[{"month":"01","author":[{"full_name":"Chiossi, Heloisa","first_name":"Heloisa","orcid":"0009-0004-2973-278X","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi"}],"ddc":["570"],"publication_status":"published","date_updated":"2026-04-07T13:21:56Z","status":"public","file":[{"embargo_to":"open_access","date_created":"2024-01-19T11:04:05Z","date_updated":"2025-01-19T23:30:04Z","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_size":8656268,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"PhD_Thesis_190124.docx","creator":"hchiossi","file_id":"14838"},{"file_id":"14839","creator":"hchiossi","file_name":"PhD_Thesis_190124.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-01-19","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","file_size":6567275,"date_updated":"2025-01-19T23:30:04Z","date_created":"2024-01-19T11:03:59Z"}],"title":"Adaptive hierarchical representations in the hippocampus","_id":"14821","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2024-01-16T14:25:21Z","year":"2024","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"abstract":[{"text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour.","lang":"eng"}],"ec_funded":1,"page":"89","date_published":"2024-01-19T00:00:00Z","OA_place":"publisher","day":"19","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-5193-4036","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"citation":{"short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:14821","type":"dissertation","file_date_updated":"2025-01-19T23:30:04Z"},{"degree_awarded":"PhD","citation":{"mla":"Janik, Marian. <i>Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>.","ista":"Janik M. 2024. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. Institute of Science and Technology Austria.","apa":"Janik, M. (2024). <i>Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>","ieee":"M. Janik, “Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors,” Institute of Science and Technology Austria, 2024.","chicago":"Janik, Marian. “Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18129\">https://doi.org/10.15479/at:ista:18129</a>.","ama":"Janik M. Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18129\">10.15479/at:ista:18129</a>","short":"M. Janik, Strong Charge-Photon Coupling in Germanium Enabled by Granular Aluminium Superinductors, Institute of Science and Technology Austria, 2024."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"24","OA_place":"publisher","date_published":"2024-09-24T00:00:00Z","file_date_updated":"2025-05-23T22:30:09Z","type":"dissertation","doi":"10.15479/at:ista:18129","oa":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/","has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"corr_author":"1","language":[{"iso":"eng"}],"_id":"18129","title":"Strong charge-photon coupling in Germanium enabled by granular aluminium superinductors","file":[{"relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"janik_thesis.zip","file_id":"18130","creator":"mjanik","embargo_to":"open_access","date_created":"2024-09-23T17:15:09Z","date_updated":"2025-05-23T22:30:09Z","checksum":"dc15958f6400b5bdaa28bf58fc7a4056","file_size":156207943},{"file_id":"18131","creator":"mjanik","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-05-23","file_name":"janik_thesis_pdfa.pdf","file_size":96195684,"checksum":"74737aee285dc1f491643327350efe9c","date_created":"2024-09-23T17:15:30Z","date_updated":"2025-05-23T22:30:09Z"}],"status":"public","date_updated":"2026-04-07T13:23:25Z","publication_status":"published","ddc":["539"],"month":"09","author":[{"full_name":"Janik, Marian","first_name":"Marian","orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik"}],"page":"164","abstract":[{"lang":"eng","text":"State-of-the-art quantum computers, with roughly a thousand qubits, face a crucial technological challenge of scaling up. Spins confined in quantum dots (QDs) are a promising candidate\r\nfor qubits due to their long coherence, tunability, control, and readout. However, their natural\r\ncoupling is the short-ranged (∼ 100 nm) exchange interaction, limited to nearest neighbours.\r\nLong-ranged (∼ 1 mm) qubit interactions mediated by a photon could be engineered through a\r\ncoherent spin-photon coupling. Achieving a strong coupling to a photon is inherently challenging in QDs due to the small dipole moment of the confined charge. However, the potential of\r\nhigh-impedance resonators to compensate for this has gained significant attention in the past\r\ndecade. Nevertheless, previous QD circuit quantum electrodynamics implementations have not\r\nexceeded the impedance of ∼ 3.8 kΩ, leaving opportunities for significant improvement. The\r\nlarge kinetic inductance of granular aluminium (grAl) could provide an order-of-magnitude\r\nenhancement. However, fully exploiting the potential of disordered or granular superconductors\r\nis challenging as their impedances close to the superconductor-to-insulator transition are\r\ndifficult to control reproducibly. We report on the realization of a wireless ohmmeter which\r\nallows in situ resistance measurements during film deposition and, therefore, indirect control\r\nof the kinetic inductance of grAl films. This allows us to reproducibly fabricate resonators\r\nwith characteristic impedance exceeding the resistance quantum, even reaching 22.3 kW, due\r\nto the large sheet kinetic inductance of up to 3 nH □−1\r\n. By integrating an 8 kW resonator\r\nwith a germanium double QD, we demonstrate a strong charge-photon coupling with the\r\nhighest rate reported, 566 MHz. The demonstrated method and grAl properties make these\r\nresonators suitable for boosting the spin-photon coupling strength, a crucial requirement for\r\nfast, high-fidelity, long-distance two-qubit gates.\r\n"}],"project":[{"grant_number":"I05060","name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507"},{"name":"Towards scalable hut wire quantum devices","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235"},{"name":"Integrated Germanium Quantum Technology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"year":"2024","related_material":{"record":[{"relation":"part_of_dissertation","id":"18144","status":"public"}]},"date_created":"2024-09-23T17:25:43Z","oa_version":"Published Version"},{"acknowledged_ssus":[{"_id":"EM-Fac"}],"corr_author":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"doi":"10.15479/at:ista:15101","file_date_updated":"2024-04-02T22:30:03Z","type":"dissertation","date_published":"2024-03-11T00:00:00Z","OA_place":"publisher","day":"11","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"citation":{"mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","oa_version":"Published Version","date_created":"2024-03-11T10:09:54Z","related_material":{"record":[{"status":"public","id":"14843","relation":"part_of_dissertation"}]},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"year":"2024","ec_funded":1,"abstract":[{"text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission.","lang":"eng"}],"page":"84","author":[{"last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","first_name":"JingJing","full_name":"Chen, JingJing"}],"month":"03","ddc":["570"],"date_updated":"2026-04-07T13:24:22Z","publication_status":"published","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","file":[{"file_name":"Thesis_Jingjing CHEN.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"jchen","file_id":"15104","date_updated":"2024-04-02T22:30:03Z","date_created":"2024-03-11T14:10:58Z","embargo_to":"open_access","checksum":"db4947474ffa271e66c254b6fe876a55","file_size":11271363},{"file_id":"15105","creator":"jchen","relation":"main_file","access_level":"open_access","embargo":"2024-04-01","content_type":"application/pdf","file_name":"Thesis_Jingjing CHEN_merged.pdf","checksum":"a5eeae8b5702cd540f5d03469bc33dde","file_size":16627311,"date_created":"2024-03-11T14:11:06Z","date_updated":"2024-04-02T22:30:03Z"}],"status":"public","_id":"15101","language":[{"iso":"eng"}]},{"page":"82","abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"year":"2024","project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"}],"related_material":{"record":[{"status":"public","id":"14032","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18057","status":"public"}]},"date_created":"2024-09-08T10:23:25Z","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"17881","file":[{"date_created":"2024-09-12T10:46:04Z","date_updated":"2025-03-13T23:30:04Z","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","file_size":10297052,"embargo":"2025-03-13","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","creator":"smukhopa","file_id":"18059"},{"checksum":"e352667482701dd18a9a0e7418aef465","file_size":29178634,"date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:50:58Z","embargo_to":"open_access","file_id":"18060","creator":"smukhopa","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","relation":"source_file","content_type":"application/zip","access_level":"closed"}],"status":"public","title":"Thermal effects in one dimensional Josephson chains","publication_status":"published","date_updated":"2026-04-07T13:04:06Z","ddc":["539"],"month":"09","author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","first_name":"Soham","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham"}],"type":"dissertation","file_date_updated":"2025-03-13T23:30:04Z","doi":"10.15479/at:ista:17881","oa":1,"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"article_processing_charge":"No","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"day":"10","OA_place":"publisher","date_published":"2024-09-10T00:00:00Z"},{"date_published":"2024-11-11T00:00:00Z","OA_place":"publisher","day":"11","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"has_accepted_license":"1","keyword":["Sex chromosomes","evolution","selection","sheltering"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","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)"},"oa":1,"doi":"10.15479/at:ista:18531","file_date_updated":"2025-05-11T22:30:04Z","type":"dissertation","author":[{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"}],"month":"11","ddc":["576"],"date_updated":"2026-04-07T13:22:45Z","publication_status":"published","title":"Early stages of sex chromosome evolution","file":[{"file_name":"AMrnjavac_thesis_library.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"amrnjava","title":"Early stages of sex chromosome evolution","file_id":"18551","date_updated":"2025-05-11T22:30:04Z","date_created":"2024-11-13T12:15:28Z","embargo_to":"open_access","checksum":"3e48b163c22114ef5d5371f758668289","file_size":26870629},{"file_size":4228766,"checksum":"3ead60c1b678e7dcf018043aef3b5db2","date_created":"2024-11-13T12:15:54Z","date_updated":"2025-05-11T22:30:04Z","file_id":"18552","creator":"amrnjava","title":"Early stages of sex chromosome evolution","relation":"main_file","embargo":"2025-05-11","access_level":"open_access","content_type":"application/pdf","file_name":"AMrnjavac_thesis_library.pdf"}],"status":"public","_id":"18531","language":[{"iso":"eng"}],"OA_embargo":"6","oa_version":"Published Version","date_created":"2024-11-11T08:40:45Z","related_material":{"record":[{"id":"12521","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18549","status":"public"}]},"year":"2024","abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"page":"181"},{"day":"17","OA_place":"publisher","date_published":"2024-12-17T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"AnSa"}],"citation":{"mla":"Santana de Freitas Amaral, Miguel. <i>Archaeal Membranes : In Silico Modelling and Design</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>.","ista":"Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.","chicago":"Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>.","ieee":"M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.","apa":"Santana de Freitas Amaral, M. (2024). <i>Archaeal membranes : In silico modelling and design</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18661\">https://doi.org/10.15479/at:ista:18661</a>","ama":"Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18661\">10.15479/at:ista:18661</a>","short":"M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-046-6"],"issn":["2663-337X"]},"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/","has_accepted_license":"1","corr_author":"1","type":"dissertation","file_date_updated":"2025-06-18T22:30:03Z","doi":"10.15479/at:ista:18661","oa":1,"publication_status":"published","date_updated":"2026-04-07T13:22:29Z","ddc":["572","530"],"author":[{"last_name":"Santana de Freitas Amaral","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel"}],"month":"12","language":[{"iso":"eng"}],"_id":"18661","file":[{"access_level":"closed","content_type":"application/zip","relation":"source_file","file_name":"2024_msfa_thesis.zip","creator":"mamaral","file_id":"18671","date_created":"2024-12-18T12:27:01Z","embargo_to":"open_access","date_updated":"2025-06-18T22:30:03Z","file_size":19161387,"checksum":"eca06497a29078558395455c890a32d9"},{"date_updated":"2025-06-18T22:30:03Z","date_created":"2024-12-18T12:26:30Z","file_size":16530084,"checksum":"2dc30ea46c5daf48d07e4cccb3c3de00","file_name":"2024_msfa_thesis.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2025-06-18","file_id":"18672","creator":"mamaral"}],"status":"public","title":"Archaeal membranes : In silico modelling and design","date_created":"2024-12-16T10:53:39Z","related_material":{"record":[{"status":"public","id":"18670","relation":"part_of_dissertation"}]},"oa_version":"Published Version","page":"57","abstract":[{"lang":"eng","text":"Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n"}],"year":"2024"},{"abstract":[{"lang":"eng","text":"We introduce a new all-electric platform, that strong couples light to mechanical motion\r\nby ensuring that the external environmental coupling dominates over internal mechanical\r\ndissipation. The system only has three everyday components: AC, DC, and a fip-chip, in which\r\na metallized silicon nitride membrane is fipped on top of the device under test. This everyday\r\nelectromechanical device can be operated at low or room temperature and has 10000× lower\r\ninsertion loss than a comparable commercial quartz crystal, achieves a position imprecision\r\nmatching state-of-the-art optical interferometer, and enables remote cooling of mechanical\r\nmotion. The spatial properties of higher order mechanical modes are a promising feature for\r\nreconstructing unknown charge distributions.\r\n"}],"page":"63","year":"2024","project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"_id":"62843413-2b32-11ec-9570-c4ec6eabfae7","name":"Surface Charge and Tunneling Multi-Mode Imaging","grant_number":"26088"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18143","status":"public"}]},"date_created":"2024-09-20T12:13:30Z","oa_version":"Published Version","_id":"18104","language":[{"iso":"eng"}],"file":[{"relation":"main_file","embargo":"2025-05-20","content_type":"application/pdf","access_level":"open_access","file_name":"PhD_DPuglia_Final.pdf","file_id":"18105","creator":"cchlebak","date_created":"2024-09-20T12:07:48Z","date_updated":"2025-05-20T22:30:05Z","file_size":10778238,"checksum":"7969263451b2356bfa0924725aa9de10"},{"date_created":"2024-09-20T12:13:09Z","embargo_to":"open_access","date_updated":"2025-05-20T22:30:05Z","checksum":"98dfe7675775e30efffa03f7ff7c091b","file_size":385419748,"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"PhD_DPuglia_Thesis.zip","file_id":"18106","creator":"cchlebak"}],"status":"public","title":"Everyday electromechanics: Capacitive strong coupling to mechanical motion","ddc":["530"],"publication_status":"published","date_updated":"2026-04-07T13:22:10Z","author":[{"full_name":"Puglia, Denise","first_name":"Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia"}],"month":"09","type":"dissertation","file_date_updated":"2025-05-20T22:30:05Z","oa":1,"doi":"10.15479/at:ista:18104","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ista":"Puglia D. 2024. Everyday electromechanics: Capacitive strong coupling to mechanical motion. Institute of Science and Technology Austria.","chicago":"Puglia, Denise. “Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>.","apa":"Puglia, D. (2024). <i>Everyday electromechanics: Capacitive strong coupling to mechanical motion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18104\">https://doi.org/10.15479/at:ista:18104</a>","ieee":"D. Puglia, “Everyday electromechanics: Capacitive strong coupling to mechanical motion,” Institute of Science and Technology Austria, 2024.","mla":"Puglia, Denise. <i>Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>.","short":"D. Puglia, Everyday Electromechanics: Capacitive Strong Coupling to Mechanical Motion, Institute of Science and Technology Austria, 2024.","ama":"Puglia D. Everyday electromechanics: Capacitive strong coupling to mechanical motion. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18104\">10.15479/at:ista:18104</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"}],"day":"20","date_published":"2024-09-20T00:00:00Z","OA_place":"publisher"},{"date_updated":"2026-04-07T13:23:06Z","publication_status":"published","ddc":["576"],"author":[{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","last_name":"Machnik","first_name":"Nick N","orcid":"0000-0001-6617-9742","full_name":"Machnik, Nick N"}],"month":"12","language":[{"iso":"eng"}],"_id":"18642","title":"Algorithms for causal learning and comparative analysis for genomic data","status":"public","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2025-06-12","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","file_id":"18649","creator":"nmachnik","date_created":"2024-12-11T11:59:54Z","date_updated":"2025-06-12T22:30:02Z","file_size":12845009,"checksum":"d45e4d170f9a70a1f69b44b99bd058e4"},{"file_id":"18650","creator":"nmachnik","file_name":"thesis.zip","relation":"source_file","content_type":"application/zip","access_level":"closed","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","file_size":14189810,"date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-11T11:59:34Z","embargo_to":"open_access"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18648","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8707"}]},"date_created":"2024-12-10T13:49:15Z","oa_version":"Published Version","page":"138","abstract":[{"text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n","lang":"eng"}],"project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"year":"2024","day":"11","OA_place":"publisher","date_published":"2024-12-11T00:00:00Z","degree_awarded":"PhD","citation":{"mla":"Machnik, Nick N. <i>Algorithms for Causal Learning and Comparative Analysis for Genomic Data</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>.","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","apa":"Machnik, N. N. (2024). <i>Algorithms for causal learning and comparative analysis for genomic data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024."},"department":[{"_id":"GradSch"},{"_id":"MaRo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","corr_author":"1","file_date_updated":"2025-06-12T22:30:02Z","type":"dissertation","doi":"10.15479/at:ista:18642","oa":1},{"author":[{"full_name":"Gupta, Divyansh","first_name":"Divyansh","orcid":"0000-0001-7400-6665","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"}],"month":"11","ddc":["573"],"publication_status":"published","date_updated":"2026-04-07T13:24:48Z","status":"public","file":[{"file_name":"PhD Thesis - Divyansh Gupta.zip","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"18589","creator":"dgupta","date_updated":"2025-11-11T23:30:02Z","embargo_to":"open_access","date_created":"2024-11-25T14:44:03Z","checksum":"ebb000d361c36b22ed6e639a931c6b7c","file_size":75512262},{"checksum":"1282401eb71598bc311058b0fcefc6a1","file_size":6412619,"date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-26T11:43:19Z","file_id":"18591","creator":"dgupta","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","relation":"main_file","access_level":"open_access","embargo":"2025-11-11","content_type":"application/pdf"}],"title":"Visual adaptations to natural statistics","_id":"18574","OA_embargo":"12","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"12349","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","id":"12370","status":"public"}]},"date_created":"2024-11-20T21:30:44Z","year":"2024","project":[{"_id":"bdaf81a8-d553-11ed-ba76-c95961984540","name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","grant_number":"101086580"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n","lang":"eng"}],"page":"86","date_published":"2024-11-22T00:00:00Z","OA_place":"publisher","day":"22","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"article_processing_charge":"No","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>"},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"corr_author":"1","acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","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"},"oa":1,"doi":"10.15479/at:ista:18574","type":"dissertation","file_date_updated":"2025-11-11T23:30:02Z"},{"OA_place":"publisher","date_published":"2024-10-28T00:00:00Z","day":"28","article_processing_charge":"No","supervisor":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-044-2"]},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"corr_author":"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"},"has_accepted_license":"1","doi":"10.15479/at:ista:18471","oa":1,"file_date_updated":"2025-05-05T22:30:04Z","type":"dissertation","month":"10","author":[{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie"}],"date_updated":"2026-04-14T08:34:37Z","publication_status":"published","ddc":["570"],"title":"Visualizing the neuronal transcriptional landscape with tissue context","file":[{"file_size":183077763,"checksum":"6d7c7725d040d8debc070dcb35ac965d","embargo_to":"open_access","date_created":"2024-10-26T22:29:06Z","date_updated":"2025-05-05T22:30:04Z","file_id":"18475","creator":"nagudelo","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx"},{"creator":"nagudelo","file_id":"18476","access_level":"open_access","content_type":"application/pdf","embargo":"2025-05-05","relation":"main_file","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","file_size":47027710,"checksum":"52f9c0bf2bdafa3baf827b73814a53ff","date_created":"2024-10-26T23:13:33Z","date_updated":"2025-05-05T22:30:04Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"18471","oa_version":"Published Version","date_created":"2024-10-26T20:02:42Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"}],"year":"2024","page":"97","abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"ec_funded":1},{"project":[{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention","call_identifier":"H2020"}],"year":"2023","abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"ec_funded":1,"page":"178","oa_version":"Published Version","date_created":"2023-03-08T15:19:45Z","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","status":"public","file":[{"file_name":"Burnett_Thesis_2023.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"lburnett","file_id":"12717","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_size":23029260},{"file_name":"Burnett_Thesis_2023_pdfA.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"12718","creator":"lburnett","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","success":1,"file_size":11959869,"checksum":"cebc77705288bf4382db9b3541483cd0"}],"_id":"12716","language":[{"iso":"eng"}],"author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","first_name":"Laura","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura"}],"month":"03","ddc":["599","573"],"date_updated":"2026-04-07T13:25:15Z","publication_status":"published","oa":1,"doi":"10.15479/at:ista:12716","file_date_updated":"2023-03-08T15:08:46Z","type":"dissertation","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"corr_author":"1","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>.","apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2023-03-10T00:00:00Z","OA_place":"publisher","day":"10"},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13264"},{"id":"10851","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-11-17T13:45:26Z","year":"2023","abstract":[{"text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.","lang":"eng"}],"page":"80","author":[{"last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T","first_name":"Duc T"}],"month":"11","ddc":["530"],"publication_status":"published","date_updated":"2026-04-07T13:25:52Z","file":[{"checksum":"db0c37d213bc002125bd59690e9db246","file_size":34828019,"date_created":"2023-11-17T13:36:44Z","date_updated":"2023-11-22T09:46:06Z","file_id":"14548","creator":"pduc","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Phan_Thesis_pdfa.pdf"},{"file_name":"dissertation_src.zip","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"14549","creator":"pduc","date_updated":"2023-11-17T13:47:54Z","date_created":"2023-11-17T13:44:53Z","file_size":279319709,"checksum":"8d3bd6afa279a0078ffd13e06bb6d56d"}],"status":"public","title":"Resonant microwave spectroscopy of Al-InAs","_id":"14547","language":[{"iso":"eng"}],"corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"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"},"keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"oa":1,"doi":"10.15479/14547","type":"dissertation","file_date_updated":"2023-11-22T09:46:06Z","date_published":"2023-11-16T00:00:00Z","OA_place":"publisher","day":"16","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","mla":"Phan, Duc T. <i>Resonant Microwave Spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14547\">10.15479/14547</a>.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","apa":"Phan, D. T. (2023). <i>Resonant microwave spectroscopy of Al-InAs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14547\">https://doi.org/10.15479/14547</a>.","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"AnHi"}],"degree_awarded":"PhD"},{"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"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"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"alternative_title":["ISTA Thesis"],"citation":{"apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>"},"degree_awarded":"PhD","date_published":"2023-08-15T00:00:00Z","OA_place":"publisher","day":"15","oa":1,"doi":"10.15479/at:ista:14058","type":"dissertation","file_date_updated":"2023-08-18T10:47:55Z","corr_author":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","file":[{"access_level":"closed","content_type":"application/zip","relation":"source_file","file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","file_id":"14075","date_created":"2023-08-16T18:15:17Z","date_updated":"2023-08-17T06:55:24Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_size":10891454},{"creator":"gpuixeus","file_id":"14079","file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":19856686,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_updated":"2023-08-18T10:47:55Z","success":1,"date_created":"2023-08-18T10:47:55Z"}],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","_id":"14058","language":[{"iso":"eng"}],"author":[{"last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"}],"month":"08","ddc":["576"],"publication_status":"published","date_updated":"2026-04-07T13:25:34Z","year":"2023","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"page":"230","oa_version":"Published Version","date_created":"2023-08-15T10:20:40Z","related_material":{"record":[{"relation":"research_data","id":"9803","status":"public"},{"status":"public","id":"12933","relation":"research_data"},{"relation":"part_of_dissertation","id":"6831","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14077"}]}},{"_id":"12885","language":[{"iso":"eng"}],"status":"public","file":[{"date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z","checksum":"9347b0e09425f56fdcede5d3528404dc","file_size":99627036,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Calcabrini.docx","creator":"mcalcabr","file_id":"12887"},{"checksum":"2d188b76621086cd384f0b9264b0a576","file_size":8742220,"date_updated":"2023-05-02T07:42:45Z","date_created":"2023-05-02T07:42:45Z","success":1,"creator":"mcalcabr","file_id":"12888","file_name":"Thesis_Calcabrini_pdfa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","ddc":["546","541"],"publication_status":"published","date_updated":"2026-04-07T13:26:14Z","author":[{"last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","full_name":"Calcabrini, Mariano"}],"month":"04","ec_funded":1,"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"page":"82","year":"2023","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_created":"2023-05-02T07:58:57Z","related_material":{"record":[{"status":"public","id":"12237","relation":"part_of_dissertation"},{"status":"public","id":"10806","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10123","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10042"},{"status":"public","relation":"part_of_dissertation","id":"9118"}]},"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-028-2"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria"}],"article_processing_charge":"No","day":"28","date_published":"2023-04-28T00:00:00Z","OA_place":"publisher","type":"dissertation","file_date_updated":"2023-05-02T07:43:18Z","oa":1,"doi":"10.15479/at:ista:12885","has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}]},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"12750","relation":"part_of_dissertation"},{"id":"11470","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8308"},{"id":"11469","relation":"part_of_dissertation","status":"public"}]},"date_created":"2023-03-17T13:30:48Z","year":"2023","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"page":"158","ec_funded":1,"abstract":[{"lang":"eng","text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings."}],"author":[{"full_name":"Brighi, Pietro","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi"}],"month":"03","publication_status":"published","date_updated":"2026-04-07T13:26:32Z","ddc":["530"],"file":[{"date_updated":"2023-03-23T16:42:56Z","date_created":"2023-03-23T16:42:56Z","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_size":42167561,"file_name":"Thesis_sub_PBrighi.zip","access_level":"closed","content_type":"application/zip","relation":"source_file","creator":"pbrighi","file_id":"12753"},{"file_id":"12754","creator":"pbrighi","file_name":"Thesis_PBrighi.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7caa153d4a5b0873a79358787d2dfe1e","file_size":13977000,"date_updated":"2023-03-23T16:43:14Z","date_created":"2023-03-23T16:43:14Z","success":1}],"status":"public","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","language":[{"iso":"eng"}],"_id":"12732","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","doi":"10.15479/at:ista:12732","oa":1,"type":"dissertation","file_date_updated":"2023-03-23T16:43:14Z","OA_place":"publisher","date_published":"2023-03-21T00:00:00Z","day":"21","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","apa":"Brighi, P. (2023). <i>Ergodicity breaking in disordered and kinetically constrained quantum many-body systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>.","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","mla":"Brighi, Pietro. <i>Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>."}},{"oa_version":"Published Version","date_created":"2023-04-14T14:56:04Z","year":"2023","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"page":"106","abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"ec_funded":1,"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria"}],"month":"04","publication_status":"published","date_updated":"2026-04-07T13:26:49Z","ddc":["570","571"],"file":[{"creator":"vpokusae","file_id":"12857","file_name":"Thesis_Pokusaeva.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"5f589a9af025f7eeebfd0c186209913e","file_size":14507243,"date_updated":"2023-04-20T09:26:51Z","date_created":"2023-04-20T09:14:38Z"},{"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","file_size":10090711,"date_updated":"2023-04-20T09:14:44Z","date_created":"2023-04-20T09:14:44Z","success":1,"creator":"vpokusae","file_id":"12858","file_name":"Thesis_Pokusaeva.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"status":"public","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","language":[{"iso":"eng"}],"_id":"12826","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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"},"has_accepted_license":"1","doi":"10.15479/at:ista:12826","oa":1,"type":"dissertation","file_date_updated":"2023-04-20T09:26:51Z","OA_place":"publisher","date_published":"2023-04-18T00:00:00Z","day":"18","supervisor":[{"full_name":"Jösch, Maximilian A","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"citation":{"ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. <i>Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","apa":"Pokusaeva, V. (2023). <i>Neural control of optic flow-based navigation in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"article_processing_charge":"No","supervisor":[{"first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Valentini, Marco. <i>Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>.","apa":"Valentini, M. (2023). <i>Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>.","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2023-07-21T00:00:00Z","day":"21","doi":"10.15479/at:ista:13286","oa":1,"file_date_updated":"2023-08-11T14:39:17Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"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","title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","file":[{"date_created":"2023-08-11T09:27:39Z","date_updated":"2023-08-11T10:01:34Z","checksum":"666ee31c7eade89679806287c062fa14","file_size":56121429,"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_name":"PhD_thesis_Valentini_final.zip","creator":"mvalenti","file_id":"14033"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"PhD_thesis_Valentini_final_validated.pdf","file_id":"14035","creator":"mvalenti","date_created":"2023-08-11T14:39:17Z","date_updated":"2023-08-11T14:39:17Z","file_size":38199711,"checksum":"0992f2ebef152dee8e70055350ebbb55"}],"status":"public","language":[{"iso":"eng"}],"_id":"13286","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco","first_name":"Marco"}],"month":"07","date_updated":"2026-04-07T13:27:22Z","publication_status":"published","ddc":["530"],"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","grant_number":"862046"},{"grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors"}],"year":"2023","page":"184","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"12522"},{"status":"public","relation":"part_of_dissertation","id":"13312"},{"relation":"part_of_dissertation","id":"12118","status":"public"},{"status":"public","id":"8910","relation":"part_of_dissertation"}]},"date_created":"2023-07-24T14:10:45Z"},{"date_published":"2023-09-30T00:00:00Z","OA_place":"publisher","day":"30","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Roos, Barbara. <i>Boundary Superconductivity in BCS Theory</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>.","ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","apa":"Roos, B. (2023). <i>Boundary superconductivity in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"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:14374","type":"dissertation","file_date_updated":"2023-10-06T11:38:01Z","month":"09","author":[{"last_name":"Roos","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","first_name":"Barbara"}],"ddc":["515","539"],"publication_status":"published","date_updated":"2026-04-07T13:27:39Z","file":[{"date_updated":"2023-10-06T11:35:56Z","date_created":"2023-10-06T11:35:56Z","file_size":2365702,"checksum":"ef039ffc3de2cb8dee5b14110938e9b6","file_name":"phd-thesis-draft_pdfa_acrobat.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"broos","file_id":"14398"},{"date_created":"2023-10-06T11:38:01Z","date_updated":"2023-10-06T11:38:01Z","file_size":4691734,"checksum":"81dcac33daeefaf0111db52f41bb1fd0","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"Version5.zip","file_id":"14399","creator":"broos"}],"status":"public","title":"Boundary superconductivity in BCS theory","_id":"14374","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2023-09-28T14:23:04Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"10850","status":"public"},{"status":"public","id":"13207","relation":"part_of_dissertation"}]},"year":"2023","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"},{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap  in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}],"ec_funded":1,"page":"206"},{"OA_place":"publisher","date_published":"2023-11-15T00:00:00Z","day":"15","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-036-7"]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","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"},"doi":"10.15479/14539","oa":1,"file_date_updated":"2023-11-15T13:44:24Z","type":"dissertation","author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","orcid":"0000-0002-4681-1699"}],"month":"11","date_updated":"2026-04-07T13:27:56Z","publication_status":"published","ddc":["000"],"title":"Automated verification and control of infinite state stochastic systems","status":"public","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"main.pdf","file_id":"14540","creator":"cchlebak","date_created":"2023-11-15T13:43:28Z","success":1,"date_updated":"2023-11-15T13:43:28Z","file_size":2116426,"checksum":"f23e002b0059ca78e1fbb864da52dd7e"},{"creator":"cchlebak","file_id":"14541","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_size":35884057,"checksum":"80ca37618a3c7b59866875f8be9b15ed","date_updated":"2023-11-15T13:44:24Z","date_created":"2023-11-15T13:44:24Z"}],"language":[{"iso":"eng"}],"_id":"14539","oa_version":"Published Version","related_material":{"record":[{"id":"10414","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12000"},{"relation":"part_of_dissertation","id":"9644","status":"public"},{"id":"12511","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14600"},{"relation":"part_of_dissertation","id":"14601","status":"public"},{"status":"public","id":"1194","relation":"part_of_dissertation"}]},"date_created":"2023-11-15T13:39:10Z","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2023","page":"256","ec_funded":1,"abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}]},{"doi":"10.15479/at:ista:14587","oa":1,"type":"dissertation","file_date_updated":"2024-03-20T12:28:32Z","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"},"acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","has_accepted_license":"1","supervisor":[{"last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","full_name":"Fischer, Julian L"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Marveggio, Alice. <i>Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>.","apa":"Marveggio, A. (2023). <i>Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14587\">https://doi.org/10.15479/at:ista:14587</a>","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14587\">10.15479/at:ista:14587</a>","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"JuFi"}],"OA_place":"publisher","date_published":"2023-11-21T00:00:00Z","day":"21","year":"2023","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","call_identifier":"H2020"}],"page":"228","ec_funded":1,"abstract":[{"text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-11-21T11:41:05Z","related_material":{"record":[{"id":"11842","relation":"part_of_dissertation","status":"public"},{"id":"14597","relation":"part_of_dissertation","status":"public"}]},"file":[{"file_size":2881100,"checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","date_created":"2023-11-29T09:09:31Z","success":1,"date_updated":"2023-11-29T09:09:31Z","creator":"amarvegg","file_id":"14626","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"thesis_Marveggio.pdf"},{"relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis_Marveggio.zip","file_id":"14627","creator":"amarvegg","date_created":"2023-11-29T09:10:19Z","date_updated":"2024-03-20T12:28:32Z","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","file_size":10189696}],"status":"public","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","language":[{"iso":"eng"}],"_id":"14587","month":"11","author":[{"id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice","first_name":"Alice"}],"publication_status":"published","date_updated":"2026-04-07T13:28:13Z","ddc":["515"]}]