--- _id: '14711' abstract: - lang: eng text: "In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management." acknowledged_ssus: - _id: SSU alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 citation: ama: Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711 apa: Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711 chicago: Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711. ieee: O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024. ista: Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. mla: Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711. short: O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024. date_created: 2023-12-26T22:49:53Z date_published: 2024-01-19T00:00:00Z date_updated: 2024-01-26T12:00:54Z day: '19' ddc: - '576' degree_awarded: PhD department: - _id: NiBa - _id: GradSch doi: 10.15479/at:ista:14711 ec_funded: 1 file: - access_level: closed checksum: de179b1c6758f182ff0c70d8b38c1501 content_type: application/zip creator: oolusany date_created: 2024-01-03T18:30:13Z date_updated: 2024-01-03T18:30:13Z file_id: '14730' file_name: FinalSubmission_Thesis_OLUSANYA.zip file_size: 16986244 relation: source_file - access_level: open_access checksum: 0e331585e3cd4823320aab4e69e64ccf content_type: application/pdf creator: oolusany date_created: 2024-01-03T18:31:34Z date_updated: 2024-01-03T18:31:34Z file_id: '14731' file_name: FinalSubmission2_Thesis_OLUSANYA.pdf file_size: 6460403 relation: main_file success: 1 file_date_updated: 2024-01-03T18:31:34Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '183' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6 grant_number: '26380' name: Polygenic Adaptation in a Metapopulation publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10658' relation: part_of_dissertation status: public - id: '10787' relation: part_of_dissertation status: public - id: '14732' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jitka full_name: Polechova, Jitka last_name: Polechova - first_name: Himani full_name: Sachdeva, Himani last_name: Sachdeva title: Local adaptation, genetic load and extinction in metapopulations tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- _id: '14821' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Heloisa full_name: Chiossi, Heloisa id: 2BBA502C-F248-11E8-B48F-1D18A9856A87 last_name: Chiossi citation: ama: Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821 apa: Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821 chicago: Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821. ieee: H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024. ista: Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. mla: Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821. short: H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024. date_created: 2024-01-16T14:25:21Z date_published: 2024-01-19T00:00:00Z date_updated: 2024-02-01T09:50:29Z day: '19' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:14821 ec_funded: 1 file: - access_level: closed checksum: d3fa3de1abd5af5204c13e9d55375615 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchiossi date_created: 2024-01-19T11:04:05Z date_updated: 2024-01-19T11:04:05Z file_id: '14838' file_name: PhD_Thesis_190124.docx file_size: 8656268 relation: source_file - access_level: closed checksum: 13adc8dcfb5b6b18107f89f0a98fa8bd content_type: application/pdf creator: hchiossi date_created: 2024-01-19T11:03:59Z date_updated: 2024-01-19T11:03:59Z embargo: 2025-01-19 embargo_to: open_access file_id: '14839' file_name: PhD_Thesis_190124.pdf file_size: 6567275 relation: main_file file_date_updated: 2024-01-19T11:04:05Z has_accepted_license: '1' language: - iso: eng month: '01' oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Adaptive hierarchical representations in the hippocampus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- _id: '15020' abstract: - lang: eng text: "This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik citation: ama: Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020 apa: Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020 chicago: Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020. ieee: M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024. ista: Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria. mla: Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020. short: M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024. date_created: 2024-02-23T14:02:04Z date_published: 2024-02-23T00:00:00Z date_updated: 2024-03-06T14:22:52Z day: '23' ddc: - '576' - '519' degree_awarded: PhD department: - _id: GradSch - _id: NiBa - _id: GaTk doi: 10.15479/at:ista:15020 ec_funded: 1 file: - access_level: open_access checksum: b2d3da47c98d481577a4baf68944fe41 content_type: application/pdf creator: mhledik date_created: 2024-02-23T13:50:53Z date_updated: 2024-02-23T13:50:53Z file_id: '15021' file_name: hledik thesis pdfa 2b.pdf file_size: 7102089 relation: main_file success: 1 - access_level: closed checksum: eda9b9430da2610fee7ce1c1419a479a content_type: application/zip creator: mhledik date_created: 2024-02-23T13:50:54Z date_updated: 2024-02-23T14:20:16Z file_id: '15022' file_name: hledik thesis source.zip file_size: 14014790 relation: source_file file_date_updated: 2024-02-23T14:20:16Z has_accepted_license: '1' keyword: - Theoretical biology - Optimality - Evolution - Information language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '158' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7553' relation: part_of_dissertation status: public - id: '12081' relation: part_of_dissertation status: public - id: '7606' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 title: Genetic information and biological optimization type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- _id: '15101' acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101 apa: 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. https://doi.org/10.15479/at:ista:15101 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. https://doi.org/10.15479/at:ista:15101. 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. mla: 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, doi:10.15479/at:ista:15101. 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. date_created: 2024-03-11T10:09:54Z date_published: 2024-03-11T00:00:00Z date_updated: 2024-03-14T13:14:19Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: PeJo doi: 10.15479/at:ista:15101 ec_funded: 1 file: - access_level: closed checksum: db4947474ffa271e66c254b6fe876a55 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jchen date_created: 2024-03-11T14:10:58Z date_updated: 2024-03-12T07:12:17Z file_id: '15104' file_name: Thesis_Jingjing CHEN.docx file_size: 11271363 relation: source_file - access_level: closed checksum: a5eeae8b5702cd540f5d03469bc33dde content_type: application/pdf creator: jchen date_created: 2024-03-11T14:11:06Z date_updated: 2024-03-11T14:11:06Z embargo: 2024-04-01 embargo_to: open_access file_id: '15105' file_name: Thesis_Jingjing CHEN_merged.pdf file_size: 16627311 relation: main_file file_date_updated: 2024-03-12T07:12:17Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: Published Version page: '84' project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14843' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- _id: '15094' abstract: - lang: eng text: "Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastiano full_name: Cultrera di Montesano, Sebastiano id: 34D2A09C-F248-11E8-B48F-1D18A9856A87 last_name: Cultrera di Montesano orcid: 0000-0001-6249-0832 citation: ama: Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094 apa: Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094 chicago: Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094. ieee: S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024. ista: Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. mla: Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094. short: S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024. date_created: 2024-03-08T15:28:10Z date_published: 2024-03-08T00:00:00Z date_updated: 2024-03-20T09:36:57Z day: '08' ddc: - '514' - '500' - '516' degree_awarded: PhD department: - _id: GradSch - _id: HeEd doi: 10.15479/at:ista:15094 ec_funded: 1 file: - access_level: open_access checksum: 1e468bfa42a7dcf04d89f4dadc621c87 content_type: application/pdf creator: scultrer date_created: 2024-03-14T08:55:07Z date_updated: 2024-03-14T08:55:07Z file_id: '15112' file_name: Thesis Sebastiano.pdf file_size: 4106872 relation: main_file success: 1 - access_level: closed checksum: bcbd213490f5a7e68855a092bbce93f1 content_type: application/zip creator: scultrer date_created: 2024-03-14T08:56:24Z date_updated: 2024-03-14T14:14:35Z file_id: '15113' file_name: Thesis (1).zip file_size: 4746234 relation: source_file file_date_updated: 2024-03-14T14:14:35Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '108' project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize - _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316 grant_number: I4887 name: Discretization in Geometry and Dynamics - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11660' relation: part_of_dissertation status: public - id: '11658' relation: part_of_dissertation status: public - id: '13182' relation: part_of_dissertation status: public - id: '15090' relation: part_of_dissertation status: public - id: '15091' relation: part_of_dissertation status: public - id: '15093' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Persistence and Morse theory for discrete geometric structures tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- _id: '12716' abstract: - lang: eng 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." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: LifeSc - _id: M-Shop - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X 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:10.15479/at:ista:12716 apa: 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. https://doi.org/10.15479/at:ista:12716 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. https://doi.org/10.15479/at:ista:12716. 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. mla: 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, doi:10.15479/at:ista:12716. 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. date_created: 2023-03-08T15:19:45Z date_published: 2023-03-10T00:00:00Z date_updated: 2023-04-05T10:59:04Z day: '10' ddc: - '599' - '573' degree_awarded: PhD department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:12716 ec_funded: 1 file: - access_level: closed checksum: 6c6d9cc2c4cdacb74e6b1047a34d7332 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lburnett date_created: 2023-03-08T15:08:46Z date_updated: 2023-03-08T15:08:46Z file_id: '12717' file_name: Burnett_Thesis_2023.docx file_size: 23029260 relation: source_file - access_level: open_access checksum: cebc77705288bf4382db9b3541483cd0 content_type: application/pdf creator: lburnett date_created: 2023-03-08T15:08:46Z date_updated: 2023-03-08T15:08:46Z file_id: '12718' file_name: Burnett_Thesis_2023_pdfA.pdf file_size: 11959869 relation: main_file success: 1 file_date_updated: 2023-03-08T15:08:46Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '178' project: - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 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 type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12809' abstract: - lang: eng text: "Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. " acknowledged_ssus: - _id: EM-Fac - _id: Bio - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Catarina full_name: Alcarva, Catarina id: 3A96634C-F248-11E8-B48F-1D18A9856A87 last_name: Alcarva citation: ama: 'Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809' apa: 'Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809' chicago: 'Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.' ieee: 'C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.' ista: 'Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.' mla: 'Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.' short: 'C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.' date_created: 2023-04-06T07:54:09Z date_published: 2023-04-06T00:00:00Z date_updated: 2023-04-26T12:16:56Z day: '06' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: RySh doi: 10.15479/at:ista:12809 file: - access_level: closed checksum: 35b5997d2b0acb461f9d33d073da0df5 content_type: application/pdf creator: cchlebak date_created: 2023-04-07T06:16:06Z date_updated: 2023-04-07T06:16:06Z embargo: 2024-04-07 embargo_to: open_access file_id: '12814' file_name: Thesis_CatarinaAlcarva_final pdfA.pdf file_size: 9881969 relation: main_file - access_level: closed checksum: 81198f63c294890f6d58e8b29782efdc content_type: application/pdf creator: cchlebak date_created: 2023-04-07T06:17:11Z date_updated: 2023-04-07T06:17:11Z file_id: '12815' file_name: Thesis_CatarinaAlcarva_final_for printing.pdf file_size: 44201583 relation: source_file - access_level: closed checksum: 0317bf7f457bb585f99d453ffa69eb53 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-04-07T06:18:05Z date_updated: 2023-04-07T06:18:05Z file_id: '12816' file_name: Thesis_CatarinaAlcarva_final.docx file_size: 84731244 relation: source_file file_date_updated: 2023-04-07T06:18:05Z has_accepted_license: '1' language: - iso: eng month: '04' oa_version: Published Version page: '115' project: - _id: 267DFB90-B435-11E9-9278-68D0E5697425 name: 'Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 title: 'Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12826' abstract: - lang: eng 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." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X citation: ama: Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826 apa: Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826 chicago: Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826. ieee: V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023. ista: Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. mla: Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826. short: V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023. date_created: 2023-04-14T14:56:04Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-06-23T09:47:36Z day: '18' ddc: - '570' - '571' degree_awarded: PhD department: - _id: MaJö - _id: GradSch doi: 10.15479/at:ista:12826 ec_funded: 1 file: - access_level: closed checksum: 5f589a9af025f7eeebfd0c186209913e content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vpokusae date_created: 2023-04-20T09:14:38Z date_updated: 2023-04-20T09:26:51Z file_id: '12857' file_name: Thesis_Pokusaeva.docx file_size: 14507243 relation: source_file - access_level: open_access checksum: bbeed76db45a996b4c91a9abe12ce0ec content_type: application/pdf creator: vpokusae date_created: 2023-04-20T09:14:44Z date_updated: 2023-04-20T09:14:44Z file_id: '12858' file_name: Thesis_Pokusaeva.pdf file_size: 10090711 relation: main_file success: 1 file_date_updated: 2023-04-20T09:26:51Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '106' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Neural control of optic flow-based navigation in Drosophila melanogaster tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12781' abstract: - lang: eng text: "Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n" acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vladyslav full_name: Kravchuk, Vladyslav id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87 last_name: Kravchuk citation: ama: Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781 apa: Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781 chicago: Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781. ieee: V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023. ista: Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. mla: Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781. short: V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023. date_created: 2023-03-31T12:24:42Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-08-04T08:54:51Z day: '23' ddc: - '570' - '572' degree_awarded: PhD department: - _id: GradSch - _id: LeSa doi: 10.15479/at:ista:12781 ec_funded: 1 file: - access_level: closed checksum: 5ebb6345cb4119f93460c81310265a6d content_type: application/pdf creator: vkravchu date_created: 2023-04-19T14:33:41Z date_updated: 2023-04-19T14:33:41Z embargo: 2024-04-20 embargo_to: local file_id: '12852' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf file_size: 6071553 relation: main_file - access_level: closed checksum: c12055c48411d030d2afa51de2166221 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vkravchu date_created: 2023-04-19T14:33:52Z date_updated: 2023-04-20T07:02:59Z embargo: 2024-04-20 embargo_to: local file_id: '12853' file_name: VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx file_size: 19468766 relation: source_file file_date_updated: 2023-04-20T07:02:59Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: Published Version page: '127' project: - _id: 238A0A5A-32DE-11EA-91FC-C7463DDC885E grant_number: '25541' name: 'Structural characterization of E. coli complex I: an important mechanistic model' - _id: 627abdeb-2b32-11ec-9570-ec31a97243d3 call_identifier: H2020 grant_number: '101020697' name: Structure and mechanism of respiratory chain molecular machines publication_identifier: isbn: - 978-3-99078-029-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12138' relation: part_of_dissertation status: public status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13074' abstract: - lang: eng text: "Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elena-Alexandra full_name: Peste, Elena-Alexandra id: 32D78294-F248-11E8-B48F-1D18A9856A87 last_name: Peste citation: ama: Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074 apa: Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074 chicago: Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074. ieee: E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023. ista: Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. mla: Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074. short: E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T17:07:53Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-08-04T10:33:27Z day: '23' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: ChLa doi: 10.15479/at:ista:13074 ec_funded: 1 file: - access_level: open_access checksum: 6b3354968403cb9d48cc5a83611fb571 content_type: application/pdf creator: epeste date_created: 2023-05-24T16:11:16Z date_updated: 2023-05-24T16:11:16Z file_id: '13087' file_name: PhD_Thesis_Alexandra_Peste_final.pdf file_size: 2152072 relation: main_file success: 1 - access_level: closed checksum: 8d0df94bbcf4db72c991f22503b3fd60 content_type: application/zip creator: epeste date_created: 2023-05-24T16:12:59Z date_updated: 2023-05-24T16:12:59Z file_id: '13088' file_name: PhD_Thesis_APeste.zip file_size: 1658293 relation: source_file file_date_updated: 2023-05-24T16:12:59Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11458' relation: part_of_dissertation status: public - id: '13053' relation: part_of_dissertation status: public - id: '12299' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: Efficiency and generalization of sparse neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12964' abstract: - lang: eng text: "Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Daniel R full_name: Boocock, Daniel R id: 453AF628-F248-11E8-B48F-1D18A9856A87 last_name: Boocock orcid: 0000-0002-1585-2631 citation: ama: Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964 apa: Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964 chicago: Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964. ieee: D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023. ista: Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. mla: Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964. short: D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023. date_created: 2023-05-15T14:52:36Z date_published: 2023-05-17T00:00:00Z date_updated: 2023-08-04T11:02:40Z day: '17' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: EdHa doi: 10.15479/at:ista:12964 ec_funded: 1 file: - access_level: closed checksum: d51240675fc6dc0e3f5dc0c902695d3a content_type: application/pdf creator: dboocock date_created: 2023-05-17T13:39:54Z date_updated: 2023-05-19T07:04:25Z embargo: 2024-05-17 embargo_to: open_access file_id: '12988' file_name: thesis_boocock.pdf file_size: 40414730 relation: main_file - access_level: closed checksum: 581a2313ffeb40fe77e8a122a25a7795 content_type: application/zip creator: dboocock date_created: 2023-05-17T13:39:53Z date_updated: 2023-05-17T14:35:13Z file_id: '12989' file_name: thesis_boocock.zip file_size: 34338567 relation: source_file file_date_updated: 2023-05-19T07:04:25Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '146' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-032-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8602' relation: part_of_dissertation status: public status: public supervisor: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Mechanochemical pattern formation across biological scales tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12885' 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. ' acknowledged_ssus: - _id: EM-Fac - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mariano full_name: Calcabrini, Mariano id: 45D7531A-F248-11E8-B48F-1D18A9856A87 last_name: Calcabrini orcid: 0000-0003-4566-5877 citation: ama: 'Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885' apa: 'Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885' chicago: 'Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.' ieee: 'M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.' ista: 'Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.' mla: 'Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.' short: 'M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-02T07:58:57Z date_published: 2023-04-28T00:00:00Z date_updated: 2023-08-14T07:25:26Z day: '28' ddc: - '546' - '541' degree_awarded: PhD department: - _id: GradSch - _id: MaIb doi: 10.15479/at:ista:12885 ec_funded: 1 file: - access_level: closed checksum: 9347b0e09425f56fdcede5d3528404dc content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mcalcabr date_created: 2023-05-02T07:43:18Z date_updated: 2023-05-02T07:43:18Z file_id: '12887' file_name: Thesis_Calcabrini.docx file_size: 99627036 relation: source_file - access_level: open_access checksum: 2d188b76621086cd384f0b9264b0a576 content_type: application/pdf creator: mcalcabr date_created: 2023-05-02T07:42:45Z date_updated: 2023-05-02T07:42:45Z file_id: '12888' file_name: Thesis_Calcabrini_pdfa.pdf file_size: 8742220 relation: main_file success: 1 file_date_updated: 2023-05-02T07:43:18Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '82' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-028-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10806' relation: part_of_dissertation status: public - id: '10042' relation: part_of_dissertation status: public - id: '12237' relation: part_of_dissertation status: public - id: '9118' relation: part_of_dissertation status: public - id: '10123' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 title: 'Nanoparticle-based semiconductor solids: From synthesis to consolidation' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12891' abstract: - lang: eng text: "The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 citation: ama: 'Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891' apa: 'Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891' chicago: 'Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.' ieee: 'A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.' ista: 'Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.' mla: 'Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.' short: 'A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-05T08:48:20Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-21T06:25:48Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:12891 ec_funded: 1 file: - access_level: closed checksum: 59b0303dc483f40a96a610a90aab7ee9 content_type: application/pdf creator: aschauer date_created: 2023-05-05T13:01:14Z date_updated: 2023-05-05T13:01:14Z embargo: 2024-05-05 embargo_to: open_access file_id: '12907' file_name: Thesis_Schauer_final.pdf file_size: 31434230 relation: main_file - access_level: closed checksum: 25f54e12479b6adaabd129a20568e6c1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: aschauer date_created: 2023-05-05T13:04:15Z date_updated: 2023-05-05T13:04:15Z file_id: '12908' file_name: Thesis_Schauer_final.docx file_size: 43809109 relation: source_file file_date_updated: 2023-05-05T13:04:15Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '190' project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 26B1E39C-B435-11E9-9278-68D0E5697425 grant_number: '25239' name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8966' relation: part_of_dissertation status: public - id: '7888' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: 'Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13175' abstract: - lang: eng text: "About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. " acknowledged_ssus: - _id: M-Shop - _id: SSU - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 citation: ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175 apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175 chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175. ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023. ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria. mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175. short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023. date_created: 2023-06-30T08:07:43Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-24T11:16:35Z day: '05' ddc: - '537' - '535' - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:13175 ec_funded: 1 file: - access_level: open_access checksum: 7d03f1a5a5258ee43dfc3323dea4e08f content_type: application/pdf creator: cchlebak date_created: 2023-06-30T08:17:25Z date_updated: 2023-06-30T08:17:25Z file_id: '13176' file_name: thesis_pdfa.pdf file_size: 18688376 relation: main_file success: 1 - access_level: closed checksum: c3b45317ae58e0527533f98c202d81b7 content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-07-06T11:35:15Z date_updated: 2023-07-06T11:35:15Z file_id: '13196' file_name: thesis.zip file_size: 37847025 relation: source_file file_date_updated: 2023-07-06T11:35:15Z has_accepted_license: '1' keyword: - quantum optics - electrooptics - quantum networks - quantum communication - transduction language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '202' project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: isbn: - 978-3-99078-030-5 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12900' relation: old_edition status: public - id: '10924' relation: part_of_dissertation status: public - id: '9114' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Cavity quantum electrooptics tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12900' abstract: - lang: eng text: "About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. " acknowledged_ssus: - _id: M-Shop - _id: SSU - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 citation: ama: Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900 apa: Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900 chicago: Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900. ieee: R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023. ista: Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria. mla: Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900. short: R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023. date_created: 2023-05-05T11:08:50Z date_published: 2023-05-05T00:00:00Z date_updated: 2023-08-24T11:16:35Z day: '05' ddc: - '537' - '535' - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:12900 ec_funded: 1 file: - access_level: closed checksum: 8cbdab9c37ee55e591092a6f66b272c4 content_type: application/x-zip-compressed creator: rsahu date_created: 2023-05-09T08:45:14Z date_updated: 2023-06-06T22:30:03Z embargo_to: open_access file_id: '12928' file_name: thesis.zip file_size: 36767177 relation: source_file - access_level: closed checksum: 439659ead46618147309be39d9dd5a8c content_type: application/pdf creator: rsahu date_created: 2023-05-09T08:51:17Z date_updated: 2023-07-06T11:37:40Z file_id: '12929' file_name: thesis_pdfa_final.pdf file_size: 17501990 relation: main_file file_date_updated: 2023-07-06T11:37:40Z has_accepted_license: '1' keyword: - quantum optics - electrooptics - quantum networks - quantum communication - transduction language: - iso: eng month: '05' oa_version: Published Version page: '190' project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: isbn: - 978-3-99078-030-5 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13175' relation: new_edition status: public - id: '10924' relation: part_of_dissertation status: public - id: '9114' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: Cavity quantum electrooptics tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12732' 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." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pietro full_name: Brighi, Pietro id: 4115AF5C-F248-11E8-B48F-1D18A9856A87 last_name: Brighi orcid: 0000-0002-7969-2729 citation: ama: Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732 apa: Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732 chicago: Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732. ieee: P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023. ista: Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. mla: Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732. short: P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023. date_created: 2023-03-17T13:30:48Z date_published: 2023-03-21T00:00:00Z date_updated: 2023-09-20T10:44:12Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:12732 ec_funded: 1 file: - access_level: closed checksum: 5d2de651ef9449c1b8dc27148ca74777 content_type: application/zip creator: pbrighi date_created: 2023-03-23T16:42:56Z date_updated: 2023-03-23T16:42:56Z file_id: '12753' file_name: Thesis_sub_PBrighi.zip file_size: 42167561 relation: source_file - access_level: open_access checksum: 7caa153d4a5b0873a79358787d2dfe1e content_type: application/pdf creator: pbrighi date_created: 2023-03-23T16:43:14Z date_updated: 2023-03-23T16:43:14Z file_id: '12754' file_name: Thesis_PBrighi.pdf file_size: 13977000 relation: main_file success: 1 file_date_updated: 2023-03-23T16:43:14Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: None page: '158' project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11470' relation: part_of_dissertation status: public - id: '8308' relation: part_of_dissertation status: public - id: '11469' relation: part_of_dissertation status: public - id: '12750' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: Ergodicity breaking in disordered and kinetically constrained quantum many-body systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13081' abstract: - lang: eng text: During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis. acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Bocanegra, Laura id: 4896F754-F248-11E8-B48F-1D18A9856A87 last_name: Bocanegra citation: ama: Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081 apa: Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081 chicago: Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081. ieee: L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023. ista: Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. mla: Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081. short: L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023. date_created: 2023-05-23T19:10:42Z date_published: 2023-05-23T00:00:00Z date_updated: 2023-10-04T11:14:04Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:13081 file: - access_level: closed checksum: 74f3f89e59a0189bee53ebfad9c1b9af content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lbocaneg date_created: 2023-05-25T06:32:12Z date_updated: 2023-05-25T06:32:12Z file_id: '13089' file_name: Thesis_final_LauraBocanegra.docx file_size: 25615534 relation: source_file - access_level: closed checksum: c6cdef6323eacfb4b7a8af20f32eae97 content_type: application/pdf creator: lbocaneg date_created: 2023-05-25T06:32:16Z date_updated: 2023-05-25T06:32:16Z embargo: 2024-05-31 embargo_to: open_access file_id: '13090' file_name: TotalFinal_Thesis_LauraBocanegraArx.pdf file_size: 12386046 relation: main_file file_date_updated: 2023-05-25T06:32:16Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '93' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9349' relation: part_of_dissertation status: public - id: '12837' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Epithelial dynamics during mouse neural tube development tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13331' abstract: - lang: eng text: "The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n" alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Seyda full_name: Köse, Seyda id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb last_name: Köse citation: ama: Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331 apa: Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331 chicago: Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331. ieee: S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023. ista: Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria. mla: Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331. short: S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023. date_created: 2023-07-31T10:20:55Z date_published: 2023-07-31T00:00:00Z date_updated: 2023-10-04T11:54:56Z day: '31' ddc: - '510' - '516' degree_awarded: MS department: - _id: GradSch - _id: UlWa doi: 10.15479/at:ista:13331 file: - access_level: closed checksum: 96ee518d796d02af71395622c45de03c content_type: application/x-zip-compressed creator: skoese date_created: 2023-07-31T10:16:32Z date_updated: 2023-07-31T10:16:32Z file_id: '13333' file_name: Exterior Algebra and Combinatorics.zip file_size: 28684 relation: source_file - access_level: open_access checksum: f610f4713f88bc477de576aaa46b114e content_type: application/pdf creator: skoese date_created: 2023-08-03T15:28:55Z date_updated: 2023-08-03T15:28:55Z file_id: '13480' file_name: thesis-pdfa.pdf file_size: 4953418 relation: main_file success: 1 file_date_updated: 2023-08-03T15:28:55Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '26' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12680' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: Exterior algebra and combinatorics type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14422' abstract: - lang: eng text: "Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Basile J full_name: Confavreux, Basile J id: C7610134-B532-11EA-BD9F-F5753DDC885E last_name: Confavreux citation: ama: 'Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422' apa: 'Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422' chicago: 'Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.' ieee: 'B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.' ista: 'Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.' mla: 'Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.' short: 'B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.' date_created: 2023-10-12T14:13:25Z date_published: 2023-10-12T00:00:00Z date_updated: 2023-10-18T09:20:56Z day: '12' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: TiVo doi: 10.15479/at:ista:14422 ec_funded: 1 file: - access_level: closed checksum: 7f636555eae7803323df287672fd13ed content_type: application/pdf creator: cchlebak date_created: 2023-10-12T14:53:50Z date_updated: 2023-10-12T14:54:52Z embargo: 2024-10-12 embargo_to: open_access file_id: '14424' file_name: Confavreux_Thesis_2A.pdf file_size: 30599717 relation: main_file - access_level: closed checksum: 725e85946db92290a4583a0de9779e1b content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-10-18T07:38:34Z date_updated: 2023-10-18T07:56:08Z file_id: '14440' file_name: Confavreux Thesis.zip file_size: 68406739 relation: source_file file_date_updated: 2023-10-18T07:56:08Z has_accepted_license: '1' language: - iso: eng month: '10' oa_version: Published Version page: '148' project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9633' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 title: 'Synapseek: Meta-learning synaptic plasticity rules' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14374' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Barbara full_name: Roos, Barbara id: 5DA90512-D80F-11E9-8994-2E2EE6697425 last_name: Roos orcid: 0000-0002-9071-5880 citation: ama: Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374 apa: Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374 chicago: Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374. ieee: B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023. ista: Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. mla: Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374. short: B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023. date_created: 2023-09-28T14:23:04Z date_published: 2023-09-30T00:00:00Z date_updated: 2023-10-27T10:37:30Z day: '30' ddc: - '515' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:14374 ec_funded: 1 file: - access_level: open_access checksum: ef039ffc3de2cb8dee5b14110938e9b6 content_type: application/pdf creator: broos date_created: 2023-10-06T11:35:56Z date_updated: 2023-10-06T11:35:56Z file_id: '14398' file_name: phd-thesis-draft_pdfa_acrobat.pdf file_size: 2365702 relation: main_file - access_level: closed checksum: 81dcac33daeefaf0111db52f41bb1fd0 content_type: application/x-zip-compressed creator: broos date_created: 2023-10-06T11:38:01Z date_updated: 2023-10-06T11:38:01Z file_id: '14399' file_name: Version5.zip file_size: 4691734 relation: source_file file_date_updated: 2023-10-06T11:38:01Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '206' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13207' relation: part_of_dissertation status: public - id: '10850' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Boundary superconductivity in BCS theory tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14506' abstract: - lang: eng text: "Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506 apa: Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506 chicago: Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506. ieee: M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023. ista: Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. mla: Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506. short: M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023. date_created: 2023-11-10T08:10:43Z date_published: 2023-11-10T00:00:00Z date_updated: 2023-11-30T10:54:51Z day: '10' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/14506 ec_funded: 1 file: - access_level: closed checksum: 521c72818d720a52b377207b2ee87b6a content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-11-23T10:29:55Z date_updated: 2023-11-23T10:29:55Z file_id: '14598' file_name: thesis_yeo.zip file_size: 3037720 relation: source_file - access_level: open_access checksum: 0ed5d16899687aecf13d843c9878c9f2 content_type: application/pdf creator: cchlebak date_created: 2023-11-23T10:30:08Z date_updated: 2023-11-23T10:30:08Z file_id: '14599' file_name: thesis_yeo.pdf file_size: 2717256 relation: main_file success: 1 file_date_updated: 2023-11-23T10:30:08Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '162' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9969' relation: part_of_dissertation status: public - id: '13238' relation: part_of_dissertation status: public - id: '14490' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Advances in efficiency and privacy in payment channel network analysis type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12726' abstract: - lang: eng text: "Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex." acknowledged_ssus: - _id: M-Shop - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 citation: ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726 apa: Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726 chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726. ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023. ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria. mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726. short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023. date_created: 2023-03-15T13:22:13Z date_published: 2023-03-23T00:00:00Z date_updated: 2023-11-30T10:55:13Z day: '23' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:12726 file: - access_level: closed checksum: eba0e19fe57a8c15e7aeab55a845efb7 content_type: application/pdf creator: cchlebak date_created: 2023-03-23T12:49:23Z date_updated: 2023-11-24T11:57:46Z description: the main file is missing the bibliography. See new thesis record 14530 for updated files. file_id: '12745' file_name: Thesis_Riedl_2023.pdf file_size: 63734746 relation: main_file - access_level: closed checksum: 0eb7b650cc8ae843bcec7c8a6109ae03 content_type: application/octet-stream creator: cchlebak date_created: 2023-03-23T12:54:34Z date_updated: 2023-09-24T22:30:03Z embargo_to: open_access file_id: '12746' file_name: Thesis_Riedl_2023_source.rar file_size: 339473651 relation: source_file file_date_updated: 2023-11-24T11:57:46Z has_accepted_license: '1' language: - iso: eng month: '03' oa_version: None page: '260' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10703' relation: part_of_dissertation status: public - id: '10791' relation: part_of_dissertation status: public - id: '7932' relation: part_of_dissertation status: public - id: '461' relation: part_of_dissertation status: public - id: '14530' relation: new_edition status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Synchronization in collectively moving active matter type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14530' abstract: - lang: eng text: 'Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ' acknowledged_ssus: - _id: M-Shop - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 citation: ama: Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530 apa: Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530 chicago: Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530. ieee: M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023. ista: Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria. mla: Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530. short: M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023. date_created: 2023-11-15T09:59:03Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-11-30T10:55:13Z day: '16' ddc: - '530' - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/14530 file: - access_level: open_access checksum: 52e1d0ab6c1abe59c82dfe8c9ff5f83a content_type: application/pdf creator: mriedl date_created: 2023-11-15T09:52:54Z date_updated: 2023-11-15T09:52:54Z file_id: '14536' file_name: Thesis_Riedl_2023_corr.pdf file_size: 36743942 relation: main_file success: 1 file_date_updated: 2023-11-15T09:52:54Z has_accepted_license: '1' keyword: - Synchronization - Collective Movement - Active Matter - Cell Migration - Active Colloids language: - iso: eng month: '11' oa: 1 oa_version: Updated Version page: '260' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10703' relation: part_of_dissertation status: public - id: '10791' relation: part_of_dissertation status: public - id: '7932' relation: part_of_dissertation status: public - id: '461' relation: part_of_dissertation status: public - id: '12726' relation: old_edition status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Synchronization in collectively moving active matter type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14547' abstract: - lang: eng 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." acknowledged_ssus: - _id: NanoFab - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan citation: ama: Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547 apa: Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547 chicago: Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547. ieee: D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023. ista: Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. mla: Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547. short: D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023. date_created: 2023-11-17T13:45:26Z date_published: 2023-11-16T00:00:00Z date_updated: 2023-11-30T10:56:04Z day: '16' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/14547 file: - access_level: open_access checksum: db0c37d213bc002125bd59690e9db246 content_type: application/pdf creator: pduc date_created: 2023-11-17T13:36:44Z date_updated: 2023-11-22T09:46:06Z file_id: '14548' file_name: Phan_Thesis_pdfa.pdf file_size: 34828019 relation: main_file - access_level: closed checksum: 8d3bd6afa279a0078ffd13e06bb6d56d content_type: application/zip creator: pduc date_created: 2023-11-17T13:44:53Z date_updated: 2023-11-17T13:47:54Z file_id: '14549' file_name: dissertation_src.zip file_size: 279319709 relation: source_file file_date_updated: 2023-11-22T09:46:06Z has_accepted_license: '1' keyword: - superconductor-semiconductor - superconductivity - Al - InAs - p-wave - superconductivity - JPA - microwave language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '80' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10851' relation: part_of_dissertation status: public - id: '13264' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Resonant microwave spectroscopy of Al-InAs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14058' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 citation: 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:10.15479/at:ista:14058' apa: '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. https://doi.org/10.15479/at:ista:14058' 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. https://doi.org/10.15479/at:ista:14058.' 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.' 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. 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, doi:10.15479/at:ista:14058.' 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.' date_created: 2023-08-15T10:20:40Z date_published: 2023-08-15T00:00:00Z date_updated: 2023-12-13T12:15:36Z day: '15' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa - _id: BeVi doi: 10.15479/at:ista:14058 ec_funded: 1 file: - access_level: closed checksum: 4e44e169f2724ee8c9324cd60bcc2b71 content_type: application/zip creator: gpuixeus date_created: 2023-08-16T18:15:17Z date_updated: 2023-08-17T06:55:24Z file_id: '14075' file_name: Thesis_latex_forpdfa.zip file_size: 10891454 relation: source_file - access_level: open_access checksum: e10b04cd8f3fecc0d9ef6e6868b6e1e8 content_type: application/pdf creator: gpuixeus date_created: 2023-08-18T10:47:55Z date_updated: 2023-08-18T10:47:55Z file_id: '14079' file_name: PhDThesis_PuixeuG.pdf file_size: 19856686 relation: main_file success: 1 file_date_updated: 2023-08-18T10:47:55Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '230' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A grant_number: '25817' name: 'Sexual conflict: resolution, constraints and biomedical implications' publication_identifier: isbn: - 978-3-99078-035-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9803' relation: research_data status: public - id: '12933' relation: research_data status: public - id: '6831' relation: part_of_dissertation status: public - id: '14077' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: 'The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14622' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Sack, Stefan id: dd622248-f6e0-11ea-865d-ce382a1c81a5 last_name: Sack orcid: 0000-0001-5400-8508 citation: ama: 'Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622' apa: 'Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622' chicago: 'Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.' ieee: 'S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.' ista: 'Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.' mla: 'Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.' short: 'S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.' date_created: 2023-11-28T10:58:13Z date_published: 2023-11-30T00:00:00Z date_updated: 2023-12-13T14:47:25Z day: '30' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:14622 ec_funded: 1 file: - access_level: closed checksum: 068fd3570506ec42b2faa390de784bc4 content_type: application/pdf creator: ssack date_created: 2023-11-30T15:53:10Z date_updated: 2023-12-01T11:10:46Z embargo: 2024-11-30 embargo_to: open_access file_id: '14635' file_name: PhD_Thesis.pdf file_size: 11947523 relation: main_file - access_level: closed checksum: 0fa3bc0d108aed0ac59d2c6beef2220a content_type: application/zip creator: ssack date_created: 2023-11-30T15:54:11Z date_updated: 2023-12-01T11:10:46Z file_id: '14636' file_name: PhD Thesis (1).zip file_size: 18422964 relation: source_file file_date_updated: 2023-12-01T11:10:46Z has_accepted_license: '1' language: - iso: eng month: '11' oa_version: Published Version page: '142' project: - _id: bd660c93-d553-11ed-ba76-fb0fb6f49c0d name: Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11471' relation: part_of_dissertation status: public - id: '13125' relation: part_of_dissertation status: public - id: '9760' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: 'Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14697' acknowledged_ssus: - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp citation: ama: 'Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697' apa: 'Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697' chicago: 'Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.' ieee: 'J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.' ista: 'Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.' mla: 'Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697.' short: 'J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.' date_created: 2023-12-18T19:14:28Z date_published: 2023-12-20T00:00:00Z date_updated: 2023-12-21T14:30:02Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:14697 ec_funded: 1 file: - access_level: closed checksum: 457927165d5d556305d3086f6b83e5c7 content_type: application/pdf creator: jstopp date_created: 2023-12-20T09:35:34Z date_updated: 2023-12-20T09:35:34Z embargo: 2024-12-20 embargo_to: open_access file_id: '14699' file_name: Thesis.pdf file_size: 51585778 relation: main_file - access_level: closed checksum: e8d26449ac461f5e8478a62c9507506f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jstopp date_created: 2023-12-20T09:35:35Z date_updated: 2023-12-20T10:41:42Z file_id: '14700' file_name: Thesis.docx file_size: 69625950 relation: source_file file_date_updated: 2023-12-20T10:41:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '226' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-038-1 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6328' relation: part_of_dissertation status: public - id: '7885' relation: part_of_dissertation status: public - id: '12272' relation: part_of_dissertation status: public - id: '14274' relation: part_of_dissertation status: public - id: '14360' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: 'Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14651' abstract: - lang: eng text: 'For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.' acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651 apa: Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651 chicago: Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651. ieee: L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023. ista: Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. mla: Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651. short: L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023. date_created: 2023-12-11T19:30:37Z date_published: 2023-12-12T00:00:00Z date_updated: 2023-12-22T11:04:45Z day: '12' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:14651 ec_funded: 1 file: - access_level: open_access checksum: 520bdb61e95e66070e02824947d2c5fa content_type: application/pdf creator: larathoo date_created: 2023-12-13T15:37:55Z date_updated: 2023-12-13T15:37:55Z file_id: '14684' file_name: Phd_Thesis_LA.pdf file_size: 34101468 relation: main_file success: 1 - access_level: closed checksum: d8e59afd0817c98fba2564a264508e5c content_type: application/zip creator: larathoo date_created: 2023-12-13T15:42:23Z date_updated: 2023-12-14T08:58:18Z file_id: '14685' file_name: Phd_Thesis_LA.zip file_size: 31052872 relation: source_file - access_level: closed checksum: 9a778c949932286f4519e1f1fca2820d content_type: application/zip creator: larathoo date_created: 2023-12-11T19:24:59Z date_updated: 2023-12-14T08:58:18Z file_id: '14681' file_name: Supplementary_Materials.zip file_size: 10713896 relation: supplementary_material file_date_updated: 2023-12-14T08:58:18Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '96' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14539' abstract: - lang: eng 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" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 citation: ama: Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539 apa: Zikelic, D. (2023). Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539 chicago: Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539. 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. mla: Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539. short: D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023. date_created: 2023-11-15T13:39:10Z date_published: 2023-11-15T00:00:00Z date_updated: 2024-01-16T11:58:15Z day: '15' ddc: - '000' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/14539 ec_funded: 1 file: - access_level: open_access checksum: f23e002b0059ca78e1fbb864da52dd7e content_type: application/pdf creator: cchlebak date_created: 2023-11-15T13:43:28Z date_updated: 2023-11-15T13:43:28Z file_id: '14540' file_name: main.pdf file_size: 2116426 relation: main_file success: 1 - access_level: closed checksum: 80ca37618a3c7b59866875f8be9b15ed content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-11-15T13:44:24Z date_updated: 2023-11-15T13:44:24Z file_id: '14541' file_name: thesis_source.zip file_size: 35884057 relation: source_file file_date_updated: 2023-11-15T13:44:24Z language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '256' project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-036-7 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1194' relation: part_of_dissertation status: public - id: '12000' relation: part_of_dissertation status: public - id: '9644' relation: part_of_dissertation status: public - id: '12511' relation: part_of_dissertation status: public - id: '14600' relation: part_of_dissertation status: public - id: '14601' relation: part_of_dissertation status: public - id: '10414' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Automated verification and control of infinite state stochastic systems tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13107' abstract: - lang: eng text: "Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus citation: ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107' apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107' chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.' ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.' ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.' mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.' short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.' date_created: 2023-06-01T09:05:24Z date_published: 2023-05-31T00:00:00Z date_updated: 2024-02-07T08:03:33Z day: '31' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/at:ista:13107 ec_funded: 1 file: - access_level: closed checksum: 4b69a4ac0bbf4163d59c0b58dcb4f2c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lknaus date_created: 2023-06-01T13:48:41Z date_updated: 2023-06-01T13:48:41Z file_id: '13112' file_name: Thesis_Lisa Knaus_approved_final.docx file_size: 12991551 relation: source_file - access_level: open_access checksum: 6903d152aa01181d87a696085af31c83 content_type: application/pdf creator: lknaus date_created: 2023-06-02T09:47:29Z date_updated: 2023-06-07T08:41:49Z file_id: '13114' file_name: Thesis_Lisa Knaus_approved_final_pdfa2b.pdf file_size: 9309015 relation: main_file file_date_updated: 2023-06-07T08:41:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: 'The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14280' abstract: - lang: eng text: "Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation." acknowledged_ssus: - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' citation: ama: Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280 apa: Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280 chicago: Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280. ieee: P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023. ista: Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. mla: Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280. short: P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023. date_created: 2023-09-06T10:58:25Z date_published: 2023-09-25T00:00:00Z date_updated: 2024-02-21T12:35:18Z day: '25' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: MaLo doi: 10.15479/at:ista:14280 ec_funded: 1 file: - access_level: closed checksum: 87eef11fbc5c7df0826f12a3a629b444 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pradler date_created: 2023-10-04T10:11:53Z date_updated: 2023-10-04T10:28:35Z file_id: '14390' file_name: PhD Thesis_Philipp Radler_20231004.docx file_size: 114932847 relation: source_file - access_level: closed checksum: 3253e099b7126469d941fd9419d68b4f content_type: application/pdf creator: pradler date_created: 2023-10-04T10:11:21Z date_updated: 2023-10-04T10:28:35Z embargo: 2024-10-04 embargo_to: open_access file_id: '14391' file_name: PhD Thesis_Philipp Radler_20231004.pdf file_size: 37838778 relation: main_file file_date_updated: 2023-10-04T10:28:35Z has_accepted_license: '1' keyword: - Cell Division - Reconstitution - FtsZ - FtsA - Divisome - E.coli language: - iso: eng month: '09' oa_version: Published Version page: '156' project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall - _id: 259B655A-B435-11E9-9278-68D0E5697425 grant_number: LT000824/2016 name: Reconstitution of bacterial cell wall sythesis publication_identifier: isbn: - 978-3-99078-033-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11373' relation: part_of_dissertation status: public - id: '7387' relation: part_of_dissertation status: public - id: '10934' relation: research_data status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Spatiotemporal signaling during assembly of the bacterial divisome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13286' 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. acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini citation: ama: 'Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286' apa: '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. https://doi.org/10.15479/at:ista:13286' 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. https://doi.org/10.15479/at:ista:13286.' 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.' mla: '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, doi:10.15479/at:ista:13286.' 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.' date_created: 2023-07-24T14:10:45Z date_published: 2023-07-21T00:00:00Z date_updated: 2024-02-21T12:35:34Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:13286 ec_funded: 1 file: - access_level: closed checksum: 666ee31c7eade89679806287c062fa14 content_type: application/x-zip-compressed creator: mvalenti date_created: 2023-08-11T09:27:39Z date_updated: 2023-08-11T10:01:34Z file_id: '14033' file_name: PhD_thesis_Valentini_final.zip file_size: 56121429 relation: source_file - access_level: open_access checksum: 0992f2ebef152dee8e70055350ebbb55 content_type: application/pdf creator: mvalenti date_created: 2023-08-11T14:39:17Z date_updated: 2023-08-11T14:39:17Z file_id: '14035' file_name: PhD_thesis_Valentini_final_validated.pdf file_size: 38199711 relation: main_file file_date_updated: 2023-08-11T14:39:17Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '184' project: - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: Conventional and unconventional topological superconductors publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13312' relation: part_of_dissertation status: public - id: '12118' relation: part_of_dissertation status: public - id: '8910' relation: part_of_dissertation status: public - id: '12522' relation: research_data status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: 'Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13984' abstract: - lang: eng text: "Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Anna full_name: Franschitz, Anna id: 480826C8-F248-11E8-B48F-1D18A9856A87 last_name: Franschitz citation: ama: Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984 apa: Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984 chicago: Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984. ieee: A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023. ista: Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. mla: Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984. short: A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023. date_created: 2023-08-08T15:33:29Z date_published: 2023-08-08T00:00:00Z date_updated: 2024-03-01T15:25:17Z day: '08' ddc: - '570' - '577' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/at:ista:13984 file: - access_level: closed checksum: 27220243d5d51c3b0d7d61c0879d7a0c content_type: application/pdf creator: afransch date_created: 2023-08-08T18:01:28Z date_updated: 2024-03-01T08:51:42Z embargo: 2024-08-08 embargo_to: open_access file_id: '13986' file_name: Thesis_AnnaFranschitz_202308.pdf file_size: 10797612 relation: main_file - access_level: closed checksum: 40abf7ccca14a3893f72dc7fb88585d6 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: afransch date_created: 2023-08-08T18:02:25Z date_updated: 2023-08-09T07:25:27Z file_id: '13987' file_name: Thesis_AnnaFranschitz_202308.docx file_size: 2619085 relation: source_file - access_level: closed checksum: 8b991ecc2d59d045cc3cf0d676785ec7 content_type: application/pdf creator: cchlebak date_created: 2024-03-01T08:37:15Z date_updated: 2024-03-01T12:13:29Z description: Minor modifications and clarifications - Feb 2024 embargo: 2024-08-08 embargo_to: open_access file_id: '15042' file_name: Addendum_AnnaFranschitz202402.pdf file_size: 85956 relation: erratum title: Addendum - access_level: closed checksum: 66745aa01f960f17472c024875c049ed content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-03-01T08:39:20Z date_updated: 2024-03-01T08:51:42Z file_id: '15043' file_name: Addendum_AnnaFranschitz202402.docx file_size: 11818 relation: source_file title: Addendum - source file - access_level: closed checksum: 55c876b73d49db15228a7f571592ec77 content_type: application/pdf creator: cchlebak date_created: 2024-03-01T08:56:06Z date_updated: 2024-03-01T12:58:14Z description: For printing purposes file_id: '15044' file_name: Print_Version_Franschitz_Anna_Thesis.pdf file_size: 10416761 relation: other title: Print Version file_date_updated: 2024-03-01T12:58:14Z has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '89' publication_identifier: isbn: - 978-3-99078-034-3 issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Individual and social immunity against viral infections in ants type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14323' abstract: - lang: eng text: Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube. acknowledged_ssus: - _id: Bio - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Katarzyna full_name: Kuzmicz-Kowalska, Katarzyna id: 4CED352A-F248-11E8-B48F-1D18A9856A87 last_name: Kuzmicz-Kowalska citation: ama: Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323 apa: Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323 chicago: Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323. ieee: K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023. ista: Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. mla: Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323. short: K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023. date_created: 2023-09-13T10:07:18Z date_published: 2023-09-13T00:00:00Z date_updated: 2024-03-07T15:02:59Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: AnKi doi: 10.15479/at:ista:14323 file: - access_level: closed checksum: bd83596869c814b24aeff7077d031c0e content_type: application/pdf creator: kkuzmicz date_created: 2023-09-13T09:52:52Z date_updated: 2023-09-13T10:08:25Z embargo: 2025-03-13 embargo_to: open_access file_id: '14324' file_name: PhDThesis_KK_final_pdfA.pdf file_size: 10147911 relation: main_file - access_level: closed checksum: aa2757ae4c3478041fd7e62c587d3e4d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: kkuzmicz date_created: 2023-09-13T09:53:29Z date_updated: 2023-09-13T09:53:29Z file_id: '14325' file_name: thesis_KK_final_corrections_092023.docx file_size: 103980668 relation: source_file file_date_updated: 2023-09-13T10:08:25Z has_accepted_license: '1' language: - iso: eng month: '09' oa_version: Published Version page: '151' project: - _id: 267AF0E4-B435-11E9-9278-68D0E5697425 name: The role of morphogens in the regulation of neural tube growth publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7883' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 title: Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14641' acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mike full_name: Hennessey-Wesen, Mike id: 3F338C72-F248-11E8-B48F-1D18A9856A87 last_name: Hennessey-Wesen citation: ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641 apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641 chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641. ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023. ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641. short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023. date_created: 2023-12-04T13:17:37Z date_published: 2023-11-30T00:00:00Z date_updated: 2024-03-22T13:21:17Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:14641 ec_funded: 1 file: - access_level: closed checksum: 4127c285b34f4bf7fb31ef24f9d14c25 content_type: application/vnd.oasis.opendocument.text creator: mhenness date_created: 2023-12-06T13:13:26Z date_updated: 2023-12-06T13:13:26Z file_id: '14648' file_name: mike_thesis_v06-12-2023.odt file_size: 46405919 relation: source_file - access_level: closed checksum: f5203a61eddaf35235bbc51904d73982 content_type: application/pdf creator: mhenness date_created: 2023-12-06T13:14:15Z date_updated: 2023-12-06T13:14:15Z embargo: 2024-11-30 embargo_to: open_access file_id: '14649' file_name: mike_thesis_v06-12-2023.pdf file_size: 21282155 relation: main_file - access_level: closed checksum: 9f7b4d646f1cfb57e3b9106a8a9cdd9d content_type: application/pdf creator: cchlebak date_created: 2024-03-20T13:19:36Z date_updated: 2024-03-20T13:19:36Z file_id: '15145' file_name: 2023_Hennessey_Michael_Thesis_from_source.pdf file_size: 2930287 relation: other file_date_updated: 2024-03-20T13:19:36Z has_accepted_license: '1' keyword: - microfluidics - miceobiology - mutations - quorum sensing language: - iso: eng month: '11' oa_version: Published Version page: '104' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Adaptive mutation in E. coli modulated by luxS type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14587' abstract: - lang: eng 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." 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). alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio citation: ama: Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587 apa: 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. https://doi.org/10.15479/at:ista:14587 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. https://doi.org/10.15479/at:ista:14587. 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. 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. mla: 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, doi:10.15479/at:ista:14587. 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. date_created: 2023-11-21T11:41:05Z date_published: 2023-11-21T00:00:00Z date_updated: 2024-03-22T13:21:28Z day: '21' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: JuFi doi: 10.15479/at:ista:14587 ec_funded: 1 file: - access_level: open_access checksum: 6c7db4cc86da6cdc79f7f358dc7755d4 content_type: application/pdf creator: amarvegg date_created: 2023-11-29T09:09:31Z date_updated: 2023-11-29T09:09:31Z file_id: '14626' file_name: thesis_Marveggio.pdf file_size: 2881100 relation: main_file success: 1 - access_level: closed checksum: 52f28bdf95ec82cff39f3685f9c48e7d content_type: application/zip creator: amarvegg date_created: 2023-11-29T09:10:19Z date_updated: 2024-03-20T12:28:32Z file_id: '14627' file_name: Thesis_Marveggio.zip file_size: 10189696 relation: source_file file_date_updated: 2024-03-20T12:28:32Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '228' project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11842' relation: part_of_dissertation status: public - id: '14597' relation: part_of_dissertation status: public status: public supervisor: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X title: Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12491' abstract: - lang: eng text: "The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 citation: ama: Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491 apa: Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491 chicago: Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491. ieee: B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023. ista: Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. mla: Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491. short: B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023. date_created: 2023-02-02T14:50:20Z date_published: 2023-02-02T00:00:00Z date_updated: 2024-03-25T23:30:05Z day: '02' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:12491 file: - access_level: open_access checksum: 069d87f025e0799bf9e3c375664264f2 content_type: application/pdf creator: bzens date_created: 2023-02-07T13:07:38Z date_updated: 2024-02-08T23:30:04Z embargo: 2024-02-07 file_id: '12527' file_name: PhDThesis_BettinaZens_2023_final.pdf file_size: 23082464 relation: main_file - access_level: closed checksum: 8c66ed203495d6e078ed1002a866520c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: bzens date_created: 2023-02-07T13:09:05Z date_updated: 2024-02-08T23:30:04Z embargo_to: open_access file_id: '12528' file_name: PhDThesis_BettinaZens_2023_final.docx file_size: 106169509 relation: source_file file_date_updated: 2024-02-08T23:30:04Z has_accepted_license: '1' keyword: - cryo-EM - cryo-ET - FIB milling - method development - FIBSEM - extracellular matrix - ECM - cell-derived matrices - CDMs - cell culture - high pressure freezing - HPF - structural biology - tomography - collagen language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '187' project: - _id: eba3b5f6-77a9-11ec-83b8-cf0905748aa3 name: Integrated visual proteomics of reciprocal cell-extracellular matrix interactions - _id: 059B463C-7A3F-11EA-A408-12923DDC885E name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria publication_identifier: isbn: - 978-3-99078-027-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8586' relation: part_of_dissertation status: public status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 title: Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14226' abstract: - lang: eng text: "We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Elizabeth R full_name: Stephenson, Elizabeth R id: 2D04F932-F248-11E8-B48F-1D18A9856A87 last_name: Stephenson orcid: 0000-0002-6862-208X citation: ama: Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226 apa: Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226 chicago: Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226. ieee: E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023. ista: Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria. mla: Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226. short: E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023. date_created: 2023-08-24T13:01:18Z date_published: 2023-08-24T00:00:00Z date_updated: 2024-02-26T23:30:04Z day: '24' ddc: - '500' degree_awarded: MS department: - _id: GradSch - _id: HeEd doi: 10.15479/at:ista:14226 file: - access_level: closed checksum: 453caf851d75c3478c10ed09bd242a91 content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-08-24T13:02:49Z date_updated: 2024-02-26T23:30:03Z embargo_to: open_access file_id: '14227' file_name: documents-export-2023-08-24.zip file_size: 15501411 relation: source_file - access_level: open_access checksum: 7349d29963d6695e555e171748648d9a content_type: application/pdf creator: cchlebak date_created: 2023-08-24T13:03:42Z date_updated: 2024-02-26T23:30:03Z embargo: 2024-02-25 file_id: '14228' file_name: thesis_pdf_a.pdf file_size: 6854783 relation: main_file file_date_updated: 2024-02-26T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '43' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Generalizing medial axes with homology switches type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12470' abstract: - lang: eng text: "The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\x02resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\x02resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl - _id: EM-Fac - _id: M-Shop - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 citation: ama: Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470 apa: Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470 chicago: Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470. ieee: J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023. ista: Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. mla: Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470. short: J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023. date_created: 2023-01-31T15:10:53Z date_published: 2023-01-09T00:00:00Z date_updated: 2023-08-31T12:26:58Z day: '09' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:12470 ec_funded: 1 file: - access_level: open_access checksum: 1a2306e5f59f52df598e7ecfadf921ac content_type: application/pdf creator: cchlebak date_created: 2023-01-31T15:11:42Z date_updated: 2023-07-27T22:30:54Z embargo: 2023-07-09 file_id: '12471' file_name: 20230109_PhD_thesis_JM_final.pdf file_size: 41771714 relation: main_file - access_level: closed checksum: 0bebbdee0773443959e1f6ab8caf281f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-01-31T15:11:51Z date_updated: 2023-07-10T22:30:04Z embargo_to: open_access file_id: '12472' file_name: 20230109_PhD_thesis_JM_final.docx file_size: 66983464 relation: source_file file_date_updated: 2023-07-27T22:30:54Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '201' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: isbn: - ' 978-3-99078-026-8' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11943' relation: part_of_dissertation status: public - id: '11950' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12531' abstract: - lang: eng text: "All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Kseniia full_name: Kirillova, Kseniia id: 8e3f931e-dc85-11ea-9058-e7b957bf23f0 last_name: Kirillova citation: ama: Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531 apa: Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531 chicago: Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531. ieee: K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023. ista: Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. mla: Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531. short: K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023. date_created: 2023-02-09T07:45:05Z date_published: 2023-02-08T00:00:00Z date_updated: 2024-02-09T23:30:04Z day: '08' ddc: - '570' degree_awarded: MS department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:12531 file: - access_level: open_access checksum: 57d8da3a6c749eb1556b7435fe266a5f content_type: application/pdf creator: cchlebak date_created: 2023-02-09T08:03:32Z date_updated: 2024-02-09T23:30:03Z embargo: 2024-02-08 file_id: '12532' file_name: Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf file_size: 8369317 relation: main_file - access_level: closed checksum: 87fb44318e4f9eb9da2ad9ad6ca8e76f content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-02-10T09:32:06Z date_updated: 2024-02-09T23:30:03Z embargo_to: open_access file_id: '12535' file_name: Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip file_size: 11204408 relation: source_file file_date_updated: 2024-02-09T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '46' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Panoramic functional gradients across the mouse retina tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2023' ... --- _id: '12800' abstract: - lang: eng text: 'The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ' alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Mara full_name: Julseth, Mara id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1 last_name: Julseth citation: ama: Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800 apa: Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800 chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800. ieee: M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023. ista: Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800. short: M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023. date_created: 2023-04-04T18:57:11Z date_published: 2023-04-05T00:00:00Z date_updated: 2023-06-02T22:30:05Z day: '05' ddc: - '576' degree_awarded: MS department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:12800 file: - access_level: closed checksum: b76cf6d69f2093d8248f6a3f9d4654a4 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: mjulseth date_created: 2023-04-06T06:09:40Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12805' file_name: Dispersaldata.xlsx file_size: 52795 relation: supplementary_material - access_level: open_access checksum: 5a13b6d204371572e249f03795bc0d04 content_type: application/vnd.wolfram.nb creator: mjulseth date_created: 2023-04-06T06:11:27Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12806' file_name: 2023_MSc_ThesisMaraJulseth_Notebook.nb file_size: 787239 relation: supplementary_material - access_level: closed checksum: c3ec842839ed1e66bf2618ae33047df8 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mjulseth date_created: 2023-04-06T08:26:12Z date_updated: 2023-06-02T22:30:04Z embargo_to: open_access file_id: '12812' file_name: ThesisMaraJulseth_04_23.docx file_size: 1061763 relation: source_file - access_level: open_access checksum: 3132cc998fbe3ae2a3a83c2a69367f37 content_type: application/pdf creator: mjulseth date_created: 2023-04-06T08:26:37Z date_updated: 2023-06-02T22:30:04Z embargo: 2023-06-01 file_id: '12813' file_name: ThesisMaraJulseth_04_23.pdf file_size: 1741364 relation: main_file file_date_updated: 2023-06-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14510' acknowledged_ssus: - _id: EM-Fac - _id: Bio - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nataliia full_name: Gnyliukh, Nataliia id: 390C1120-F248-11E8-B48F-1D18A9856A87 last_name: Gnyliukh orcid: 0000-0002-2198-0509 citation: ama: Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510 apa: Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510 chicago: Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510. ieee: N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023. ista: Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria. mla: Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510. short: N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023. date_created: 2023-11-10T09:10:06Z date_published: 2023-11-10T00:00:00Z date_updated: 2024-03-27T23:30:45Z day: '10' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JiFr - _id: MaLo doi: 10.15479/at:ista:14510 ec_funded: 1 file: - access_level: closed checksum: 3d5e680bfc61f98e308c434f45cc9bd6 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: ngnyliuk date_created: 2023-11-20T09:18:51Z date_updated: 2023-11-20T09:18:51Z file_id: '14567' file_name: Thesis_Gnyliukh_final_08_11_23.docx file_size: 20824903 relation: source_file - access_level: closed checksum: bfc96d47fc4e7e857dd71656097214a4 content_type: application/pdf creator: ngnyliuk date_created: 2023-11-20T09:23:11Z date_updated: 2023-11-23T13:10:55Z embargo: 2024-11-23 embargo_to: open_access file_id: '14568' file_name: Thesis_Gnyliukh_final_20_11_23.pdf file_size: 24871844 relation: main_file file_date_updated: 2023-11-23T13:10:55Z has_accepted_license: '1' keyword: - Clathrin-Mediated Endocytosis - vesicle scission - Dynamin-Related Protein 2 - SH3P2 - TPLATE complex - Total internal reflection fluorescence microscopy - Arabidopsis thaliana language: - iso: eng month: '11' oa_version: Published Version page: '180' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-037-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14591' relation: part_of_dissertation status: public - id: '9887' relation: part_of_dissertation status: public - id: '8139' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Mechanism of clathrin-coated vesicle formation during endocytosis in plants tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12897' abstract: - lang: eng text: "Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will." acknowledged_ssus: - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner citation: ama: 'Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897' apa: 'Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897' chicago: 'Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.' ieee: 'C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.' ista: 'Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.' mla: 'Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.' short: 'C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.' date_created: 2023-05-05T10:40:14Z date_published: 2023-05-05T00:00:00Z date_updated: 2024-01-29T10:47:51Z day: '05' ddc: - '516' - '004' - '518' - '531' degree_awarded: PhD department: - _id: GradSch - _id: BeBi doi: 10.15479/at:ista:12897 ec_funded: 1 file: - access_level: open_access checksum: cc2094e92fa27000b70eb4bfb76d6b5a content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:20Z date_updated: 2023-12-08T23:30:04Z embargo: 2023-12-07 file_id: '12942' file_name: thesis-hafner-2023may11-a2b.pdf file_size: 50714445 relation: main_file - access_level: closed checksum: a6b51334be2b81672357b1549afab40c content_type: application/pdf creator: chafner date_created: 2023-05-11T10:43:44Z date_updated: 2023-12-08T23:30:04Z embargo_to: open_access file_id: '12943' file_name: thesis-release-form.pdf file_size: 265319 relation: source_file file_date_updated: 2023-12-08T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '180' project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: isbn: - 978-3-99078-031-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9817' relation: part_of_dissertation status: public - id: '7117' relation: part_of_dissertation status: public - id: '13188' relation: dissertation_contains status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: 'Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models' type: dissertation user_id: 400429CC-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12072' abstract: - lang: eng text: "In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm\r\nform associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.\r\nIn the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or\r\nintegral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.\r\nMore precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in\r\nthe power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. " acknowledgement: I acknowledge the received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska Curie Grant Agreement No. 665385. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alec L full_name: Shute, Alec L id: 440EB050-F248-11E8-B48F-1D18A9856A87 last_name: Shute orcid: 0000-0002-1812-2810 citation: ama: 'Shute AL. Existence and density problems in Diophantine geometry: From norm forms to Campana points. 2022. doi:10.15479/at:ista:12072' apa: 'Shute, A. L. (2022). Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12072' chicago: 'Shute, Alec L. “Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12072.' ieee: 'A. L. Shute, “Existence and density problems in Diophantine geometry: From norm forms to Campana points,” Institute of Science and Technology Austria, 2022.' ista: 'Shute AL. 2022. Existence and density problems in Diophantine geometry: From norm forms to Campana points. Institute of Science and Technology Austria.' mla: 'Shute, Alec L. Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12072.' short: 'A.L. Shute, Existence and Density Problems in Diophantine Geometry: From Norm Forms to Campana Points, Institute of Science and Technology Austria, 2022.' date_created: 2022-09-08T21:53:03Z date_published: 2022-09-08T00:00:00Z date_updated: 2023-02-21T16:37:35Z day: '08' ddc: - '512' degree_awarded: PhD department: - _id: GradSch - _id: TiBr doi: 10.15479/at:ista:12072 ec_funded: 1 file: - access_level: open_access checksum: bf073344320e05d92c224786cec2e92d content_type: application/pdf creator: ashute date_created: 2022-09-08T21:50:34Z date_updated: 2022-09-08T21:50:34Z file_id: '12073' file_name: Thesis_final_draft.pdf file_size: 1907386 relation: main_file success: 1 - access_level: closed checksum: b054ac6baa09f70e8235403a4abbed80 content_type: application/octet-stream creator: ashute date_created: 2022-09-08T21:50:42Z date_updated: 2022-09-12T11:24:21Z file_id: '12074' file_name: athesis.tex file_size: 495393 relation: source_file - access_level: closed checksum: 0a31e905f1cff5eb8110978cc90e1e79 content_type: application/x-zip-compressed creator: ashute date_created: 2022-09-09T12:05:00Z date_updated: 2022-09-12T11:24:21Z file_id: '12078' file_name: qfcjsfmtvtbfrjjvhdzrnqxfvgjvxtbf.zip file_size: 944534 relation: source_file file_date_updated: 2022-09-12T11:24:21Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '208' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-023-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12076' relation: part_of_dissertation status: public - id: '12077' relation: part_of_dissertation status: public status: public supervisor: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 title: 'Existence and density problems in Diophantine geometry: From norm forms to Campana points' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11777' abstract: - lang: eng text: "In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pascal full_name: Wild, Pascal id: 4C20D868-F248-11E8-B48F-1D18A9856A87 last_name: Wild citation: ama: Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:10.15479/at:ista:11777 apa: Wild, P. (2022). High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. https://doi.org/10.15479/at:ista:11777 chicago: Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. https://doi.org/10.15479/at:ista:11777. ieee: P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022. ista: Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology. mla: Wild, Pascal. High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes. Institute of Science and Technology, 2022, doi:10.15479/at:ista:11777. short: P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022. date_created: 2022-08-10T15:51:19Z date_published: 2022-08-11T00:00:00Z date_updated: 2023-06-22T09:56:36Z day: '11' ddc: - '500' - '516' - '514' degree_awarded: PhD department: - _id: GradSch - _id: UlWa doi: 10.15479/at:ista:11777 ec_funded: 1 file: - access_level: open_access checksum: f5f3af1fb7c8a24b71ddc88ad7f7c5b4 content_type: text/x-python creator: pwild date_created: 2022-08-10T15:34:04Z date_updated: 2022-08-10T15:34:04Z description: Code for computer-assisted proofs in Section 8.4.7 in Thesis file_id: '11780' file_name: flags.py file_size: 16828 relation: supplementary_material - access_level: open_access checksum: 1f7c12dfe3bdaa9b147e4fbc3d34e3d5 content_type: text/x-c++src creator: pwild date_created: 2022-08-10T15:34:10Z date_updated: 2022-08-10T15:34:10Z description: Code for proof of Lemma 8.20 in Thesis file_id: '11781' file_name: lowerbound.cpp file_size: 12226 relation: supplementary_material - access_level: open_access checksum: 4cf81455c49e5dec3b9b2e3980137eeb content_type: text/x-python creator: pwild date_created: 2022-08-10T15:34:17Z date_updated: 2022-08-10T15:34:17Z description: Code for proof of Proposition 7.9 in Thesis file_id: '11782' file_name: upperbound.py file_size: 3240 relation: supplementary_material - access_level: open_access checksum: 4e96575b10cbe4e0d0db2045b2847774 content_type: application/pdf creator: pwild date_created: 2022-08-11T16:08:33Z date_updated: 2022-08-11T16:08:33Z file_id: '11809' file_name: finalthesisPascalWildPDFA.pdf file_size: 5086282 relation: main_file title: High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes - access_level: closed checksum: 92d94842a1fb6dca5808448137573b2e content_type: application/zip creator: pwild date_created: 2022-08-11T16:09:19Z date_updated: 2022-08-11T16:09:19Z file_id: '11810' file_name: ThesisSubmission.zip file_size: 18150068 relation: source_file file_date_updated: 2022-08-11T16:09:19Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '170' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-021-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: High-dimensional expansion and crossing numbers of simplicial complexes type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11128' abstract: - lang: eng text: "Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline." acknowledged_ssus: - _id: ScienComp - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lenka full_name: Matejovicova, Lenka id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87 last_name: Matejovicova citation: ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128 apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128 chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128. ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022. ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128. short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022. date_created: 2022-04-07T08:19:54Z date_published: 2022-04-06T00:00:00Z date_updated: 2023-06-23T06:26:41Z day: '06' ddc: - '576' - '582' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11128 file: - access_level: open_access checksum: e9609bc4e8f8e20146fc1125fd4f1bf7 content_type: application/pdf creator: cchlebak date_created: 2022-04-07T08:11:34Z date_updated: 2022-04-07T08:11:34Z file_id: '11129' file_name: LenkaPhD_Official_PDFA.pdf file_size: 11906472 relation: main_file - access_level: closed checksum: 99d67040432fd07a225643a212ee8588 content_type: application/x-zip-compressed creator: cchlebak date_created: 2022-04-07T08:11:51Z date_updated: 2022-04-07T08:11:51Z file_id: '11130' file_name: LenkaPhD Official_source.zip file_size: 23036766 relation: source_file file_date_updated: 2022-04-07T08:11:51Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '112' publication_identifier: isbn: - 978-3-99078-016-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Genetic basis of flower colour as a model for adaptive evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '11945' abstract: - lang: eng text: "G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.\r\nWe validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.\r\nOur DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level." acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X citation: ama: Schulz R. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. 2022. doi:10.15479/at:ista:11945 apa: Schulz, R. (2022). Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11945 chicago: Schulz, Rouven. “Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11945. ieee: R. Schulz, “Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function,” Institute of Science and Technology Austria, 2022. ista: Schulz R. 2022. Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function. Institute of Science and Technology Austria. mla: Schulz, Rouven. Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11945. short: R. Schulz, Chimeric G Protein-Coupled Receptors Mimic Distinct Signaling Pathways and Modulate Microglia Function, Institute of Science and Technology Austria, 2022. date_created: 2022-08-23T11:33:11Z date_published: 2022-08-23T00:00:00Z date_updated: 2023-08-03T13:02:26Z day: '23' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/at:ista:11945 file: - access_level: open_access checksum: 61b1b666a210ff7cdd0e95ea75207a13 content_type: application/pdf creator: rschulz date_created: 2022-08-25T08:59:57Z date_updated: 2022-08-25T08:59:57Z file_id: '11970' file_name: Thesis_Rouven_Schulz_2022_final.pdf file_size: 28079331 relation: main_file success: 1 - access_level: closed checksum: 2b8f95ea1c134dbdb927b41b1dbeeeb5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rschulz date_created: 2022-08-25T09:00:11Z date_updated: 2022-08-25T09:33:31Z file_id: '11971' file_name: Thesis_Rouven_Schulz_2022_final.docx file_size: 27226963 relation: source_file file_date_updated: 2022-08-25T09:33:31Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '133' project: - _id: 267F75D8-B435-11E9-9278-68D0E5697425 name: Modulating microglia through G protein-coupled receptor (GPCR) signaling publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11995' relation: dissertation_contains status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12390' abstract: - lang: eng text: "The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that\r\nis broken on the level of the corresponding effective theory. In particular we are going to\r\ninvestigate translation-invariant Bose gases in the mean field limit, effectively described by\r\nthe Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively\r\ndescribed by the Pekar functional. The latter is a model describing the interaction between a\r\ncharged particle and the optical modes of a polar crystal. Regarding the former, we assume in\r\naddition that the particles in the gas are unconfined, and typically we will consider particles\r\nthat are subject to an attractive interaction. In both cases the ground state energy of the\r\nHamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on\r\nthe contrary there exists a whole invariant orbit of minimizers for the corresponding effective\r\nfunctionals. Both, the absence of proper eigenstates and the broken symmetry of the effective\r\ntheory, make the study significantly more involved and it is the content of this thesis to\r\ndevelop a frameworks which allows for a systematic way to circumvent these issues.\r\nIt is a well-established result that the ground state energy of Bose gases in the mean field limit,\r\nas well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is\r\nto leading order given by the minimal energy of the corresponding effective theory. As part\r\nof this thesis we identify the sub-leading term in the expansion of the ground state energy,\r\nwhich can be interpreted as the quantum correction to the classical energy, since the effective\r\ntheories under consideration can be seen as classical counterparts.\r\nWe are further going to establish an asymptotic expression for the energy-momentum relation\r\nof the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta,\r\nthis asymptotic expression agrees with the energy-momentum relation of a free particle having\r\nan effectively increased mass, and we find that this effectively increased mass agrees with the\r\nconjectured value in the physics literature.\r\nIn addition we will discuss two unrelated papers written by the author during his stay at ISTA\r\nin the appendix. The first one concerns the realization of anyons, which are quasi-particles\r\nacquiring a non-trivial phase under the exchange of two particles, as molecular impurities.\r\nThe second one provides a classification of those vector fields defined on a given manifold\r\nthat can be written as the gradient of a given functional with respect to a suitable metric,\r\nprovided that some mild smoothness assumptions hold. This classification is subsequently\r\nused to identify those quantum Markov semigroups that can be written as a gradient flow of\r\nthe relative entropy.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 citation: ama: Brooks M. Translation-invariant quantum systems with effectively broken symmetry. 2022. doi:10.15479/at:ista:12390 apa: Brooks, M. (2022). Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12390 chicago: Brooks, Morris. “Translation-Invariant Quantum Systems with Effectively Broken Symmetry.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12390. ieee: M. Brooks, “Translation-invariant quantum systems with effectively broken symmetry,” Institute of Science and Technology Austria, 2022. ista: Brooks M. 2022. Translation-invariant quantum systems with effectively broken symmetry. Institute of Science and Technology Austria. mla: Brooks, Morris. Translation-Invariant Quantum Systems with Effectively Broken Symmetry. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12390. short: M. Brooks, Translation-Invariant Quantum Systems with Effectively Broken Symmetry, Institute of Science and Technology Austria, 2022. date_created: 2023-01-26T10:00:42Z date_published: 2022-12-15T00:00:00Z date_updated: 2023-08-07T13:32:09Z day: '15' ddc: - '500' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:12390 ec_funded: 1 file: - access_level: open_access checksum: b31460e937f33b557abb40ebef02b567 content_type: application/pdf creator: cchlebak date_created: 2023-01-26T10:02:34Z date_updated: 2023-01-26T10:02:34Z file_id: '12391' file_name: Brooks_Thesis.pdf file_size: 3095225 relation: main_file success: 1 - access_level: closed checksum: 9751869fa5e7981588ad4228f4fd4bd6 content_type: application/octet-stream creator: cchlebak date_created: 2023-01-26T10:02:42Z date_updated: 2023-01-26T10:02:42Z file_id: '12392' file_name: Brooks_Thesis.tex file_size: 809842 relation: source_file file_date_updated: 2023-01-26T10:02:42Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '196' project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9005' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Translation-invariant quantum systems with effectively broken symmetry tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ... --- _id: '12368' abstract: - lang: eng text: "Metazoan development relies on the formation and remodeling of cell-cell contacts. The \r\nbinding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell \r\ninteraction sites have been implicated in cell-cell contact formation. Yet, how these two \r\nprocesses functionally interact to drive cell-cell contact expansion and strengthening \r\nremains unclear. Here, we study how primary germ layer progenitor cells from zebrafish \r\nbind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an \r\nassay system for monitoring cell-cell contact formation at high spatiotemporal resolution. \r\nWe show that cell-cell contact formation represents a two-tiered process: E-cadherin\x02mediated downregulation of the small GTPase RhoA at the forming contact leads to both \r\ndepletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin \r\nnetwork flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the \r\ncontact zone, with Myosin-2 displaying higher cortical localization outside than inside of \r\nthe contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin \r\nnetwork at the contact disc, but also lead to an accumulation of both F-actin and E\x02cadherin at the contact rim. Eventually, this combination of actomyosin downregulation \r\nand flows at the contact contribute to the characteristic molecular organization implicated \r\nin contact formation and maintenance: depletion of cortical actomyosin at the contact disc, \r\ndriving contact expansion by lowering interfacial tension at the contact, and accumulation \r\nof both E-cadherin and F-actin at the contact rim, mechanically linking the contractile \r\ncortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how \r\nadhesion signaling and cell mechanics function together to modulate the spatial \r\norganization of cell-cell contacts." acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: NanoFab alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 citation: ama: Arslan FN. Remodeling of E-cadherin-mediated contacts via cortical  flows. 2022. doi:10.15479/at:ista:12153 apa: Arslan, F. N. (2022). Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12153 chicago: Arslan, Feyza N. “Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12153. ieee: F. N. Arslan, “Remodeling of E-cadherin-mediated contacts via cortical  flows,” Institute of Science and Technology Austria, 2022. ista: Arslan FN. 2022. Remodeling of E-cadherin-mediated contacts via cortical  flows. Institute of Science and Technology Austria. mla: Arslan, Feyza N. Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12153. short: F.N. Arslan, Remodeling of E-Cadherin-Mediated Contacts via Cortical  Flows, Institute of Science and Technology Austria, 2022. date_created: 2023-01-25T10:43:24Z date_published: 2022-09-29T00:00:00Z date_updated: 2023-08-08T13:14:10Z day: '29' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: CaHe doi: 10.15479/at:ista:12153 ec_funded: 1 file: - access_level: open_access checksum: e54a3e69b83ebf166544164afd25608e content_type: application/pdf creator: cchlebak date_created: 2023-01-25T10:52:46Z date_updated: 2023-01-25T10:52:46Z file_id: '12369' file_name: THESIS_FINAL_FArslan_pdfa.pdf file_size: 14581024 relation: main_file success: 1 file_date_updated: 2023-01-25T10:52:46Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation publication_identifier: isbn: - ' 978-3-99078-025-1 ' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9350' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: Remodeling of E-cadherin-mediated contacts via cortical flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11362' abstract: - lang: eng text: "Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner citation: ama: Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362 apa: Lechner, M. (2022). Learning verifiable representations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11362 chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362. ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022. ista: Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria. mla: Lechner, Mathias. Learning Verifiable Representations. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11362. short: M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022. date_created: 2022-05-12T07:14:01Z date_published: 2022-05-12T00:00:00Z date_updated: 2023-08-17T06:58:38Z day: '12' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: ToHe doi: 10.15479/at:ista:11362 ec_funded: 1 file: - access_level: closed checksum: 8eefa9c7c10ca7e1a2ccdd731962a645 content_type: application/zip creator: mlechner date_created: 2022-05-13T12:33:26Z date_updated: 2022-05-13T12:49:00Z file_id: '11378' file_name: src.zip file_size: 13210143 relation: source_file - access_level: open_access checksum: 1b9e1e5a9a83ed9d89dad2f5133dc026 content_type: application/pdf creator: mlechner date_created: 2022-05-16T08:02:28Z date_updated: 2022-05-17T15:19:39Z file_id: '11382' file_name: thesis_main-a2.pdf file_size: 2732536 relation: main_file file_date_updated: 2022-05-17T15:19:39Z has_accepted_license: '1' keyword: - neural networks - verification - machine learning language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: '124' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication_identifier: isbn: - 978-3-99078-017-6 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10665' relation: part_of_dissertation status: public - id: '10667' relation: part_of_dissertation status: public - id: '11366' relation: part_of_dissertation status: public - id: '7808' relation: part_of_dissertation status: public - id: '10666' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: Learning verifiable representations tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2022' ...