--- OA_place: publisher _id: '19836' abstract: - lang: eng text: "Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo citation: ama: 'Saez Mollejo J. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . 2025. doi:10.15479/AT-ISTA-19836' apa: 'Saez Mollejo, J. (2025). Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19836' chicago: 'Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19836.' ieee: 'J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.' ista: 'Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria.' mla: 'Saez Mollejo, Jaime. Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning . Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19836.' short: 'J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-06-13T09:01:50Z date_published: 2025-06-13T00:00:00Z date_updated: 2026-05-20T06:42:16Z day: '13' ddc: - '530' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/AT-ISTA-19836 file: - access_level: closed checksum: 643bfddead59857536cce4d57c775b32 content_type: application/x-zip-compressed creator: jsaezmol date_created: 2025-06-16T09:38:49Z date_updated: 2026-04-01T22:30:07Z embargo_to: open_access file_id: '19849' file_name: istaustriathesis-master - Copy.zip file_size: 59892829 relation: source_file - access_level: open_access checksum: e3dcb767fcc2b1787a455fdda991cefb content_type: application/pdf creator: jsaezmol date_created: 2025-06-18T08:50:16Z date_updated: 2026-04-01T22:30:07Z embargo: 2026-04-01 file_id: '19851' file_name: SaezMollejo_PhDFinal_pdfa-1b.pdf file_size: 22382376 relation: main_file file_date_updated: 2026-04-01T22:30:07Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '06' oa: 1 oa_version: Published Version page: '175' project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19424' relation: part_of_dissertation 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: 'Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ' 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: '2025' ... --- OA_place: publisher _id: '20449' abstract: - lang: eng text: "Males and females of many species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. " acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett citation: ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449 apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449 chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449. ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025. ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449. short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-11T08:18:51Z date_published: 2025-10-10T00:00:00Z date_updated: 2026-06-12T08:32:16Z day: '10' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-20449 file: - access_level: open_access checksum: 26905c22bca417198a733d792d8ce422 content_type: application/pdf creator: vbett date_created: 2025-10-20T13:32:29Z date_updated: 2026-06-01T22:30:04Z embargo: 2026-06-01 file_id: '20507' file_name: 2025_Bett_Vincent_Thesis.pdf file_size: 18507283 relation: main_file - access_level: closed checksum: 6a09a8d126d3628bfd8a35202735f267 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vbett date_created: 2025-10-20T13:35:34Z date_updated: 2026-06-01T22:30:04Z embargo_to: open_access file_id: '20508' file_name: 2025_Bett_Vincent_Thesis.docx file_size: 17163921 relation: source_file file_date_updated: 2026-06-01T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '114' project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19735' relation: part_of_dissertation status: public - id: '15009' 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 title: Evolution and regulation of the Z chromosome 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: '2025' ... --- OA_place: publisher _id: '19993' abstract: - lang: eng text: "Ants are frequently challenged by different pathogens, which they counter with\r\nindividual and collective responses. Usually, the pathogens like fungi or viruses are\r\nsolitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These\r\nentomopathogenic nematodes are active parasites with an own behavior and chasing\r\npray.\r\nIn the first chapter, we investigated the basic biology of the host-pathogen relationship.\r\nWe tested different ant life stages and found that adult ants display defense behaviors\r\nand are generally resistant to nematode infection, whereas brood is highly susceptible.\r\nIn the case of worker pupae, we found a slight protective effect of the cocoon. When\r\nlarvae are accompanied by adults, meaning a queen or a group of workers, survival is\r\nsignificantly enhanced. Moreover, we found that nematodes can transmit from infected\r\ncadavers to healthy worker larvae, confirming a transmissible disease in ants. Again,\r\nworker presence significantly reduces transmission risk. In the end, we were also able\r\nto disentangle the pathogen system and investigate the pathogenic effect of the\r\nbacterial and nematode components.\r\nIn the second chapter, we studied the effect of multiple infections in adult queens and\r\nqueen larvae. By multiple exposures in the mode of coinfection and superinfections,\r\nwe wanted to assess the detrimental effect of combined fungal and nematode\r\nexposure to better understand how the pathogens interact with each other in an ant\r\nhost. We found instances where combined exposure lead to higher mortality in a given\r\ntime frame in both, adult queens and queen larvae.\r\nOverall entomopathogenic nematodes are a promising model to study worm infections\r\nin ants which extend our knowledge on collective disease defense." acknowledged_ssus: - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Florian full_name: Strahodinsky, Florian id: 979E35EE-C996-11E9-8C7C-CF13E6697425 last_name: Strahodinsky citation: ama: Strahodinsky F. Social immunity in a tri-partite host-pathogen relationship. 2025. doi:10.15479/AT-ISTA-19993 apa: Strahodinsky, F. (2025). Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19993 chicago: Strahodinsky, Florian. “Social Immunity in a Tri-Partite Host-Pathogen Relationship.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19993. ieee: F. Strahodinsky, “Social immunity in a tri-partite host-pathogen relationship,” Institute of Science and Technology Austria, 2025. ista: Strahodinsky F. 2025. Social immunity in a tri-partite host-pathogen relationship. Institute of Science and Technology Austria. mla: Strahodinsky, Florian. Social Immunity in a Tri-Partite Host-Pathogen Relationship. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19993. short: F. Strahodinsky, Social Immunity in a Tri-Partite Host-Pathogen Relationship, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-10T14:12:20Z date_published: 2025-07-11T00:00:00Z date_updated: 2026-04-07T12:39:58Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SyCr doi: 10.15479/AT-ISTA-19993 file: - access_level: closed checksum: df3a02f0d937ea9a3d79d5fb94fff097 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fstrahod date_created: 2025-07-14T13:18:37Z date_updated: 2026-01-15T23:30:03Z embargo_to: open_access file_id: '20021' file_name: Thesis_Florian_Strahodinsky_DOCX.docx file_size: 9857392 relation: source_file - access_level: open_access checksum: 7164c21fe1946e839f7b8acd255ce803 content_type: application/pdf creator: fstrahod date_created: 2025-07-14T13:18:38Z date_updated: 2026-01-15T23:30:03Z embargo: 2026-01-15 file_id: '20022' file_name: Thesis_Florian_Strahodinsky_PDF.pdf file_size: 6439602 relation: main_file file_date_updated: 2026-01-15T23:30:03Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: '138' publication_identifier: 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: Social immunity in a tri-partite host-pathogen relationship 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19906' abstract: - lang: eng text: "Flows of ordinary fluids such as water or air transition from laminar to turbulent\r\nmotion as the velocity increases. This simple dependence of the flow state\r\nsolely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here\r\nvarious different instabilities and turbulent states can arise at low and even\r\nvanishing inertia, while high inertia turbulence counterintuitively is suppressed\r\nand its drag strongly reduced. We here show in experiments of a viscoelastic\r\nmodel fluid that the phenomena observed at low and high inertia have a\r\ncommon origin and that the same dynamical state, elasto-inertial turbulence,\r\npersists across four orders of magnitude in Reynolds number, ranging from\r\nvery low inertia, all the way to high inertia Maximum drag reduction (MDR)\r\nasymptote. We also explore the transitions from Newtonian turbulence to\r\nMDR, and specific cases of flow at high polymer concentrations, exploring the\r\nrelationship between flow at these wide range of control parameters.\r\n" acknowledged_ssus: - _id: M-Shop acknowledgement: "This work was partially funded by the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie grant agreement\r\nNo. 665385." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sarath S full_name: Suresh, Sarath S id: 3D126CC4-F248-11E8-B48F-1D18A9856A87 last_name: Suresh citation: ama: 'Suresh SS. Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. 2025. doi:10.15479/AT-ISTA-19906' apa: 'Suresh, S. S. (2025). Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19906' chicago: 'Suresh, Sarath S. “Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19906.' ieee: 'S. S. Suresh, “Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote,” Institute of Science and Technology Austria, 2025.' ista: 'Suresh SS. 2025. Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote. Institute of Science and Technology Austria.' mla: 'Suresh, Sarath S. Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19906.' short: 'S.S. Suresh, Turbulence in Polymeric Flows : A Characterisation of Elasto-Inertial Turbulence and the Maximum Drag Reduction Asymptote, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-06-26T08:39:08Z date_published: 2025-06-26T00:00:00Z date_updated: 2026-04-07T12:39:19Z day: '26' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/AT-ISTA-19906 ec_funded: 1 file: - access_level: open_access checksum: 302a07605a9e64ac247c2036d5f5b1cd content_type: application/pdf creator: cchlebak date_created: 2025-06-26T08:40:53Z date_updated: 2025-12-27T23:30:02Z embargo: 2025-12-27 file_id: '19907' file_name: Thesis_v9_PDFA2b.pdf file_size: 6504571 relation: main_file - access_level: closed checksum: 5d69d10bdacc24c27f02924379405bd9 content_type: application/x-zip-compressed creator: cchlebak date_created: 2025-06-26T08:41:24Z date_updated: 2025-12-27T23:30:02Z embargo_to: open_access file_id: '19908' file_name: Thesis Template - ISTA [istaustriathesis].zip file_size: 59092991 relation: source_file file_date_updated: 2025-12-27T23:30:02Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '06' 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: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10299' relation: part_of_dissertation 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: 'Turbulence in polymeric flows : A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20470' abstract: - lang: eng text: "Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bryan full_name: Wu, Bryan id: 3C521EBA-F248-11E8-B48F-1D18A9856A87 last_name: Wu citation: ama: Wu B. An examination on phages as a naturally composable system. 2025. doi:10.15479/AT-ISTA-20470 apa: Wu, B. (2025). An examination on phages as a naturally composable system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20470 chicago: Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20470. ieee: B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025. ista: Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria. mla: Wu, Bryan. An Examination on Phages as a Naturally Composable System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20470. short: B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-15T13:30:21Z date_published: 2025-10-30T00:00:00Z date_updated: 2026-05-06T08:01:28Z day: '30' ddc: - '579' degree_awarded: PhD department: - _id: GradSch - _id: CaGu doi: 10.15479/AT-ISTA-20470 file: - access_level: closed checksum: d32ea83f259f6b0506325cd57b1d44c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: brwu date_created: 2025-10-21T17:33:27Z date_updated: 2026-04-30T22:30:02Z embargo_to: open_access file_id: '20516' file_name: 2025_Wu_Bryan_Thesis.docx file_size: 10603235 relation: source_file - access_level: open_access checksum: 53590046fd3244c5550b4022282449d2 content_type: application/pdf creator: brwu date_created: 2025-10-21T17:33:26Z date_updated: 2026-04-30T22:30:02Z embargo: 2026-04-30 file_id: '20517' file_name: 2025_Wu_Bryan_Thesis.pdf file_size: 6251936 relation: main_file file_date_updated: 2026-04-30T22:30:02Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: An examination on phages as a naturally composable system type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20694' abstract: - lang: eng text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.\r\nA persistent challenge in the field is to identify loci that contribute to reproductive isolation,\r\nwhile disentangling signals of selection from demography, linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches that rely on site-based statistics in\r\narbitrary fixed windows face inherent limitations, as they conflate historical and\r\ncontemporary processes of divergence and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce and recombine through time. By directly analysing haplotype clustering by species\r\nor phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow, and tracing their evolutionary history.\r\nIn this thesis, I explore the utility of genealogical approaches for studying species\r\ndivergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks\r\nthrough the structure of the ARG, using simulations and empirical data to highlight how\r\ngenealogical processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter 3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails Littorina. These snails offer a unique opportunity to study an innovation because they\r\ninclude a very recent transition from egg-laying to live bearing, yet snails with the different\r\nreproductive modes are not reciprocally monophyletic. I exploited this by using topology\r\nclustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying\r\nto live-bearing involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale, phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging, then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy combines molecular phasing with statistical phasing to generate phased whole\r\ngenome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn chapter 5, I analyse hybridising populations from two replicate hybrid zones to find\r\na parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape\r\ndriven by variation in demographic history. While outlier genome scans of FST failed to dissect\r\nthe causes of differentiation, ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes across hybrid zones. In addition to the biological insight, this chapter\r\nalso presents a comparison of the latest ARG inference tools, showing that signals of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods, despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association studies of floral pigmentation with genealogical\r\ninference, to test for additional colour loci, and confirm the effect of previously described loci.\r\nThis work demonstrates that flower colour variation is driven by a small number of large effect\r\nloci, while also hinting at the presence of a new candidate regulatory factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary origins. My results show that it\r\nconsists of 5 highly divergent loci, each of which is associated with flower colour. Using\r\npatterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent localized barrier to gene flow within an otherwise permeable genome.\r\nTogether, these chapters add to the increasing pool of studies using genealogical\r\napproaches to complement and extend site-based statistics to use haplotype structures in\r\nspeciation research. By tracking haplotypes directly and connecting genealogical clustering to\r\npopulation processes, ARG-based inference promises to provide new insights into how local\r\nselective pressures, demographic history, and long-term barriers interact to shape the\r\ngenomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about\r\nthe benefits of using genealogical inference to learn more than what site-based statistics\r\ncould tell us." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 citation: ama: Pal A. Using genealogies to study the genomic basis of species divergence. 2025. doi:10.15479/AT-ISTA-20694 apa: Pal, A. (2025). Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694 chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694. ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,” Institute of Science and Technology Austria, 2025. ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence. Institute of Science and Technology Austria. mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694. short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-11-25T13:19:11Z date_published: 2025-11-25T00:00:00Z date_updated: 2026-04-28T13:20:36Z day: '25' ddc: - '576' - '578' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/AT-ISTA-20694 file: - access_level: open_access checksum: 7a10a738d58524aebb5dcbd9b34c21c5 content_type: application/pdf creator: apal date_created: 2025-12-01T13:53:36Z date_updated: 2026-03-01T23:30:03Z embargo: 2026-03-01 file_id: '20721' file_name: 2025_Pal_Arka_Thesis.pdf file_size: 42723135 relation: main_file - access_level: closed checksum: 166d832b08d0434ce407f8f3cb930fe5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: apal date_created: 2025-12-01T13:53:39Z date_updated: 2026-03-01T23:30:03Z embargo_to: open_access file_id: '20722' file_name: 2025_Pal_Arka_Thesis.docx file_size: 60632116 relation: source_file file_date_updated: 2026-03-01T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '268' project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12159' relation: part_of_dissertation status: public - id: '14796' relation: part_of_dissertation status: public - id: '20190' 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: Using genealogies to study the genomic basis of species divergence tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20777' abstract: - lang: eng text: "A major challenge in neuroscience is deciphering how the brain orchestrates behavior in\r\nresponse to changes in environmental conditions. This process is characterized by several\r\nprocessing stages, from perception to the storage of important information. Information\r\nstorage is performed by a memory system implemented through complex networks of highly\r\ninterconnected neurons. The collective operational principles of neuronal networks that support\r\nformation and storage are the main topics of this thesis.\r\nTo investigate the collective dynamics of the hippocampus from the perspective of the brain\r\ncriticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches\r\n¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures\r\nderived from neuronal avalanches suggested that during wakefulness the hippocampus operated\r\nfurther away from criticality than during sleep/rest. In addition, neural activity propagated\r\ndifferently in these two brain states, as indicated by different collapses of the avalanche shapes.\r\nNext, the Phenomenological Renormalization Group approach also indicated conceptually\r\nsimilar differences, through the scaling exponent of activity variance α, which was higher during\r\nsleep/rest than during awake. These results confirmed that the activity of the hippocampus\r\nexhibits signatures of criticality and that these signatures change with the state of the brain.\r\nNext, I found that memory retention was predicted by the scaling exponent of activity variance\r\nα. The exponent α measured during the sleep/rest session that followed learning correlated\r\nwith memory retention during the subsequent unrewarded testing session. Moreover, α\r\npredicted performance even when controlled for reactivation that occurs in parallel. Second, α\r\nmeasured in the sleep/rest phase that preceded learning was correlated with the learning speed.\r\nI analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day\r\nvariability of these distributions, during sleep/rest that followed learning, correlated with the\r\nscaling exponent of activity variance α, as well as with memory retention. These findings\r\nconfirmed that variance scaling and functional heterogeneity provide behaviorally meaningful\r\nperspectives on hippocampal activity, as they are directly related to memory consolidation.\r\nI further investigated the process of memory acquisition and consolidation between the\r\nhippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards\r\nthe goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals\r\nduring sleep/rest that followed learning. This shift during sleep/rest was supported by the\r\nreactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and\r\nindependently of the hippocampal SWRs. Both types of reactivation predicted subsequent\r\nmemory retention, as well as the amount of goal-related remapping. Again, the day-to-day\r\nvariability of the distribution of the cell timescales correlated with the goal-related remapping,\r\nin CA1 during the learning session and in mEC during sleep/rest. These results suggest that\r\nin spatial navigation tasks, the functional responsibilities of CA1 and mEC change between\r\nlearning and sleep/rest and that their function benefits from increased functional heterogeneity\r\namong cells.\r\n" acknowledgement: "My work has been funded through the project \"Functional Advantages of Critical Brain\r\nDynamics\" of the ISTA interdisciplinary fund and through the FWF.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Predrag full_name: Zivadinovic, Predrag id: 68AA0E5A-AFDA-11E9-9994-141DE6697425 last_name: Zivadinovic citation: ama: Zivadinovic P. Scale-free activity as a basis for spatial learning and memory in the brain. 2025. doi:10.15479/AT-ISTA-20777 apa: Zivadinovic, P. (2025). Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20777 chicago: Zivadinovic, Predrag. “Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20777. ieee: P. Zivadinovic, “Scale-free activity as a basis for spatial learning and memory in the brain,” Institute of Science and Technology Austria, 2025. ista: Zivadinovic P. 2025. Scale-free activity as a basis for spatial learning and memory in the brain. Institute of Science and Technology Austria. mla: Zivadinovic, Predrag. Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20777. short: P. Zivadinovic, Scale-Free Activity as a Basis for Spatial Learning and Memory in the Brain, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-12-10T19:37:41Z date_published: 2025-12-11T00:00:00Z date_updated: 2026-07-24T08:14:37Z day: '11' ddc: - '570' - '539' - '571' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/AT-ISTA-20777 doi_confirm: '1' file: - access_level: open_access checksum: aae9d1ed53f7b67f75e289c26a02b72f content_type: application/pdf creator: pzivadin date_created: 2025-12-10T19:28:20Z date_updated: 2026-06-11T22:30:02Z embargo: 2026-06-11 file_id: '20778' file_name: 2025_Zivadinovic_Predrag_PhD_thesis.pdf file_size: 8105379 relation: main_file - access_level: closed checksum: 8a08a3804ce7d9d625fdf1631113da8c content_type: application/zip creator: pzivadin date_created: 2025-12-10T19:28:10Z date_updated: 2026-06-11T22:30:02Z embargo_to: open_access file_id: '20779' file_name: 2025_Zivadinovic_Predrag_PhD_thesis_source.zip file_size: 8512240 relation: source_file file_date_updated: 2026-06-11T22:30:02Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '104' project: - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics 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: Scale-free activity as a basis for spatial learning and memory in the brain type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20563' abstract: - lang: eng text: "The theory of optimal transport provides an elegant and powerful description of many evolution\r\nequations as gradient flows. The primary objective of this thesis is to adapt and extend the\r\ntheory to deal with important equations that are not covered by the classical framework,\r\nspecifically boundary value problems and kinetic equations. Additionally, we establish new\r\nresults in periodic homogenization for discrete dynamical optimal transport and in quantization\r\nof measures.\r\nSection 1.1 serves as an invitation to the classical theory of optimal transport, including the\r\nmain definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the\r\nmain results of this thesis, outline the motivations, and review the current state of the art.\r\nIn Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet\r\nboundary conditions. We construct a time-discrete scheme involving a modification of the\r\nWasserstein distance and, under weak assumptions, prove its convergence to a solution of this\r\nboundary value problem. In dimension 1, we show that this solution is a gradient flow in a\r\nsuitable space of measures.\r\nChapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory\r\nof optimal transport to describe and study particle systems at the mesoscopic scale. We prove\r\nadapted versions of some fundamental theorems, including the Benamou–Brenier formula and\r\nthe identification of absolutely continuous curves of measures.\r\nChapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical\r\ntransportation functionals on periodic graphs in the large-scale limit when the cost functional\r\nis asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge\r\nto 1-Wasserstein distances constructed from crystalline norms on R\r\nd\r\n.\r\nChapter 5 concerns optimal empirical quantization: the problem of approximating a measure\r\nby the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein\r\ndistance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for\r\nthe minimal error as n tends to infinity.\r\n" acknowledgement: "The research contained in this thesis has received funding from the Austrian Science\r\nFund (FWF) project 10.55776/F65." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Quattrocchi F. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. 2025. doi:10.15479/AT-ISTA-20563 apa: Quattrocchi, F. (2025). Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20563 chicago: Quattrocchi, Filippo. “Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20563. ieee: F. Quattrocchi, “Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures,” Institute of Science and Technology Austria, 2025. ista: Quattrocchi F. 2025. Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures. Institute of Science and Technology Austria. mla: Quattrocchi, Filippo. Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20563. short: F. Quattrocchi, Optimal Transport Methods for Kinetic Equations, Boundary Value Problems, and Discretization of Measures, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-28T13:10:49Z date_published: 2025-11-03T00:00:00Z date_updated: 2026-07-23T06:09:20Z day: '03' ddc: - '515' - '519' degree_awarded: PhD department: - _id: GradSch - _id: JaMa doi: 10.15479/AT-ISTA-20563 file: - access_level: open_access checksum: 6f55275bdf99992be3a6457d949dd664 content_type: application/pdf creator: fquattro date_created: 2025-11-17T21:04:15Z date_updated: 2026-01-01T23:30:03Z embargo: 2026-01-01 file_id: '20653' file_name: 2025_quattrocchi_filippo_thesis.pdf file_size: 4326411 relation: main_file - access_level: closed checksum: 707e580f5d993a214c0dba456b75837b content_type: application/zip creator: fquattro date_created: 2025-11-17T21:05:43Z date_updated: 2026-01-01T23:30:03Z embargo_to: open_access file_id: '20654' file_name: 2025_quattrocchi_thesis.zip file_size: 11726509 relation: source_file file_date_updated: 2026-01-01T23:30:03Z has_accepted_license: '1' keyword: - optimal transport - kinetic equations - boundary value problems - quantization - gradient flows - homogenization language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '240' project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20569' relation: part_of_dissertation status: public - id: '20571' relation: part_of_dissertation status: public - id: '20570' relation: part_of_dissertation status: public - id: '18706' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 title: Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_embargo: '6' OA_place: publisher _id: '20798' abstract: - lang: eng text: "Atom interferometers measure the relative phase shifts between coherent matter-wave paths\r\nthat arise from interactions with external fields or inertial forces. Due to their exceptional\r\nphase sensitivity, atom interferometers became an essential tool for precision measurements\r\nand fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial\r\nnavigation. However, their measurement precision is limited by quantum projection noise,\r\nwhich arises from the Heisenberg uncertainty principle, preventing the measurement of atomic\r\nstates with absolute precision. The generation of entanglement between the atoms offers a\r\npath to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s\r\nphase sensitivity beyond classical measurement bounds.\r\nThis thesis reports on the development of an atom interferometer experiment designed to\r\nrealize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms.\r\nThe experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder\r\ninterferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is\r\ncentered on a triangular optical cavity that mediates all relevant atom-light interactions. The\r\ncavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling\r\nto perform interferometry on a continuously trapped atomic ensemble.\r\nThe thesis elaborates on the fundamental theoretical framework, the cavity design, and the full\r\noptical setup, including the detailed configuration of the developed laser stabilization methods.\r\nExperimentally, continuous loading methods were explored, resulting in an accumulation of\r\nup to 4 × 106\r\natoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift\r\ncompensation method developed for continuous loading was further applied for in-trap cooling\r\nto 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control\r\nwas verified via observation of microwave-driven Rabi oscillations, and used to characterize\r\natom-cavity coupling.\r\nThese presented results establish the experimental groundwork for the future development of\r\ncavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sebastian full_name: Wald, Sebastian id: 133F200A-B015-11E9-AD41-0EDAE5697425 last_name: Wald orcid: 0000-0002-5869-1604 citation: ama: Wald S. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. 2025. doi:10.15479/AT-ISTA-20798 apa: Wald, S. (2025). Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20798 chicago: Wald, Sebastian. “Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20798. ieee: S. Wald, “Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry,” Institute of Science and Technology Austria, 2025. ista: Wald S. 2025. Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry. Institute of Science and Technology Austria. mla: Wald, Sebastian. Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20798. short: S. Wald, Atoms in a Propagating-Wave Cavity for Squeezed Mach-Zehnder Atom Interferometry, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-12-11T11:48:11Z date_published: 2025-12-11T00:00:00Z date_updated: 2026-07-24T08:07:28Z day: '11' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: OnHo doi: 10.15479/AT-ISTA-20798 doi_confirm: '1' file: - access_level: open_access checksum: 1be72faf529a5e8a2d03cb3d5f808b77 content_type: application/pdf creator: swald date_created: 2025-12-12T11:53:42Z date_updated: 2026-06-15T22:30:03Z embargo: 2026-06-15 file_id: '20809' file_name: 2025_Wald_Sebastian_Thesis.pdf file_size: 47536855 relation: main_file - access_level: closed checksum: 8c3a1904dceb4bcd04bc9f14b2594bab content_type: application/x-zip-compressed creator: swald date_created: 2025-12-12T11:54:55Z date_updated: 2026-06-15T22:30:03Z embargo_to: open_access file_id: '20810' file_name: 2025_Wald_Sebastian_Thesis.zip file_size: 40127601 relation: source_file file_date_updated: 2026-06-15T22:30:03Z has_accepted_license: '1' keyword: - entanglement-enhanced atom interferometry - cavity QED - spin-squeezing - dipole trap - quantum optics language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '12' oa: 1 oa_version: Published Version page: '152' publication_identifier: isbn: - 978-3-99078-075-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14759' relation: part_of_dissertation status: public status: public supervisor: - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X title: Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2023-12-26T22:49:53Z date_published: 2024-01-19T00:00:00Z date_updated: 2026-04-07T12:54:29Z 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: '10787' relation: part_of_dissertation status: public - id: '10658' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2024-02-23T14:02:04Z date_published: 2024-02-23T00:00:00Z date_updated: 2026-04-07T12:59:25Z 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: '7606' relation: part_of_dissertation status: public - id: '12081' relation: part_of_dissertation status: public - id: '7553' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _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. corr_author: '1' date_created: 2024-03-08T15:28:10Z date_published: 2024-03-08T00:00:00Z date_updated: 2026-04-07T12:58:48Z 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: Mathematics, Computer Science - _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316 grant_number: I4887 name: Persistent Homology, Algorithms and Stochastic Geometry - _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: '15091' relation: part_of_dissertation status: public - id: '11660' relation: part_of_dissertation status: public - id: '15090' relation: part_of_dissertation status: public - id: '15093' relation: part_of_dissertation status: public - id: '13182' relation: part_of_dissertation status: public - id: '11658' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17133' abstract: - lang: eng text: "An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 citation: ama: Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:10.15479/at:ista:17133 apa: Hassani, F. (2024). Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17133 chicago: Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17133. ieee: F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024. ista: Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria. mla: Hassani, Farid. Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17133. short: F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-06-11T18:20:05Z date_published: 2024-06-11T00:00:00Z date_updated: 2026-04-15T06:43:02Z day: '11' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/at:ista:17133 file: - access_level: open_access checksum: 258c353d47fa37ea63ea43b1e10a34a0 content_type: application/pdf creator: fhassani date_created: 2024-06-12T07:53:19Z date_updated: 2024-06-20T11:52:22Z file_id: '17137' file_name: Thesis_main_final.pdf file_size: 28370759 relation: main_file - access_level: closed checksum: deffa5d0db88093f74812fa71520d5e1 content_type: text/x-tex creator: fhassani date_created: 2024-06-12T07:54:27Z date_updated: 2024-06-12T07:54:27Z file_id: '17138' file_name: Thesis_main.tex file_size: 445735 relation: source_file file_date_updated: 2024-06-20T11:52:22Z has_accepted_license: '1' keyword: - Quantum information - Qubits - Superconducting devices language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '161' project: - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication_identifier: isbn: - 978-3-99078-040-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13227' relation: part_of_dissertation status: public - id: '9928' relation: part_of_dissertation status: public - id: '8755' 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: Superconducting qubits capable of dynamic switching between protected and high-speed control regimes 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17156' abstract: - lang: eng text: "This dissertation is the summary of the author’s work, concerning the relations between\r\ncohomology rings of algebraic varieties and rings of functions on zero schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth complex varieties with\r\nan action of a principally paired group, e.g. a parabolic subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored article [66] says that if the principal\r\nnilpotent has a unique zero, then the zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant cohomology ring, remembering the grading in terms of\r\na C^* action. A similar statement is proved also for the G-invariant functions on the total\r\nzero scheme over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult for the GKM spaces, which poses the question on a joint generalisation.\r\nWe also tackle the situation of a singular variety. As long as it is embedded in a smooth\r\nvariety with regular action, we are able to study its cohomology as well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines the cohomology ring\r\ncompletely. In largest generality, this allows us to see a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1) that the cohomology ring of spherical varieties appears as\r\nthe ring of functions on the zero scheme. The computational aspect is not easy, but one\r\ncan hope that this can bring some concrete information about such cohomology rings.\r\nLastly, the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe thesis includes also an introduction to group actions on algebraic varieties. In\r\nparticular, the vector fields associated to the actions are extensively studied. We also\r\nprovide a version of the Kostant section for arbitrary principally paired group, which\r\nparametrises the regular orbits in the Lie algebra of an algebraic group. Before proving\r\nthe main theorem, we also include a historical overview of the field. In particular we bring\r\ntogether the results of Akyildiz, Carrell and Lieberman on non-equivariant cohomology\r\nrings." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kamil P full_name: Rychlewicz, Kamil P id: 85A07246-A8BF-11E9-B4FA-D9E3E5697425 last_name: Rychlewicz citation: ama: Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:10.15479/at:ista:17156 apa: Rychlewicz, K. P. (2024). Equivariant cohomology and rings of functions. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17156 chicago: Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17156. ieee: K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute of Science and Technology Austria, 2024. ista: Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute of Science and Technology Austria. mla: Rychlewicz, Kamil P. Equivariant Cohomology and Rings of Functions. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17156. short: K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-06-23T15:07:06Z date_published: 2024-06-25T00:00:00Z date_updated: 2026-04-07T12:55:46Z day: '25' ddc: - '516' degree_awarded: PhD department: - _id: TaHa - _id: GradSch doi: 10.15479/at:ista:17156 file: - access_level: closed checksum: 1610063569f5452f8a5acef728c2fc26 content_type: application/zip creator: krychlew date_created: 2024-06-26T20:56:27Z date_updated: 2024-06-26T21:00:14Z file_id: '17179' file_name: thesis.zip file_size: 2761814 relation: source_file - access_level: open_access checksum: 7bbadb1fbc9ed2a1ecf54597f88af99c content_type: application/pdf creator: krychlew date_created: 2024-06-26T20:58:24Z date_updated: 2024-06-26T20:58:24Z file_id: '17180' file_name: thesis.pdf file_size: 3695952 relation: main_file file_date_updated: 2024-06-26T21:00:14Z has_accepted_license: '1' keyword: - equivariant cohomology - zero schemes - algebraic groups - Lie algebras language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '117' project: - _id: 34cd0f74-11ca-11ed-8bc3-bf0492a14a24 grant_number: '26525' name: Topology of open smooth varieties with a torus action publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17157' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel orcid: 0000-0002-9582-2634 title: Equivariant cohomology and rings of functions 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17164' abstract: - lang: eng text: "This thesis is structured into two parts. In the first part, we consider the random\r\nvariable X := Tr(f1(W)A1 . . . fk(W)Ak) where W is an N × N Hermitian Wigner matrix, k ∈ N, and we choose (possibly N-dependent) regular functions f1, . . . , fk as well as\r\nbounded deterministic matrices A1, . . . , Ak. In this context, we prove a functional central\r\nlimit theorem on macroscopic and mesoscopic scales, showing that the fluctuations of X\r\naround its expectation are Gaussian and that the limiting covariance structure is given\r\nby a deterministic recursion. We further give explicit error bounds in terms of the scaling\r\nof f1, . . . , fk and the number of traceless matrices among A1, . . . , Ak, thus extending\r\nthe results of Cipolloni, Erdős and Schröder [40] to products of arbitrary length k ≥ 2.\r\nAnalyzing the underlying combinatorics leads to a non-recursive formula for the variance\r\nof X as well as the covariance of X and Y := Tr(fk+1(W)Ak+1 . . . fk+ℓ(W)Ak+ℓ) of similar\r\nbuild. When restricted to polynomials, these formulas reproduce recent results of Male,\r\nMingo, Peché, and Speicher [107], showing that the underlying combinatorics of noncrossing partitions and annular non-crossing permutations continue to stay valid beyond\r\nthe setting of second-order free probability theory. As an application, we consider the\r\nfluctuation of Tr(eitW A1e\r\n−itW A2)/N around its thermal value Tr(A1) Tr(A2)/N2 when t\r\nis large and give an explicit formula for the variance.\r\nThe second part of the thesis collects three smaller projects focusing on different random\r\nmatrix models. In the first project, we show that a class of weakly perturbed Hamiltonians\r\nof the form Hλ = H0 + λW, where W is a Wigner matrix, exhibits prethermalization.\r\nThat is, the time evolution generated by Hλ relaxes to its ultimate thermal state via an\r\nintermediate prethermal state with a lifetime of order λ\r\n−2\r\n. As the main result, we obtain\r\na general relaxation formula, expressing the perturbed dynamics via the unperturbed\r\ndynamics and the ultimate thermal state. The proof relies on a two-resolvent global law\r\nfor the deformed Wigner matrix Hλ.\r\nThe second project focuses on correlated random matrices, more precisely on a correlated N × N Hermitian random matrix with a polynomially decaying metric correlation\r\nstructure. A trivial a priori bound shows that the operator norm of this model is stochastically dominated by √\r\nN. However, by calculating the trace of the moments of the matrix\r\nand using the summable decay of the cumulants, the norm estimate can be improved to a\r\nbound of order one.\r\nIn the third project, we consider a multiplicative perturbation of the form UA(t) where U\r\nis a unitary random matrix and A = diag(t, 1, ..., 1). This so-called UA model was\r\nfirst introduced by Fyodorov [73] for its applications in scattering theory. We give a\r\ngeneral description of the eigenvalue trajectories obtained by varying the parameter t and\r\nintroduce a flow of deterministic domains that separates the outlier resulting from the\r\nrank-one perturbation from the typical eigenvalues for all sub-critical timescales. The\r\nresults are obtained under generic assumptions on U that hold for various unitary random\r\nmatrices, including the circular unitary ensemble (CUE) in the original formulation of\r\nthe model." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker citation: ama: 'Reker J. Central limit theorems for random matrices: From resolvents to free probability. 2024. doi:10.15479/at:ista:17164' apa: 'Reker, J. (2024). Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17164' chicago: 'Reker, Jana. “Central Limit Theorems for Random Matrices: From Resolvents to Free Probability.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17164.' ieee: 'J. Reker, “Central limit theorems for random matrices: From resolvents to free probability,” Institute of Science and Technology Austria, 2024.' ista: 'Reker J. 2024. Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria.' mla: 'Reker, Jana. Central Limit Theorems for Random Matrices: From Resolvents to Free Probability. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17164.' short: 'J. Reker, Central Limit Theorems for Random Matrices: From Resolvents to Free Probability, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-06-24T11:23:29Z date_published: 2024-06-26T00:00:00Z date_updated: 2026-04-07T13:02:13Z day: '26' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: LaEr doi: 10.15479/at:ista:17164 ec_funded: 1 file: - access_level: open_access checksum: fb16d86e1f2753dc3a9e14d2bdfd84cd content_type: application/pdf creator: jreker date_created: 2024-06-26T12:39:36Z date_updated: 2024-06-26T12:44:53Z file_id: '17176' file_name: ISTA_Thesis_JReker.pdf file_size: 2783027 relation: main_file - access_level: closed checksum: cb1e54009d47c1dcf5b866c4566fa27f content_type: application/zip creator: jreker date_created: 2024-06-26T12:39:42Z date_updated: 2024-06-26T12:44:53Z file_id: '17177' file_name: ISTA_Thesis_JReker_SourceFiles.zip file_size: 3054878 relation: source_file file_date_updated: 2024-06-26T12:44:53Z has_accepted_license: '1' keyword: - Random Matrices - Spectrum - Central Limit Theorem - Resolvent - Free Probability language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '206' project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17173' relation: part_of_dissertation status: public - id: '11135' relation: part_of_dissertation status: public - id: '17047' relation: part_of_dissertation status: public - id: '17154' relation: part_of_dissertation status: public - id: '17174' relation: part_of_dissertation status: public status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: 'Central limit theorems for random matrices: From resolvents to free probability' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18515' abstract: - lang: eng text: "Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations." acknowledged_ssus: - _id: ScienComp acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh orcid: 0000-0001-6395-386X citation: ama: Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515 apa: Surendranadh, P. (2024). Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18515 chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18515. ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024. ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria. mla: Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18515. short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-06T21:25:37Z date_published: 2024-11-07T00:00:00Z date_updated: 2026-04-07T12:56:52Z day: '07' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:18515 file: - access_level: open_access checksum: c32cf7bc75748d9c551d8eb70178bbec content_type: application/pdf creator: psurendr date_created: 2024-11-07T10:59:29Z date_updated: 2024-11-07T10:59:29Z file_id: '18519' file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf file_size: 37019760 relation: main_file success: 1 - access_level: closed checksum: 4417e02d54084d89e75734e18caaa96d content_type: application/zip creator: psurendr date_created: 2024-11-07T10:59:42Z date_updated: 2024-11-07T10:59:42Z file_id: '18520' file_name: PhD Thesis- Parvathy_071124.zip file_size: 41198857 relation: source_file file_date_updated: 2024-11-07T10:59:42Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '219' project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation - _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 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: Effect of population structure on neutral genetic variation and barriers to gene exchange 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18568' abstract: - lang: eng text: "Locomotion is ubiquitous in the animal kingdom because an animal's survival depends on its ability to navigate its environment to find food, avoid predators and locate potential mates. These behaviours require control mechanisms that can extract information from the environment, particularly visual cues. Selective evolutionary pressures have thus refined such visuomotor transformations in a species-specific manner to meet the specific ecological and ethological challenges of each organism. However, a common challenge across organisms as visual information processing\r\nbecomes increasingly detailed is the mechanisms required to synthesise disparate pieces of information into a coherent percept or unified picture of the world. In this thesis, I investigate how disparate visual information is combined in the brain of Drosophila melanogaster to effectively guide locomotion.\r\nFor this, I first designed and built a behavioural setup to record locomotion and present visual stimuli to freely-walking fruit flies in a closed-loop manner. This setup allowed the investigation of innate visually-guided behaviours, including the optomotor reflex and courtship.\r\nSecond, taking advantage of my system I investigated the optomotor response, a reflexive visual stabilisation behaviour in which flies turn in the direction of global motion to minimise retinal slip. This behaviour is thought to be mediated by Lobula plate tangential cells (LPTCs); a complex network of optic-flow-sensitive neurons essential for self-motion estimation. Using a novel genetic mutant, I demonstrate that electrical coupling between two LPTC subtypes, contralateral HS and H2 neurons, regulates the balance between smooth optomotor turning and saccadic anti-optomotor responses. These findings underscore the critical role of binocular motion cue integration in guiding course control. Finally, I developed a novel behavioural paradigm in which a sexually aroused male fruit fly is presented with an optomotor distractor. This setup creates competition between two visual behaviours, courtship tracking and the optomotor response, enabling me to explore how the visual system resolves this conflict. In this setting, males\r\nengaged in courtship selectively suppress their optomotor response based on the female's location. Furthermore, when this experiment is replicated with an “artificial female”, optogenetically aroused males alternate between tracking and optomotor responses. The probability and dynamics of this switching are determined by the relative strengths of the two competing stimuli. In summary, the results presented in this thesis explore two mechanisms – integration and competition - through which visual information is combined in the brain of the fruit fly to drive locomotion." acknowledged_ssus: - _id: M-Shop acknowledgement: I am incredibly thankful for the outstanding support provided by ISTA, especially the Machine Shop team, who made conducting research much easier and more efficient. I am also grateful for the funding provided by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie programme (665385) and The German Research Foundation grant DFG (SPP2205) “Evolutionary optimization of neuronal processing”. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Roshan K full_name: Satapathy, Roshan K id: 46046B7A-F248-11E8-B48F-1D18A9856A87 last_name: Satapathy orcid: 0009-0006-2974-5075 citation: ama: Satapathy RK. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. 2024. doi:10.15479/at:ista:18568 apa: Satapathy, R. K. (2024). Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18568 chicago: Satapathy, Roshan K. “Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18568. ieee: R. K. Satapathy, “Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster,” Institute of Science and Technology Austria, 2024. ista: Satapathy RK. 2024. Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster. Institute of Science and Technology Austria. mla: Satapathy, Roshan K. Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18568. short: R.K. Satapathy, Mechanisms of Visual Integration and Competition in Innate Behaviours in Drosophila Melanogaster, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-19T12:34:30Z date_published: 2024-11-20T00:00:00Z date_updated: 2026-04-07T13:00:36Z day: '20' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:18568 ec_funded: 1 file: - access_level: open_access checksum: 340f2bfe882c8a85e11ec0687ca15f5e content_type: application/pdf creator: rsatapat date_created: 2024-11-19T12:39:55Z date_updated: 2024-11-19T12:39:55Z file_id: '18570' file_name: Roshan PhD thesis-Final.pdf file_size: 10960975 relation: main_file success: 1 - access_level: closed checksum: 0f846fce60d6ea511e07f77eff59a6a1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rsatapat date_created: 2024-11-19T12:46:47Z date_updated: 2024-12-13T10:27:25Z file_id: '18571' file_name: Roshan PhD thesis-Final.docx file_size: 36695917 relation: source_file file_date_updated: 2024-12-13T10:27:25Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: '114' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-047-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18444' relation: part_of_dissertation status: public 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: Mechanisms of visual integration and competition in innate behaviours in Drosophila melanogaster tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18674' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue. acknowledged_ssus: - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik citation: ama: Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:10.15479/at:ista:18674 apa: Lyudchik, J. (2024). Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18674 chicago: Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18674. ieee: J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024. ista: Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria. mla: Lyudchik, Julia. Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18674. short: J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-12-18T14:24:43Z date_published: 2024-12-18T00:00:00Z date_updated: 2026-04-14T08:34:35Z day: '18' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18674 ec_funded: 1 file: - access_level: open_access checksum: 1b42b8073e2bc09fc504da52372248c1 content_type: application/pdf creator: jlyudchi date_created: 2024-12-18T14:17:34Z date_updated: 2024-12-18T14:17:34Z file_id: '18675' file_name: 18122024_PhDthesis_corrected_final_pdfa.pdf file_size: 160536833 relation: main_file success: 1 - access_level: closed checksum: b4da84624060745519723698f7ddf54b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jlyudchi date_created: 2024-12-18T14:21:06Z date_updated: 2024-12-18T14:41:53Z file_id: '18676' file_name: 18122024_PhDthesis_corrected_final_JL_markup.docx file_size: 99172203 relation: source_file file_date_updated: 2024-12-18T14:41:53Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '217' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - ' 978-3-99078-051-0' issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11160' relation: part_of_dissertation status: public - id: '18677' relation: part_of_dissertation status: public - id: '13267' relation: part_of_dissertation status: public - id: '14257' 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: Image analysis for brain tissue reconstruction with super-resolution light microscopy 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_embargo: '20' OA_place: publisher _id: '18681' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 citation: ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:10.15479/at:ista:18681' apa: 'Tavakoli, M. (2024). Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18681' chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18681.' ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.' ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.' mla: 'Tavakoli, Mojtaba. Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18681.' short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-12-19T02:30:39Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-04-07T12:56:37Z day: '20' ddc: - '600' - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18681 file: - access_level: closed checksum: b61651d417cafddd740a8528f46068c5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mtavakol date_created: 2024-12-20T10:23:17Z date_updated: 2024-12-20T10:31:37Z file_id: '18699' file_name: Thesis_Mojtaba Tavakoli_.docx file_size: 118593521 relation: source_file - access_level: closed checksum: c80bcfd1a34c23afc3538052325283e5 content_type: application/pdf creator: mtavakol date_created: 2024-12-20T10:25:12Z date_updated: 2024-12-20T10:25:12Z embargo: 2026-08-01 embargo_to: open_access file_id: '18700' file_name: Thesis_Mojtaba Tavakoli_.pdf file_size: 63885521 relation: main_file file_date_updated: 2024-12-20T10:31:37Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '230' project: - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: isbn: - 978-3-99078-048-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11160' relation: part_of_dissertation status: public - id: '18688' relation: part_of_dissertation status: public - id: '18677' relation: part_of_dissertation status: public - id: '18689' 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: 'Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18766' abstract: - lang: eng text: Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses. acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp acknowledgement: "This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample." alternative_title: - ISTA thesis article_processing_charge: No author: - first_name: Julia full_name: Datler, Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 citation: ama: Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766 apa: Datler, J. (2024). Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18766 chicago: Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18766. ieee: J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024. ista: Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria. mla: Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18766. short: J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2025-01-07T10:23:12Z date_published: 2024-12-30T00:00:00Z date_updated: 2026-04-07T12:59:44Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:18766 file: - access_level: closed checksum: 3e51cab327c754045c3d29c1a50cc9a9 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jstanger date_created: 2025-01-07T12:15:11Z date_updated: 2025-01-07T12:15:11Z file_id: '18769' file_name: PhD_thesis_Julia_Datler.docx file_size: 38814932 relation: source_file - access_level: open_access checksum: 22fabe5b97950bf852212f6edb555173 content_type: application/pdf creator: jstanger date_created: 2025-01-07T12:15:14Z date_updated: 2025-01-07T12:15:14Z file_id: '18770' file_name: PhD_thesis_Julia_Datler.pdf file_size: 12044865 relation: main_file success: 1 file_date_updated: 2025-01-07T12:15:14Z has_accepted_license: '1' keyword: - cryo-EM - cryo-ET - cryo-SPA - Structural Virology - Poxvirus - Vaccinia Virus - Structural Biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '106' project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication_identifier: isbn: - 978-3-99078-049-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12334' relation: part_of_dissertation status: public - id: '14979' 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: Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ...