--- OA_place: publisher OA_type: gold _id: '19393' abstract: - lang: eng text: "Rotations constitute one of the fundamental symmetries in physics, characterized by their intricate group structure and infinite dimensional representations. In contrast to classical rotations, quantum mechanics unveils the SO(3) symmetry group structure, manifesting in phenomena without classical counterparts, from angular momentum quantization to non-trivial addition of angular momenta.\r\nWhile most studies of topological physics have focused on two-band systems, the SO(3) symmetry group of quantum rotors offers an inherently more complex platform with unprecedented possibilities for exploring topological phenomena. Despite their ubiquity in nature– from molecules to nanorotors– their potential for hosting topological phases has remained largely unexamined.\r\nIn this thesis, we mainly focus on periodically driven linear molecules as a prototype for studying topological phenomena in quantum rotors. Recent technological advances in coherent control of molecules, particularly through precisely shaped laser pulses, have made it possible to investigate linear rotors in the context of topology. While planar rotors have received some attention in recent years, threedimensional rotors–particularly linear molecules–harbor substantially richer topological phenomena due to their non-abelian nature and their additional angular degrees of freedom. We demonstrate that these systems can host novel edge states and topological features fundamentally impossible in planar systems.\r\nWe begin by establishing a theoretical bridge between periodically kicked rotors and \"crystalline\" lattices in angular momentum space. Using non-interacting linear molecules as our primary example, we show how quantum interference and revival patterns lead to the possibility to simulate band models with arbitrary number of bands N. While our framework applies to various quantum rotors, including nanorotors and kicked Bose-Einstein condensates, linear\r\nmolecules provide an ideal experimental platform due to their abovementioned precise controllability.\r\nThe core of this work examines adiabatic dynamics of 3D quantum rotors, establishing a geometric framework based on the Euler class to characterize its non-abelian topology. The non-Hermitian nature of the system enables novel braiding behaviors and topological transitions impossible in static systems, leading to an anomalous Dirac string phase with edge states in each gap, even though the Berry phases are all zero. These features can be directly observed through\r\nmolecular alignment and rotational level populations.\r\nThese findings establish quantum rotors as an alternative platform for studying multi-band topological physics, while suggesting practical implementations for quantum computation where topological protection could offer natural resilience against decoherence. The rich structure of three-dimensional rotation groups, combined with the tunability of topological features through driving parameters, makes this platform particularly valuable for exploring fundamental\r\nphysics and developing quantum technologies." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Volker full_name: Karle, Volker id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425 last_name: Karle orcid: 0000-0002-6963-0129 citation: ama: Karle V. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. 2025. doi:10.15479/AT-ISTA-19393 apa: Karle, V. (2025). Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19393 chicago: Karle, Volker. “Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19393. ieee: V. Karle, “Non-equilibrium topological phases with periodically driven molecules and quantum rotors,” Institute of Science and Technology Austria, 2025. ista: Karle V. 2025. Non-equilibrium topological phases with periodically driven molecules and quantum rotors. Institute of Science and Technology Austria. mla: Karle, Volker. Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19393. short: V. Karle, Non-Equilibrium Topological Phases with Periodically Driven Molecules and Quantum Rotors, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-03-12T13:04:59Z date_published: 2025-03-13T00:00:00Z date_updated: 2026-07-29T08:59:30Z day: '13' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MiLe doi: 10.15479/AT-ISTA-19393 file: - access_level: open_access checksum: d3ab25782c7ea38ce9910e57d25f6733 content_type: application/pdf creator: vkarle date_created: 2025-03-12T12:56:46Z date_updated: 2025-03-12T12:56:46Z file_id: '19394' file_name: thesis_final.pdf file_size: 10625143 relation: main_file success: 1 - access_level: closed checksum: 3ccfb0aeba4d860d71e18347913034e4 content_type: application/zip creator: vkarle date_created: 2025-03-13T13:15:10Z date_updated: 2025-03-20T08:02:35Z file_id: '19400' file_name: thesis.zip file_size: 23119202 relation: source_file file_date_updated: 2025-03-20T08:02:35Z fulldoi: https://doi.org/10.15479/AT-ISTA-19393 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '192' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14851' relation: part_of_dissertation status: public - id: '12788' relation: part_of_dissertation status: public - id: '9903' relation: part_of_dissertation status: public - id: '15004' relation: part_of_dissertation status: public - id: '19425' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Non-equilibrium topological phases with periodically driven molecules and quantum rotors tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20735' abstract: - lang: eng text: "Left–right alternation is a defining feature of spinal locomotor circuits, yet the level of neuronal\r\ndetail required to generate and maintain this pattern remains unclear. This thesis investigates how\r\nmodels spanning multiple levels of abstraction—from biophysically detailed Hodgkin–Huxley (HH)\r\nneurons to adaptive integrate–and–fire (I&F) formulations and synfire-chain modules—can account\r\nfor the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole. The guiding\r\nhypothesis is that a small set of neuronal mechanisms is sufficient to reproduce the essential features\r\nof rhythmic alternation, and that moving between modeling scales helps distinguish core principles\r\nfrom biological detail.\r\nA minimal bilateral HH network comprising only four canonical neuron classes—excitatory\r\ndescending interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory\r\ninterneurons (aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce\r\nexperimentally observed firing modes, the model demonstrated that rebound-prone dIN excitability,\r\ncontralateral inhibition and modest electrical coupling are sufficient to generate stable alternating\r\nactivity, even in very small networks. These results motivated the transition to simpler models\r\ncapable of efficient analysis and scaling.\r\nAdaptive exponential I&F (AdEx) neurons were calibrated to physiological recordings using\r\nsimulation-based inference, yielding tonic and phasic/rebound templates that preserved the key\r\ndynamical signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying\r\nsingle-spike responses and rebound firing in dINs. At network level, the I&F models robustly\r\nreproduced left–right alternation, while highlighting constraints on synaptic kinetics and adaptation\r\nneeded to avoid multi-spike responses.\r\nFinally, a synfire-chain framework provided a complementary, timing-centric perspective, demonstrating how precise spike synchrony, synaptic delays and minimal inhibitory coupling can generate\r\nalternating left–right sequences in a feedforward setting. Together, these approaches converge on a\r\ncommon conclusion: rebound-prone ipsilateral excitation combined with precisely timed contralateral inhibition constitutes a sufficient substrate for alternating spinal rhythms.\r\nBy integrating bottom-up and top-down modeling strategies, this thesis provides a unified, extensible framework for studying spinal pattern generation. The results show that essential locomotor\r\ndynamics can be captured across multiple abstraction levels, offering both mechanistic insight and\r\npractical tools for future data-driven investigations of spinal circuit development, robustness and\r\nmodulation." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Alexia C full_name: Wilson, Alexia C id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d last_name: Wilson orcid: 0000-0001-6191-1367 citation: ama: 'Wilson AC. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. 2025. doi:10.15479/AT-ISTA-20735' apa: 'Wilson, A. C. (2025). Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20735' chicago: 'Wilson, Alexia C. “Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20735.' ieee: 'A. C. Wilson, “Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog,” Institute of Science and Technology Austria, 2025.' ista: 'Wilson AC. 2025. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology Austria.' mla: 'Wilson, Alexia C. Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20735.' short: 'A.C. Wilson, Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-12-08T09:49:41Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-07-29T12:55:12Z day: '09' ddc: - '570' - '596' - '005' degree_awarded: MS department: - _id: GradSch - _id: TiVo - _id: LoSw doi: 10.15479/AT-ISTA-20735 doi_confirm: '1' file: - access_level: closed checksum: 9e3b6b73f8cbec2c3687d17fe8e30410 content_type: application/zip creator: awilson date_created: 2026-01-01T17:26:30Z date_updated: 2026-01-02T13:05:07Z file_id: '20919' file_name: tadpoleAdEx.zip file_size: 566072368 relation: source_file - access_level: open_access checksum: 13f4c0d33923e9d5c9d56731345cf21d content_type: application/pdf creator: awilson date_created: 2026-01-04T12:58:49Z date_updated: 2026-01-04T12:58:49Z file_id: '20923' file_name: Masters_Thesis_Alexia_Wilson_FINAL_pdfA.pdf file_size: 7170097 relation: main_file success: 1 file_date_updated: 2026-01-04T12:58:49Z fulldoi: https://doi.org/10.15479/AT-ISTA-20735 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '110' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13097' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 title: 'Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '21398' abstract: - lang: eng text: Seymour's decomposition theorem is a hallmark result in matroid theory presenting a structural characterization of the class of regular matroids. Formalization of matroid theory faces many challenges, most importantly that only a limited number of notions and results have been implemented so far. In this work, we formalize the proof of the forward (composition) direction of Seymour's theorem for regular matroids. To this end, we develop a library in Lean 4 that implements definitions and results about totally unimodular matrices, vector matroids, their standard representations, regular matroids, and 1-, 2-, and 3-sums of matrices and binary matroids given by their standard representations. Using this framework, we formally state Seymour's decomposition theorem and implement a formally verified proof of the composition direction in the setting where the matroids have finite rank and may have infinite ground sets. acknowledgement: "We would like to dedicate the paper to the memory of Klaus Truemper, whose monograph Matroid Decomposition [12]\r\nlaid the foundation for our entire work." article_number: '2509.20539' article_processing_charge: No arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Tristan full_name: Figueroa-Reid, Tristan last_name: Figueroa-Reid - first_name: Rida full_name: Hamadani, Rida last_name: Hamadani - first_name: Byung-Hak full_name: Hwang, Byung-Hak last_name: Hwang - first_name: Evgenia full_name: Karunus, Evgenia last_name: Karunus - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Alexander full_name: Meiburg, Alexander last_name: Meiburg - first_name: Alexander full_name: Nelson, Alexander last_name: Nelson - first_name: Peter full_name: Nelson, Peter last_name: Nelson - first_name: Mark full_name: Sandey, Mark last_name: Sandey - first_name: Ivan full_name: Sergeev, Ivan id: ca3c9187-9a72-11ee-a009-8af825d896b0 last_name: Sergeev orcid: 0009-0004-9145-8785 citation: ama: Dvorak M, Figueroa-Reid T, Hamadani R, et al. Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv. doi:10.48550/arXiv.2509.20539 apa: Dvorak, M., Figueroa-Reid, T., Hamadani, R., Hwang, B.-H., Karunus, E., Kolmogorov, V., … Sergeev, I. (n.d.). Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv. https://doi.org/10.48550/arXiv.2509.20539 chicago: Dvorak, Martin, Tristan Figueroa-Reid, Rida Hamadani, Byung-Hak Hwang, Evgenia Karunus, Vladimir Kolmogorov, Alexander Meiburg, et al. “Composition Direction of Seymour’s Theorem for Regular Matroids — Formally Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2509.20539. ieee: M. Dvorak et al., “Composition direction of Seymour’s theorem for regular matroids — Formally verified,” arXiv. . ista: Dvorak M, Figueroa-Reid T, Hamadani R, Hwang B-H, Karunus E, Kolmogorov V, Meiburg A, Nelson A, Nelson P, Sandey M, Sergeev I. Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv, 2509.20539. mla: Dvorak, Martin, et al. “Composition Direction of Seymour’s Theorem for Regular Matroids — Formally Verified.” ArXiv, 2509.20539, doi:10.48550/arXiv.2509.20539. short: M. Dvorak, T. Figueroa-Reid, R. Hamadani, B.-H. Hwang, E. Karunus, V. Kolmogorov, A. Meiburg, A. Nelson, P. Nelson, M. Sandey, I. Sergeev, ArXiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-03-04T11:56:29Z date_published: 2025-09-23T00:00:00Z date_updated: 2026-07-29T12:56:51Z day: '23' department: - _id: GradSch - _id: VlKo doi: 10.48550/arXiv.2509.20539 external_id: arxiv: - '2509.20539' fulldoi: https://doi.org/10.48550/arXiv.2509.20539 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2509.20539 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '21393' relation: dissertation_contains status: public status: public title: Composition direction of Seymour's theorem for regular matroids — Formally verified type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20811' abstract: - lang: eng text: "\tThis thesis is organized into two parts, each comprising two chapters: Chapter 1 and 2 offer models for the evolution of vaccine resistance in response to diverse vaccination strategies. Chapter 3 and 4 review the statistics of records, their connection to models of innovation and an application to the cultural evolution of sports.\r\n\tIn chapter 1 we present a modelling study from 2021 on the evolution of SARS-CoV-2. At that time the vaccine-resistant Omicron variant had not yet evolved. In our model we consider a population that is becoming vaccinated over time, while a pathogen is spreading in the population and eventually becoming resistant to the vaccine. We explore effective pharmaceutical and non-pharmaceutical interventions to prevent the emergence of vaccine resistance. \r\n\tIn chapter 2 we model a particular set of complex vaccination strategies, mosaic and pyramid vaccination, where an immunologically diverse portfolio of vaccines is considered. We find that a bet-hatching strategy, in which vaccine types are distributed in the population, is effective at hindering the evolution of vaccine resistance if mutation rates are high. \r\n\tIn chapter 3 we switch gears and present a review on the statistics of records. We highlight similarities and analogies to other models in the fields of statistical physics, evolution and innovation. This offers interesting complimentary perspectives on well-known models. \r\n\tIn chapter 4 we apply models of record statistics and innovation to study cultural evolution in sport. We propose a model of sport evolution that combines deterministic improvements in performance and stochastic bursts of improvements due to innovation. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella citation: ama: 'Rella S. Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation. 2025. doi:10.15479/AT-ISTA-20811' apa: 'Rella, S. (2025). Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20811' chicago: 'Rella, Simon. “Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20811.' ieee: 'S. Rella, “Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation,” Institute of Science and Technology Austria, 2025.' ista: 'Rella S. 2025. Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation. Institute of Science and Technology Austria.' mla: 'Rella, Simon. Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20811.' short: 'S. Rella, Adaptive Processes in Biology and Culture: Models of Evolving Vaccine Resistance and the Record Statistics of Innovation, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-12-12T14:39:56Z date_published: 2025-12-15T00:00:00Z date_updated: 2026-07-29T12:57:49Z day: '15' ddc: - '616' - '576' - '614' - '519' degree_awarded: PhD department: - _id: GradSch - _id: GaTk - _id: FyKo doi: 10.15479/AT-ISTA-20811 doi_confirm: '1' file: - access_level: open_access checksum: a0bd7a585720e60df284101b8afdf6bb content_type: application/pdf creator: srella date_created: 2025-12-16T21:49:52Z date_updated: 2025-12-16T21:49:52Z file_id: '20831' file_name: 2025_Rella_Simon_Thesis.pdf file_size: 29019662 relation: main_file success: 1 - access_level: open_access checksum: b8b3a90932ae1d96d307838710f46e32 content_type: application/zip creator: srella date_created: 2025-12-16T21:52:19Z date_updated: 2025-12-16T21:52:19Z file_id: '20832' file_name: 2025_Rella_Simon_Thesis_Sourcefiles.zip file_size: 42094025 relation: source_file file_date_updated: 2025-12-16T21:52:19Z fulldoi: https://doi.org/10.15479/AT-ISTA-20811 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '95' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18307' relation: part_of_dissertation status: public - id: '9905' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 title: 'Adaptive processes in biology and culture: Models of evolving vaccine resistance and the record statistics of innovation' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20276' abstract: - lang: eng text: "Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations\r\neither preserve the intrinsic material geometry (e.g., folding paper) or modify it through\r\nlocalized contraction. Once transformed, the 3D shape can be further controlled to achieve a\r\ntarget functionality. A key challenge is to take the material specifications and the actuation\r\nprocess as input to automatically design the target 3D shape and its functionality. This thesis\r\npresents two novel computational pipelines for the design and control of shape-morphing\r\nstructures used to create functional prototypes.\r\nThe first pipeline borrows from the art of origami to fold paper into intricate shapes and\r\napplies this principle to make 3D lighting displays. We introduce, PCBend a computational\r\ndesign approach that covers a surface with individually addressable RGB LEDs, effectively\r\nforming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize\r\ncut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and\r\nfabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated\r\nstandard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs\r\nare cut along the contour and folded onto a 3D-printed support. The 3D lighting display is\r\nthen controlled to display complex surface light patterns.\r\nCreating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion\r\nor require multiple patches, which are unsuitable for fabrication pipelines that rely on folding\r\nnon-stretchable materials. We reinforce such fabrication pipelines by providing a geometric\r\nrelaxation to the problem, where the input shape is modified to admit overlap-free unfolding.\r\nThe second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s\r\nblueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots\r\nusing modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable\r\nartificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is\r\naltered to enable untethered actuation through infrared radiation, allowing active control of\r\nindividual muscles and their corresponding bones. The combined motion of individual bones\r\ndefines the robot’s overall shape and functionality. Our proposed system significantly expands\r\nboth the design and control spaces of soft robots, which we harness using our computational\r\ndesign tools. We build several physical robots that exhibit complex shape morphing and varied\r\nterrain navigation, showcasing the versatility of our pipeline.\r\nThis thesis explores applications ranging from intricate light patterns displayed on 3D shapes\r\nformed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit\r\nshape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform\r\npassive structures into functional prototypes." acknowledgement: "Financial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design\r\nand Modeling that I gratefully acknowledge.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Manas full_name: Bhargava, Manas id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425 last_name: Bhargava orcid: 0009-0007-6138-6890 citation: ama: 'Bhargava M. Design and control of deformable structures: From PCB lighting displays to elastomer robots. 2025. doi:10.15479/AT-ISTA-20276' apa: 'Bhargava, M. (2025). Design and control of deformable structures: From PCB lighting displays to elastomer robots. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20276' chicago: 'Bhargava, Manas. “Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20276.' ieee: 'M. Bhargava, “Design and control of deformable structures: From PCB lighting displays to elastomer robots,” Institute of Science and Technology Austria, 2025.' ista: 'Bhargava M. 2025. Design and control of deformable structures: From PCB lighting displays to elastomer robots. Institute of Science and Technology Austria.' mla: 'Bhargava, Manas. Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20276.' short: 'M. Bhargava, Design and Control of Deformable Structures: From PCB Lighting Displays to Elastomer Robots, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-02T14:48:39Z date_published: 2025-09-02T00:00:00Z date_updated: 2026-07-29T13:03:31Z day: '02' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: BeBi doi: 10.15479/AT-ISTA-20276 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 5baf8ca46c86a94fc8380ff1007aabd4 content_type: application/pdf creator: mbhargav date_created: 2025-09-03T10:40:52Z date_updated: 2025-09-03T10:40:52Z file_id: '20284' file_name: 2025-Bhargava-Manas-Thesis.pdf file_size: 161436245 relation: main_file success: 1 - access_level: closed checksum: 66878fafbc0074f88ddd18f24a9fc647 content_type: application/x-zip-compressed creator: mbhargav date_created: 2025-09-03T13:18:05Z date_updated: 2025-09-04T09:22:29Z file_id: '20285' file_name: manas_phd_thesis_source_files.zip file_size: 198831315 relation: source_file file_date_updated: 2025-09-04T09:22:29Z fulldoi: https://doi.org/10.15479/AT-ISTA-20276 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '96' project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: isbn: - 978-3-99078-065-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13049' relation: part_of_dissertation status: public - id: '18565' relation: part_of_dissertation status: public - id: '20286' relation: part_of_dissertation status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: 'Design and control of deformable structures: From PCB lighting displays to elastomer robots' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20203' abstract: - lang: eng text: Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon. acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: EM-Fac - _id: LifeSc - _id: ScienComp acknowledgement: "The project in Chapter 2 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 3 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 4 has received financing from the European Research Council grant\r\nagreement No. 949120 under the European Union’s Horizon 2020 research and innovation\r\nprogramme. The Analytical Instrumentation Center of the TU Wien acknowledges support by\r\nthe FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state\r\nof Lower Austria and the European Regional Development Fund under grant no. WST3-F542638/004-2021.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce citation: ama: 'Sobarzo Ponce JCA. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. 2025. doi:10.15479/AT-ISTA-20203' apa: 'Sobarzo Ponce, J. C. A. (2025). Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20203' chicago: 'Sobarzo Ponce, Juan Carlos A. “Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20203.' ieee: 'J. C. A. Sobarzo Ponce, “Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges,” Institute of Science and Technology Austria, 2025.' ista: 'Sobarzo Ponce JCA. 2025. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria.' mla: 'Sobarzo Ponce, Juan Carlos A. Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20203.' short: 'J.C.A. Sobarzo Ponce, Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-08-21T11:42:59Z date_published: 2025-08-27T00:00:00Z date_updated: 2026-07-29T13:11:25Z day: '27' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-20203 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 661b9d3786cfc985be811befc3262bf5 content_type: application/pdf creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-27T14:50:32Z file_id: '20237' file_name: 2025_Sobarzo_JuanCarlos_Thesis.pdf file_size: 12667200 relation: main_file success: 1 - access_level: closed checksum: ca2f24e6c3b55912982521707552a0f5 content_type: application/x-zip-compressed creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-28T08:19:07Z file_id: '20238' file_name: 2025_Sobarzo_JuanCarlos_Thesis.zip file_size: 18940521 relation: source_file file_date_updated: 2025-08-28T08:19:07Z fulldoi: https://doi.org/10.15479/AT-ISTA-20203 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '96' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-062-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12109' relation: part_of_dissertation status: public - id: '15322' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: 'Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18565' abstract: - lang: eng text: 'We present a computational approach for unfolding 3D shapes isometrically into the plane as a single patch without overlapping triangles. This is a hard, sometimes impossible, problem, which existing methods are forced to soften by allowing for map distortions or multiple patches. Instead, we propose a geometric relaxation of the problem: We modify the input shape until it admits an overlap‐free unfolding. We achieve this by locally displacing vertices and collapsing edges, guided by the unfolding process. We validate our algorithm quantitatively and qualitatively on a large dataset of complex shapes and show its proficiency by fabricating real shapes from paper.' acknowledgement: Researchers from INRIA received support from the DORNELL Inria Challenge. Silvia Sellán acknowledges support from NSERC Vanier Doctoral Scholarship and an MIT SoE Postdoctoral Fellowship for Engineering Excellence. article_number: e15269 article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Manas full_name: Bhargava, Manas id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425 last_name: Bhargava orcid: 0009-0007-6138-6890 - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: M. full_name: Freire, M. last_name: Freire - first_name: P. A. full_name: Hugron, P. A. last_name: Hugron - first_name: S. full_name: Lefebvre, S. last_name: Lefebvre - first_name: S. full_name: Sellán, S. last_name: Sellán - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Bhargava M, Schreck C, Freire M, et al. Mesh simplification for unfolding. Computer Graphics Forum. 2025;44(1). doi:10.1111/cgf.15269 apa: Bhargava, M., Schreck, C., Freire, M., Hugron, P. A., Lefebvre, S., Sellán, S., & Bickel, B. (2025). Mesh simplification for unfolding. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.15269 chicago: Bhargava, Manas, Camille Schreck, M. Freire, P. A. Hugron, S. Lefebvre, S. Sellán, and Bernd Bickel. “Mesh Simplification for Unfolding.” Computer Graphics Forum. Wiley, 2025. https://doi.org/10.1111/cgf.15269. ieee: M. Bhargava et al., “Mesh simplification for unfolding,” Computer Graphics Forum, vol. 44, no. 1. Wiley, 2025. ista: Bhargava M, Schreck C, Freire M, Hugron PA, Lefebvre S, Sellán S, Bickel B. 2025. Mesh simplification for unfolding. Computer Graphics Forum. 44(1), e15269. mla: Bhargava, Manas, et al. “Mesh Simplification for Unfolding.” Computer Graphics Forum, vol. 44, no. 1, e15269, Wiley, 2025, doi:10.1111/cgf.15269. short: M. Bhargava, C. Schreck, M. Freire, P.A. Hugron, S. Lefebvre, S. Sellán, B. Bickel, Computer Graphics Forum 44 (2025). corr_author: '1' date_created: 2024-11-19T09:14:32Z date_published: 2025-02-01T00:00:00Z date_updated: 2026-07-29T13:03:30Z day: '01' ddc: - '006' department: - _id: GradSch - _id: BeBi doi: 10.1111/cgf.15269 external_id: arxiv: - '2408.06944' isi: - '001357046100001' file: - access_level: open_access checksum: 34acdd9bfbe43f00eb6c7656afef3ac6 content_type: video/mp4 creator: mbhargav date_created: 2024-11-19T09:23:20Z date_updated: 2024-11-19T09:23:20Z file_id: '18567' file_name: Mesh_Simplification_For_Unfolding_cgf_submission_supplemental_video.mp4 file_size: 36999751 relation: main_file success: 1 - access_level: open_access checksum: efb06b01bae37f470954601bc004374d content_type: application/pdf creator: dernst date_created: 2025-04-16T09:06:45Z date_updated: 2025-04-16T09:06:45Z file_id: '19576' file_name: 2025_CompGraphicsForum_Bhargava.pdf file_size: 5188265 relation: main_file success: 1 file_date_updated: 2025-04-16T09:06:45Z fulldoi: https://doi.org/10.1111/cgf.15269 has_accepted_license: '1' intvolume: ' 44' isi: 1 issue: '1' keyword: - fabrication - single patch unfolding - mesh simplification language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '20276' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mesh simplification for unfolding tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2025' ... --- OA_place: publisher _id: '20371' abstract: - lang: eng text: "Quantum mechanics reveals a world that defies classical determinism, where uncertainty, superposition, and fluctuations are fundamental aspects. Engineering devices that harness these quantum features requires not only precision, but also a deep understanding of how they interact with their surrounding environment. Superconducting circuits, which exploit\r\nmacroscopic quantum coherence in low-loss superconducting materials, provide a scalable platform for implementing such systems. Among the critical elements in these circuits, superinductors—high-impedance, dissipation-free inductive components—play a central role by suppressing charge fluctuations. They allow quantum states to be delocalized in phase space, protect qubits from environmental noise, and facilitate access to phenomena such as dual Josephson physics and ultra-strong coupling regimes. \r\nThis thesis explores two complementary implementations of high-impedance circuits: geometric superinductors, demonstrating that high impedance can be achieved beyond kinetic inductance,\r\nand Josephson junction chains, used to investigate both microwave mode properties and DC transport across the superconductor-to-insulator transition. \r\nPart I addresses geometric superinductors. Contrary to the common belief that high-impedance superconducting circuits require kinetic inductance, we demonstrate that purely geometric designs can achieve characteristic impedance exceeding the resistance quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors achieve enhanced self-inductance, creating a reliable platform for qubits and resonators. Modeling, simulation, fabrication, and\r\ncharacterization confirm that these elements behave as superinductor. With low loss, high linearity, and minimal stray capacitance, these elements are reproducible, free of uncontrolled tunneling events, and capable of strong magnetic coupling. This establishes geometric superinductors as robust, single-wave-function superconducting devices suitable for hardware protected qubits and hybrid systems.\r\nPart II presents classical numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps. The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive environment with a parasitic capacitance.\r\nPart III extends the investigation of high characteristic-impedance circuit elements to one-dimensional Josephson junction chains, which act as a quantum simulator for many-body physics and the superconductor–insulator transition. Different devices are realized on both sides of the DC phase transition, showing either a supercurrent branch or Coulomb blockade at zero bias. The effect of the crossover on microwave modes, however, remains insufficiently investigated. Studying these modes provides insight into the interplay between disorder and phase-slip events. Small differences in circuit component sizes determine which side of the transition a device falls on, making these results relevant not only for fundamental understanding but also for the design of quantum devices, emphasizing the crucial role of the\r\nelectromagnetic environment in stabilizing and controlling fragile quantum states. \r\nTogether, these results illustrate how carefully engineered high characteristic-impedance elements provide a link between macroscopic circuits and the inherently uncertain quantum world, enabling experiments that probe, control, and ultimately exploit quantum fluctuations for applications in quantum information, metrology, solid state physics and beyond.\r\n\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "I also gratefully acknowledge the generous support of the NOMIS Foundation Project \"Protected\r\nStates of Quantum Matter\" and the grant from the Beyond-C consortium. Their funding\r\nmade this research possible and gave me the freedom to ask ambitious questions, and try to\r\nanswer them.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni citation: ama: 'Trioni A. High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. 2025. doi:10.15479/AT-ISTA-20371' apa: 'Trioni, A. (2025). High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20371' chicago: 'Trioni, Andrea. “High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20371.' ieee: 'A. Trioni, “High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains,” Institute of Science and Technology Austria, 2025.' ista: 'Trioni A. 2025. High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. Institute of Science and Technology Austria.' mla: 'Trioni, Andrea. High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20371.' short: 'A. Trioni, High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-23T09:57:57Z date_published: 2025-09-23T00:00:00Z date_updated: 2026-07-29T13:12:10Z day: '23' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-20371 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 6fb925648dfa5f4384814c552ee2f099 content_type: application/pdf creator: atrioni date_created: 2025-09-25T07:15:05Z date_updated: 2025-09-25T14:25:31Z file_id: '20392' file_name: 2025_Trioni_Andrea_Thesis.pdf file_size: 22351676 relation: main_file - access_level: closed checksum: 619dc614bdfbf3999b76ac8890b2cebd content_type: application/x-zip-compressed creator: atrioni date_created: 2025-09-25T14:45:43Z date_updated: 2025-09-26T07:20:48Z file_id: '20396' file_name: 2025_Trioni_Andrea_Thesis.zip file_size: 60079009 relation: source_file file_date_updated: 2025-09-26T07:20:48Z fulldoi: https://doi.org/10.15479/AT-ISTA-20371 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '202' project: - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-067-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8755' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: 'High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20339' abstract: - lang: eng text: "This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights.\r\n\r\nWe first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations.\r\n\r\nIn the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gianluca full_name: Tasinato, Gianluca id: 0433290C-AF8F-11E9-A4C7-F729E6697425 last_name: Tasinato citation: ama: 'Tasinato G. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. 2025. doi:10.15479/AT-ISTA-20339' apa: 'Tasinato, G. (2025). Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20339' chicago: 'Tasinato, Gianluca. “Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20339.' ieee: 'G. Tasinato, “Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems,” Institute of Science and Technology Austria, 2025.' ista: 'Tasinato G. 2025. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria.' mla: 'Tasinato, Gianluca. Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20339.' short: 'G. Tasinato, Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-10T12:17:55Z date_published: 2025-09-10T00:00:00Z date_updated: 2026-07-29T13:13:18Z day: '10' ddc: - '516' degree_awarded: PhD department: - _id: GradSch - _id: UlWa doi: 10.15479/AT-ISTA-20339 doi_confirm: '1' file: - access_level: closed checksum: ae097a515b9bb4d4b025ca854ae2ed76 content_type: application/x-zip-compressed creator: gtasinat date_created: 2025-09-11T12:24:12Z date_updated: 2025-09-11T12:24:12Z file_id: '20344' file_name: thesis-source.zip file_size: 2218562 relation: source_file - access_level: open_access checksum: 04b2e016409e52167ce42b0eef839fbf content_type: application/pdf creator: gtasinat date_created: 2025-09-11T12:26:14Z date_updated: 2025-09-11T12:26:14Z file_id: '20345' file_name: 2025_Tasinato_Gianluca_Thesis.pdf file_size: 10071982 relation: main_file success: 1 file_date_updated: 2025-09-11T12:26:14Z fulldoi: https://doi.org/10.15479/AT-ISTA-20339 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '106' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20008' relation: part_of_dissertation status: public - id: '15168' relation: part_of_dissertation status: public - id: '19860' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: 'Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '19540' abstract: - lang: eng text: "This thesis deals with several different models for complex quantum mechanical systems and is structured in three main parts. \r\n\t\r\nIn Part I, we study mean field random matrices as models for quantum Hamiltonians. Our focus lies on proving concentration estimates for resolvents of random matrices, so-called local laws, mostly in the setting of multiple resolvents. These estimates have profound consequences for eigenvector overlaps and thermalization problems. More concretely, we obtain, e.g., the optimal eigenstate thermalization hypothesis (ETH) uniformly in the spectrum for Wigner matrices, an optimal lower bound on non-Hermitian eigenvector overlaps, and prethermalization for deformed Wigner matrices.\tIn order to prove our novel multi-resolvent local laws, we develop and devise two main methods, the static Psi-method and the dynamical Zigzag strategy. \r\n\t\r\nIn Part II, we study Bardeen-Cooper-Schrieffer (BCS) theory, the standard mean field microscopic theory of superconductivity. We focus on asymptotic formulas for the characteristic critical temperature and energy gap of a superconductor and prove universality of their ratio in various physical regimes. Additionally, we investigate multi-band superconductors and show that inter-band coupling effects can only enhance the critical temperature. \r\n\t\r\nIn Part III, we study quantum lattice systems. On the one hand, we show a strong version of the local-perturbations-perturb-locally (LPPL) principle for the ground state of weakly interacting quantum spin systems with a uniform on-site gap. On the other hand, we introduce a notion of a local gap and rigorously justify response theory and the Kubo formula under the weakened assumption of a local gap. \r\n\t\r\nAdditionally, we discuss two classes of problems which do not fit into the three main parts of the thesis. These are deformational rigidity of Liouville metrics on the torus and relativistic toy models of particle creation via interior-boundary-conditions (IBCs). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X citation: ama: 'Henheik SJ. Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems. 2025. doi:10.15479/AT-ISTA-19540' apa: 'Henheik, S. J. (2025). Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19540' chicago: 'Henheik, Sven Joscha. “Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19540.' ieee: 'S. J. Henheik, “Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems,” Institute of Science and Technology Austria, 2025.' ista: 'Henheik SJ. 2025. Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems. Institute of Science and Technology Austria.' mla: 'Henheik, Sven Joscha. Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19540.' short: 'S.J. Henheik, Modeling Complex Quantum Systems: Random Matrices, BCS Theory, and Quantum Lattice Systems, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-04-10T21:21:18Z date_published: 2025-04-10T00:00:00Z date_updated: 2026-07-29T13:18:17Z day: '10' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: LaEr doi: 10.15479/AT-ISTA-19540 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: b8477ae5578436c72c3bb4193ad34ac5 content_type: application/zip creator: shenheik date_created: 2025-04-10T21:14:18Z date_updated: 2025-04-10T21:14:18Z file_id: '19542' file_name: Henheik-Thesis_source_final.zip file_size: 4107587 relation: source_file - access_level: open_access checksum: e9fc0ea12ec46c9f71110c33217c4140 content_type: application/pdf creator: shenheik date_created: 2025-04-11T13:16:05Z date_updated: 2025-04-11T13:16:05Z file_id: '19553' file_name: Henheik-Thesis-pdfa_FINAL.pdf file_size: 9999492 relation: main_file success: 1 - access_level: closed checksum: f94580f86c785e7108eb116cd189e225 content_type: application/pdf creator: cchlebak date_created: 2025-04-23T14:10:27Z date_updated: 2025-04-23T14:10:27Z file_id: '19615' file_name: Henheik-Thesis-Volume1_print.pdf file_size: 13276442 relation: other - access_level: closed checksum: b927ead3c78020ffb32918911deedb74 content_type: application/pdf creator: cchlebak date_created: 2025-04-23T14:11:05Z date_updated: 2025-04-23T14:11:05Z file_id: '19616' file_name: Henheik-Thesis-Volume2_print.pdf file_size: 7628767 relation: other file_date_updated: 2025-04-23T14:11:05Z fulldoi: https://doi.org/10.15479/AT-ISTA-19540 has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '720' project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication_identifier: isbn: - 978-3-99078-057-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14343' relation: part_of_dissertation status: public - id: '13317' relation: part_of_dissertation status: public - id: '11732' relation: part_of_dissertation status: public - id: '12184' relation: part_of_dissertation status: public - id: '14421' relation: part_of_dissertation status: public - id: '10623' relation: part_of_dissertation status: public - id: '18112' relation: part_of_dissertation status: public - id: '19001' relation: part_of_dissertation status: public - id: '10642' relation: part_of_dissertation status: public - id: '19545' relation: part_of_dissertation status: public - id: '19546' relation: part_of_dissertation status: public - id: '19550' relation: part_of_dissertation status: public - id: '19551' relation: part_of_dissertation status: public - id: '19552' relation: part_of_dissertation status: public - id: '14542' relation: part_of_dissertation status: public - id: '17049' relation: part_of_dissertation status: public - id: '18764' relation: part_of_dissertation status: public - id: '19547' relation: part_of_dissertation status: public - id: '19548' relation: part_of_dissertation status: public - id: '18656' relation: part_of_dissertation status: public status: public supervisor: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 title: 'Modeling complex quantum systems: Random matrices, BCS theory, and quantum lattice systems' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- _id: '20641' abstract: - lang: eng text: 'Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ' acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011." article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Schanda P. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2025. doi:10.15479/AT-ISTA-20641 apa: Becker, L. M., & Schanda, P. (2025). Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20641 chicago: Becker, Lea Marie, and Paul Schanda. “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20641. ieee: L. M. Becker and P. Schanda, “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. ista: Becker LM, Schanda P. 2025. Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20641. mla: Becker, Lea Marie, and Paul Schanda. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20641. short: L.M. Becker, P. Schanda, (2025). contributor: - contributor_type: researcher first_name: 'Haohao ' last_name: Fu - contributor_type: researcher first_name: Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - contributor_type: researcher first_name: Matthias last_name: Dreydoppel - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - contributor_type: researcher first_name: Ulrich last_name: Weininger - contributor_type: researcher first_name: Sylvain last_name: Engilberge - contributor_type: researcher first_name: Christophe last_name: Chipot corr_author: '1' date_created: 2025-11-13T09:29:58Z date_published: 2025-11-18T00:00:00Z date_updated: 2026-08-04T09:32:44Z day: '18' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-20641 file: - access_level: open_access checksum: a73a0550c644957e7f62241e239d3a1d content_type: application/zip creator: lbecker date_created: 2025-11-13T09:38:35Z date_updated: 2026-02-17T10:16:57Z file_id: '20643' file_name: Research_Data.zip file_size: 1806589513 relation: main_file - access_level: open_access checksum: 7176b257f753c213a0460ee06f802363 content_type: application/pdf creator: lbecker date_created: 2025-11-17T11:54:17Z date_updated: 2026-02-17T10:16:57Z file_id: '20652' file_name: README.pdf file_size: 191376 relation: table_of_contents file_date_updated: 2026-02-17T10:16:57Z fulldoi: https://doi.org/10.15479/AT-ISTA-20641 has_accepted_license: '1' month: '11' oa: 1 oa_version: Published Version project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publisher: Institute of Science and Technology Austria related_material: record: - id: '21145' relation: later_version status: public - id: '22105' relation: used_in_publication status: public status: public title: Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- OA_place: repository OA_type: green _id: '20926' abstract: - lang: eng text: Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs. acknowledgement: Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating discussions. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Dongjin full_name: Kim, Dongjin last_name: Kim - first_name: Xiaoyu full_name: Wang, Xiaoyu id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3 last_name: Wang - first_name: Santiago full_name: Vargas, Santiago last_name: Vargas - first_name: Peichen full_name: Zhong, Peichen last_name: Zhong - first_name: Daniel S. full_name: King, Daniel S. last_name: King - first_name: Theo Jaffrelot full_name: Inizan, Theo Jaffrelot last_name: Inizan - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400 apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., & Cheng, B. (2025). A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400 chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King, Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400. ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials,” Journal of Chemical Theory and Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724, 2025. ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724. mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24, doi:10.1021/acs.jctc.5c01400. short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 12709–12724. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training sets, training scripts, and trained potentials are available at https://github.com/ChengUCB/les_fit. The LES library is publicly available at https://github.com/ChengUCB/les. The CACE package with the LES implementation is available at https://github.com/BingqingCheng/cace. The MACE package with the LES implementation is available at https://github.com/ACEsuit/mace. The NequIP and Allegro LES extension package is available at https://github.com/ChengUCB/NequIP-LES. The MatGL package with the LES implementation is available at https://github.com/ChengUCB/matgl. The UMA package with the LES implementation is available at https://github.com/santi921/fairchem/tree/les_branch. date_created: 2026-01-04T23:01:33Z date_published: 2025-12-10T00:00:00Z date_updated: 2026-08-07T09:35:25Z day: '10' department: - _id: GradSch - _id: BiCh doi: 10.1021/acs.jctc.5c01400 external_id: arxiv: - '2507.14302' pmid: - '41368735 ' fulldoi: https://doi.org/10.1021/acs.jctc.5c01400 intvolume: ' 21' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2507.14302 month: '12' oa: 1 oa_version: Preprint page: 12709-12724 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2025' ... --- OA_place: publisher _id: '20074' abstract: - lang: eng text: "Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann citation: ama: Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074 apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074 chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074. ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025. ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074. short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-24T12:37:22Z date_published: 2025-07-24T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20074 doi_confirm: '1' file: - access_level: closed checksum: d09f9984002353ad7442358394919bf3 content_type: application/x-zip-compressed creator: vhuebsch date_created: 2025-07-30T08:47:53Z date_updated: 2025-07-30T08:47:53Z file_id: '20086' file_name: PhD_Thesis_Schmied.zip file_size: 43566093 relation: source_file - access_level: open_access checksum: 4833690d7283c587f518ba98eeb2c946 content_type: application/pdf creator: vhuebsch date_created: 2025-07-30T08:47:46Z date_updated: 2025-07-30T09:29:09Z file_id: '20087' file_name: PhD_Thesis_Schmied.pdf file_size: 13120922 relation: main_file file_date_updated: 2025-07-30T09:29:09Z fulldoi: https://doi.org/10.15479/AT-ISTA-20074 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '151' project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation publication_identifier: isbn: - 978-3-99078-060-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11478' relation: part_of_dissertation status: public - id: '19593' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Human microglia impact neuronal development in retinal organoids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20342' abstract: - lang: eng text: Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication. article_number: '13149' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 2025;21(2). doi:10.46298/lmcs-21(2:2)2025 apa: Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025 chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025. ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” Logical Methods in Computer Science, vol. 21, no. 2. EPI Sciences, 2025. ista: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149. mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:10.46298/lmcs-21(2:2)2025. short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025). corr_author: '1' date_created: 2025-09-11T12:17:52Z date_published: 2025-04-08T00:00:00Z date_updated: 2026-08-12T08:46:05Z day: '08' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.46298/lmcs-21(2:2)2025 ec_funded: 1 external_id: arxiv: - '2307.06016' isi: - '001468887900001' file: - access_level: open_access checksum: 0b4d477bd981379724c35a4de2c176e5 content_type: application/pdf creator: esarac date_created: 2025-09-11T12:17:12Z date_updated: 2025-09-11T12:17:12Z file_id: '20343' file_name: 2307.06016.pdf file_size: 709584 relation: main_file success: 1 file_date_updated: 2025-09-11T12:17:12Z fulldoi: https://doi.org/10.46298/lmcs-21(2:2)2025 has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Logical Methods in Computer Science publication_identifier: eissn: - 1860-5974 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '13221' relation: earlier_version status: public - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: Safety and liveness of quantitative properties and automata tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2025' ... --- OA_place: publisher _id: '20147' abstract: - lang: eng text: "Quantitative properties offer a framework for specifying and verifying system behaviors beyond the traditional boolean perspective. For example, while a boolean property may specify whether a server eventually grants every request it receives, a quantitative one may map each server execution to its average response time. This quantitative view is relatively well-studied in the context of static verification. However, although such properties often appear in practice as performance or robustness measures in a dynamic verification context, a general theoretical framework for their analysis and classification from a monitoring perspective is still missing.\r\n\r\nIn this thesis, we aim to develop such a framework that takes resource-precision tradeoffs of monitors as a central consideration. We present the first theory of monitorability for quantitative properties where monitors can be naturally approximate and compared regarding their precision and resource use. In particular, we show that additional monitor resources such as registers or states lead to strictly better approximations for some properties. To enable such analyses in a machine-model independent way, we describe an abstract notion of monitors that can be instantiated with concrete models of monitors. Within this framework, we study how abstract monitors behave and identify classes of properties amenable to approximate monitoring with resource-precision considerations. We then extend the boolean safety-liveness dichotomy and safety-progress hierarchy to the quantitative setting with a monitoring perspective. In particular, we prove that every property is the pointwise minimum of a safety property and a liveness property, and properties that are both safe and co-safe can be approximately monitored arbitrarily precisely using only finitely many states. We also study the classes of quantitative properties definable by finite-state quantitative automata and provide algorithms for deciding their safety or liveness as well as their safety-liveness decompositions. Finally, we present the first general-purpose tool for automating the analysis, verification, and monitoring of quantitative automata.\r\n\r\n\r\n" acknowledgement: "This work was supported in part by the Austrian Science Fund (FWF)\r\nunder grant Z211-N23 (Wittgenstein Award) and the ERC-2020-AdG 101020093.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Sarac NE. A monitoring-oriented theory and classification of quantitative specifications. 2025. doi:10.15479/AT-ISTA-20147 apa: Sarac, N. E. (2025). A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20147 chicago: Sarac, Naci E. “A Monitoring-Oriented Theory and Classification of Quantitative Specifications.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20147. ieee: N. E. Sarac, “A monitoring-oriented theory and classification of quantitative specifications,” Institute of Science and Technology Austria, 2025. ista: Sarac NE. 2025. A monitoring-oriented theory and classification of quantitative specifications. Institute of Science and Technology Austria. mla: Sarac, Naci E. A Monitoring-Oriented Theory and Classification of Quantitative Specifications. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20147. short: N.E. Sarac, A Monitoring-Oriented Theory and Classification of Quantitative Specifications, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-07T15:57:57Z date_published: 2025-08-07T00:00:00Z date_updated: 2026-08-12T08:46:04Z day: '07' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ToHe doi: 10.15479/AT-ISTA-20147 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 0f3015f1db36576a23d8d669afb60b41 content_type: application/x-zip-compressed creator: esarac date_created: 2025-08-21T09:40:28Z date_updated: 2025-09-10T08:19:51Z file_id: '20200' file_name: 2025_Sarac_NaciEge_Thesis.zip file_size: 8884801 relation: source_file - access_level: open_access checksum: 332ed2fe61f580641664ec3f05d30f14 content_type: application/pdf creator: esarac date_created: 2025-08-21T09:40:34Z date_updated: 2025-08-21T09:40:34Z file_id: '20201' file_name: 2025_Sarac_NaciEge_Thesis.pdf file_size: 2955584 relation: main_file success: 1 file_date_updated: 2025-09-10T08:19:51Z fulldoi: https://doi.org/10.15479/AT-ISTA-20147 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '149' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: Formal methods for the design and analysis of complex systems - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: "In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not\r\nendorse any of ISTA's products or services. Internal or personal use of this\r\nmaterial is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional\r\npurposes or for creating new collective works for resale or redistribution, please go to\r\nhttp://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from\r\nRightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation." related_material: record: - id: '11775' relation: part_of_dissertation status: public - id: '13140' relation: part_of_dissertation status: deleted - id: '19741' relation: part_of_dissertation status: public - id: '19643' relation: part_of_dissertation status: deleted - id: '17634' relation: part_of_dissertation status: public - id: '13221' relation: part_of_dissertation status: public - id: '9356' relation: part_of_dissertation status: public - id: '20342' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: A monitoring-oriented theory and classification of quantitative specifications tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20167' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön citation: ama: Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:10.15479/AT-ISTA-20167 apa: Schön, H. (2025). The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20167 chicago: Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20167. ieee: H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025. ista: Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. mla: Schön, Hanna. The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20167. short: H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-13T11:13:13Z date_published: 2025-08-13T00:00:00Z date_updated: 2026-08-13T13:05:37Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MaDe doi: 10.15479/AT-ISTA-20167 doi_confirm: '1' file: - access_level: closed checksum: b40c74404b8d9593802dabf57bfdf10f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hschoen date_created: 2025-09-08T14:33:50Z date_updated: 2025-09-09T08:57:04Z file_id: '20311' file_name: 2025_Schoen_Hanna_Thesis.docx file_size: 78812587 relation: source_file - access_level: closed checksum: 16abc3ff66396ce2457fe07ffa8bed90 content_type: application/pdf creator: hschoen date_created: 2025-09-11T14:20:59Z date_updated: 2026-08-13T13:05:36Z embargo: 2027-03-15 embargo_to: open_access file_id: '20347' file_name: 2025_Schoen_Hanna_Thesis.pdf file_size: 9667057 relation: main_file file_date_updated: 2026-08-13T13:05:36Z fulldoi: https://doi.org/10.15479/AT-ISTA-20167 has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '171' project: - _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E grant_number: 209504/A/17/Z name: Molecular mechanisms of neural circuit function - _id: 23813290-32DE-11EA-91FC-C7463DDC885E grant_number: ALTF 302-2019 name: Control of gene expression at the endoplasmic reticulum publication_identifier: isbn: - 978-3-99078-061-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 title: The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20538' abstract: - lang: eng text: In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70. article_number: '169465' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sonja full_name: Knödlstorfer, Sonja last_name: Knödlstorfer - first_name: Giorgia full_name: Toscano, Giorgia id: 334a5e40-8747-11f0-b671-ba1f5154b4b4 last_name: Toscano - first_name: Aleksandra L. full_name: Ptaszek, Aleksandra L. last_name: Ptaszek - first_name: Georg full_name: Kontaxis, Georg last_name: Kontaxis - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Jakob full_name: Schneider, Jakob id: 64368429-eb97-11eb-a6c2-c980b1f44415 last_name: Schneider - first_name: Katharina full_name: Maier, Katharina last_name: Maier - first_name: Anna full_name: Kapitonova, Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - first_name: Roman J. full_name: Lichtenecker, Roman J. last_name: Lichtenecker - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Robert full_name: Konrat, Robert last_name: Konrat citation: ama: Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169465 apa: Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169465 chicago: Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology. Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169465. ieee: S. Knödlstorfer et al., “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025. ista: Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465. mla: Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology, vol. 437, no. 23, 169465, Elsevier, 2025, doi:10.1016/j.jmb.2025.169465. short: S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025). date_created: 2025-10-26T23:01:35Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-08-13T14:19:02Z day: '01' ddc: - '540' department: - _id: PaSc - _id: GradSch doi: 10.1016/j.jmb.2025.169465 external_id: pmid: - '41016549' file: - access_level: open_access checksum: feb92f9c79032c261165f4ca573f444a content_type: application/pdf creator: dernst date_created: 2025-12-30T10:29:08Z date_updated: 2025-12-30T10:29:08Z file_id: '20915' file_name: 2025_JourMolecularBiology_Knoedlstorfer.pdf file_size: 3076611 relation: main_file success: 1 file_date_updated: 2025-12-30T10:29:08Z fulldoi: https://doi.org/10.1016/j.jmb.2025.169465 has_accepted_license: '1' intvolume: ' 437' issue: '23' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0 grant_number: I06223 name: Structure and mechanism of the mitochondrial MIM insertase - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Journal of Molecular Biology publication_identifier: eissn: - 1089-8638 issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 437 year: '2025' ... --- OA_place: publisher _id: '19395' abstract: - lang: eng text: "Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood." acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer citation: ama: 'Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant development. 2025. doi:10.15479/AT-ISTA-19395' apa: 'Monzer, A. (2025). Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395' chicago: 'Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.' ieee: 'A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.' ista: 'Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.' mla: 'Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395.' short: 'A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-03-12T14:25:42Z date_published: 2025-03-13T00:00:00Z date_updated: 2026-08-14T09:33:46Z day: '13' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19395 doi_confirm: '1' file: - access_level: open_access checksum: 9a3dd03bb4ec6b9907a325c3c4e8a1d7 content_type: application/pdf creator: amonzer date_created: 2025-03-12T14:14:49Z date_updated: 2025-03-12T14:14:49Z file_id: '19396' file_name: Final Thesis Aline Monzer.pdf file_size: 13119670 relation: main_file success: 1 - access_level: closed checksum: a353ce1ee2eabce37bca35499e76dbf1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amonzer date_created: 2025-03-12T14:15:19Z date_updated: 2025-04-01T07:55:27Z file_id: '19397' file_name: Thesis Aline.docx file_size: 13774837 relation: source_file file_date_updated: 2025-04-01T07:55:27Z fulldoi: https://doi.org/10.15479/AT-ISTA-19395 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: eisbn: - 978-3-99078-054-1 eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '14826' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public - id: '19398' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Cell-surface auxin signaling: Linking molecular pathways to plant development' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '19398' abstract: - lang: eng text: Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance. article_processing_charge: No author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Michael full_name: Smejkal, Michael id: 79a5a1be-04a3-11f0-ba18-a1730e0b58e9 last_name: Smejkal - first_name: Ema full_name: Cervenova, Ema id: 9f185b95-04a3-11f0-8245-f5e32eeb470f last_name: Cervenova - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv. doi:10.1101/2025.02.28.640727 apa: Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv. https://doi.org/10.1101/2025.02.28.640727 chicago: Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, n.d. https://doi.org/10.1101/2025.02.28.640727. ieee: A. Monzer et al., “TMK interacting network of receptor like kinases for auxin canalization and beyond,” bioRxiv. . ista: Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, 10.1101/2025.02.28.640727. mla: Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, doi:10.1101/2025.02.28.640727. short: A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2025-03-12T14:28:53Z date_published: 2025-03-02T00:00:00Z date_updated: 2026-08-14T09:33:45Z day: '02' ddc: - '580' department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 10.1101/2025.02.28.640727 fulldoi: https://doi.org/10.1101/2025.02.28.640727 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.02.28.640727 month: '03' oa: 1 oa_version: Published Version publication: bioRxiv publication_status: draft related_material: record: - id: '19395' relation: dissertation_contains status: public status: public title: TMK interacting network of receptor like kinases for auxin canalization and beyond tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19684' 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." acknowledged_ssus: - _id: ScienComp acknowledgement: "The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 citation: ama: 'Yalniz G. Transition to turbulence: Data-, solution-, and pattern-driven approaches. 2025. doi:10.15479/AT-ISTA-19684' apa: 'Yalniz, G. (2025). Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19684' 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.' ieee: 'G. Yalniz, “Transition to turbulence: Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.' ista: 'Yalniz G. 2025. Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.' 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.' short: 'G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-05-12T15:12:28Z date_published: 2025-05-13T00:00:00Z date_updated: 2026-09-02T08:16:32Z day: '13' ddc: - '514' - '519' - '532' - '004' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/AT-ISTA-19684 doi_confirm: '1' file: - access_level: open_access checksum: 0e452642b79f13633f1595bde71a67e3 content_type: application/pdf creator: gyalniz date_created: 2025-05-12T15:13:28Z date_updated: 2025-05-12T15:13:28Z file_id: '19685' file_name: Gökhan Yalnız - PhD thesis.pdf file_size: 20058169 relation: main_file success: 1 - access_level: open_access checksum: 921099d76adab2df784ce12ce41cfb22 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:15:59Z date_updated: 2025-05-12T15:43:28Z description: '3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).' file_id: '19686' file_name: Movie 2A.1.mp4 file_size: 37763743 relation: supplementary_material title: Chapter 2 - Movie 2A.1 - access_level: open_access checksum: 0ae5ac7d9896003c0c4207dd746808dc content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:09Z date_updated: 2025-05-12T15:43:28Z description: 'Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19687' file_name: Movie 3A.1.mp4 file_size: 3902655 relation: supplementary_material title: Chapter 3 - Movie 3A.1 - access_level: open_access checksum: ef8d270e066c1a9c3cb5ae46acf945e6 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:21Z date_updated: 2025-05-12T15:43:28Z description: 'Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19688' file_name: Movie 3A.2.mp4 file_size: 7043169 relation: supplementary_material title: Chapter 3 - Movie 3A.2 - access_level: open_access checksum: 7ed871f428100d6827ac9b0e8ca8e985 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:36Z date_updated: 2025-05-12T15:43:28Z 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_id: '19689' file_name: Movie 3A.3.mp4 file_size: 7748659 relation: supplementary_material title: Chapter 3 - Movie 3A.3 - access_level: open_access checksum: dd5a252e1da00c8f303588e22e2baeef content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:50Z date_updated: 2025-05-12T15:43:28Z 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_id: '19690' file_name: Movie 3A.4.mp4 file_size: 5873052 relation: supplementary_material title: Chapter 3 - Movie 3A.4 - access_level: open_access checksum: 5ac58b86810698db28cbfc28f351ff70 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:11Z date_updated: 2025-05-12T15:43:28Z description: Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit. file_id: '19691' file_name: Movie 4A.1.mp4 file_size: 9209327 relation: supplementary_material title: Chapter 4 - Movie 4A.1 - access_level: open_access checksum: ac877f1e1ef39439911bf37cb1793b8e content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:43Z date_updated: 2025-05-12T15:43:28Z 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_id: '19692' file_name: Movie 5A.1.mp4 file_size: 5893993 relation: supplementary_material title: Chapter 5 - Movie 5A.1 - access_level: open_access checksum: fd17eabb70129ceaa414e40924d1d2fe content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:49Z date_updated: 2025-05-12T15:43:28Z description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain. file_id: '19693' file_name: Movie 5A.2.mp4 file_size: 3990352 relation: supplementary_material title: Chapter 5 - Movie 5A.2 - access_level: open_access checksum: 32f904497ab0bbee38f0788d96b91454 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:58Z date_updated: 2025-05-12T15:43:28Z description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the 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. file_id: '19694' file_name: Movie 5A.3.mp4 file_size: 5171009 relation: supplementary_material title: Chapter 5 - Movie 5A.3 - access_level: closed checksum: f313261b9bb12dfb943fead8318954c6 content_type: application/x-zip-compressed creator: gyalniz date_created: 2025-05-12T15:27:10Z date_updated: 2025-05-12T15:43:28Z file_id: '19695' file_name: Gökhan Yalnız - PhD thesis.zip file_size: 18991996 relation: source_file file_date_updated: 2025-05-12T15:43:28Z fulldoi: https://doi.org/10.15479/AT-ISTA-19684 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '155' project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: Revisiting the Turbulence Problem Using Statistical Mechanics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9558' relation: part_of_dissertation status: public - id: '12105' relation: part_of_dissertation status: public - id: '13274' relation: part_of_dissertation status: public - id: '14466' relation: part_of_dissertation status: public - id: '7563' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: 'Transition to turbulence: Data-, solution-, and pattern-driven approaches' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ...