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","license":"https://creativecommons.org/licenses/by-sa/4.0/","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"doi":"10.15479/AT-ISTA-21360","file_date_updated":"2026-03-02T10:59:50Z","type":"dissertation","date_published":"2026-02-26T00:00:00Z","OA_place":"repository","day":"26","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"article_processing_charge":"No","citation":{"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","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.","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.","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.","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","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"21363"}]},"date_created":"2026-02-27T09:08:14Z","project":[{"grant_number":"101060393","_id":"34afa094-11ca-11ed-8bc3-a375845a59fb","name":"Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks"}],"year":"2026","page":"185","author":[{"full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","first_name":"Stefan","last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"}],"month":"02","ddc":["570","575","583"],"date_updated":"2026-03-09T12:20:56Z","publication_status":"published","title":"Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species","status":"public","file":[{"date_created":"2026-03-02T10:59:50Z","date_updated":"2026-03-02T10:59:50Z","file_size":31430022,"checksum":"2f1f44e8536c2538f94a440217452c9f","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"2026_Riegler_Stefan_Thesis.zip","file_id":"21386","creator":"sriegler"},{"checksum":"2e8dc39640bc26ae5684c944c619719b","file_size":11635090,"date_updated":"2026-03-02T10:59:49Z","date_created":"2026-03-02T10:59:49Z","embargo_to":"open_access","creator":"sriegler","file_id":"21387","file_name":"2026_Riegler_Stefan_Thesis.pdf","access_level":"closed","content_type":"application/pdf","embargo":"2027-02-27","relation":"main_file"}],"_id":"21360","language":[{"iso":"eng"}]},{"day":"11","date_published":"2026-03-11T00:00:00Z","OA_place":"repository","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments, Institute of Science and Technology Austria, 2026.","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.","apa":"Dunajova, Z. (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","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.","ista":"Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and chiral filaments. Institute of Science and Technology Austria.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-076-3"]},"article_processing_charge":"No","supervisor":[{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"has_accepted_license":"1","acknowledgement":"Finally, I gratefully acknowledge funding from the DOC Fellowship of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360.","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2026-03-13T11:19:21Z","type":"dissertation","doi":"10.15479/AT-ISTA-21423","ddc":["539","570"],"date_updated":"2026-03-18T14:11:35Z","publication_status":"published","month":"03","author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana"}],"_id":"21423","language":[{"iso":"eng"}],"title":"Geometry-driven self-organization of migrating cells and chiral filaments","status":"public","file":[{"file_name":"2026_Dunajova_Zuzana_Thesis_pdfA.pdf","content_type":"application/pdf","embargo":"2026-09-11","access_level":"closed","relation":"main_file","creator":"zdunajov","file_id":"21446","date_updated":"2026-03-12T20:38:52Z","date_created":"2026-03-12T20:38:52Z","embargo_to":"open_access","file_size":14662770,"checksum":"47ce6a48a0c63f28eca6e64c9ffd2c84"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"Thesis-Dunajova_source_file.docx","creator":"zdunajov","file_id":"21447","date_created":"2026-03-12T20:40:18Z","date_updated":"2026-03-13T11:19:21Z","checksum":"5dec5afdffd47c2b0b162d0fe1bed925","file_size":32961408}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"13314","status":"public"},{"status":"public","id":"13116","relation":"research_data"},{"status":"public","id":"21427","relation":"part_of_dissertation"},{"relation":"research_data","id":"21439","status":"public"}]},"date_created":"2026-03-11T08:30:49Z","oa_version":"Published Version","page":"110","project":[{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"year":"2026"},{"status":"public","file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2026_Dvorak_Martin_Thesis.pdf","creator":"mdvorak","file_id":"21394","success":1,"date_created":"2026-03-04T08:56:15Z","date_updated":"2026-03-04T08:56:15Z","file_size":1771231,"checksum":"cface6dc18152680962b5361575f6e4f"},{"file_id":"21395","creator":"mdvorak","file_name":"2026_Dvorak_Martin_Thesis.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"290ddfacfb7e07fb07e6f0b334e67c90","file_size":864585,"date_updated":"2026-03-04T09:03:37Z","date_created":"2026-03-04T09:03:37Z"}],"title":"Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids","_id":"21393","language":[{"iso":"eng"}],"month":"03","author":[{"last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","first_name":"Martin","full_name":"Dvorak, Martin"}],"ddc":["511","000"],"publication_status":"published","date_updated":"2026-03-27T12:37:00Z","year":"2026","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."}],"page":"160","oa_version":"Published Version","date_created":"2026-03-04T09:26:46Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"13120","status":"public"},{"id":"21398","relation":"part_of_dissertation","status":"public"},{"id":"20071","relation":"part_of_dissertation","status":"public"}],"link":[{"url":"https://github.com/madvorak/duality/tree/v3.5.0","relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)"},{"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)","url":"https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0","relation":"software"},{"description":"Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars)","relation":"software","url":"https://github.com/madvorak/chomsky/tree/v1.2.0"},{"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"}]},"publication_identifier":{"isbn":["978-3-99078-074-9"],"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Blanchette, Jasmin","first_name":"Jasmin","last_name":"Blanchette"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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.","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","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.","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.","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."},"alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"degree_awarded":"PhD","date_published":"2026-03-04T00:00:00Z","OA_place":"repository","day":"04","oa":1,"doi":"10.15479/AT-ISTA-21393","type":"dissertation","file_date_updated":"2026-03-04T09:03:37Z","corr_author":"1","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"date_published":"2026-02-09T00:00:00Z","OA_place":"publisher","day":"09","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"citation":{"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.","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.","mla":"Scott, Jonathan A. Data Heterogeneity and Personalization in Federated Learning. Institute of Science and Technology Austria, 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.","ama":"Scott JA. Data heterogeneity and personalization in federated learning. 2026. doi:10.15479/AT-ISTA-21198"},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","has_accepted_license":"1","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).","oa":1,"doi":"10.15479/AT-ISTA-21198","file_date_updated":"2026-02-27T10:25:41Z","type":"dissertation","month":"02","author":[{"first_name":"Jonathan A","full_name":"Scott, Jonathan A","last_name":"Scott","id":"e499926b-f6e0-11ea-865d-9c63db0031e8"}],"ddc":["005"],"date_updated":"2026-04-07T11:46:11Z","publication_status":"published","title":"Data heterogeneity and personalization in federated learning","file":[{"date_updated":"2026-02-17T11:46:22Z","date_created":"2026-02-17T11:46:22Z","checksum":"121c1d968bd86f3630aa7e81d5bbbcb0","file_size":272379252,"file_name":"2026_Scott_Jonathan_Thesis_Source.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","creator":"jscott","file_id":"21298"},{"file_size":15220298,"checksum":"6e3e08ba474bbee8511cc8a839ab2077","date_updated":"2026-02-27T10:25:41Z","date_created":"2026-02-27T10:25:41Z","success":1,"file_id":"21366","creator":"jscott","file_name":"2026_Jonathan_Scott_Thesis.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"status":"public","_id":"21198","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20819"},{"status":"public","relation":"part_of_dissertation","id":"17411"},{"status":"public","relation":"part_of_dissertation","id":"18120"},{"status":"public","id":"21207","relation":"part_of_dissertation"}]},"date_created":"2026-02-09T14:59:53Z","year":"2026","abstract":[{"lang":"eng","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."}],"page":"158"},{"oa":1,"doi":"10.15479/AT-ISTA-21021","type":"dissertation","file_date_updated":"2026-01-30T11:40:09Z","corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"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","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"HeEd"},{"_id":"UlWa"}],"citation":{"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","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.","ista":"Fillmore CD. 2026. Braiding geometry and topology to study shapes and data. Institute of Science and Technology Austria.","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.","short":"C.D. Fillmore, Braiding Geometry and Topology to Study Shapes and Data, Institute of Science and Technology Austria, 2026.","ama":"Fillmore CD. Braiding geometry and topology to study shapes and data. 2026. doi:10.15479/AT-ISTA-21021"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","date_published":"2026-01-21T00:00:00Z","OA_place":"publisher","day":"21","year":"2026","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."}],"page":"122","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"20260","relation":"part_of_dissertation"},{"status":"public","id":"21050","relation":"part_of_dissertation"},{"status":"public","id":"21051","relation":"part_of_dissertation"}]},"date_created":"2026-01-20T21:38:40Z","status":"public","file":[{"file_size":55954297,"checksum":"4c0889130095c31d4e5088c5b8dfd607","date_updated":"2026-01-30T11:40:09Z","date_created":"2026-01-26T19:44:46Z","file_id":"21046","creator":"cfillmor","file_name":"2025_Fillmore_Christopher_Thesis.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","file_name":"Thesis.zip","creator":"cfillmor","file_id":"21047","date_created":"2026-01-26T19:46:20Z","date_updated":"2026-01-26T19:46:20Z","file_size":166080788,"checksum":"d69afb71d82ab98f856886126ee7303a"}],"title":"Braiding geometry and topology to study shapes and data","_id":"21021","language":[{"iso":"eng"}],"month":"01","author":[{"id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore","full_name":"Fillmore, Christopher D","first_name":"Christopher D"}],"ddc":["514","516"],"publication_status":"published","date_updated":"2026-04-07T11:42:49Z"},{"date_published":"2026-03-04T00:00:00Z","OA_place":"publisher","day":"04","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-078-7"]},"article_processing_charge":"No","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}],"department":[{"_id":"GradSch"},{"_id":"KrPi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Baig MA. 2026. On secure chain selection rules from physical resources in a permissionless setting. Institute of Science and Technology Austria.","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.","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","ieee":"M. A. Baig, “On secure chain selection rules from physical resources in a permissionless setting,” Institute of Science and Technology Austria, 2026.","ama":"Baig MA. On secure chain selection rules from physical resources in a permissionless setting. 2026. doi: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."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"oa":1,"doi":"10.15479/AT-ISTA-21651","file_date_updated":"2026-04-15T07:37:25Z","type":"dissertation","author":[{"id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","first_name":"Mirza Ahad","full_name":"Baig, Mirza Ahad"}],"month":"03","ddc":["000"],"date_updated":"2026-04-15T08:45:19Z","publication_status":"published","title":"On secure chain selection rules from physical resources in a permissionless setting","status":"public","file":[{"file_name":"PhD-Thesis-Mirza-Ahad-Baig - Library Submission.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_id":"21655","creator":"mbaig","date_updated":"2026-04-13T08:24:13Z","date_created":"2026-04-03T17:28:48Z","checksum":"c3986dba90653dac97adba662ebff238","file_size":139353434},{"date_created":"2026-04-03T17:29:30Z","date_updated":"2026-04-15T07:37:25Z","file_size":1942037,"checksum":"292a5989262521f7c145a109d1f348cb","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2026_Baig_Mirza_Ahad_Thesis.pdf","file_id":"21656","creator":"mbaig"}],"_id":"21651","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"21134","status":"public"},{"id":"20587","relation":"part_of_dissertation","status":"public"}]},"date_created":"2026-04-02T09:31:34Z","year":"2026","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"}]},{"day":"16","date_published":"2026-01-16T00:00:00Z","OA_place":"publisher","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:10.15479/AT-ISTA-20991","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","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.","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.","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","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-077-0"],"issn":["2663-337X"]},"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","orcid":"0000-0003-1050-4969"}],"article_processing_charge":"No","has_accepted_license":"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)","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"corr_author":"1","file_date_updated":"2026-01-16T13:08:59Z","type":"dissertation","oa":1,"doi":"10.15479/AT-ISTA-20991","ddc":["576"],"date_updated":"2026-04-16T12:20:37Z","publication_status":"published","month":"01","author":[{"last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","full_name":"Garcia Castillo, Diego Fernando"}],"_id":"20991","language":[{"iso":"eng"}],"title":"The genomic architecture of local adaptation in introduced populations","file":[{"date_created":"2026-01-16T12:25:13Z","date_updated":"2026-01-16T12:25:13Z","file_size":22456421,"checksum":"841f1bc073d667125729b2a017f8c37a","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"2026_Garcia_Diego_Thesis.docx","creator":"dgarciac","file_id":"20996"},{"creator":"dgarciac","file_id":"20997","file_name":"2026_Garcia_Diego_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":9556719,"checksum":"a1f33d4f183ce7072eee42a6ccf5340b","date_updated":"2026-01-16T12:25:13Z","success":1,"date_created":"2026-01-16T12:25:13Z"},{"date_created":"2026-01-16T13:08:14Z","date_updated":"2026-01-16T13:08:14Z","file_size":54491433,"checksum":"98a80691067174c30fe53f38ce7344e6","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.","access_level":"closed","content_type":"application/x-compressed","relation":"supplementary_material","file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","creator":"dgarciac","file_id":"20998"},{"file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar","relation":"supplementary_material","access_level":"open_access","content_type":"application/x-compressed","file_id":"20999","creator":"dgarciac","date_updated":"2026-01-16T13:08:14Z","date_created":"2026-01-16T13:08:14Z","file_size":7982811,"checksum":"99a3cab2fa36666b9a92eefc27d586da"},{"date_created":"2026-01-16T13:08:59Z","date_updated":"2026-01-16T13:08:59Z","file_size":732,"checksum":"255fdf56b2932c46bf27c63aa6106a4f","relation":"supplementary_material","access_level":"open_access","content_type":"text/plain","file_name":"README.txt","file_id":"21000","creator":"dgarciac"}],"status":"public","date_created":"2026-01-16T09:47:59Z","related_material":{"record":[{"relation":"research_data","id":"18498","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"18491"}]},"oa_version":"Published Version","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."}],"page":"199","year":"2026"},{"month":"05","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","last_name":"Yalniz","full_name":"Yalniz, Gökhan","first_name":"Gökhan","orcid":"0000-0002-8490-9312"}],"date_updated":"2026-04-07T11:47:06Z","publication_status":"published","ddc":["514","519","532","004"],"title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Gökhan Yalnız - PhD thesis.pdf","file_id":"19685","creator":"gyalniz","date_created":"2025-05-12T15:13:28Z","success":1,"date_updated":"2025-05-12T15:13:28Z","file_size":20058169,"checksum":"0e452642b79f13633f1595bde71a67e3"},{"date_created":"2025-05-12T15:15:59Z","date_updated":"2025-05-12T15:43:28Z","checksum":"921099d76adab2df784ce12ce41cfb22","file_size":37763743,"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).","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","file_name":"Movie 2A.1.mp4","title":"Chapter 2 - Movie 2A.1","creator":"gyalniz","file_id":"19686"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:09Z","checksum":"0ae5ac7d9896003c0c4207dd746808dc","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). 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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":"2025-05-12T15:16:21Z","date_updated":"2025-05-12T15:43:28Z","creator":"gyalniz","title":"Chapter 3 - Movie 3A.2","file_id":"19688","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","file_name":"Movie 3A.2.mp4"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:36Z","file_size":7748659,"checksum":"7ed871f428100d6827ac9b0e8ca8e985","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_name":"Movie 3A.3.mp4","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","creator":"gyalniz","title":"Chapter 3 - Movie 3A.3","file_id":"19689"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:16:50Z","checksum":"dd5a252e1da00c8f303588e22e2baeef","file_size":5873052,"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).","file_name":"Movie 3A.4.mp4","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","creator":"gyalniz","title":"Chapter 3 - Movie 3A.4","file_id":"19690"},{"file_name":"Movie 4A.1.mp4","relation":"supplementary_material","content_type":"video/mp4","access_level":"open_access","file_id":"19691","title":"Chapter 4 - Movie 4A.1","creator":"gyalniz","date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:11Z","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit.","file_size":9209327,"checksum":"5ac58b86810698db28cbfc28f351ff70"},{"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:17:43Z","checksum":"ac877f1e1ef39439911bf37cb1793b8e","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.","file_size":5893993,"file_name":"Movie 5A.1.mp4","relation":"supplementary_material","access_level":"open_access","content_type":"video/mp4","file_id":"19692","title":"Chapter 5 - Movie 5A.1","creator":"gyalniz"},{"file_size":3990352,"checksum":"fd17eabb70129ceaa414e40924d1d2fe","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.","date_created":"2025-05-12T15:17:49Z","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 5 - Movie 5A.2","creator":"gyalniz","file_id":"19693","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","file_name":"Movie 5A.2.mp4"},{"date_created":"2025-05-12T15:17:58Z","date_updated":"2025-05-12T15:43:28Z","file_size":5171009,"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.","checksum":"32f904497ab0bbee38f0788d96b91454","access_level":"open_access","content_type":"video/mp4","relation":"supplementary_material","file_name":"Movie 5A.3.mp4","creator":"gyalniz","title":"Chapter 5 - Movie 5A.3","file_id":"19694"},{"file_id":"19695","creator":"gyalniz","file_name":"Gökhan Yalnız - PhD thesis.zip","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","checksum":"f313261b9bb12dfb943fead8318954c6","file_size":18991996,"date_updated":"2025-05-12T15:43:28Z","date_created":"2025-05-12T15:27:10Z"}],"status":"public","language":[{"iso":"eng"}],"_id":"19684","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7563","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9558","status":"public"},{"id":"12105","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"13274","status":"public"},{"relation":"part_of_dissertation","id":"14466","status":"public"}]},"date_created":"2025-05-12T15:12:28Z","project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"year":"2025","page":"155","abstract":[{"lang":"eng","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."}],"OA_place":"publisher","date_published":"2025-05-13T00:00:00Z","day":"13","supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"short":"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","ieee":"G. Yalniz, “Transition to turbulence : Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","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","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.","ista":"Yalniz G. 2025. Transition to turbulence : Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","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."},"publisher":"Institute of Science and Technology Austria","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","doi":"10.15479/AT-ISTA-19684","oa":1,"file_date_updated":"2025-05-12T15:43:28Z","type":"dissertation"},{"article_processing_charge":"No","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"citation":{"ista":"Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria.","ieee":"O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025.","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.","mla":"Draganov, Ondrej. Structures and Computations in Topological Data Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18979.","short":"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"},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2025-02-03T00:00:00Z","day":"03","doi":"10.15479/at:ista:18979","oa":1,"file_date_updated":"2025-02-04T16:22:07Z","type":"dissertation","corr_author":"1","keyword":["topological data analysis","chromatic point set","alpha complex","persistent homology","six pack","sheaf","microlocal discrete Morse","injective resolution","collapse","knot","discrete Morse theory"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","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","title":"Structures and computations in topological data analysis","status":"public","file":[{"file_name":"Thesis.zip","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"18983","creator":"odragano","date_updated":"2025-01-31T16:58:30Z","date_created":"2025-01-31T16:58:30Z","file_size":11899491,"checksum":"af6567e5d35e5eb330b8925ae37f1998"},{"file_size":8857514,"checksum":"c3fef68e35b9dc2020b2ca6006da6343","date_created":"2025-02-04T16:22:07Z","date_updated":"2025-02-04T16:22:07Z","creator":"odragano","file_id":"19000","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"Thesis.pdf"}],"language":[{"iso":"eng"}],"_id":"18979","month":"02","author":[{"id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","full_name":"Draganov, Ondrej","first_name":"Ondrej","orcid":"0000-0003-0464-3823"}],"date_updated":"2026-04-07T11:47:30Z","publication_status":"published","ddc":["514","004"],"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"}],"year":"2025","page":"140","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."}],"oa_version":"Published Version","date_created":"2025-01-31T17:04:40Z","related_material":{"record":[{"id":"15091","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18981","relation":"part_of_dissertation"}]}},{"day":"25","OA_place":"publisher","date_published":"2025-08-25T00:00:00Z","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"citation":{"ama":"Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi: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.","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.","ieee":"J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025.","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","ista":"Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"has_accepted_license":"1","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","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file_date_updated":"2025-08-25T13:49:56Z","type":"dissertation","doi":"10.15479/AT-ISTA-20206","oa":1,"date_updated":"2026-04-07T11:48:07Z","publication_status":"published","ddc":["621","535"],"author":[{"orcid":"0009-0000-7590-3501","first_name":"Jakob","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"}],"month":"08","language":[{"iso":"eng"}],"_id":"20206","title":"Construction of a cryo-super-resolution microscope to guide in situ structure analysis","file":[{"file_id":"20228","creator":"jvorlauf","file_name":"2025_Vorlaufer_Jakob_Thesis.docx","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"191db3367c19c9b32b65f4bc3a7c19de","file_size":39735535,"date_updated":"2025-08-25T13:49:55Z","date_created":"2025-08-25T13:49:55Z"},{"file_name":"2025_Vorlaufer_Jakob_Thesis.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"20229","creator":"jvorlauf","date_updated":"2025-08-25T13:49:56Z","success":1,"date_created":"2025-08-25T13:49:56Z","checksum":"104400e6036921569610230c1d4899dc","file_size":10947446}],"status":"public","date_created":"2025-08-22T08:12:55Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"19795","status":"public"}]},"oa_version":"Published Version","page":"107","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"}],"project":[{"grant_number":"CZI01","name":"CryoMinflux-guided in-situ molecular census and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308"}],"year":"2025"},{"status":"public","file":[{"file_size":8292363,"checksum":"847ec70b2e40f50e0ddc7b8da201d52c","date_updated":"2025-05-28T11:59:11Z","embargo_to":"open_access","date_created":"2025-05-28T11:59:11Z","file_id":"19757","creator":"sinumell","file_name":"Final Thesis_Syamala Inumella.pdf","relation":"main_file","access_level":"closed","embargo":"2026-05-23","content_type":"application/pdf"},{"creator":"sinumell","file_id":"19758","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Final Thesis_Syamala Inumella.docx","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","file_size":7145703,"date_created":"2025-05-28T11:59:11Z","date_updated":"2025-05-28T11:59:11Z"}],"title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","OA_embargo":"12","language":[{"iso":"eng"}],"_id":"19722","month":"05","author":[{"last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425","orcid":"0009-0002-5890-120X","first_name":"Syamala","full_name":"Inumella, Syamala"}],"publication_status":"published","date_updated":"2026-04-07T11:47:52Z","ddc":["580"],"year":"2025","page":"113","oa_version":"Published Version","date_created":"2025-05-23T15:21:29Z","article_processing_charge":"No","supervisor":[{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-059-6"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi: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.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","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","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.","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"OA_place":"publisher","date_published":"2025-05-23T00:00:00Z","day":"23","doi":"10.15479/AT-ISTA-19722","type":"dissertation","file_date_updated":"2025-05-28T11:59:11Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","acknowledgement":"Special thanks to the Plant Facility.","has_accepted_license":"1"},{"author":[{"last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","first_name":"Jakub"}],"month":"08","ddc":["000","519"],"date_updated":"2026-04-07T11:49:12Z","publication_status":"published","title":"Structural properties of games on graphs","status":"public","file":[{"date_updated":"2025-08-14T09:54:43Z","success":1,"date_created":"2025-08-14T09:54:43Z","checksum":"c6c4df9777f4537940de7ab392ad57e2","file_size":5927291,"file_name":"2025_Svoboda_Jakub_Thesis.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"20177","creator":"jsvoboda"},{"date_created":"2025-08-14T09:55:20Z","date_updated":"2025-08-21T11:48:39Z","file_size":6731815,"checksum":"485e9f9822821bc03666d245d80aaa08","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"2025_Svoboda_Jakub_Thesis.zip","file_id":"20178","creator":"jsvoboda"}],"_id":"20138","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"12787","status":"public"},{"id":"12101","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"12257","status":"public"},{"relation":"part_of_dissertation","id":"15297","status":"public"},{"id":"18703","relation":"part_of_dissertation","status":"public"}]},"date_created":"2025-08-05T14:33:59Z","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"year":"2025","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"}],"ec_funded":1,"page":"167","date_published":"2025-08-05T00:00:00Z","OA_place":"publisher","day":"05","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ama":"Svoboda J. Structural properties of games on graphs. 2025. doi:10.15479/AT-ISTA-20138","short":"J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025.","mla":"Svoboda, Jakub. Structural Properties of Games on Graphs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20138.","ista":"Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria.","chicago":"Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20138.","apa":"Svoboda, J. (2025). Structural properties of games on graphs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20138","ieee":"J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","corr_author":"1","has_accepted_license":"1","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"oa":1,"doi":"10.15479/AT-ISTA-20138","file_date_updated":"2025-08-21T11:48:39Z","type":"dissertation"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"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.","has_accepted_license":"1","doi":"10.15479/AT-ISTA-20117","type":"dissertation","file_date_updated":"2025-09-03T09:36:52Z","date_published":"2025-08-04T00:00:00Z","OA_place":"publisher","day":"04","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ama":"Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117","short":"Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025.","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.","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.","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","ista":"Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 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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"}],"oa_version":"Published Version","date_created":"2025-05-28T16:20:48Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"15039","status":"public"},{"status":"public","id":"18874","relation":"part_of_dissertation"},{"id":"17426","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11839"}]},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"citation":{"apa":"Prach, B. (2025). 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Thaliana Developmental Transitions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20364.","ieee":"C. Giannini, “Nuclear and cell surface auxin signaling in A. thaliana developmental transitions,” Institute of Science and Technology Austria, 2025."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2025-09-19T00:00:00Z","OA_place":"publisher","day":"19","doi":"10.15479/AT-ISTA-20364","file_date_updated":"2025-09-30T14:31:29Z","type":"dissertation","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","has_accepted_license":"1","acknowledgement":"Plant Facility,\r\nProtein Service Facility","keyword":["Auxin Signaling","Plant Development"]},{"file":[{"date_updated":"2025-10-28T13:10:08Z","success":1,"date_created":"2025-10-28T13:10:08Z","checksum":"2892f04d4a5c18677871c3e06ac1244a","file_size":6846189,"file_name":"Thesis_PDFA_.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"20567","creator":"snaik"},{"checksum":"15934d4465cd0e9b7c32678da9a33a2f","file_size":8839300,"date_created":"2025-10-28T13:10:26Z","date_updated":"2025-10-28T13:10:26Z","file_id":"20568","creator":"snaik","relation":"source_file","access_level":"open_access","content_type":"application/zip","file_name":"Thesis.zip"}],"status":"public","title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","_id":"20441","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-8421-5508","first_name":"Suyash","full_name":"Naik, Suyash","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"}],"month":"10","ddc":["596","597","532"],"publication_status":"published","date_updated":"2026-04-07T11:58:57Z","year":"2025","project":[{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"grant_number":"W 1250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"25AA5F24-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium."}],"page":"105","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"20465","relation":"part_of_dissertation"}]},"date_created":"2025-10-10T14:58:30Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-069-5"]},"article_processing_charge":"No","supervisor":[{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"publisher":"Institute of Science and Technology Austria","citation":{"ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:10.15479/AT-ISTA-20441","short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.","mla":"Naik, Suyash. Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20441.","ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20441.","apa":"Naik, S. (2025). Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20441","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"degree_awarded":"PhD","date_published":"2025-10-12T00:00:00Z","OA_place":"publisher","day":"12","oa":1,"doi":"10.15479/AT-ISTA-20441","type":"dissertation","file_date_updated":"2025-10-28T13:10:26Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","has_accepted_license":"1","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"}},{"doi":"10.15479/AT-ISTA-20485","file_date_updated":"2025-11-06T11:08:06Z","type":"dissertation","corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"I would also like to acknowledge the funding that I received from the European Union’s\r\nHorizon 2020 research and Innovation programme under the Marie Sklodowska-Curie\r\nGrant Agreement No. 665385. This work would not have been possible without the contribution and support of people\r\nbehind the scientific service units at ISTA: the Life Science Facility (LSF), Imaging and\r\nOptics Facility (IOF), the Bioinformatics Unit, Protein Services Unit and\r\nElectrophysiology Unit. I would also like to recognize the work of people at the Vienna\r\nBiocenter (VBC) Mass Spectrometry Facility, particularly Markus Hartl and WeiQiang\r\nChen. ","article_processing_charge":"No","supervisor":[{"full_name":"de Bono, Mario","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-068-8"]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"citation":{"short":"M. Misova, Dissecting Gap Junction Biology Using the C. Elegans Nervous System, Institute of Science and Technology Austria, 2025.","ama":"Misova M. Dissecting gap junction biology using the C. elegans nervous system. 2025. doi:10.15479/AT-ISTA-20485","ieee":"M. Misova, “Dissecting gap junction biology using the C. elegans nervous system,” Institute of Science and Technology Austria, 2025.","apa":"Misova, M. (2025). Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20485","chicago":"Misova, Michaela. “Dissecting Gap Junction Biology Using the C. Elegans Nervous System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20485.","ista":"Misova M. 2025. Dissecting gap junction biology using the C. elegans nervous system. Institute of Science and Technology Austria.","mla":"Misova, Michaela. Dissecting Gap Junction Biology Using the C. Elegans Nervous System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20485."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","OA_place":"publisher","date_published":"2025-10-23T00:00:00Z","day":"23","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"year":"2025","page":"155","ec_funded":1,"oa_version":"Published Version","date_created":"2025-10-17T16:15:09Z","title":"Dissecting gap junction biology using the C. elegans nervous system","file":[{"date_created":"2025-10-23T08:22:35Z","date_updated":"2025-11-06T11:08:06Z","checksum":"e042ea314e7e13fce76c6c95e126779a","file_size":75070995,"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2025-Misova-Michaela-Thesis.docx","file_id":"20518","creator":"mmisova"},{"file_size":10974630,"checksum":"fcd8973d6a025256eb0eb1a82c02172c","date_created":"2025-10-23T08:21:21Z","embargo_to":"open_access","date_updated":"2025-10-23T08:21:21Z","creator":"mmisova","file_id":"20519","content_type":"application/pdf","embargo":"2026-10-23","access_level":"closed","relation":"main_file","file_name":"2025-Misova-Michaela-Thesis.pdf"}],"status":"public","language":[{"iso":"eng"}],"_id":"20485","author":[{"id":"495A3C32-F248-11E8-B48F-1D18A9856A87","last_name":"Misova","first_name":"Michaela","orcid":"0000-0003-2427-6856","full_name":"Misova, Michaela"}],"month":"10","date_updated":"2026-04-07T11:54:00Z","publication_status":"published","ddc":["570"]}]