[{"publisher":"Institute of Science and Technology Austria","file":[{"checksum":"2f1f44e8536c2538f94a440217452c9f","content_type":"application/x-zip-compressed","file_size":31430022,"access_level":"closed","date_updated":"2026-03-02T10:59:50Z","date_created":"2026-03-02T10:59:50Z","file_name":"2026_Riegler_Stefan_Thesis.zip","creator":"sriegler","file_id":"21386","relation":"source_file"},{"creator":"sriegler","file_name":"2026_Riegler_Stefan_Thesis.pdf","embargo":"2027-02-27","relation":"main_file","file_id":"21387","content_type":"application/pdf","checksum":"2e8dc39640bc26ae5684c944c619719b","file_size":11635090,"date_updated":"2026-03-02T10:59:49Z","access_level":"closed","embargo_to":"open_access","date_created":"2026-03-02T10:59:49Z"}],"has_accepted_license":"1","status":"public","ddc":["570","575","583"],"page":"185","citation":{"ista":"Riegler S. 2026. Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. Institute of Science and Technology Austria.","chicago":"Riegler, Stefan. “Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.","short":"S. Riegler, Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species, Institute of Science and Technology Austria, 2026.","ama":"Riegler S. Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. 2026. doi:10.15479/AT-ISTA-21360","apa":"Riegler, S. (2026). Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360","mla":"Riegler, Stefan. Root System Plasticity under Nutrient Limitation : Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.","ieee":"S. Riegler, “Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species,” Institute of Science and Technology Austria, 2026."},"author":[{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343","last_name":"Riegler","first_name":"Stefan","full_name":"Riegler, Stefan"}],"year":"2026","date_updated":"2026-03-09T12:20:56Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"day":"26","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"repository","supervisor":[{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication_status":"published","_id":"21360","related_material":{"record":[{"status":"public","id":"21363","relation":"research_data"}]},"date_published":"2026-02-26T00:00:00Z","file_date_updated":"2026-03-02T10:59:50Z","month":"02","type":"dissertation","project":[{"_id":"34afa094-11ca-11ed-8bc3-a375845a59fb","grant_number":"101060393","name":"Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). ","corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species","date_created":"2026-02-27T09:08:14Z","doi":"10.15479/AT-ISTA-21360","oa_version":"Published Version","article_processing_charge":"No"},{"date_published":"2026-03-05T00:00:00Z","keyword":["Privacy-preserving verification","Runtime verification","Monitoring","Reactive functionalities","Cryptographic protocols"],"_id":"21401","related_material":{"record":[{"relation":"part_of_dissertation","id":"21020","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.15479/AT-ISTA-21401","date_created":"2026-03-05T15:20:47Z","oa_version":"Published Version","title":"Privacy-preserving runtime verification","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"degree_awarded":"MS","corr_author":"1","acknowledgement":"This work is part of the project VAMOS, which has received funding from the European\r\nResearch Council (ERC) under grant agreement No. 101020093, and the Austrian Science\r\nFund (FWF) SFB project SpyCoDe F8502.\r\n","publication_identifier":{"issn":["2791-4585"]},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"},{"name":"Security and Privacy by Design for Complex Systems","grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"abstract":[{"text":"Runtime verification offers scalable solutions to improve the safety and reliability of systems. However, systems that require verification or monitoring by a third party to ensure compliance with a specification might contain sensitive information, causing privacy concerns when usual runtime verification approaches are used. Privacy is compromised if protected information about the system, or sensitive data that is processed by the system, is revealed. In addition, revealing the specification being monitored may undermine the essence of third-party verification.\r\n\r\nIn this thesis, we propose a protocol for privacy-preserving runtime verification of systems against formal sequential specifications. We develop the protocol in two steps. In the first step, the monitor verifies whether the system satisfies the specification without learning anything else, though both parties are aware of the specification. In the second step, we extend the protocol to ensure that the system remains oblivious to the monitored specification, while the monitor learns only whether the system satisfies the specification and nothing more. Our protocol adapts and improves existing techniques used in cryptography, and more specifically, multi-party computation.\r\n\r\nThe sequential specification defines the observation step of the monitor, whose granularity depends on the situation (e.g., banks may be monitored on a daily basis). Our protocol exchanges a single message per observation step, after an initialization phase. This design minimizes communication overhead, enabling relatively lightweight privacy-preserving monitoring. We implement our approach for monitoring specifications described by register automata and evaluate it experimentally.\r\n","lang":"eng"}],"type":"dissertation","month":"03","file_date_updated":"2026-03-10T15:20:09Z","date_updated":"2026-03-13T13:37:20Z","year":"2026","author":[{"id":"6e5417ba-5355-11ee-ae5a-94c2e510b26b","orcid":"0009-0005-0820-1696","full_name":"Karimi, Mahyar","last_name":"Karimi","first_name":"Mahyar"}],"citation":{"chicago":"Karimi, Mahyar. “Privacy-Preserving Runtime Verification.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21401.","ista":"Karimi M. 2026. Privacy-preserving runtime verification. Institute of Science and Technology Austria.","short":"M. Karimi, Privacy-Preserving Runtime Verification, Institute of Science and Technology Austria, 2026.","apa":"Karimi, M. (2026). Privacy-preserving runtime verification. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21401","ama":"Karimi M. 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(2026). Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423","mla":"Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423.","ama":"Dunajova Z. Geometry-driven self-organization of migrating cells and chiral filaments. 2026. doi:10.15479/AT-ISTA-21423","ieee":"Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral filaments,” Institute of Science and Technology Austria, 2026.","short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026.","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria.","chicago":"Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423."},"ddc":["539","570"],"status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"embargo":"2026-09-11","relation":"main_file","file_id":"21446","creator":"zdunajov","file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","file_size":14662770,"content_type":"application/pdf","checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84","date_created":"2026-03-12T20:38:52Z","embargo_to":"open_access","date_updated":"2026-03-12T20:38:52Z","access_level":"closed"},{"file_name":"Thesis-Dunajova_source_file.docx","creator":"zdunajov","file_id":"21447","relation":"source_file","date_updated":"2026-03-13T11:19:21Z","access_level":"closed","date_created":"2026-03-12T20:40:18Z","file_size":32961408,"checksum":"5dec5afdffd47c2b0b162d0fe1bed925","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"article_processing_charge":"No","date_created":"2026-03-11T08:30:49Z","oa_version":"Published Version","doi":"10.15479/AT-ISTA-21423","title":"Geometry-driven self-organization of migrating cells and chiral filaments","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"degree_awarded":"PhD","corr_author":"1","acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-076-3"]},"project":[{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"month":"03","type":"dissertation","file_date_updated":"2026-03-13T11:19:21Z","date_published":"2026-03-11T00:00:00Z","_id":"21423","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13314"},{"status":"public","id":"13116","relation":"research_data"},{"relation":"part_of_dissertation","id":"21427","status":"public"},{"relation":"research_data","id":"21439","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}]},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"},{"first_name":"Jasmin","last_name":"Blanchette","full_name":"Blanchette, Jasmin"}],"day":"04","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"repository","status":"public","citation":{"short":"M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.","ista":"Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.","chicago":"Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21393.","ama":"Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. 2026. doi:10.15479/AT-ISTA-21393","ieee":"M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.","apa":"Dvorak, M. (2026). Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21393","mla":"Dvorak, Martin. Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21393."},"page":"160","ddc":["511","000"],"publisher":"Institute of Science and Technology Austria","file":[{"success":1,"date_created":"2026-03-04T08:56:15Z","access_level":"open_access","date_updated":"2026-03-04T08:56:15Z","file_size":1771231,"content_type":"application/pdf","checksum":"cface6dc18152680962b5361575f6e4f","file_id":"21394","relation":"main_file","file_name":"2026_Dvorak_Martin_Thesis.pdf","creator":"mdvorak"},{"date_updated":"2026-03-04T09:03:37Z","access_level":"closed","date_created":"2026-03-04T09:03:37Z","file_size":864585,"checksum":"290ddfacfb7e07fb07e6f0b334e67c90","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mdvorak","file_name":"2026_Dvorak_Martin_Thesis.docx","relation":"source_file","file_id":"21395"}],"has_accepted_license":"1","date_updated":"2026-03-27T12:37:00Z","author":[{"orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","full_name":"Dvorak, Martin","first_name":"Martin","last_name":"Dvorak"}],"year":"2026","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-074-9"]},"corr_author":"1","type":"dissertation","month":"03","file_date_updated":"2026-03-04T09:03:37Z","abstract":[{"lang":"eng","text":"This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion."}],"title":"Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids","oa_version":"Published Version","date_created":"2026-03-04T09:26:46Z","doi":"10.15479/AT-ISTA-21393","article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2026-03-04T00:00:00Z","related_material":{"link":[{"description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)","url":"https://github.com/madvorak/duality/tree/v3.5.0","relation":"software"},{"description":"Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems)","url":"https://github.com/madvorak/vcsp/tree/v8.2.0","relation":"software"},{"description":"Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project)","relation":"software","url":"https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0"},{"description":"Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars)","url":"https://github.com/madvorak/chomsky/tree/v1.2.0","relation":"software"},{"url":"https://github.com/madvorak/grammars","relation":"software","description":"Old version (Lean 3) of the project about grammars"},{"description":"Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis","relation":"software","url":"https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean"}],"record":[{"status":"public","relation":"part_of_dissertation","id":"13120"},{"status":"public","id":"21398","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"20071","status":"public"}]},"_id":"21393"},{"day":"14","alternative_title":["ISTA Master’s Thesis"],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"file":[{"checksum":"812857b2fbe3f6113bef22fd04bccd3e","content_type":"application/pdf","file_size":2867531,"date_created":"2026-01-21T14:12:13Z","embargo_to":"open_access","date_updated":"2026-01-21T14:12:13Z","access_level":"closed","file_id":"21033","relation":"main_file","embargo":"2027-01-01","file_name":"2026_Vladimirtsev_Dmitrii_Thesis.pdf","creator":"dvladimi"},{"date_updated":"2026-01-28T12:38:19Z","access_level":"closed","date_created":"2026-01-21T14:41:58Z","content_type":"application/x-zip-compressed","checksum":"2b969f97f8d7461bea3d255f48c2219c","file_size":25023066,"file_name":"Source Files.zip","creator":"dvladimi","file_id":"21034","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","status":"public","page":"22","ddc":["570"],"citation":{"ama":"Vladimirtsev D. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. 2026. doi:10.15479/AT-ISTA-20964","mla":"Vladimirtsev, Dmitrii. Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20964.","apa":"Vladimirtsev, D. (2026). Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20964","ieee":"D. Vladimirtsev, “Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels,” Institute of Science and Technology Austria, 2026.","chicago":"Vladimirtsev, Dmitrii. “Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20964.","short":"D. Vladimirtsev, Armadillo Repeat Only Proteins Are Master Regulators of Plant Cyclic-Nucleotide Gated Channels, Institute of Science and Technology Austria, 2026.","ista":"Vladimirtsev D. 2026. Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels. Institute of Science and Technology Austria."},"author":[{"id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","last_name":"Vladimirtsev","first_name":"Dmitrii","full_name":"Vladimirtsev, Dmitrii"}],"year":"2026","date_updated":"2026-04-07T11:41:44Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"type":"dissertation","month":"01","file_date_updated":"2026-01-28T12:38:19Z","project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"}],"publication_identifier":{"issn":["2791-4585"]},"corr_author":"1","degree_awarded":"MS","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"title":"Armadillo repeat only proteins are master regulators of plant cyclic-nucleotide gated channels","doi":"10.15479/AT-ISTA-20964","oa_version":"Published Version","date_created":"2026-01-09T09:22:48Z","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"20982","relation":"part_of_dissertation","status":"public"}]},"_id":"20964","date_published":"2026-01-14T00:00:00Z"},{"date_updated":"2026-04-07T11:46:11Z","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"id":"e499926b-f6e0-11ea-865d-9c63db0031e8","first_name":"Jonathan A","last_name":"Scott","full_name":"Scott, Jonathan A"}],"year":"2026","status":"public","page":"158","ddc":["005"],"citation":{"mla":"Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21198.","apa":"Scott, J. A. (2026). Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21198","ieee":"J. A. Scott, “Data heterogeneity and personalization in federated learning,” Institute of Science and Technology Austria, 2026.","ama":"Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:10.15479/AT-ISTA-21198","short":"J.A. Scott, Data Heterogeneity and Personalization in Federated Learning, Institute of Science and Technology Austria, 2026.","ista":"Scott JA. 2026. Data heterogeneity and personalization in federated learning. Institute of Science and Technology Austria.","chicago":"Scott, Jonathan A. “Data Heterogeneity and Personalization in Federated Learning.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21198."},"publisher":"Institute of Science and Technology Austria","file":[{"creator":"jscott","file_name":"2026_Scott_Jonathan_Thesis_Source.zip","relation":"source_file","file_id":"21298","access_level":"closed","date_updated":"2026-02-17T11:46:22Z","date_created":"2026-02-17T11:46:22Z","checksum":"121c1d968bd86f3630aa7e81d5bbbcb0","file_size":272379252,"content_type":"application/zip"},{"checksum":"6e3e08ba474bbee8511cc8a839ab2077","content_type":"application/pdf","file_size":15220298,"access_level":"open_access","date_updated":"2026-02-27T10:25:41Z","success":1,"date_created":"2026-02-27T10:25:41Z","file_name":"2026_Jonathan_Scott_Thesis.pdf","creator":"jscott","file_id":"21366","relation":"main_file"}],"has_accepted_license":"1","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph"}],"day":"09","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","oa":1,"date_published":"2026-02-09T00:00:00Z","related_material":{"record":[{"status":"public","id":"20819","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"17411"},{"id":"18120","relation":"part_of_dissertation","status":"public"},{"id":"21207","relation":"part_of_dissertation","status":"public"}]},"_id":"21198","publication_status":"published","language":[{"iso":"eng"}],"title":"Data heterogeneity and personalization in federated learning","date_created":"2026-02-09T14:59:53Z","doi":"10.15479/AT-ISTA-21198","oa_version":"Published Version","article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"This research was funded in part by the Austrian Science Fund (FWF)\r\n[10.55776/COE12]. Furthermore, the candidate acknowledges the support from the Scientific\r\nService Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","corr_author":"1","file_date_updated":"2026-02-27T10:25:41Z","type":"dissertation","month":"02","abstract":[{"text":"In recent years there has been a massive increase in the amount of data generated in a\r\ndecentralized manner. Ever more powerful edge devices, such as smartphones, have become\r\nubiquitous in most societies on earth. Through text typed, photos taken and apps used,\r\nthese devices, which we refer to as clients, generate enormous amounts of high quality and\r\ncomplex data. Moreover, the nature of these devices means the data they generate is often\r\nsensitive and privacy concerns prevent it being gathered and stored in a central location. This\r\npresents a challenge to the modern machine learning paradigm that requires central access\r\nto large amounts of data. Federated learning (FL) has emerged as one of the answers to\r\nthis problem. Rather than bringing the data to the model, FL sends the model to the data.\r\nModel training takes place on device, with periodically synchronized updates, allowing data to\r\nremain locally stored. While this approach offers significant privacy advantages it comes with\r\nits own set of unique challenges. These include: data heterogeneity, the notion that different\r\ndevices generate data in distinct ways which can negatively impact training dynamics; systems\r\nheterogeneity, meaning that different devices may have differing hardware specifications; high\r\ncommunication costs, which are induced by the repeated transferring of models over the\r\nnetwork and low device computational power, which limits the use of larger models on device.\r\nIn this thesis we present a range of methods for federated learning. We focus primarily on\r\nthe challenge of data heterogeneity, though the methods presented are designed to be well\r\nadapted to the other challenges of a federated setting, such as the constraints of limited\r\ncompute and communication overhead. We first present a method for explicitly modeling client\r\ndata heterogeneity. The approach formulates clients as samples from a certain probability\r\ndistribution and infers the parameters of this distribution from the available training clients.\r\nThis learned distribution then represents the heterogeneity present among the clients and can\r\nbe sampled from in order to create new simulated clients that are similar to the real clients we\r\nhave observed so far. Following this we present two methods for directly dealing with data\r\nheterogeneity through personalization. Highly heterogeneous client data distributions can mean\r\nthat learning a single global model becomes suboptimal, and some form of personalization of\r\nmodels to each individual client is required. Our approaches are based around hypernetworks,\r\nwhich we use to generate personalized model parameters without the need for additional\r\ntraining or finetuning. In the first approach we focus on generating full parameterizations of\r\nclient models using learned embeddings of client data and labels, with a hypernetwork located\r\non the central server. In the second approach we address the more challenging scenario where\r\nwe want to generate a personalized model for a client without any label information. The\r\nhypernetwork is trained to generate a low dimensional representation of a client’s personalized\r\nmodel parameters, allowing it to be transferred to and run on the client devices. In our final\r\npresented method, we change our focus and rather than aim to directly address the challenge\r\nof data heterogeneity, we instead ensure we are unaffected by it. This is done in the context\r\nof k-means clustering and we present a method for federated clustering with a focus on added\r\nprivacy guarantees.","lang":"eng"}]},{"alternative_title":["ISTA Thesis"],"day":"21","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2026","author":[{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D","first_name":"Christopher D","last_name":"Fillmore"}],"date_updated":"2026-04-07T11:42:49Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/pdf","file_size":55954297,"checksum":"4c0889130095c31d4e5088c5b8dfd607","date_updated":"2026-01-30T11:40:09Z","access_level":"open_access","date_created":"2026-01-26T19:44:46Z","file_name":"2025_Fillmore_Christopher_Thesis.pdf","creator":"cfillmor","file_id":"21046","relation":"main_file"},{"content_type":"application/x-zip-compressed","checksum":"d69afb71d82ab98f856886126ee7303a","file_size":166080788,"date_created":"2026-01-26T19:46:20Z","date_updated":"2026-01-26T19:46:20Z","access_level":"closed","file_id":"21047","relation":"source_file","file_name":"Thesis.zip","creator":"cfillmor"}],"status":"public","page":"122","ddc":["514","516"],"citation":{"ama":"Fillmore CD. Braiding geometry and topology to study shapes and data. 2026. doi:10.15479/AT-ISTA-21021","ieee":"C. D. Fillmore, “Braiding geometry and topology to study shapes and data,” Institute of Science and Technology Austria, 2026.","apa":"Fillmore, C. D. (2026). Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21021","mla":"Fillmore, Christopher D. Braiding Geometry and Topology to Study Shapes and Data. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21021.","ista":"Fillmore CD. 2026. Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria.","chicago":"Fillmore, Christopher D. “Braiding Geometry and Topology to Study Shapes and Data.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21021.","short":"C.D. Fillmore, Braiding Geometry and Topology to Study Shapes and Data, Institute of Science and Technology Austria, 2026."},"department":[{"_id":"GradSch"},{"_id":"HeEd"},{"_id":"UlWa"}],"degree_awarded":"PhD","title":"Braiding geometry and topology to study shapes and data","article_processing_charge":"No","date_created":"2026-01-20T21:38:40Z","oa_version":"Published Version","doi":"10.15479/AT-ISTA-21021","abstract":[{"lang":"eng","text":"This thesis examines how geometry and topology intersect in the representation, transformation, and analysis of complex shapes. It considers how continuous manifolds relate to their discrete analogues, how topological structures evolve in persistence vineyards, and how tools from topological data analysis can illuminate problems in mathematical physics. Central to this exploration is the question of how structure, both geometric and topological, persists or changes under approximation, sampling, or deformation. The work develops new approaches to skeletal and grid-based representations of surfaces, reveals the full expressive capacity of persistence vineyards, and applies topological methods to the longstanding problem of equilibria in electrostatic fields. These threads braid together into a broader understanding of how topology and geometry inform one another across theory, computation, and application."}],"file_date_updated":"2026-01-30T11:40:09Z","month":"01","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","acknowledgement":"The research presented in this thesis was funded by the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’.\r\n","related_material":{"record":[{"status":"public","id":"20260","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21050","status":"public"},{"id":"21051","relation":"part_of_dissertation","status":"public"}]},"_id":"21021","date_published":"2026-01-21T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published"},{"date_updated":"2026-04-15T08:45:19Z","author":[{"last_name":"Baig","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"}],"year":"2026","status":"public","ddc":["000"],"citation":{"ama":"Baig MA. On secure chain selection rules from physical resources in a permissionless setting. 2026. doi:10.15479/AT-ISTA-21651","apa":"Baig, M. A. (2026). On secure chain selection rules from physical resources in a permissionless setting. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21651","mla":"Baig, Mirza Ahad. On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21651.","ieee":"M. A. Baig, “On secure chain selection rules from physical resources in a permissionless setting,” Institute of Science and Technology Austria, 2026.","chicago":"Baig, Mirza Ahad. “On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21651.","short":"M.A. Baig, On Secure Chain Selection Rules from Physical Resources in a Permissionless Setting, Institute of Science and Technology Austria, 2026.","ista":"Baig MA. 2026. On secure chain selection rules from physical resources in a permissionless setting. Institute of Science and Technology Austria."},"file":[{"content_type":"application/x-zip-compressed","checksum":"c3986dba90653dac97adba662ebff238","file_size":139353434,"date_updated":"2026-04-13T08:24:13Z","access_level":"closed","date_created":"2026-04-03T17:28:48Z","creator":"mbaig","file_name":"PhD-Thesis-Mirza-Ahad-Baig - Library Submission.zip","relation":"source_file","file_id":"21655"},{"file_id":"21656","relation":"main_file","file_name":"2026_Baig_Mirza_Ahad_Thesis.pdf","creator":"mbaig","date_created":"2026-04-03T17:29:30Z","date_updated":"2026-04-15T07:37:25Z","access_level":"open_access","content_type":"application/pdf","checksum":"292a5989262521f7c145a109d1f348cb","file_size":1942037}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"day":"04","alternative_title":["ISTA Thesis"],"OA_place":"publisher","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","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)"},"oa":1,"date_published":"2026-03-04T00:00:00Z","_id":"21651","related_material":{"record":[{"id":"21134","relation":"part_of_dissertation","status":"public"},{"id":"20587","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","language":[{"iso":"eng"}],"title":"On secure chain selection rules from physical resources in a permissionless setting","date_created":"2026-04-02T09:31:34Z","doi":"10.15479/AT-ISTA-21651","oa_version":"Published Version","article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_identifier":{"isbn":["978-3-99078-078-7"],"issn":["2663-337X"]},"corr_author":"1","type":"dissertation","month":"03","file_date_updated":"2026-04-15T07:37:25Z","abstract":[{"text":"Blockchains enable distributed consensus in permissionless settings, where participants\r\nare unknown, dynamically changing, and do not trust each other. While Bitcoin,\r\nbased on Proof-of-Work (PoW), was the first protocol in this model, significant\r\nresearch has focused on permissionless protocols using alternative physical resources,\r\nspecifically Proof-of-Space (PoSpace) and Verifiable Delay Functions (VDFs). This\r\nthesis investigates the theoretical limits and design space of longest-chain protocols in\r\nthe fully permissionless and dynamically available settings using these three resources.\r\nFirst, we address the feasibility of blockchains relying solely on storage as a resource.\r\nWe prove a fundamental impossibility result: there exists no secure longest-chain\r\nprotocol based exclusively on Proof-of-Space in the fully permissionless or dynamically\r\navailable settings. Further, we quantify the adversarial capabilities required to execute\r\na double-spend attack. Our result formally justifies the necessity of coupling PoSpace\r\nwith time-dependent primitives (such as VDFs) or to move to less permissive settings\r\n(quasi-permissionless or permissioned) to ensure security.\r\nSecond, we generalize Nakamoto-like heaviest chain consensus to protocols utilizing\r\ncombinations of multiple physical resources. We analyze chain selection rules governed\r\nby a weight function Γ(S, V,W), which assigns weight to blocks based on recorded\r\nSpace (S), VDF speed (V ), and Work (W). We provide a complete classification\r\nof secure weight functions, proving that a weight function is secure against private\r\ndouble-spend attacks if and only if it is homogeneous in the timed resources (V,W)\r\nand sub-homogeneous in S. This framework unifies existing protocols like Bitcoin and\r\nChia under a single theoretical model and provides a powerful tool for designing new\r\nlongest-chain blockchains from a mix of physical resources.","lang":"eng"}]},{"alternative_title":["ISTA Thesis"],"day":"16","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M"}],"oa":1,"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","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)"},"year":"2026","author":[{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"}],"date_updated":"2026-04-16T12:20:37Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"access_level":"closed","date_updated":"2026-01-16T12:25:13Z","date_created":"2026-01-16T12:25:13Z","file_size":22456421,"checksum":"841f1bc073d667125729b2a017f8c37a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dgarciac","file_name":"2026_Garcia_Diego_Thesis.docx","relation":"source_file","file_id":"20996"},{"date_updated":"2026-01-16T12:25:13Z","access_level":"open_access","success":1,"date_created":"2026-01-16T12:25:13Z","file_size":9556719,"checksum":"a1f33d4f183ce7072eee42a6ccf5340b","content_type":"application/pdf","file_name":"2026_Garcia_Diego_Thesis.pdf","creator":"dgarciac","file_id":"20997","relation":"main_file"},{"content_type":"application/x-compressed","checksum":"98a80691067174c30fe53f38ce7344e6","file_size":54491433,"date_created":"2026-01-16T13:08:14Z","date_updated":"2026-01-16T13:08:14Z","access_level":"closed","description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","relation":"supplementary_material","file_id":"20998","creator":"dgarciac","file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar"},{"content_type":"application/x-compressed","checksum":"99a3cab2fa36666b9a92eefc27d586da","file_size":7982811,"access_level":"open_access","date_updated":"2026-01-16T13:08:14Z","date_created":"2026-01-16T13:08:14Z","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","creator":"dgarciac","file_id":"20999","relation":"supplementary_material"},{"file_name":"README.txt","creator":"dgarciac","file_id":"21000","relation":"supplementary_material","date_updated":"2026-01-16T13:08:59Z","access_level":"open_access","date_created":"2026-01-16T13:08:59Z","content_type":"text/plain","checksum":"255fdf56b2932c46bf27c63aa6106a4f","file_size":732}],"status":"public","citation":{"short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20991.","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria.","ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991","mla":"Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation in Introduced Populations. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-20991.","ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","apa":"Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991"},"ddc":["576"],"page":"199","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"degree_awarded":"PhD","title":"The genomic architecture of local adaptation in introduced populations","article_processing_charge":"No","doi":"10.15479/AT-ISTA-20991","oa_version":"Published Version","date_created":"2026-01-16T09:47:59Z","abstract":[{"lang":"eng","text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms."}],"file_date_updated":"2026-01-16T13:08:59Z","type":"dissertation","month":"01","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-077-0"]},"corr_author":"1","acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","_id":"20991","related_material":{"record":[{"relation":"research_data","id":"18498","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18491"}]},"date_published":"2026-01-16T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published"},{"author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","first_name":"Gökhan","last_name":"Yalniz"}],"year":"2025","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-04-07T11:47:06Z","file":[{"access_level":"open_access","date_updated":"2025-05-12T15:13:28Z","success":1,"date_created":"2025-05-12T15:13:28Z","checksum":"0e452642b79f13633f1595bde71a67e3","content_type":"application/pdf","file_size":20058169,"file_name":"Gökhan Yalnız - PhD thesis.pdf","creator":"gyalniz","file_id":"19685","relation":"main_file"},{"file_size":37763743,"content_type":"video/mp4","checksum":"921099d76adab2df784ce12ce41cfb22","date_created":"2025-05-12T15:15:59Z","title":"Chapter 2 - Movie 2A.1","access_level":"open_access","date_updated":"2025-05-12T15:43:28Z","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","relation":"supplementary_material","file_id":"19686","creator":"gyalniz","file_name":"Movie 2A.1.mp4"},{"creator":"gyalniz","file_name":"Movie 3A.1.mp4","relation":"supplementary_material","file_id":"19687","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 3 - Movie 3A.1","access_level":"open_access","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","date_created":"2025-05-12T15:16:09Z","content_type":"video/mp4","file_size":3902655,"checksum":"0ae5ac7d9896003c0c4207dd746808dc"},{"file_id":"19688","relation":"supplementary_material","file_name":"Movie 3A.2.mp4","creator":"gyalniz","date_created":"2025-05-12T15:16:21Z","description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 3 - Movie 3A.2","access_level":"open_access","file_size":7043169,"checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","content_type":"video/mp4"},{"date_created":"2025-05-12T15:16:36Z","date_updated":"2025-05-12T15:43:28Z","access_level":"open_access","title":"Chapter 3 - Movie 3A.3","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","file_size":7748659,"content_type":"video/mp4","checksum":"7ed871f428100d6827ac9b0e8ca8e985","relation":"supplementary_material","file_id":"19689","creator":"gyalniz","file_name":"Movie 3A.3.mp4"},{"date_created":"2025-05-12T15:16:50Z","access_level":"open_access","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 3 - Movie 3A.4","description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","checksum":"dd5a252e1da00c8f303588e22e2baeef","content_type":"video/mp4","file_size":5873052,"relation":"supplementary_material","file_id":"19690","creator":"gyalniz","file_name":"Movie 3A.4.mp4"},{"relation":"supplementary_material","file_id":"19691","creator":"gyalniz","file_name":"Movie 4A.1.mp4","file_size":9209327,"checksum":"5ac58b86810698db28cbfc28f351ff70","content_type":"video/mp4","date_created":"2025-05-12T15:17:11Z","title":"Chapter 4 - Movie 4A.1","date_updated":"2025-05-12T15:43:28Z","access_level":"open_access","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit."},{"date_created":"2025-05-12T15:17:43Z","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 5 - Movie 5A.1","access_level":"open_access","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","content_type":"video/mp4","checksum":"ac877f1e1ef39439911bf37cb1793b8e","file_size":5893993,"relation":"supplementary_material","file_id":"19692","creator":"gyalniz","file_name":"Movie 5A.1.mp4"},{"date_created":"2025-05-12T15:17:49Z","access_level":"open_access","title":"Chapter 5 - Movie 5A.2","date_updated":"2025-05-12T15:43:28Z","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_size":3990352,"content_type":"video/mp4","checksum":"fd17eabb70129ceaa414e40924d1d2fe","relation":"supplementary_material","file_id":"19693","creator":"gyalniz","file_name":"Movie 5A.2.mp4"},{"date_created":"2025-05-12T15:17:58Z","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain.","title":"Chapter 5 - Movie 5A.3","date_updated":"2025-05-12T15:43:28Z","access_level":"open_access","file_size":5171009,"content_type":"video/mp4","checksum":"32f904497ab0bbee38f0788d96b91454","file_id":"19694","relation":"supplementary_material","file_name":"Movie 5A.3.mp4","creator":"gyalniz"},{"checksum":"f313261b9bb12dfb943fead8318954c6","content_type":"application/x-zip-compressed","file_size":18991996,"date_created":"2025-05-12T15:27:10Z","date_updated":"2025-05-12T15:43:28Z","access_level":"closed","relation":"source_file","file_id":"19695","creator":"gyalniz","file_name":"Gökhan Yalnız - PhD thesis.zip"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","page":"155","citation":{"mla":"Yalniz, Gökhan. Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19684.","ieee":"G. Yalniz, “Transition to turbulence : Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","ama":"Yalniz G. Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:10.15479/AT-ISTA-19684","apa":"Yalniz, G. (2025). Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19684","short":"G. Yalniz, Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.","ista":"Yalniz G. 2025. Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","chicago":"Yalniz, Gökhan. “Transition to Turbulence : Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19684."},"ddc":["514","519","532","004"],"status":"public","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"13","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn"}],"oa":1,"_id":"19684","related_material":{"record":[{"id":"7563","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9558","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"12105"},{"status":"public","relation":"part_of_dissertation","id":"13274"},{"status":"public","relation":"part_of_dissertation","id":"14466"}]},"date_published":"2025-05-13T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"doi":"10.15479/AT-ISTA-19684","oa_version":"Published Version","date_created":"2025-05-12T15:12:28Z","article_processing_charge":"No","title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"month":"05","type":"dissertation","file_date_updated":"2025-05-12T15:43:28Z","abstract":[{"text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate.","lang":"eng"}],"acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","corr_author":"1","publication_identifier":{"issn":["2663-337X"]}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"}],"day":"03","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","status":"public","citation":{"ieee":"O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025.","ama":"Draganov O. Structures and computations in topological data analysis. 2025. doi:10.15479/at:ista:18979","mla":"Draganov, Ondrej. Structures and Computations in Topological Data Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18979.","apa":"Draganov, O. (2025). Structures and computations in topological data analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18979","chicago":"Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18979.","short":"O. Draganov, Structures and Computations in Topological Data Analysis, Institute of Science and Technology Austria, 2025.","ista":"Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria."},"ddc":["514","004"],"page":"140","file":[{"checksum":"af6567e5d35e5eb330b8925ae37f1998","file_size":11899491,"content_type":"application/zip","access_level":"closed","date_updated":"2025-01-31T16:58:30Z","date_created":"2025-01-31T16:58:30Z","creator":"odragano","file_name":"Thesis.zip","relation":"source_file","file_id":"18983"},{"file_id":"19000","relation":"main_file","file_name":"Thesis.pdf","creator":"odragano","date_created":"2025-02-04T16:22:07Z","date_updated":"2025-02-04T16:22:07Z","access_level":"open_access","checksum":"c3fef68e35b9dc2020b2ca6006da6343","file_size":8857514,"content_type":"application/pdf"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","date_updated":"2026-04-07T11:47:30Z","author":[{"first_name":"Ondrej","last_name":"Draganov","full_name":"Draganov, Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0464-3823"}],"year":"2025","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"The research presented in this thesis was funded with the Wittgenstein Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n","corr_author":"1","month":"02","file_date_updated":"2025-02-04T16:22:07Z","type":"dissertation","abstract":[{"lang":"eng","text":"Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe describe a construction of a chromatic alpha complex, which enables efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot."}],"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"title":"Structures and computations in topological data analysis","date_created":"2025-01-31T17:04:40Z","oa_version":"Published Version","doi":"10.15479/at:ista:18979","article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publication_status":"published","language":[{"iso":"eng"}],"date_published":"2025-02-03T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"15091","status":"public"},{"relation":"part_of_dissertation","id":"18981","status":"public"}]},"_id":"18979","keyword":["topological data analysis","chromatic point set","alpha complex","persistent homology","six pack","sheaf","microlocal discrete Morse","injective resolution","collapse","knot","discrete Morse theory"]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"25","alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","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)"},"author":[{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","first_name":"Jakob","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob"}],"year":"2025","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_updated":"2026-04-07T11:48:07Z","file":[{"date_created":"2025-08-25T13:49:55Z","access_level":"closed","date_updated":"2025-08-25T13:49:55Z","file_size":39735535,"checksum":"191db3367c19c9b32b65f4bc3a7c19de","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"20228","relation":"source_file","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","creator":"jvorlauf"},{"file_size":10947446,"content_type":"application/pdf","checksum":"104400e6036921569610230c1d4899dc","access_level":"open_access","date_updated":"2025-08-25T13:49:56Z","date_created":"2025-08-25T13:49:56Z","success":1,"file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","creator":"jvorlauf","file_id":"20229","relation":"main_file"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","page":"107","citation":{"apa":"Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20206","ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","mla":"Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20206.","chicago":"Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20206.","short":"J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025.","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria."},"ddc":["621","535"],"status":"public","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"oa_version":"Published Version","date_created":"2025-08-22T08:12:55Z","doi":"10.15479/AT-ISTA-20206","article_processing_charge":"No","title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","project":[{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","name":"CryoMinflux-guided in-situ molecular census and structure determination","grant_number":"CZI01"}],"file_date_updated":"2025-08-25T13:49:56Z","month":"08","type":"dissertation","abstract":[{"lang":"eng","text":"The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n"}],"acknowledgement":"The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. ","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"_id":"20206","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"19795"}]},"date_published":"2025-08-25T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_status":"published","_id":"19722","date_published":"2025-05-23T00:00:00Z","file_date_updated":"2025-05-28T11:59:11Z","type":"dissertation","month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-059-6"]},"corr_author":"1","acknowledgement":"Special thanks to the Plant Facility.","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"OA_embargo":"12","degree_awarded":"PhD","title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","article_processing_charge":"No","doi":"10.15479/AT-ISTA-19722","oa_version":"Published Version","date_created":"2025-05-23T15:21:29Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"file_size":8292363,"checksum":"847ec70b2e40f50e0ddc7b8da201d52c","content_type":"application/pdf","date_created":"2025-05-28T11:59:11Z","embargo_to":"open_access","access_level":"closed","date_updated":"2025-05-28T11:59:11Z","embargo":"2026-05-23","relation":"main_file","file_id":"19757","creator":"sinumell","file_name":"Final Thesis_Syamala Inumella.pdf"},{"date_updated":"2025-05-28T11:59:11Z","access_level":"closed","date_created":"2025-05-28T11:59:11Z","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","file_size":7145703,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"sinumell","file_name":"Final Thesis_Syamala Inumella.docx","relation":"source_file","file_id":"19758"}],"status":"public","ddc":["580"],"citation":{"ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria.","chicago":"Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19722.","short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","mla":"Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19722.","apa":"Inumella, S. (2025). Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19722","ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025."},"page":"113","year":"2025","author":[{"id":"F8660870-D756-11E9-98C5-34DFE5697425","orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","first_name":"Syamala","last_name":"Inumella"}],"date_updated":"2026-04-07T11:47:52Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"day":"23","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}]},{"year":"2025","author":[{"full_name":"Monzer, Aline","first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"}],"date_updated":"2026-04-07T11:48:32Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_id":"19396","creator":"amonzer","file_name":"Final Thesis Aline Monzer.pdf","success":1,"date_created":"2025-03-12T14:14:49Z","date_updated":"2025-03-12T14:14:49Z","access_level":"open_access","file_size":13119670,"checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7","content_type":"application/pdf"},{"file_size":13774837,"checksum":"a353ce1ee2eabce37bca35499e76dbf1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2025-04-01T07:55:27Z","date_created":"2025-03-12T14:15:19Z","file_name":"Thesis Aline.docx","creator":"amonzer","file_id":"19397","relation":"source_file"}],"status":"public","citation":{"ama":"Monzer A. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. 2025. doi:10.15479/AT-ISTA-19395","ieee":"A. Monzer, “Cell-Surface Auxin Signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","mla":"Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395.","apa":"Monzer, A. (2025). Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395","chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.","ista":"Monzer A. 2025. Cell-Surface Auxin Signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025."},"page":"160","ddc":["580"],"alternative_title":["ISTA Thesis"],"day":"13","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"19398","status":"public"},{"relation":"part_of_dissertation","id":"19399","status":"public"},{"id":"12291","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14826","relation":"part_of_dissertation"}]},"_id":"19395","date_published":"2025-03-13T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"degree_awarded":"PhD","title":"Cell-Surface Auxin Signaling: Linking molecular pathways to plant development","article_processing_charge":"No","date_created":"2025-03-12T14:25:42Z","doi":"10.15479/AT-ISTA-19395","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood."}],"file_date_updated":"2025-04-01T07:55:27Z","type":"dissertation","month":"03","publication_identifier":{"eissn":["2663-337X"],"eisbn":["978-3-99078-054-1"]},"corr_author":"1","acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research."},{"related_material":{"record":[{"id":"14851","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"12788","relation":"part_of_dissertation"},{"id":"19425","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9903","relation":"part_of_dissertation"},{"id":"15004","relation":"part_of_dissertation","status":"public"}]},"_id":"19393","date_published":"2025-03-13T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"MiLe"}],"oa_version":"Published Version","date_created":"2025-03-12T13:04:59Z","doi":"10.15479/AT-ISTA-19393","article_processing_charge":"No","title":"Non-equilibrium topological phases with periodically driven molecules and quantum rotors","month":"03","file_date_updated":"2025-03-20T08:02:35Z","type":"dissertation","abstract":[{"text":"Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies.","lang":"eng"}],"corr_author":"1","publication_identifier":{"eissn":["2663-337X"]},"author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","orcid":"0000-0002-6963-0129","full_name":"Karle, Volker","last_name":"Karle","first_name":"Volker"}],"year":"2025","date_updated":"2026-04-07T11:48:53Z","file":[{"relation":"main_file","file_id":"19394","creator":"vkarle","file_name":"thesis_final.pdf","file_size":10625143,"checksum":"d3ab25782c7ea38ce9910e57d25f6733","content_type":"application/pdf","date_created":"2025-03-12T12:56:46Z","success":1,"access_level":"open_access","date_updated":"2025-03-12T12:56:46Z"},{"date_updated":"2025-03-20T08:02:35Z","access_level":"closed","date_created":"2025-03-13T13:15:10Z","content_type":"application/zip","checksum":"3ccfb0aeba4d860d71e18347913034e4","file_size":23119202,"file_name":"thesis.zip","creator":"vkarle","file_id":"19400","relation":"source_file"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","ddc":["530"],"OA_type":"gold","citation":{"ista":"Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria.","short":"V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025.","chicago":"Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19393.","apa":"Karle, V. (2025). Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19393","ama":"Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:10.15479/AT-ISTA-19393","mla":"Karle, Volker. Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19393.","ieee":"V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025."},"page":"192","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"13","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"}},{"date_published":"2025-08-05T00:00:00Z","_id":"20138","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12787"},{"relation":"part_of_dissertation","id":"12101","status":"public"},{"relation":"part_of_dissertation","id":"12257","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"15297"},{"status":"public","relation":"part_of_dissertation","id":"18703"}]},"publication_status":"published","language":[{"iso":"eng"}],"title":"Structural properties of games on graphs","article_processing_charge":"No","doi":"10.15479/AT-ISTA-20138","oa_version":"Published Version","date_created":"2025-08-05T14:33:59Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n","abstract":[{"text":"The evolution shapes the world around us.\r\nNot only in biology, where the fittest individuals spread their genes but also in physics and social dynamics, the evolutionary forces determine the development of a state of matter or public opinions.\r\nMany models describe these dynamics.\r\nThis thesis examines the role of the structure in the models of selection.\r\nThe population structure is represented as a graph or a network, and each vertex is occupied by one individual.\r\nEvery individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors.\r\nThe evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness.\r\n\r\n\r\n\r\nThe role of the networks is widely examined in the literature.\r\nThe structures that promote the spread of the desired type compared to the structureless case are called amplifiers.\r\nThe existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified.\r\nMoreover, there are other important questions about the number of steps until one type spreads over the whole network (fixation time), the computational complexity, and the questions about the robustness of these processes.\r\n\r\n\r\nThis thesis explores the role of structure in evolution from many perspectives.\r\nFirst, it introduces different models and various choices that can be made in the models of evolution.\r\nIt highlights the role of the structure in the real world and how this is reflected in these models.\r\nThen, it describes the previous results and open problems.\r\nSecond, the thesis describes an amplifier for two variants of the Moran process: one with a constant birth rate and the other with a constant death rate.\r\nThis is an important contribution to the robustness of the amplification.\r\nThird, the thesis determines the complexity of spatial games.\r\nThese are processes where the fitness comes from a game, and the strength of selection is high.\r\nIt shows that determining the fate of cooperation in these games is a PSPACE-complete problem.\r\nFourth, the thesis describes the amplifier of cooperation for spatial games.\r\nThis is the first amplifier in this setting.\r\nFifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity.\r\nIn this setting, the fitness depends not only on the type of the individual but also on the occupied vertex.\r\nThe chapter determines the relationship between the interactions of vertices of different types and the coexistence time.\r\nSixth, the thesis examines the social balance on networks and proposes a stochastic dynamic partially aware of the state of the graph, which reaches a balanced position quickly.\r\nFinally, the thesis presents conclusions and outlines the directions for future work.\r\n\r\n\r\n","lang":"eng"}],"file_date_updated":"2025-08-21T11:48:39Z","type":"dissertation","month":"08","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"date_updated":"2026-04-07T11:49:12Z","year":"2025","author":[{"orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"status":"public","ddc":["000","519"],"page":"167","citation":{"apa":"Svoboda, J. (2025). Structural properties of games on graphs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20138","ama":"Svoboda J. Structural properties of games on graphs. 2025. doi:10.15479/AT-ISTA-20138","mla":"Svoboda, Jakub. Structural Properties of Games on Graphs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20138.","ieee":"J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025.","chicago":"Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20138.","short":"J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025.","ista":"Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria."},"has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"2025_Svoboda_Jakub_Thesis.pdf","creator":"jsvoboda","file_id":"20177","relation":"main_file","access_level":"open_access","date_updated":"2025-08-14T09:54:43Z","date_created":"2025-08-14T09:54:43Z","success":1,"content_type":"application/pdf","file_size":5927291,"checksum":"c6c4df9777f4537940de7ab392ad57e2"},{"file_size":6731815,"checksum":"485e9f9822821bc03666d245d80aaa08","content_type":"application/zip","date_created":"2025-08-14T09:55:20Z","access_level":"closed","date_updated":"2025-08-21T11:48:39Z","file_id":"20178","relation":"source_file","file_name":"2025_Svoboda_Jakub_Thesis.zip","creator":"jsvoboda"}],"supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"}],"alternative_title":["ISTA Thesis"],"day":"05","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","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)"},"oa":1},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2025-08-22T08:22:10Z","date_updated":"2025-08-22T08:53:46Z","access_level":"closed","checksum":"36b87c17d12c7bf5955d6d812acb8d77","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25798848,"file_id":"20209","relation":"source_file","file_name":"2025_Wang_Yiqun_Thesis.docx","creator":"yiqwang"},{"checksum":"8d7a2383f66377da675d379ec30ea0fe","content_type":"application/pdf","file_size":12628313,"date_updated":"2025-09-03T09:36:52Z","access_level":"closed","embargo_to":"open_access","date_created":"2025-08-22T10:32:30Z","creator":"yiqwang","file_name":"2025_Wang_Yiqun_Thesis.pdf","embargo":"2026-09-03","relation":"main_file","file_id":"20211"}],"ddc":["580"],"page":"108","citation":{"chicago":"Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20117.","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria.","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025.","apa":"Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20117","mla":"Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20117.","ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117"},"status":"public","year":"2025","author":[{"id":"82F537F2-B517-11E9-84D7-6433E6697425","first_name":"Yiqun","last_name":"Wang","full_name":"Wang, Yiqun"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"date_updated":"2026-04-07T11:49:34Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","alternative_title":["ISTA Thesis"],"day":"04","supervisor":[{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"18063","relation":"part_of_dissertation"}]},"_id":"20117","date_published":"2025-08-04T00:00:00Z","file_date_updated":"2025-09-03T09:36:52Z","month":"08","type":"dissertation","corr_author":"1","acknowledgement":"I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments.","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"degree_awarded":"PhD","article_processing_charge":"No","oa_version":"Published Version","date_created":"2025-08-04T15:24:21Z","doi":"10.15479/AT-ISTA-20117","title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development"},{"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13049"},{"status":"public","relation":"part_of_dissertation","id":"18565"},{"status":"public","id":"20286","relation":"part_of_dissertation"}]},"_id":"20276","date_published":"2025-09-02T00:00:00Z","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2025-09-04T09:22:29Z","type":"dissertation","month":"09","abstract":[{"text":"Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations\r\neither preserve the intrinsic material geometry (e.g., folding paper) or modify it through\r\nlocalized contraction. Once transformed, the 3D shape can be further controlled to achieve a\r\ntarget functionality. A key challenge is to take the material specifications and the actuation\r\nprocess as input to automatically design the target 3D shape and its functionality. This thesis\r\npresents two novel computational pipelines for the design and control of shape-morphing\r\nstructures used to create functional prototypes.\r\nThe first pipeline borrows from the art of origami to fold paper into intricate shapes and\r\napplies this principle to make 3D lighting displays. We introduce, PCBend a computational\r\ndesign approach that covers a surface with individually addressable RGB LEDs, effectively\r\nforming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize\r\ncut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and\r\nfabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated\r\nstandard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs\r\nare cut along the contour and folded onto a 3D-printed support. The 3D lighting display is\r\nthen controlled to display complex surface light patterns.\r\nCreating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion\r\nor require multiple patches, which are unsuitable for fabrication pipelines that rely on folding\r\nnon-stretchable materials. We reinforce such fabrication pipelines by providing a geometric\r\nrelaxation to the problem, where the input shape is modified to admit overlap-free unfolding.\r\nThe second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s\r\nblueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots\r\nusing modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable\r\nartificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is\r\naltered to enable untethered actuation through infrared radiation, allowing active control of\r\nindividual muscles and their corresponding bones. The combined motion of individual bones\r\ndefines the robot’s overall shape and functionality. Our proposed system significantly expands\r\nboth the design and control spaces of soft robots, which we harness using our computational\r\ndesign tools. We build several physical robots that exhibit complex shape morphing and varied\r\nterrain navigation, showcasing the versatility of our pipeline.\r\nThis thesis explores applications ranging from intricate light patterns displayed on 3D shapes\r\nformed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit\r\nshape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform\r\npassive structures into functional prototypes.","lang":"eng"}],"acknowledgement":"Financial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design\r\nand Modeling that I gratefully acknowledge.\r\n","corr_author":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-065-7"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"date_created":"2025-09-02T14:48:39Z","doi":"10.15479/AT-ISTA-20276","oa_version":"Published Version","article_processing_charge":"No","title":"Design and control of deformable structures: From PCB lighting displays to elastomer robots","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_id":"20284","creator":"mbhargav","file_name":"2025-Bhargava-Manas-Thesis.pdf","success":1,"date_created":"2025-09-03T10:40:52Z","date_updated":"2025-09-03T10:40:52Z","access_level":"open_access","file_size":161436245,"content_type":"application/pdf","checksum":"5baf8ca46c86a94fc8380ff1007aabd4"},{"file_id":"20285","relation":"source_file","file_name":"manas_phd_thesis_source_files.zip","creator":"mbhargav","date_created":"2025-09-03T13:18:05Z","date_updated":"2025-09-04T09:22:29Z","access_level":"closed","content_type":"application/x-zip-compressed","file_size":198831315,"checksum":"66878fafbc0074f88ddd18f24a9fc647"}],"ec_funded":1,"has_accepted_license":"1","citation":{"apa":"Bhargava, M. (2025). Design and control of deformable structures: From PCB lighting displays to elastomer robots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20276","mla":"Bhargava, Manas. Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20276.","ama":"Bhargava M. Design and control of deformable structures: From PCB lighting displays to elastomer robots. 2025. doi:10.15479/AT-ISTA-20276","ieee":"M. Bhargava, “Design and control of deformable structures: From PCB lighting displays to elastomer robots,” Institute of Science and Technology Austria, 2025.","short":"M. Bhargava, Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots, Institute of Science and Technology Austria, 2025.","ista":"Bhargava M. 2025. Design and control of deformable structures: From PCB lighting displays to elastomer robots. Institute of Science and Technology Austria.","chicago":"Bhargava, Manas. “Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20276."},"page":"96","ddc":["000"],"status":"public","author":[{"first_name":"Manas","last_name":"Bhargava","full_name":"Bhargava, Manas","id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425","orcid":"0009-0007-6138-6890"}],"year":"2025","date_updated":"2026-04-07T11:50:10Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","day":"02","alternative_title":["ISTA Thesis"],"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd"}]},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2025-06-10T18:11:05Z","access_level":"open_access","date_created":"2025-06-10T18:11:05Z","content_type":"application/pdf","checksum":"e5108e759014e2a9020c973c778fafc9","file_size":3578077,"creator":"bprach","file_name":"ThesisFinal.pdf","relation":"main_file","file_id":"19829"},{"file_id":"19830","relation":"source_file","file_name":"ThesisFinal.zip","creator":"bprach","date_created":"2025-06-10T18:14:03Z","access_level":"closed","date_updated":"2025-06-10T18:14:03Z","checksum":"51bf6c11fb6d8a9f8010b458c600a83f","file_size":74894357,"content_type":"application/x-zip-compressed"}],"status":"public","citation":{"apa":"Prach, B. (2025). Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria. https://doi.org/10.15479/10.15479/at-ista-19759","mla":"Prach, Bernd. Robust Image Classification with 1-Lipschitz Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/10.15479/at-ista-19759.","ama":"Prach B. Robust image classification with 1-Lipschitz networks. 2025. doi:10.15479/10.15479/at-ista-19759","ieee":"B. Prach, “Robust image classification with 1-Lipschitz networks,” Institute of Science and Technology Austria, 2025.","ista":"Prach B. 2025. Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria.","short":"B. Prach, Robust Image Classification with 1-Lipschitz Networks, Institute of Science and Technology Austria, 2025.","chicago":"Prach, Bernd. “Robust Image Classification with 1-Lipschitz Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/at-ista-19759."},"page":"84","ddc":["000"],"year":"2025","author":[{"full_name":"Prach, Bernd","last_name":"Prach","first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425"}],"date_updated":"2026-04-07T11:49:52Z","oa":1,"alternative_title":["ISTA Thesis"],"day":"30","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"15039"},{"relation":"part_of_dissertation","id":"18874","status":"public"},{"relation":"part_of_dissertation","id":"17426","status":"public"},{"relation":"part_of_dissertation","id":"11839","status":"public"}]},"_id":"19759","date_published":"2025-05-30T00:00:00Z","abstract":[{"text":"Despite generating remarkable results in various computer vision tasks, deep learning comes\r\nwith some surprising shortcomings. For example, tiny perturbations, often imperceptible to\r\nthe human eye, can completely change the predictions of image classifiers. Despite a decade\r\nof research, the field has made limited progress in developing image classifiers that are both\r\naccurate and robust. This thesis aims to address this gap.\r\nAs our first contribution, we aim to simplify the process of training certifiably robust image\r\nclassifiers. We do this by designing a convolutional layer that does not require executing an\r\niterative procedure in every forward pass, but relies on an explicit bound instead. We also\r\npropose a loss function that allows optimizing for a particular margin more precisely.\r\nNext, we provide an overview and comparison of various methods that create robust image\r\nclassifiers by constraining the Lipschitz constant. This is important since generally longer\r\ntraining times and more parameters improve the performance of robust classifiers, making it\r\nchallenging to determine the most practical and effective methods from existing literature.\r\nIn 1-Lipschitz classification, the performance of current methods is still much worse than what\r\nwe expect on the simple tasks we consider. Therefore, we next investigate potential causes of\r\nthis shortcoming. We first consider the role of the activation function. We prove a theoretical\r\nshortcoming of the commonly used activation function, and provide an alternative without it.\r\nHowever this theoretical improvement does barely translate to the empirical performance of\r\nrobust classifiers, suggesting a different bottleneck.\r\nTherefore, in the final chapter, we study how the performance depends on the amount of\r\ntraining data. We prove that in the worst case, we might require far more data to train a\r\nrobust classifier compared to a normal one. We furthermore find that the amount of training\r\ndata is a key determinant of the performance current methods achieve on popular datasets.\r\nAdditionally, we show that linear subspaces exist with tiny data variance, and yet we can\r\nstill train very accurate classifiers after projecting into those subspaces. This shows that on\r\nthe datasets considered, enforcing robustness in classification makes the task strictly more\r\nchallenging.\r\n\r\n-----------------“In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of [name of university or educational entity]’s products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.”\r\n","lang":"eng"}],"type":"dissertation","month":"05","file_date_updated":"2025-06-10T18:14:03Z","publication_identifier":{"issn":["2663-337X"]},"corr_author":"1","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"degree_awarded":"PhD","title":"Robust image classification with 1-Lipschitz networks","article_processing_charge":"No","doi":"10.15479/10.15479/at-ista-19759","oa_version":"Published Version","date_created":"2025-05-28T16:20:48Z"},{"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"2025_Schoen_Hanna_Thesis.docx","creator":"hschoen","file_id":"20311","relation":"source_file","checksum":"b40c74404b8d9593802dabf57bfdf10f","file_size":78812587,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2025-09-09T08:57:04Z","date_created":"2025-09-08T14:33:50Z"},{"date_created":"2025-09-11T14:20:59Z","embargo_to":"open_access","access_level":"closed","date_updated":"2025-09-18T14:12:29Z","checksum":"16abc3ff66396ce2457fe07ffa8bed90","file_size":9667057,"content_type":"application/pdf","embargo":"2026-09-15","relation":"main_file","file_id":"20347","creator":"hschoen","file_name":"2025_Schoen_Hanna_Thesis.pdf"}],"has_accepted_license":"1","status":"public","ddc":["570"],"page":"171","citation":{"ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria.","chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20167.","short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","apa":"Schön, H. (2025). The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20167","mla":"Schön, Hanna. The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20167.","ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:10.15479/AT-ISTA-20167"},"author":[{"full_name":"Schön, Hanna","first_name":"Hanna","last_name":"Schön","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425"}],"year":"2025","date_updated":"2026-04-07T11:50:26Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"13","alternative_title":["ISTA Thesis"],"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario"}],"language":[{"iso":"eng"}],"publication_status":"published","_id":"20167","date_published":"2025-08-13T00:00:00Z","file_date_updated":"2025-09-18T14:12:29Z","type":"dissertation","month":"08","project":[{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"ALTF 302-2019","name":"Control of gene expression at the endoplasmic reticulum","_id":"23813290-32DE-11EA-91FC-C7463DDC885E"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-061-9"]},"acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","corr_author":"1","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","doi":"10.15479/AT-ISTA-20167","date_created":"2025-08-13T11:13:13Z","oa_version":"Published Version","article_processing_charge":"No"}]