--- OA_place: repository OA_type: green _id: '21309' abstract: - lang: eng text: The polarization of light is a critically under-utilized, rich source of information in astronomy. For stars in particular, surface magnetism polarization that can be detected and measured with spectro-polarimetry. Many questions about these surface fields remain unanswered due to a lack of dedicated instruments capable of probing weak and strong surface magnetic fields for the entire mass range of stars, from M-dwarfs (and even substellar objects) to massive O-type stars at different evolutionary stages and metallicities. These questions range from the origin of these fields to their true incidence rate throughout the stellar population and the dependence on metallicity. Magnetic fields, although currently often excluded from stellar evolution models, play an important role in stellar evolution. Connecting the surface fields to internal fields through asteroseismology will instigate a new era of understanding stellar evolution and the transport of angular momentum and chemical elements throughout stellar interiors, also impacting our understanding of star-planet interactions and stellar remnants. Polarimetry is also an under-utilized tool to observationally constrain the mode identification of nonradial oscillations, which lies at the basis of accurate asteroseismic parameter estimation at percentage-level for stellar radii, masses, ages, internal rotation, and magnetic field strengths. Combining strong constraints on mode identification and surface magnetic properties through the acquisition of time-resolved, high-resolution and high-signal-to-noise (S/N) spectro-polarimetry and spectroscopy promises to bring leaps forward in our understanding of stellar structure, particularly when combined with long-term space photometric data from past, current, and future missions. article_number: '2512.15170' article_processing_charge: No arxiv: 1 author: - first_name: J. full_name: Vandersnickt, J. last_name: Vandersnickt - first_name: R. Ochoa full_name: Armenta, R. Ochoa last_name: Armenta - first_name: V. full_name: Vanlaer, V. last_name: Vanlaer - first_name: A. David-Uraz full_name: A. David-Uraz, A. David-Uraz last_name: A. David-Uraz - first_name: C. full_name: Aerts, C. last_name: Aerts - first_name: S. B. full_name: Das, S. B. last_name: Das - first_name: J. -C. full_name: Bouret, J. -C. last_name: Bouret - first_name: D. M. full_name: Bowman, D. M. last_name: Bowman - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: V. full_name: Khalack, V. last_name: Khalack - first_name: J. Labadie-Bartz full_name: J. Labadie-Bartz, J. Labadie-Bartz last_name: J. Labadie-Bartz - first_name: S. full_name: Mathis, S. last_name: Mathis - first_name: Y. full_name: Nazé, Y. last_name: Nazé - first_name: C. full_name: Neiner, C. last_name: Neiner - first_name: P. full_name: Petit, P. last_name: Petit - first_name: V. full_name: Petit, V. last_name: Petit - first_name: K. Thomson-Paressant full_name: K. Thomson-Paressant, K. Thomson-Paressant last_name: K. Thomson-Paressant - first_name: T. Van full_name: Doorsselaere, T. Van last_name: Doorsselaere - first_name: M. full_name: Vanrespaille, M. last_name: Vanrespaille citation: ama: Vandersnickt J, Armenta RO, Vanlaer V, et al. Expanding stellar horizons with polarized light. arXiv. doi:10.48550/arXiv.2512.15170 apa: Vandersnickt, J., Armenta, R. O., Vanlaer, V., A. David-Uraz, A. D.-U., Aerts, C., Das, S. B., … Vanrespaille, M. (n.d.). Expanding stellar horizons with polarized light. arXiv. https://doi.org/10.48550/arXiv.2512.15170 chicago: Vandersnickt, J., R. Ochoa Armenta, V. Vanlaer, A. David-Uraz A. David-Uraz, C. Aerts, S. B. Das, J. -C. Bouret, et al. “Expanding Stellar Horizons with Polarized Light.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2512.15170. ieee: J. Vandersnickt et al., “Expanding stellar horizons with polarized light,” arXiv. . ista: Vandersnickt J, Armenta RO, Vanlaer V, A. David-Uraz AD-U, Aerts C, Das SB, Bouret J-C, Bowman DM, Bugnet LA, Khalack V, J. Labadie-Bartz JL-B, Mathis S, Nazé Y, Neiner C, Petit P, Petit V, K. Thomson-Paressant KT-P, Doorsselaere TV, Vanrespaille M. Expanding stellar horizons with polarized light. arXiv, 2512.15170. mla: Vandersnickt, J., et al. “Expanding Stellar Horizons with Polarized Light.” ArXiv, 2512.15170, doi:10.48550/arXiv.2512.15170. short: J. Vandersnickt, R.O. Armenta, V. Vanlaer, A.D.-U. A. David-Uraz, C. Aerts, S.B. Das, J.-C. Bouret, D.M. Bowman, L.A. Bugnet, V. Khalack, J.L.-B. J. Labadie-Bartz, S. Mathis, Y. Nazé, C. Neiner, P. Petit, V. Petit, K.T.-P. K. Thomson-Paressant, T.V. Doorsselaere, M. Vanrespaille, ArXiv (n.d.). date_created: 2026-02-17T13:53:50Z date_published: 2025-12-17T00:00:00Z date_updated: 2026-04-07T06:00:40Z day: '17' department: - _id: LiBu doi: 10.48550/arXiv.2512.15170 external_id: arxiv: - '2512.15170' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2512.15170 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Expanding stellar horizons with polarized light type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '20864' abstract: - lang: eng text: Studies of the distant Universe are providing key insights into our understanding of the formation of galaxies. The advent of the James Webb Space Telescope (JWST) has significantly enhanced our observational capabilities, leading to an expanded redshift frontier, providing unprecedented detail in the characterisation of early galaxies and enabling the discovery of new populations of accreting black holes. This review aims to provide an introduction to the basic processes and components that shape the observed spectra of galaxies, with a focus on their relevance to techniques with which high-redshift galaxies are selected. The review further introduces specific topics that have attracted significant attention in recent literature, including the discovery of highly efficient galaxy formation in the early Universe, the relation between galaxies and the process of reionization, new insights into the formation of the first stars and the enrichment of interstellar gas with heavy elements, and breakthroughs in our understanding of the origins of supermassive black holes. acknowledgement: I thank Claudia Di Cesare, Edoardo Iani, Gauri Kotiwale and Wendy Sun for proofreading, Daichi Kashino, Gauri Kotiwale, Sara Mascia, Benjamín Navarette and Joris Witstok for their assistance in preparing some of the Figures, and Richard Ellis and Stephen Blundell for constructive comments. Funded by the European Union (ERC, AGENTS, 101076224). article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X citation: ama: 'Matthee JJ. JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies. Contemporary Physics. 2025;66(1-4):116-151. doi:10.1080/00107514.2025.2586370' apa: 'Matthee, J. J. (2025). JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies. Contemporary Physics. Taylor & Francis. https://doi.org/10.1080/00107514.2025.2586370' chicago: 'Matthee, Jorryt J. “JWST Provides a New View of Cosmic Dawn: Latest Developments in Studies of Early Galaxies.” Contemporary Physics. Taylor & Francis, 2025. https://doi.org/10.1080/00107514.2025.2586370.' ieee: 'J. J. Matthee, “JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies,” Contemporary Physics, vol. 66, no. 1–4. Taylor & Francis, pp. 116–151, 2025.' ista: 'Matthee JJ. 2025. JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies. Contemporary Physics. 66(1–4), 116–151.' mla: 'Matthee, Jorryt J. “JWST Provides a New View of Cosmic Dawn: Latest Developments in Studies of Early Galaxies.” Contemporary Physics, vol. 66, no. 1–4, Taylor & Francis, 2025, pp. 116–51, doi:10.1080/00107514.2025.2586370.' short: J.J. Matthee, Contemporary Physics 66 (2025) 116–151. corr_author: '1' date_created: 2025-12-29T12:05:25Z date_published: 2025-12-04T00:00:00Z date_updated: 2026-04-07T08:44:00Z day: '04' department: - _id: JoMa doi: 10.1080/00107514.2025.2586370 external_id: arxiv: - '2511.04843' intvolume: ' 66' issue: 1-4 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2511.04843 month: '12' oa: 1 oa_version: Preprint page: 116-151 project: - _id: bd9b2118-d553-11ed-ba76-db24564edfea grant_number: '101076224' name: Young galaxies as tracers and agents of cosmic reionization publication: Contemporary Physics publication_identifier: eissn: - 1366-5812 issn: - 0010-7514 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: 'JWST provides a new view of cosmic dawn: Latest developments in studies of early galaxies' type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 66 year: '2025' ... --- OA_place: repository OA_type: green _id: '21322' abstract: - lang: eng text: Habitat fragmentation poses a significant risk to population survival, causing both demographic stochasticity and genetic drift within local populations to increase, thereby increasing genetic load. Higher load causes population numbers to decline, which reduces the efficiency of selection and further increases load, resulting in a positive feedback that may drive entire populations to extinction. Here, we investigate this eco-evolutionary feedback in a metapopulation consisting of local demes connected via migration, with individuals subject to deleterious mutation at a large number of loci. We first analyze the determinants of load under soft selection, where population sizes are fixed, and then build on this to understand hard selection, where population sizes and load coevolve. We show that under soft selection, very little gene flow (less than one migrant per generation) is enough to prevent fixation of deleterious alleles. By contrast, much higher levels of migration are required to mitigate load and prevent extinction when selection is hard, with critical migration thresholds for metapopulation persistence increasing sharply as the genome-wide deleterious mutation rate becomes comparable to the baseline population growth rate. Moreover, critical migration thresholds are highest if deleterious mutations have intermediate selection coefficients but lower if alleles are predominantly recessive rather than additive (due to more efficient purging of recessive load within local populations). Our analysis is based on a combination of analytical approximations and simulations, allowing for a more comprehensive understanding of the factors influencing load and extinction in fragmented populations. acknowledgement: 'This research was partially funded by the Austrian Science Fund (FWF P-32896B) and DOC Fellowships of the Austrian Academy of Sciences: grants 26380 (O.O.) and 26293 (K.K.). We thank Nick Barton for useful comments on the chapter in O.O.’s thesis that led to this article.' article_processing_charge: No article_type: original author: - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback, and extinction in metapopulations. The American Naturalist. 2025;205(6):617-636. doi:10.1086/735562 apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (2025). Genetic load, eco-evolutionary feedback, and extinction in metapopulations. The American Naturalist. University of Chicago Press. https://doi.org/10.1086/735562 chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback, and Extinction in Metapopulations.” The American Naturalist. University of Chicago Press, 2025. https://doi.org/10.1086/735562. ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback, and extinction in metapopulations,” The American Naturalist, vol. 205, no. 6. University of Chicago Press, pp. 617–636, 2025. ista: Olusanya OO, Khudiakova K, Sachdeva H. 2025. Genetic load, eco-evolutionary feedback, and extinction in metapopulations. The American Naturalist. 205(6), 617–636. mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback, and Extinction in Metapopulations.” The American Naturalist, vol. 205, no. 6, University of Chicago Press, 2025, pp. 617–36, doi:10.1086/735562. short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, The American Naturalist 205 (2025) 617–636. corr_author: '1' date_created: 2026-02-18T10:47:18Z date_published: 2025-06-01T00:00:00Z date_updated: 2026-04-07T08:45:14Z day: '01' department: - _id: JaMa - _id: NiBa doi: 10.1086/735562 external_id: pmid: - '40446297 ' intvolume: ' 205' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.12.02.569702 month: '06' oa: 1 oa_version: Preprint page: 617-636 pmid: 1 project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6 grant_number: '26380' name: Polygenic Adaptation in a Metapopulation - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations publication: The American Naturalist publication_identifier: eissn: - 1537-5323 issn: - 0003-0147 publication_status: published publisher: University of Chicago Press quality_controlled: '1' related_material: record: - id: '14732' relation: earlier_version status: public scopus_import: '1' status: public title: Genetic load, eco-evolutionary feedback, and extinction in metapopulations type: journal_article user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd volume: 205 year: '2025' ... --- OA_place: repository OA_type: gold _id: '21668' abstract: - lang: eng text: "This artifact allows to review and reproduce the experiments from the paper *A Revised Practitioner's Guide to MDP Model Checking Algorithms*.\r\nThe package contains all original logfiles and derived data used to generate the plots as in the paper. Furthermore, the artifact contains the model checking tools `Storm` and `mcsta` in the version exercised in the paper, the used Docker container, as well as benchmark instances and execution scripts to reproduce the experiments.\r\n\r\nSee also the artifact of the conference paper: https://zenodo.org/records/7509474" article_processing_charge: No author: - first_name: Arnd full_name: Hartmanns, Arnd last_name: Hartmanns - first_name: Sebastian full_name: Junges, Sebastian last_name: Junges - first_name: Tim full_name: Quatmann, Tim last_name: Quatmann - first_name: Maximilian full_name: Weininger, Maximilian id: 02ab0197-cc70-11ed-ab61-918e71f56881 last_name: Weininger orcid: 0000-0002-0163-2152 citation: ama: Hartmanns A, Junges S, Quatmann T, Weininger M. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. 2025. doi:10.5281/ZENODO.14500423 apa: Hartmanns, A., Junges, S., Quatmann, T., & Weininger, M. (2025). Benchmark data for the revised practitioner’s guide to MDP model checking algorithms. Zenodo. https://doi.org/10.5281/ZENODO.14500423 chicago: Hartmanns, Arnd, Sebastian Junges, Tim Quatmann, and Maximilian Weininger. “Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.14500423. ieee: A. Hartmanns, S. Junges, T. Quatmann, and M. Weininger, “Benchmark data for the revised practitioner’s guide to MDP model checking algorithms.” Zenodo, 2025. ista: Hartmanns A, Junges S, Quatmann T, Weininger M. 2025. Benchmark data for the revised practitioner’s guide to MDP model checking algorithms, Zenodo, 10.5281/ZENODO.14500423. mla: Hartmanns, Arnd, et al. Benchmark Data for the Revised Practitioner’s Guide to MDP Model Checking Algorithms. Zenodo, 2025, doi:10.5281/ZENODO.14500423. short: A. Hartmanns, S. Junges, T. Quatmann, M. Weininger, (2025). date_created: 2026-04-07T09:47:22Z date_published: 2025-03-07T00:00:00Z date_updated: 2026-04-07T09:52:55Z day: '07' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.14500423 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.14500423 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '21661' relation: used_for_analysis_in status: public status: public title: Benchmark data for the revised practitioner's guide to MDP model checking algorithms type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository _id: '20982' abstract: - lang: eng text: Plant cells respond to a wide range of stimuli through intracellular calcium (Ca2+) signaling. Cyclic nucleotide-gated channels (CNGCs) are a major class of plant Ca2+ channels, with 20 homologs in Arabidopsis. These tetrameric plasma membrane proteins act downstream of diverse signals, such as phytohormones, extracellular damage, cell wall integrity or temperature. Here, we identify a class of plant-specific proteins, Armadillo Repeat Only (ARO), as essential regulators of possibly all plant CNGCs. Abrogation of functional sporophytic AROs results in a phenotypic pattern strongly reminiscent of CNGC dysfunction, including defects in root gravitropism, root hair growth and morphology, stomatal movement, and responses to extracellular ATP and the phytohormone auxin. aro2/3/4 mutants are fully resistant to the toxic effects caused by overexpression of CNGCs. AROs colocalize and physically interact with multiple CNGCs and modulate CNGC-dependent currents in Xenopus oocytes. Structural modeling and site-directed mutagenesis reveal AROs tetramer formation surrounding the CNGC channel, interacting via its IQ domain. Taken together, plant CNGC channels don’t act alone, but in a larger complex - channelosome, first of a kind in plants. acknowledgement: "This project was supported by the Czech Science Foundation grant Nr. 25-16449S and by European\r\nUnion, Horizon Europe, project MOLIPEC, ID 101087030. Computational resources used for structural\r\nmodeling were provided by the e-INFRA CZ project (ID:90254), supported by the Ministry of Education,\r\nYouth and Sports of the Czech Republic. Part of the work was carried out with the support of a Growth\r\nFacility (BC Core Facilities; IPMB BC CAS). X. laevis oocytes were kindly provided by C. Korbmacher on\r\na regular basis (FAU Erlangen-Nürnberg). MF received support from the European Research Council\r\n(Grant 480 No. 101125499). We acknowledge the core facility LMH, the BC CAS supported by the MEYS\r\nCR (LM 2023050 Czech-BioImaging). DO received support from the Czech Science Foundation grant Nr.\r\n24-12107S\r\n" article_processing_charge: No author: - first_name: Ivan full_name: Kulich, Ivan id: 57a1567c-8314-11eb-9063-c9ddc3451a54 last_name: Kulich - first_name: Denisa full_name: Oulehlová, Denisa last_name: Oulehlová - first_name: Dmitrii full_name: Vladimirtsev, Dmitrii id: 60466724-5355-11ee-ae5a-fa55e8f99c3d last_name: Vladimirtsev - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Edita full_name: Lileikyte, Edita last_name: Lileikyte - first_name: Alexey full_name: Bondar, Alexey last_name: Bondar - first_name: Katarína full_name: Kulichová, Katarína last_name: Kulichová - first_name: Martin full_name: Janda, Martin last_name: Janda - first_name: Oksana full_name: Iakovenko, Oksana last_name: Iakovenko - first_name: Michaela full_name: Neubergerová, Michaela last_name: Neubergerová - first_name: Tanja full_name: Studtrucker, Tanja last_name: Studtrucker - first_name: Roman full_name: Pleskot, Roman last_name: Pleskot - first_name: Petra full_name: Dietrich, Petra last_name: Dietrich - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kulich I, Oulehlová D, Vladimirtsev D, et al. Armadillo repeat only proteins are required for the function of plant CNGC channels. bioRxiv. doi:10.1101/2025.01.06.631460 apa: Kulich, I., Oulehlová, D., Vladimirtsev, D., Zou, M., Lileikyte, E., Bondar, A., … Friml, J. (n.d.). Armadillo repeat only proteins are required for the function of plant CNGC channels. bioRxiv. https://doi.org/10.1101/2025.01.06.631460 chicago: Kulich, Ivan, Denisa Oulehlová, Dmitrii Vladimirtsev, Minxia Zou, Edita Lileikyte, Alexey Bondar, Katarína Kulichová, et al. “Armadillo Repeat Only Proteins Are Required for the Function of Plant CNGC Channels.” BioRxiv, n.d. https://doi.org/10.1101/2025.01.06.631460. ieee: I. Kulich et al., “Armadillo repeat only proteins are required for the function of plant CNGC channels,” bioRxiv. . ista: Kulich I, Oulehlová D, Vladimirtsev D, Zou M, Lileikyte E, Bondar A, Kulichová K, Janda M, Iakovenko O, Neubergerová M, Studtrucker T, Pleskot R, Dietrich P, Fendrych M, Friml J. Armadillo repeat only proteins are required for the function of plant CNGC channels. bioRxiv, 10.1101/2025.01.06.631460. mla: Kulich, Ivan, et al. “Armadillo Repeat Only Proteins Are Required for the Function of Plant CNGC Channels.” BioRxiv, doi:10.1101/2025.01.06.631460. short: I. Kulich, D. Oulehlová, D. Vladimirtsev, M. Zou, E. Lileikyte, A. Bondar, K. Kulichová, M. Janda, O. Iakovenko, M. Neubergerová, T. Studtrucker, R. Pleskot, P. Dietrich, M. Fendrych, J. Friml, BioRxiv (n.d.). corr_author: '1' date_created: 2026-01-13T14:07:58Z date_published: 2025-05-16T00:00:00Z date_updated: 2026-04-07T11:41:43Z day: '16' department: - _id: JiFr doi: 10.1101/2025.01.06.631460 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.01.06.631460 month: '05' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: draft related_material: record: - id: '20964' relation: dissertation_contains status: public status: public title: Armadillo repeat only proteins are required for the function of plant CNGC channels 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20260' abstract: - lang: eng text: The medial axis of a set consists of the points in the ambient space without a unique closest point in the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a skeleton topologically equivalent to the original set. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities, various prunings of the medial axis have been proposed in the computational geometry community. Here, we examine one type of pruning, called burning. Because of the good experimental results it was hoped that the burning method of simplifying the medial axis would be stable. In this work, we show a simple example that dashes such hopes. Based on Bing’s house with two rooms, we demonstrate an isotopy of a shape where the medial axis goes from collapsible to non-collapsible. More precisely, we consider the standard deformation retract from the closed ball to Bing’s house with two rooms, but stop just short of the point where Bing’s house becomes two dimensional. This way we obtain an isotopy from the 3-ball to a thickened version of Bing’s house. Under this isotopy, the medial axis goes from collapsible to non-collapsible. We stress that this isotopy can be made generic, in the sense of singularity theory, as developed by Arnol’d and Thom. acknowledgement: "We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan, and Tao Ju for sharing code to generate the examples. We further thank Abigail Thompson for discussion on the conjecture and James Damon for sharing his insight in singularity theory. We thank the reviewers for their detailed reviews, which helped to improve the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). Partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’ and the European Research Council (ERC), grant no. 788183, ‘Alpha Shape Theory Extended’. The first author was supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2444309. The fourth author was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) M-3073, ANR grant StratMesh, ANR-24-CE48-1899, and the welcome package from IDEX of the Université Côte d’Azur, ANR-15-IDEX-01." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Erin Wolf full_name: Chambers, Erin Wolf last_name: Chambers - first_name: Christopher D full_name: Fillmore, Christopher D id: 35638A5C-AAC7-11E9-B0BF-5503E6697425 last_name: Fillmore - first_name: Elizabeth R full_name: Stephenson, Elizabeth R id: 2D04F932-F248-11E8-B48F-1D18A9856A87 last_name: Stephenson orcid: 0000-0002-6862-208X - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: ama: Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. Burning or collapsing the medial axis is unstable. La Matematica. 2025;4:811-828. doi:10.1007/s44007-025-00170-0 apa: Chambers, E. W., Fillmore, C. D., Stephenson, E. R., & Wintraecken, M. (2025). Burning or collapsing the medial axis is unstable. La Matematica. Springer Nature. https://doi.org/10.1007/s44007-025-00170-0 chicago: Chambers, Erin Wolf, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “Burning or Collapsing the Medial Axis Is Unstable.” La Matematica. Springer Nature, 2025. https://doi.org/10.1007/s44007-025-00170-0. ieee: E. W. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “Burning or collapsing the medial axis is unstable,” La Matematica, vol. 4. Springer Nature, pp. 811–828, 2025. ista: Chambers EW, Fillmore CD, Stephenson ER, Wintraecken M. 2025. Burning or collapsing the medial axis is unstable. La Matematica. 4, 811–828. mla: Chambers, Erin Wolf, et al. “Burning or Collapsing the Medial Axis Is Unstable.” La Matematica, vol. 4, Springer Nature, 2025, pp. 811–28, doi:10.1007/s44007-025-00170-0. short: E.W. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, La Matematica 4 (2025) 811–828. corr_author: '1' date_created: 2025-08-31T22:01:33Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-04-07T11:42:48Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s44007-025-00170-0 ec_funded: 1 file: - access_level: open_access checksum: e2043259194bfcdf3d74c4da8a5a853f content_type: application/pdf creator: dernst date_created: 2025-12-30T07:52:58Z date_updated: 2025-12-30T07:52:58Z file_id: '20885' file_name: 2025_LaMatematica_Chambers.pdf file_size: 2678640 relation: main_file success: 1 file_date_updated: 2025-12-30T07:52:58Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 811-828 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc390959-9c52-11eb-aca3-afa58bd282b2 grant_number: M03073 name: Learning and triangulating manifolds via collapses publication: La Matematica publication_identifier: eissn: - 2730-9657 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21021' relation: dissertation_contains status: public scopus_import: '1' status: public title: Burning or collapsing the medial axis is unstable 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: 4 year: '2025' ... --- OA_place: publisher OA_type: gold _id: '20819' abstract: - lang: eng text: "Clustering is a cornerstone of data analysis that is particularly suited to identifying coherent subgroups or substructures in unlabeled data, as are generated continuously in large amounts these days. However, in many cases traditional clustering methods are not applicable, because data are increasingly being produced and stored in a distributed way, e.g. on edge devices, and privacy concerns prevent it from being transferred to a central server. To address this challenge, we present FedDP-KMeans, a new algorithm for \r\n-means clustering that is fully-federated as well as differentially private. Our approach leverages (potentially small and out-of-distribution) server-side data to overcome the primary challenge of differentially private clustering methods: the need for a good initialization. Combining our initialization with a simple federated DP-Lloyds algorithm we obtain an algorithm that achieves excellent results on synthetic and real-world benchmark tasks. We also provide a theoretical analysis of our method that provides bounds on the convergence speed and cluster identification success." acknowledged_ssus: - _id: ScienComp acknowledgement: "This research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE12] and supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).\r\n" alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: David full_name: Saulpic, David id: f8e48cf0-b0ff-11ed-b0e9-b4c35598f964 last_name: Saulpic citation: ama: 'Scott JA, Lampert C, Saulpic D. Differentially private federated k-means clustering with server-side data. In: 42nd International Conference on Machine Learning. Vol 267. ML Research Press; 2025:53757-53790.' apa: 'Scott, J. A., Lampert, C., & Saulpic, D. (2025). Differentially private federated k-means clustering with server-side data. In 42nd International Conference on Machine Learning (Vol. 267, pp. 53757–53790). Vancouver, Canada: ML Research Press.' chicago: Scott, Jonathan A, Christoph Lampert, and David Saulpic. “Differentially Private Federated K-Means Clustering with Server-Side Data.” In 42nd International Conference on Machine Learning, 267:53757–90. ML Research Press, 2025. ieee: J. A. Scott, C. Lampert, and D. Saulpic, “Differentially private federated k-means clustering with server-side data,” in 42nd International Conference on Machine Learning, Vancouver, Canada, 2025, vol. 267, pp. 53757–53790. ista: 'Scott JA, Lampert C, Saulpic D. 2025. Differentially private federated k-means clustering with server-side data. 42nd International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 267, 53757–53790.' mla: Scott, Jonathan A., et al. “Differentially Private Federated K-Means Clustering with Server-Side Data.” 42nd International Conference on Machine Learning, vol. 267, ML Research Press, 2025, pp. 53757–90. short: J.A. Scott, C. Lampert, D. Saulpic, in:, 42nd International Conference on Machine Learning, ML Research Press, 2025, pp. 53757–53790. conference: end_date: 2025-07-19 location: Vancouver, Canada name: 'ICML: International Conference on Machine Learning' start_date: 2025-07-13 corr_author: '1' date_created: 2025-12-14T23:02:05Z date_published: 2025-05-01T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '01' ddc: - '000' department: - _id: ChLa - _id: MoHe external_id: arxiv: - '2506.05408' file: - access_level: open_access checksum: 815b32b463023ca21e569c2158745c15 content_type: application/pdf creator: dernst date_created: 2025-12-16T12:38:29Z date_updated: 2025-12-16T12:38:29Z file_id: '20829' file_name: 2025_ICML_Scott.pdf file_size: 746612 relation: main_file success: 1 file_date_updated: 2025-12-16T12:38:29Z has_accepted_license: '1' intvolume: ' 267' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 53757-53790 publication: 42nd International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '21198' relation: dissertation_contains status: public scopus_import: '1' status: public title: Differentially private federated k-means clustering with server-side data 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 267 year: '2025' ... --- OA_place: repository _id: '21207' abstract: - lang: eng text: Personalized federated learning has emerged as a popular approach to training on devices holding statistically heterogeneous data, known as clients. However, most existing approaches require a client to have labeled data for training or finetuning in order to obtain their own personalized model. In this paper we address this by proposing FLowDUP, a novel method that is able to generate a personalized model using only a forward pass with unlabeled data. The generated model parameters reside in a low-dimensional subspace, enabling efficient communication and computation. FLowDUP's learning objective is theoretically motivated by our new transductive multi-task PAC-Bayesian generalization bound, that provides performance guarantees for unlabeled clients. The objective is structured in such a way that it allows both clients with labeled data and clients with only unlabeled data to contribute to the training process. To supplement our theoretical results we carry out a thorough experimental evaluation of FLowDUP, demonstrating strong empirical performance on a range of datasets with differing sorts of statistically heterogeneous clients. Through numerous ablation studies, we test the efficacy of the individual components of the method. article_processing_charge: No author: - first_name: Hossein full_name: Zakerinia, Hossein id: 653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4 last_name: Zakerinia orcid: 0009-0007-3977-6462 - first_name: Jonathan A full_name: Scott, Jonathan A id: e499926b-f6e0-11ea-865d-9c63db0031e8 last_name: Scott - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Zakerinia H, Scott JA, Lampert C. Federated learning with unlabeled clients: Personalization can happen in low dimensions. arXiv. doi:10.48550/ARXIV.2505.15579' apa: 'Zakerinia, H., Scott, J. A., & Lampert, C. (n.d.). Federated learning with unlabeled clients: Personalization can happen in low dimensions. arXiv. https://doi.org/10.48550/ARXIV.2505.15579' chicago: 'Zakerinia, Hossein, Jonathan A Scott, and Christoph Lampert. “Federated Learning with Unlabeled Clients: Personalization Can Happen in Low Dimensions.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2505.15579.' ieee: 'H. Zakerinia, J. A. Scott, and C. Lampert, “Federated learning with unlabeled clients: Personalization can happen in low dimensions,” arXiv. .' ista: 'Zakerinia H, Scott JA, Lampert C. Federated learning with unlabeled clients: Personalization can happen in low dimensions. arXiv, 10.48550/ARXIV.2505.15579.' mla: 'Zakerinia, Hossein, et al. “Federated Learning with Unlabeled Clients: Personalization Can Happen in Low Dimensions.” ArXiv, doi:10.48550/ARXIV.2505.15579.' short: H. Zakerinia, J.A. Scott, C. Lampert, ArXiv (n.d.). corr_author: '1' date_created: 2026-02-10T08:20:59Z date_published: 2025-05-21T00:00:00Z date_updated: 2026-04-07T11:46:11Z day: '21' department: - _id: ChLa doi: 10.48550/ARXIV.2505.15579 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2505.15579 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '21198' relation: dissertation_contains status: public status: public title: 'Federated learning with unlabeled clients: Personalization can happen in low dimensions' 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: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository _id: '21050' abstract: - lang: eng text: "In 1873, James C. Maxwell conjectured that the electric field generated by $n$ point charges in generic position has at most $(n-1)^2$ isolated zeroes. The first (non-optimal) upper bound was only obtained in 2007 by Gabrielov, Novikov and Shapiro, who also posed two additional interesting conjectures.\r\n In this article, we give the best upper bound known to date on the number of zeroes of the electric field, and construct a counterexample to a conjecture of Gabrielov, Novikov and Shapiro that the number of equilibria cannot exceed those of the distance function defined by the unit point charges.\r\n Finally, we note that it is quite possible that Maxwell's quadratic upper bound is not tight, so it is prudent to find smaller bounds. Hence, we also explore examples and construct configurations of charges achieving the highest ratios of the number of electric field zeroes by point charges found to this day." article_processing_charge: No arxiv: 1 author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Christopher D full_name: Fillmore, Christopher D id: 35638A5C-AAC7-11E9-B0BF-5503E6697425 last_name: Fillmore - first_name: Gonçalo full_name: Olivera, Gonçalo last_name: Olivera citation: ama: Edelsbrunner H, Fillmore CD, Olivera G. Counting equilibria of the electrostatic potential. arXiv. doi:10.48550/ARXIV.2501.05315 apa: Edelsbrunner, H., Fillmore, C. D., & Olivera, G. (n.d.). Counting equilibria of the electrostatic potential. arXiv. https://doi.org/10.48550/ARXIV.2501.05315 chicago: Edelsbrunner, Herbert, Christopher D Fillmore, and Gonçalo Olivera. “Counting Equilibria of the Electrostatic Potential.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2501.05315. ieee: H. Edelsbrunner, C. D. Fillmore, and G. Olivera, “Counting equilibria of the electrostatic potential,” arXiv. . ista: Edelsbrunner H, Fillmore CD, Olivera G. Counting equilibria of the electrostatic potential. arXiv, 10.48550/ARXIV.2501.05315. mla: Edelsbrunner, Herbert, et al. “Counting Equilibria of the Electrostatic Potential.” ArXiv, doi:10.48550/ARXIV.2501.05315. short: H. Edelsbrunner, C.D. Fillmore, G. Olivera, ArXiv (n.d.). corr_author: '1' date_created: 2026-01-27T14:29:27Z date_published: 2025-03-20T00:00:00Z date_updated: 2026-04-07T11:42:48Z day: '20' department: - _id: HeEd doi: 10.48550/ARXIV.2501.05315 external_id: arxiv: - '2501.05315' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2501.05315 month: '03' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '21021' relation: dissertation_contains status: public status: public title: Counting equilibria of the electrostatic potential 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: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 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: 2026-04-07T11:47:06Z day: '13' ddc: - '514' - '519' - '532' - '004' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/AT-ISTA-19684 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 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: '7563' relation: part_of_dissertation status: public - 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 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: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19795' abstract: - lang: eng text: Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases. acknowledged_ssus: - _id: M-Shop - _id: EM-Fac - _id: LifeSc acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).' article_number: '100211' article_processing_charge: Yes article_type: original author: - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Nikolai full_name: Semenov, Nikolai id: e64d39c7-72ef-11ef-b75a-ee3046860d1b last_name: Semenov - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Manjunath full_name: Javoor, Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor orcid: 0000-0003-2311-2112 - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Marek full_name: Suplata, Marek id: EE8452B8-C26A-11E9-B157-E80CE6697425 last_name: Suplata - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr orcid: 0000-0003-0201-2315 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Andreas full_name: Wartak, Andreas id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb last_name: Wartak - first_name: Florian Km full_name: Schur, Florian Km id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 2025;5(2). doi:10.1016/j.bpr.2025.100211 apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. Elsevier. https://doi.org/10.1016/j.bpr.2025.100211 chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical Reports. Elsevier, 2025. https://doi.org/10.1016/j.bpr.2025.100211. ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” Biophysical Reports, vol. 5, no. 2. Elsevier, 2025. ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211. mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical Reports, vol. 5, no. 2, 100211, Elsevier, 2025, doi:10.1016/j.bpr.2025.100211. short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025). corr_author: '1' date_created: 2025-06-08T22:01:22Z date_published: 2025-06-11T00:00:00Z date_updated: 2026-04-07T11:48:07Z day: '11' ddc: - '570' department: - _id: JoDa - _id: GradSch - _id: FlSc - _id: EM-Fac doi: 10.1016/j.bpr.2025.100211 ec_funded: 1 file: - access_level: open_access checksum: 4018c833f25a3ad3b57e3577fed70334 content_type: application/pdf creator: dernst date_created: 2025-06-10T07:24:46Z date_updated: 2025-06-10T07:24:46Z file_id: '19802' file_name: 2025_BiophysicalReports_Vorlaufer.pdf file_size: 7238179 relation: main_file success: 1 file_date_updated: 2025-06-10T07:24:46Z has_accepted_license: '1' intvolume: ' 5' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 62909c6f-2b32-11ec-9570-e1476aab5308 grant_number: CZI01 name: CryoMinflux-guided in-situ molecular census and structure determination - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 2668BFA0-B435-11E9-9278-68D0E5697425 grant_number: LT00057 name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration publication: Biophysical Reports publication_identifier: eissn: - 2667-0747 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '20206' relation: dissertation_contains status: public scopus_import: '1' status: public title: Image-based 3D active sample stabilization on the nanometer scale for optical microscopy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2025' ... --- OA_place: publisher _id: '18979' abstract: - lang: eng text: "Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA.\r\n\r\nThe first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue.\r\n\r\nThe aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor.\r\n\r\nWe describe a construction of a chromatic alpha complex, which enables efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline.\r\n\r\nThe second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory.\r\n\r\nIn the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot." acknowledgement: "The research presented in this thesis was funded with the Wittgenstein Prize,\r\nAustrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research\r\nCenter TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF),\r\ngrant no. I 02979-N35.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ondrej full_name: Draganov, Ondrej id: 2B23F01E-F248-11E8-B48F-1D18A9856A87 last_name: Draganov orcid: 0000-0003-0464-3823 citation: ama: Draganov O. Structures and computations in topological data analysis. 2025. doi:10.15479/at:ista:18979 apa: Draganov, O. (2025). Structures and computations in topological data analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18979 chicago: Draganov, Ondrej. “Structures and Computations in Topological Data Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:18979. ieee: O. Draganov, “Structures and computations in topological data analysis,” Institute of Science and Technology Austria, 2025. ista: Draganov O. 2025. Structures and computations in topological data analysis. Institute of Science and Technology Austria. mla: Draganov, Ondrej. Structures and Computations in Topological Data Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:18979. short: O. Draganov, Structures and Computations in Topological Data Analysis, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-01-31T17:04:40Z date_published: 2025-02-03T00:00:00Z date_updated: 2026-04-07T11:47:30Z day: '03' ddc: - '514' - '004' degree_awarded: PhD department: - _id: GradSch - _id: HeEd doi: 10.15479/at:ista:18979 file: - access_level: closed checksum: af6567e5d35e5eb330b8925ae37f1998 content_type: application/zip creator: odragano date_created: 2025-01-31T16:58:30Z date_updated: 2025-01-31T16:58:30Z file_id: '18983' file_name: Thesis.zip file_size: 11899491 relation: source_file - access_level: open_access checksum: c3fef68e35b9dc2020b2ca6006da6343 content_type: application/pdf creator: odragano date_created: 2025-02-04T16:22:07Z date_updated: 2025-02-04T16:22:07Z file_id: '19000' file_name: Thesis.pdf file_size: 8857514 relation: main_file file_date_updated: 2025-02-04T16:22:07Z has_accepted_license: '1' keyword: - topological data analysis - chromatic point set - alpha complex - persistent homology - six pack - sheaf - microlocal discrete Morse - injective resolution - collapse - knot - discrete Morse theory language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '140' project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: Mathematics, Computer Science publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15091' relation: part_of_dissertation status: public - id: '18981' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Structures and computations in topological data analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20206' abstract: - lang: eng text: "The internal structure of biomolecules and their organization in higher-order arrangements are key factors governing the working principles of biological systems. Bioimaging has successfully revealed arrangements across relevant spatial scales. For example, cryo-electron tomography has become widely used for analyzing biomolecular structures in situ due to its comprehensive structural visualization of near-natively preserved samples, and its capability of sub-nm resolution via averaging. However, the identification of molecules within crowded cellular environments is often hindered by low contrast. Fluorescence microscopy, on the other hand, routinely visualizes specifically labeled targets at single-molecule contrast against essentially zero background. Moreover, it provides comparatively high throughput and is amenable to multiplexing. Due to this complementarity, combining datasets from both modalities acquired on the same region via correlative light and electron microscopy can reveal novel types of information. \r\nThe spatial scale at which information can be extracted depends on imaging resolution and correlation accuracy. Since diffraction of light limits the resolution of conventional fluorescence microscopy to few hundreds of nanometers, reaching the full potential of correlative imaging requires super-resolution approaches. Performing imaging at cryogenic temperature preserves structures in a near-native state and minimizes distortions between the fluorescence and the electron microscopy datasets. Implementations of this concept have achieved correlation on the scale of cellular organelles or bacterial domains.\r\nWe have worked towards pushing correlative imaging to the single-molecule scale by improving cryo-super-resolution microscopy, and devising a refined image correlation workflow. As part of this project, I constructed a microscopy setup and adopted it for super-resolution fluorescence microscopy at room temperature and cryogenic conditions. I explored different cryo-stages and acquisition strategies. Specifically, I developed a new scheme for correcting sample drift, thus increasing mechanical stability during microscopy acquisitions.\r\n" acknowledged_ssus: - _id: M-Shop - _id: EM-Fac - _id: Bio acknowledgement: "The project was supported by CZI grant DAF2021-234754 and grant\r\nDOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an\r\nadvised fund of Silicon Valley Community Foundation (funder\r\nDOI: https://doi.org/10.13039/100014989), as well as internal grants from ISTA’s Equipment\r\nInvestment Committee and Interdisciplinary Project Committee. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 citation: ama: Vorlaufer J. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. 2025. doi:10.15479/AT-ISTA-20206 apa: Vorlaufer, J. (2025). Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20206 chicago: Vorlaufer, Jakob. “Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20206. ieee: J. Vorlaufer, “Construction of a cryo-super-resolution microscope to guide in situ structure analysis,” Institute of Science and Technology Austria, 2025. ista: Vorlaufer J. 2025. Construction of a cryo-super-resolution microscope to guide in situ structure analysis. Institute of Science and Technology Austria. mla: Vorlaufer, Jakob. Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20206. short: J. Vorlaufer, Construction of a Cryo-Super-Resolution Microscope to Guide in Situ Structure Analysis, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-22T08:12:55Z date_published: 2025-08-25T00:00:00Z date_updated: 2026-04-07T11:48:07Z day: '25' ddc: - '621' - '535' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/AT-ISTA-20206 file: - access_level: closed checksum: 191db3367c19c9b32b65f4bc3a7c19de content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jvorlauf date_created: 2025-08-25T13:49:55Z date_updated: 2025-08-25T13:49:55Z file_id: '20228' file_name: 2025_Vorlaufer_Jakob_Thesis.docx file_size: 39735535 relation: source_file - access_level: open_access checksum: 104400e6036921569610230c1d4899dc content_type: application/pdf creator: jvorlauf date_created: 2025-08-25T13:49:56Z date_updated: 2025-08-25T13:49:56Z file_id: '20229' file_name: 2025_Vorlaufer_Jakob_Thesis.pdf file_size: 10947446 relation: main_file success: 1 file_date_updated: 2025-08-25T13:49:56Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '08' oa: 1 oa_version: Published Version page: '107' project: - _id: 62909c6f-2b32-11ec-9570-e1476aab5308 grant_number: CZI01 name: CryoMinflux-guided in-situ molecular census and structure determination publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19795' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: Construction of a cryo-super-resolution microscope to guide in situ structure analysis tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19722' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: Special thanks to the Plant Facility. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Syamala full_name: Inumella, Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella orcid: 0009-0002-5890-120X citation: ama: Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722 apa: Inumella, S. (2025). Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19722 chicago: Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19722. ieee: S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025. ista: Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. mla: Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19722. short: S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-23T15:21:29Z date_published: 2025-05-23T00:00:00Z date_updated: 2026-04-07T11:47:52Z day: '23' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-19722 file: - access_level: closed checksum: 847ec70b2e40f50e0ddc7b8da201d52c content_type: application/pdf creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2025-05-28T11:59:11Z embargo: 2026-05-23 embargo_to: open_access file_id: '19757' file_name: Final Thesis_Syamala Inumella.pdf file_size: 8292363 relation: main_file - access_level: closed checksum: 17cdffdae13a5f65bdad9c84e9e0e3bd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2025-05-28T11:59:11Z file_id: '19758' file_name: Final Thesis_Syamala Inumella.docx file_size: 7145703 relation: source_file file_date_updated: 2025-05-28T11:59:11Z has_accepted_license: '1' language: - iso: eng month: '05' oa_version: Published Version page: '113' publication_identifier: isbn: - 978-3-99078-059-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of microtubule reorganization in elongating root epidermal cells type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd 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: 2026-04-07T11:48:32Z day: '13' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19395 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 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: '19398' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public - id: '12291' relation: part_of_dissertation status: public - id: '14826' 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: ba8df636-2132-11f1-aed0-ed93e2281fdd 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. Cold Spring Harbor Laboratory. 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. Cold Spring Harbor Laboratory, 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. Cold Spring Harbor Laboratory. 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, Cold Spring Harbor Laboratory, 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' date_created: 2025-03-12T14:28:53Z date_published: 2025-03-02T00:00:00Z date_updated: 2026-04-07T11:48:31Z day: '02' department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 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 publisher: Cold Spring Harbor Laboratory 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 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: 2026-04-07T11:48:53Z 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 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: '19425' relation: part_of_dissertation status: public - id: '9903' relation: part_of_dissertation status: public - id: '15004' 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: '20138' abstract: - lang: eng text: "The evolution shapes the world around us.\r\nNot only in biology, where the fittest individuals spread their genes but also in physics and social dynamics, the evolutionary forces determine the development of a state of matter or public opinions.\r\nMany models describe these dynamics.\r\nThis thesis examines the role of the structure in the models of selection.\r\nThe population structure is represented as a graph or a network, and each vertex is occupied by one individual.\r\nEvery individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors.\r\nThe evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness.\r\n\r\n\r\n\r\nThe role of the networks is widely examined in the literature.\r\nThe structures that promote the spread of the desired type compared to the structureless case are called amplifiers.\r\nThe existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified.\r\nMoreover, there are other important questions about the number of steps until one type spreads over the whole network (fixation time), the computational complexity, and the questions about the robustness of these processes.\r\n\r\n\r\nThis thesis explores the role of structure in evolution from many perspectives.\r\nFirst, it introduces different models and various choices that can be made in the models of evolution.\r\nIt highlights the role of the structure in the real world and how this is reflected in these models.\r\nThen, it describes the previous results and open problems.\r\nSecond, the thesis describes an amplifier for two variants of the Moran process: one with a constant birth rate and the other with a constant death rate.\r\nThis is an important contribution to the robustness of the amplification.\r\nThird, the thesis determines the complexity of spatial games.\r\nThese are processes where the fitness comes from a game, and the strength of selection is high.\r\nIt shows that determining the fate of cooperation in these games is a PSPACE-complete problem.\r\nFourth, the thesis describes the amplifier of cooperation for spatial games.\r\nThis is the first amplifier in this setting.\r\nFifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity.\r\nIn this setting, the fitness depends not only on the type of the individual but also on the occupied vertex.\r\nThe chapter determines the relationship between the interactions of vertices of different types and the coexistence time.\r\nSixth, the thesis examines the social balance on networks and proposes a stochastic dynamic partially aware of the state of the graph, which reaches a balanced position quickly.\r\nFinally, the thesis presents conclusions and outlines the directions for future work.\r\n\r\n\r\n" acknowledgement: "This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 citation: ama: Svoboda J. Structural properties of games on graphs. 2025. doi:10.15479/AT-ISTA-20138 apa: Svoboda, J. (2025). Structural properties of games on graphs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20138 chicago: Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20138. ieee: J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025. ista: Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria. mla: Svoboda, Jakub. Structural Properties of Games on Graphs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20138. short: J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-05T14:33:59Z date_published: 2025-08-05T00:00:00Z date_updated: 2026-04-07T11:49:12Z day: '05' ddc: - '000' - '519' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/AT-ISTA-20138 ec_funded: 1 file: - access_level: open_access checksum: c6c4df9777f4537940de7ab392ad57e2 content_type: application/pdf creator: jsvoboda date_created: 2025-08-14T09:54:43Z date_updated: 2025-08-14T09:54:43Z file_id: '20177' file_name: 2025_Svoboda_Jakub_Thesis.pdf file_size: 5927291 relation: main_file success: 1 - access_level: closed checksum: 485e9f9822821bc03666d245d80aaa08 content_type: application/zip creator: jsvoboda date_created: 2025-08-14T09:55:20Z date_updated: 2025-08-21T11:48:39Z file_id: '20178' file_name: 2025_Svoboda_Jakub_Thesis.zip file_size: 6731815 relation: source_file file_date_updated: 2025-08-21T11:48:39Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '167' project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12787' relation: part_of_dissertation status: public - id: '12101' relation: part_of_dissertation status: public - id: '12257' relation: part_of_dissertation status: public - id: '15297' relation: part_of_dissertation status: public - id: '18703' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Structural properties of games on graphs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20117' acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl acknowledgement: "I would also like to acknowledge the invaluable assistance provided by the Plant\r\nFacility, Imaging & Optics Facility, and the Lab Support Facility. The technical support and\r\nresources offered by these facilities were indispensable to the successful completion of my\r\nexperiments." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Yiqun full_name: Wang, Yiqun id: 82F537F2-B517-11E9-84D7-6433E6697425 last_name: Wang citation: ama: Wang Y. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. 2025. doi:10.15479/AT-ISTA-20117 apa: Wang, Y. (2025). The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20117 chicago: Wang, Yiqun. “The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20117. ieee: Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025. ista: Wang Y. 2025. The role of dynamin related protein 2A in cytokinin regulated plant growth and development. Institute of Science and Technology Austria. mla: Wang, Yiqun. The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20117. short: Y. Wang, The Role of Dynamin Related Protein 2A in Cytokinin Regulated Plant Growth and Development, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-04T15:24:21Z date_published: 2025-08-04T00:00:00Z date_updated: 2026-04-07T11:49:34Z day: '04' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-20117 file: - access_level: closed checksum: 36b87c17d12c7bf5955d6d812acb8d77 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: yiqwang date_created: 2025-08-22T08:22:10Z date_updated: 2025-08-22T08:53:46Z file_id: '20209' file_name: 2025_Wang_Yiqun_Thesis.docx file_size: 25798848 relation: source_file - access_level: closed checksum: 8d7a2383f66377da675d379ec30ea0fe content_type: application/pdf creator: yiqwang date_created: 2025-08-22T10:32:30Z date_updated: 2025-09-03T09:36:52Z embargo: 2026-09-03 embargo_to: open_access file_id: '20211' file_name: 2025_Wang_Yiqun_Thesis.pdf file_size: 12628313 relation: main_file file_date_updated: 2025-09-03T09:36:52Z has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '108' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18063' relation: part_of_dissertation status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: The role of dynamin related protein 2A in cytokinin regulated plant growth and development type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19759' abstract: - lang: eng text: "Despite generating remarkable results in various computer vision tasks, deep learning comes\r\nwith some surprising shortcomings. For example, tiny perturbations, often imperceptible to\r\nthe human eye, can completely change the predictions of image classifiers. Despite a decade\r\nof research, the field has made limited progress in developing image classifiers that are both\r\naccurate and robust. This thesis aims to address this gap.\r\nAs our first contribution, we aim to simplify the process of training certifiably robust image\r\nclassifiers. We do this by designing a convolutional layer that does not require executing an\r\niterative procedure in every forward pass, but relies on an explicit bound instead. We also\r\npropose a loss function that allows optimizing for a particular margin more precisely.\r\nNext, we provide an overview and comparison of various methods that create robust image\r\nclassifiers by constraining the Lipschitz constant. This is important since generally longer\r\ntraining times and more parameters improve the performance of robust classifiers, making it\r\nchallenging to determine the most practical and effective methods from existing literature.\r\nIn 1-Lipschitz classification, the performance of current methods is still much worse than what\r\nwe expect on the simple tasks we consider. Therefore, we next investigate potential causes of\r\nthis shortcoming. We first consider the role of the activation function. We prove a theoretical\r\nshortcoming of the commonly used activation function, and provide an alternative without it.\r\nHowever this theoretical improvement does barely translate to the empirical performance of\r\nrobust classifiers, suggesting a different bottleneck.\r\nTherefore, in the final chapter, we study how the performance depends on the amount of\r\ntraining data. We prove that in the worst case, we might require far more data to train a\r\nrobust classifier compared to a normal one. We furthermore find that the amount of training\r\ndata is a key determinant of the performance current methods achieve on popular datasets.\r\nAdditionally, we show that linear subspaces exist with tiny data variance, and yet we can\r\nstill train very accurate classifiers after projecting into those subspaces. This shows that on\r\nthe datasets considered, enforcing robustness in classification makes the task strictly more\r\nchallenging.\r\n\r\n-----------------“In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of [name of university or educational entity]’s products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation.”\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach citation: ama: Prach B. Robust image classification with 1-Lipschitz networks. 2025. doi:10.15479/10.15479/at-ista-19759 apa: Prach, B. (2025). Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria. https://doi.org/10.15479/10.15479/at-ista-19759 chicago: Prach, Bernd. “Robust Image Classification with 1-Lipschitz Networks.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/at-ista-19759. ieee: B. Prach, “Robust image classification with 1-Lipschitz networks,” Institute of Science and Technology Austria, 2025. ista: Prach B. 2025. Robust image classification with 1-Lipschitz networks. Institute of Science and Technology Austria. mla: Prach, Bernd. Robust Image Classification with 1-Lipschitz Networks. Institute of Science and Technology Austria, 2025, doi:10.15479/10.15479/at-ista-19759. short: B. Prach, Robust Image Classification with 1-Lipschitz Networks, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-28T16:20:48Z date_published: 2025-05-30T00:00:00Z date_updated: 2026-04-07T11:49:52Z day: '30' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/10.15479/at-ista-19759 file: - access_level: open_access checksum: e5108e759014e2a9020c973c778fafc9 content_type: application/pdf creator: bprach date_created: 2025-06-10T18:11:05Z date_updated: 2025-06-10T18:11:05Z file_id: '19829' file_name: ThesisFinal.pdf file_size: 3578077 relation: main_file - access_level: closed checksum: 51bf6c11fb6d8a9f8010b458c600a83f content_type: application/x-zip-compressed creator: bprach date_created: 2025-06-10T18:14:03Z date_updated: 2025-06-10T18:14:03Z file_id: '19830' file_name: ThesisFinal.zip file_size: 74894357 relation: source_file file_date_updated: 2025-06-10T18:14:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '84' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15039' relation: part_of_dissertation status: public - id: '18874' relation: part_of_dissertation status: public - id: '17426' relation: part_of_dissertation status: public - id: '11839' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Robust image classification with 1-Lipschitz networks type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ...