . . , fk and the number of traceless matrices among A1, . . . , Ak, thus extending\r\nthe results of Cipolloni, Erdős and Schröder [40] to products of arbitrary length k ≥ 2.\r\nAnalyzing the underlying combinatorics leads to a non-recursive formula for the variance\r\nof X as well as the covariance of X and Y := Tr(fk+1(W)Ak+1 . . . fk+ℓ(W)Ak+ℓ) of similar\r\nbuild. When restricted to polynomials, these formulas reproduce recent results of Male,\r\nMingo, Peché, and Speicher [107], showing that the underlying combinatorics of noncrossing partitions and annular non-crossing permutations continue to stay valid beyond\r\nthe setting of second-order free probability theory. As an application, we consider the\r\nfluctuation of Tr(eitW A1e\r\n−itW A2)/N around its thermal value Tr(A1) Tr(A2)/N2 when t\r\nis large and give an explicit formula for the variance.\r\nThe second part of the thesis collects three smaller projects focusing on different random\r\nmatrix models. In the first project, we show that a class of weakly perturbed Hamiltonians\r\nof the form Hλ = H0 + λW, where W is a Wigner matrix, exhibits prethermalization.\r\nThat is, the time evolution generated by Hλ relaxes to its ultimate thermal state via an\r\nintermediate prethermal state with a lifetime of order λ\r\n−2\r\n. As the main result, we obtain\r\na general relaxation formula, expressing the perturbed dynamics via the unperturbed\r\ndynamics and the ultimate thermal state. The proof relies on a two-resolvent global law\r\nfor the deformed Wigner matrix Hλ.\r\nThe second project focuses on correlated random matrices, more precisely on a correlated N × N Hermitian random matrix with a polynomially decaying metric correlation\r\nstructure. A trivial a priori bound shows that the operator norm of this model is stochastically dominated by √\r\nN. However, by calculating the trace of the moments of the matrix\r\nand using the summable decay of the cumulants, the norm estimate can be improved to a\r\nbound of order one.\r\nIn the third project, we consider a multiplicative perturbation of the form UA(t) where U\r\nis a unitary random matrix and A = diag(t, 1, ..., 1). This so-called UA model was\r\nfirst introduced by Fyodorov [73] for its applications in scattering theory. We give a\r\ngeneral description of the eigenvalue trajectories obtained by varying the parameter t and\r\nintroduce a flow of deterministic domains that separates the outlier resulting from the\r\nrank-one perturbation from the typical eigenvalues for all sub-critical timescales. The\r\nresults are obtained under generic assumptions on U that hold for various unitary random\r\nmatrices, including the circular unitary ensemble (CUE) in the original formulation of\r\nthe model."}],"ec_funded":1,"year":"2024","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"17173","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11135"},{"id":"17047","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"17154","status":"public"},{"status":"public","id":"17174","relation":"part_of_dissertation"}]},"date_created":"2024-06-24T11:23:29Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17164","status":"public","file":[{"file_name":"ISTA_Thesis_JReker.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17176","creator":"jreker","date_updated":"2024-06-26T12:44:53Z","date_created":"2024-06-26T12:39:36Z","checksum":"fb16d86e1f2753dc3a9e14d2bdfd84cd","file_size":2783027},{"checksum":"cb1e54009d47c1dcf5b866c4566fa27f","file_size":3054878,"date_created":"2024-06-26T12:39:42Z","date_updated":"2024-06-26T12:44:53Z","file_id":"17177","creator":"jreker","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"ISTA_Thesis_JReker_SourceFiles.zip"}],"title":"Central limit theorems for random matrices: From resolvents to free probability","publication_status":"published","date_updated":"2026-04-07T13:02:13Z","ddc":["519"],"author":[{"last_name":"Reker","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","full_name":"Reker, Jana","first_name":"Jana"}],"month":"06"},{"oa":1,"doi":"10.15479/at:ista:17850","type":"dissertation","file_date_updated":"2024-09-27T10:34:34Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1","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)"},"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"FyKo"}],"citation":{"short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","apa":"Gonzalez Somermeyer, L. (2024). <i>Fitness landscapes of orthologous green fluorescent proteins</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>.","mla":"Gonzalez Somermeyer, Louisa. <i>Fitness Landscapes of Orthologous Green Fluorescent Proteins</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_published":"2024-09-06T00:00:00Z","OA_place":"publisher","day":"06","year":"2024","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209"}],"abstract":[{"lang":"eng","text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design."}],"ec_funded":1,"page":"89","oa_version":"Published Version","date_created":"2024-09-06T12:57:44Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11448"}],"link":[{"relation":"software","url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks"}]},"file":[{"checksum":"d3303724e8d3c91321d71bbad4062048","file_size":11219837,"date_updated":"2024-09-27T10:32:33Z","date_created":"2024-09-27T10:32:33Z","creator":"lgonzale","file_id":"18151","file_name":"louisa_thesis_draft__240904b.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file"},{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"louisa_thesis_draft__240904b.docx","creator":"lgonzale","file_id":"18152","date_created":"2024-09-27T10:34:34Z","date_updated":"2024-09-27T10:34:34Z","checksum":"22e63f7f9014dffde2af7a47e7d1d014","file_size":43338677}],"status":"public","title":"Fitness landscapes of orthologous green fluorescent proteins","_id":"17850","language":[{"iso":"eng"}],"month":"09","author":[{"last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","first_name":"Louisa"}],"ddc":["570"],"publication_status":"published","date_updated":"2026-04-07T13:25:01Z"},{"article_processing_charge":"No","supervisor":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]},"degree_awarded":"PhD","citation":{"ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2024-12-18T00:00:00Z","day":"18","doi":"10.15479/at:ista:18674","oa":1,"file_date_updated":"2024-12-18T14:41:53Z","type":"dissertation","acknowledged_ssus":[{"_id":"Bio"}],"corr_author":"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)"},"has_accepted_license":"1","title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","file":[{"date_created":"2024-12-18T14:17:34Z","success":1,"date_updated":"2024-12-18T14:17:34Z","checksum":"1b42b8073e2bc09fc504da52372248c1","file_size":160536833,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","creator":"jlyudchi","file_id":"18675"},{"file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"18676","creator":"jlyudchi","date_updated":"2024-12-18T14:41:53Z","date_created":"2024-12-18T14:21:06Z","file_size":99172203,"checksum":"b4da84624060745519723698f7ddf54b"}],"status":"public","language":[{"iso":"eng"}],"_id":"18674","author":[{"first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"}],"month":"12","date_updated":"2026-04-14T08:34:35Z","publication_status":"published","ddc":["004"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"year":"2024","page":"217","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"status":"public","id":"18677","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13267","status":"public"},{"id":"14257","relation":"part_of_dissertation","status":"public"}]},"date_created":"2024-12-18T14:24:43Z"},{"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"],"isbn":["978-3-99078-040-4"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"citation":{"ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>"},"OA_place":"publisher","date_published":"2024-06-11T00:00:00Z","day":"11","doi":"10.15479/at:ista:17133","oa":1,"type":"dissertation","file_date_updated":"2024-06-20T11:52:22Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"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"},"keyword":["Quantum information","Qubits","Superconducting devices"],"has_accepted_license":"1","status":"public","file":[{"checksum":"258c353d47fa37ea63ea43b1e10a34a0","file_size":28370759,"date_updated":"2024-06-20T11:52:22Z","date_created":"2024-06-12T07:53:19Z","file_id":"17137","creator":"fhassani","file_name":"Thesis_main_final.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access"},{"relation":"source_file","content_type":"text/x-tex","access_level":"closed","file_name":"Thesis_main.tex","file_id":"17138","creator":"fhassani","date_created":"2024-06-12T07:54:27Z","date_updated":"2024-06-12T07:54:27Z","file_size":445735,"checksum":"deffa5d0db88093f74812fa71520d5e1"}],"title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","language":[{"iso":"eng"}],"_id":"17133","author":[{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"}],"month":"06","publication_status":"published","date_updated":"2026-04-15T06:43:02Z","ddc":["530"],"year":"2024","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"page":"161","abstract":[{"lang":"eng","text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing."}],"oa_version":"Published Version","related_material":{"record":[{"id":"13227","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"9928","status":"public"},{"relation":"part_of_dissertation","id":"8755","status":"public"}]},"date_created":"2024-06-11T18:20:05Z"},{"file_date_updated":"2024-09-26T13:12:55Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:18135","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"},"license":"https://creativecommons.org/licenses/by/4.0/","corr_author":"1","citation":{"short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024.","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"article_processing_charge":"No","supervisor":[{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert"}],"day":"23","date_published":"2024-09-23T00:00:00Z","OA_place":"publisher","abstract":[{"text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$.","lang":"eng"}],"ec_funded":1,"page":"353","project":[{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"},{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"year":"2024","date_created":"2024-09-24T10:56:25Z","related_material":{"record":[{"status":"public","id":"11732","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14542","status":"public"},{"status":"public","id":"18107","relation":"part_of_dissertation"},{"id":"17240","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"14931","status":"public"}]},"oa_version":"Published Version","_id":"18135","language":[{"iso":"eng"}],"title":"Energies of dilute Fermi gases and universalities in BCS theory","status":"public","file":[{"file_name":"Lauritsen-thesis-final.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"alaurits","file_id":"18147","date_updated":"2024-09-26T13:11:24Z","success":1,"date_created":"2024-09-26T13:11:24Z","file_size":3648831,"checksum":"c7bc3b31e430d57c65393051ca439575"},{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"Lauritsen-thesis-source.zip","file_id":"18148","creator":"alaurits","date_created":"2024-09-26T13:12:55Z","date_updated":"2024-09-26T13:12:55Z","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","file_size":1625888}],"ddc":["515","539"],"date_updated":"2026-04-16T08:17:55Z","publication_status":"published","month":"09","author":[{"first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen"}]},{"publication_status":"published","date_updated":"2026-04-16T12:20:39Z","ddc":["539"],"month":"09","author":[{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi","full_name":"Sagi, Oliver","first_name":"Oliver"}],"language":[{"iso":"eng"}],"_id":"18076","file":[{"file_name":"OliverSagi_Thesis_pdfa.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18093","creator":"osagi","date_updated":"2024-09-18T14:13:01Z","date_created":"2024-09-18T14:13:01Z","success":1,"checksum":"d01d0e2846c2f3ac5bb14d321554a4cd","file_size":86679095},{"creator":"osagi","file_id":"18094","access_level":"local","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"Thesis_OliverSagi.zip","checksum":"0543f473d509ee545f4ed3a56f742f4b","file_size":172098524,"date_created":"2024-09-18T14:14:02Z","date_updated":"2024-09-19T09:20:33Z"}],"status":"public","title":"Hybrid circuits on planar Germanium","date_created":"2024-09-16T12:58:36Z","related_material":{"record":[{"status":"public","id":"17202","relation":"part_of_dissertation"}]},"oa_version":"Published Version","page":"111","abstract":[{"text":"The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge\r\nspin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track\r\nto enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson\r\njunctions have recently emerged as building blocks for such hybrid quantum circuits. In this\r\nthesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity\r\nin a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates\r\nthe superconductor from the Ge quantum well. The Josephson junction is then integrated\r\ninto an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase\r\nthe qubit tunability in a broad frequency range with resonator and two-tone spectroscopy.\r\nTime-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our\r\nresults, combined with the recent advances in the spin qubit field, pave the way towards novel\r\nhybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}],"ec_funded":1,"year":"2024","project":[{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge"},{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046"}],"day":"18","OA_place":"publisher","date_published":"2024-09-18T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"citation":{"ama":"Sagi O. Hybrid circuits on planar Germanium. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>","short":"O. Sagi, Hybrid Circuits on Planar Germanium, Institute of Science and Technology Austria, 2024.","mla":"Sagi, Oliver. <i>Hybrid Circuits on Planar Germanium</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18076\">10.15479/at:ista:18076</a>.","ista":"Sagi O. 2024. Hybrid circuits on planar Germanium. Institute of Science and Technology Austria.","ieee":"O. Sagi, “Hybrid circuits on planar Germanium,” Institute of Science and Technology Austria, 2024.","chicago":"Sagi, Oliver. “Hybrid Circuits on Planar Germanium.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>.","apa":"Sagi, O. (2024). <i>Hybrid circuits on planar Germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18076\">https://doi.org/10.15479/at:ista:18076</a>"},"alternative_title":["ISTA Thesis"],"article_processing_charge":"No","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"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","corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"type":"dissertation","file_date_updated":"2024-09-19T09:20:33Z","doi":"10.15479/at:ista:18076","oa":1},{"language":[{"iso":"eng"}],"_id":"17206","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","status":"public","file":[{"file_size":13788479,"checksum":"d5e9234bde8667b005a8cfe18bb467d3","date_updated":"2025-01-11T23:30:04Z","embargo_to":"open_access","date_created":"2024-07-11T07:18:01Z","creator":"cchlebak","file_id":"17223","file_name":"ThesisRaices2024_postDefense.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"date_created":"2024-07-11T07:22:32Z","date_updated":"2025-01-11T23:30:04Z","file_size":5580296,"checksum":"f5ed0139aa3e11ce58369f0915647c5c","access_level":"open_access","embargo":"2025-01-11","content_type":"application/pdf","relation":"main_file","file_name":"ThesisRaices2024_nosignature.pdf","creator":"cchlebak","file_id":"17224"}],"date_updated":"2026-04-07T13:03:22Z","publication_status":"published","ddc":["570"],"author":[{"first_name":"Julia","full_name":"Raices, Julia","last_name":"Raices","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"}],"month":"07","page":"82","ec_funded":1,"abstract":[{"lang":"eng","text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. "}],"project":[{"grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"year":"2024","date_created":"2024-07-05T14:15:29Z","oa_version":"Published Version","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"citation":{"ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.","ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"day":"05","OA_place":"publisher","date_published":"2024-07-05T00:00:00Z","file_date_updated":"2025-01-11T23:30:04Z","type":"dissertation","doi":"10.15479/at:ista:17206","oa":1,"tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1"},{"abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"ec_funded":1,"page":"131","year":"2024","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"25762","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms"}],"date_created":"2024-09-20T10:21:03Z","oa_version":"Published Version","_id":"18101","language":[{"iso":"eng"}],"status":"public","file":[{"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"PhD_thesis_DPorley_final_20240919.docx","file_id":"18149","creator":"dporley","embargo_to":"open_access","date_created":"2024-09-26T13:40:33Z","date_updated":"2025-03-25T23:30:03Z","file_size":14213128,"checksum":"3b8b0bacfe61112f3852744f3170e468"},{"creator":"dporley","file_id":"18150","file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","access_level":"open_access","content_type":"application/pdf","embargo":"2025-03-25","relation":"main_file","file_size":18583031,"checksum":"6c3a652a8eede874118e11d66a63652f","date_updated":"2025-03-25T23:30:03Z","date_created":"2024-09-26T13:41:39Z"}],"title":"Structural characterization of spumavirus capsid assemblies","ddc":["570"],"publication_status":"published","date_updated":"2026-04-07T13:21:01Z","author":[{"id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","last_name":"Porley","first_name":"Dario J","full_name":"Porley, Dario J"}],"month":"09","type":"dissertation","file_date_updated":"2025-03-25T23:30:03Z","oa":1,"doi":"10.15479/at:ista:18101","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-041-1"]},"supervisor":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","day":"26","date_published":"2024-09-26T00:00:00Z","OA_place":"publisher"},{"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","file_date_updated":"2024-10-05T22:30:05Z","type":"dissertation","oa":1,"doi":"10.15479/at:ista:17465","day":"29","date_published":"2024-08-29T00:00:00Z","OA_place":"repository","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["ISTA Thesis"],"citation":{"mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024."},"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"related_material":{"record":[{"id":"11420","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17469"},{"status":"public","relation":"part_of_dissertation","id":"14459"},{"status":"public","id":"9198","relation":"part_of_dissertation"}]},"date_created":"2024-08-28T15:14:25Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"page":"232","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":"W1260-N35"}],"year":"2024","ddc":["519"],"date_updated":"2025-04-25T10:32:06Z","publication_status":"published","month":"08","author":[{"full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko"}],"_id":"17465","language":[{"iso":"eng"}],"title":"High-dimensional limits in artificial neural networks","file":[{"file_id":"17482","creator":"ashevche","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2024-10-04","file_name":"thesis_a2b.pdf","file_size":4468610,"checksum":"da6dd3166078934577f6af93d27000e2","date_created":"2024-09-02T09:23:32Z","date_updated":"2024-10-05T22:30:05Z"},{"date_created":"2024-09-02T09:23:46Z","embargo_to":"open_access","date_updated":"2024-10-05T22:30:05Z","checksum":"76a39ef252239560923cdda4ce0a31a4","file_size":15930999,"relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis Alex - ISTA.zip","file_id":"17483","creator":"ashevche"}],"status":"public"},{"month":"06","author":[{"full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","first_name":"Réka K","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_updated":"2026-04-07T13:21:37Z","ddc":["576"],"file":[{"date_updated":"2025-01-10T23:30:10Z","embargo_to":"open_access","date_created":"2024-06-07T16:09:17Z","checksum":"fab59146e3b3dc2e5d214576984a2a63","file_size":180557931,"file_name":"thesis.zip","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"17121","creator":"rkelemen"},{"file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"rkelemen","file_id":"17213","date_updated":"2025-01-10T23:30:10Z","date_created":"2024-07-10T08:00:20Z","checksum":"91cc4c25a792239e8a7688e8aec7c62a","file_size":19405484}],"status":"public","title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","language":[{"iso":"eng"}],"_id":"17119","oa_version":"Published Version","date_created":"2024-06-07T16:14:13Z","related_material":{"record":[{"id":"542","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"year":"2024","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"page":"105","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"ec_funded":1,"OA_place":"publisher","date_published":"2024-06-20T00:00:00Z","day":"20","article_processing_charge":"No","supervisor":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>."},"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"},"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"has_accepted_license":"1","doi":"10.15479/at:ista:17119","oa":1,"type":"dissertation","file_date_updated":"2025-01-10T23:30:10Z"},{"corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"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"},"oa":1,"doi":"10.15479/at:ista:18477","type":"dissertation","file_date_updated":"2025-10-29T23:30:02Z","date_published":"2024-10-29T00:00:00Z","OA_place":"publisher","day":"29","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-045-9"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>"},"department":[{"_id":"GradSch"},{"_id":"CaBe"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","oa_version":"Published Version","date_created":"2024-10-27T07:35:13Z","year":"2024","abstract":[{"text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis.","lang":"eng"}],"page":"124","author":[{"full_name":"Kaczmarek, Beata M","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek"}],"month":"10","ddc":["572"],"publication_status":"published","date_updated":"2026-04-07T13:23:59Z","file":[{"file_size":23136626,"checksum":"2053294ea4d770c495e4cc501e2a218b","date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-29T11:56:36Z","embargo_to":"open_access","file_id":"18485","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.docx","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"18486","creator":"bkaczmar","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2025-10-29","file_size":11707360,"checksum":"8ce857a4cd44b776791eaf180ac9dbb3","date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-29T11:56:44Z"}],"status":"public","title":"Biochemical and structural insights into ADAR1 RNA editing","_id":"18477","language":[{"iso":"eng"}]},{"page":"224","abstract":[{"lang":"eng","text":"This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor."}],"year":"2024","date_created":"2024-07-26T09:05:55Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17319","status":"public","file":[{"checksum":"95517e697ea6a87e267e649cad560989","file_size":24639084,"date_created":"2024-07-26T13:14:24Z","date_updated":"2025-01-26T23:30:04Z","file_id":"17320","creator":"cchlebak","relation":"main_file","embargo":"2025-01-26","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Kristina_Lukic.pdf"},{"file_id":"17321","creator":"cchlebak","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Kristina_Lukic.docx","file_size":96334272,"checksum":"74325746a9a05078fb9935dbf2aef752","embargo_to":"open_access","date_created":"2024-07-26T13:14:50Z","date_updated":"2025-01-26T23:30:04Z"}],"title":"Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B","publication_status":"published","date_updated":"2026-04-07T13:20:44Z","ddc":["580"],"month":"07","author":[{"full_name":"Lukic, Kristina","orcid":"0000-0003-1581-881X","first_name":"Kristina","last_name":"Lukic","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","file_date_updated":"2025-01-26T23:30:04Z","doi":"10.15479/at:ista:17319","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"corr_author":"1","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"mla":"Lukic, Kristina. <i>Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>.","chicago":"Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>.","apa":"Lukic, K. (2024). <i>Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17319\">https://doi.org/10.15479/at:ista:17319</a>","ieee":"K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.","ista":"Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.","ama":"Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17319\">10.15479/at:ista:17319</a>","short":"K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024."},"department":[{"_id":"LeSa"},{"_id":"GradSch"}],"article_processing_charge":"No","supervisor":[{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"publication_identifier":{"issn":["2663-337X"]},"day":"26","OA_place":"publisher","date_published":"2024-07-26T00:00:00Z"},{"year":"2024","page":"103","abstract":[{"lang":"eng","text":"Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas."}],"oa_version":"Published Version","date_created":"2024-07-29T15:08:42Z","title":"Stability and change in the memory system during rest","file":[{"date_created":"2024-07-31T18:37:19Z","date_updated":"2025-01-31T23:30:03Z","file_size":12920169,"checksum":"12c76297cc27449da80c60d79127770d","relation":"main_file","embargo":"2025-01-31","content_type":"application/pdf","access_level":"open_access","file_name":"PhD_Thesis_Lars_Bollmann.pdf","file_id":"17359","creator":"lbollman"},{"date_updated":"2025-01-31T23:30:03Z","embargo_to":"open_access","date_created":"2024-07-31T18:38:39Z","checksum":"19a0265079dec8038830ad6e35c5106e","file_size":27568807,"file_name":"Latex_source.zip","relation":"source_file","content_type":"application/zip","access_level":"closed","file_id":"17360","creator":"lbollman"}],"status":"public","language":[{"iso":"eng"}],"_id":"17346","author":[{"first_name":"Lars","full_name":"Bollmann, Lars","id":"47AD3038-F248-11E8-B48F-1D18A9856A87","last_name":"Bollmann"}],"month":"07","date_updated":"2026-04-07T13:21:20Z","publication_status":"published","ddc":["573"],"doi":"10.15479/at:ista:17346","oa":1,"file_date_updated":"2025-01-31T23:30:03Z","type":"dissertation","corr_author":"1","keyword":["Memory","Hippocampus","Consolidation"],"has_accepted_license":"1","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Bollmann L. Stability and change in the memory system during rest. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>","short":"L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024.","mla":"Bollmann, Lars. <i>Stability and Change in the Memory System during Rest</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17346\">10.15479/at:ista:17346</a>.","ista":"Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria.","ieee":"L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024.","chicago":"Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>.","apa":"Bollmann, L. (2024). <i>Stability and change in the memory system during rest</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17346\">https://doi.org/10.15479/at:ista:17346</a>"},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2024-07-31T00:00:00Z","day":"31"}]