--- OA_place: publisher _id: '20737' acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: "I also want to thank ISTA and the Austrian Science Fund FWF SFB F78 (F7805) for financially\r\nsupporting my research." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Raquel full_name: Casado Polanco, Raquel id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd last_name: Casado Polanco orcid: 0000-0001-8293-4568 citation: ama: Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage progression. 2025. doi:10.15479/AT-ISTA-20737 apa: Casado Polanco, R. (2025). Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20737 chicago: Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20737. ieee: R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage progression,” Institute of Science and Technology Austria, 2025. ista: Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor lineage progression. Institute of Science and Technology Austria. mla: Casado Polanco, Raquel. Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20737. short: R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage Progression, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-12-09T09:04:18Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-04-14T08:16:58Z day: '09' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SiHi doi: 10.15479/AT-ISTA-20737 file: - access_level: closed checksum: 71e0fdf4619b0d70d03657ad7348137d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: rcasadop date_created: 2025-12-11T09:28:09Z date_updated: 2025-12-11T11:18:37Z file_id: '20793' file_name: 2025_CasadoPolanco_Raquel_Thesis.docx file_size: 78207207 relation: source_file - access_level: closed checksum: 58cf2f25c33567723bc754a019c3e396 content_type: application/pdf creator: rcasadop date_created: 2025-12-11T09:28:04Z date_updated: 2025-12-11T09:28:04Z embargo: 2026-12-01 embargo_to: open_access file_id: '20794' file_name: 2025_CasadoPolanco_Raquel_Thesis.pdf file_size: 6261874 relation: main_file file_date_updated: 2025-12-11T11:18:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-20737 has_accepted_license: '1' keyword: - NOTCH - radial glial progenitor - lineage progression - cortical development language: - iso: eng month: '12' oa_version: Published Version page: '133' project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication_identifier: isbn: - 978-3-99078-072-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 title: Role of NOTCH signaling in radial glial progenitor lineage progression type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20741' abstract: - lang: eng text: "Life on Earth emerged when biomacromolecules were membrane-enclosed in a confined space where many essential chemical reactions were more likely to happen and thereby accelerate evolution. These kinds of membranes separated internal reactions from the outside chaos while staying flexible so that those primordial cells can move, adopt their shape and, most importantly, propagate. Such membrane plasticity still remains a defining feature of all modern cell types. This remarkable ability to change their shape is most prominently observed during their propagation (i.e., cell division). Throughout division, a cell undergoes drastic change in its shape, usually at the middle of the cell, pulling the two opposite membrane sides inward, closer to each other, and, finally, culminating in pinching off to separate the cell into two daughter cells. To achieve this, a cell needs to employ a protein machinery, usually termed divisome, that can coordinate all necessary intracellular processes with membrane remodelling and synthesis of other extracellular structures that decorate a cell. The focus of this dissertation is a membrane-remodelling FtsZ system that is present across all domains of life. FtsZ forms filaments that further self-organize into ring-like structures at the cell septum and together with other division proteins perform cell envelope synthesis and constriction. However, there are still knowledge gaps in our mechanistic understanding of division in both archaea and bacteria. My work presented in this dissertation centres around a simple yet not well understood question: How is the divisome positioned correctly at the mid-cell? To achieve the proper positioning, the divisome needs to (i) be recruited to the mid-cell and (ii) localized orthogonally to the long cell axis. I tackle these processes in two different systems by applying an in vitro biochemical bottom-up reconstitution approach. I use purified components of Haloferax volcanii and Escherichia coli divisome to explore how divisome is recruited to the mid-cell in archaea and how the Z-ring positions orthogonally to the long cell axis in bacteria, respectively. \r\n\r\nFirstly, I collaborate with archaeal cell and structural biologists to explore the assembly of early division proteins in two FtsZ-containing archaeon H. volcanii, a standard model system for understudied archaeal organisms. I particularly address the hierarchy of interactions that allow a tripartite complex formation (SepF-CdpB1-CdpB2) and how the hierarchy of interactions ultimately leads to the recruitment of FtsZ filaments to the septum. This part of work has been published in (Nußbaum et al., 2024). In collaboration with evolutionary biologists, I shed light on ancient features that archaeal divisome has retained to this day and also speculate on a property that it might have lost during the course of evolution. \r\n\r\nNext, I switch my attention to E. coli divisome. Particularly, I address the FtsZ’s intrinsic biophysical property that drives the Z-ring diameter, and thereby the perpendicular orientation of the Z-ring to the long cell axis based on suggested membrane curvature sensing mechanism (Vanhille-Campos et al., 2024). This property allows formation of different Z-ring diameters that match the variety of cell diameters present in prokaryotes. The results showcase that the distribution of charged amino acids in the intrinsically disordered linker at the C-terminus (CTL) of FtsZ is the major determining factor of Z-ring diameter with inter-CTL interactions as an underlying mechanism. \r\n\r\nFinally, I thoroughly explain the methodology I used to address the abovementioned projects, and I finish with a discussion on how early archaeal divisome assembly and curvature sensing mechanism in bacteria, at first sight unrelated topics, are interconnected and important groundwork for both fundamental and translational research. " acknowledged_ssus: - _id: Bio alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marko full_name: Kojic, Marko id: 73e7ecd4-dc85-11ea-9058-88a16394b160 last_name: Kojic orcid: 0000-0001-7244-8128 citation: ama: Kojic M. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. 2025. doi:10.15479/AT-ISTA-20741 apa: Kojic, M. (2025). Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20741 chicago: Kojic, Marko. “Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20741. ieee: M. Kojic, “Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria,” Institute of Science and Technology Austria, 2025. ista: Kojic M. 2025. Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria. Institute of Science and Technology Austria. mla: Kojic, Marko. Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20741. short: M. Kojic, Towards Understanding the Assembly Mechanisms of the Z-Ring in Archaea and Bacteria, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-12-09T13:08:11Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-04-07T12:27:58Z day: '09' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: MaLo doi: 10.15479/AT-ISTA-20741 file: - access_level: closed checksum: a3643d07e93134b2490a566b02a4517d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mkojic date_created: 2025-12-10T13:09:58Z date_updated: 2025-12-10T13:09:58Z file_id: '20774' file_name: 2025_marko_kojic_thesis.docx file_size: 142876975 relation: source_file - access_level: open_access checksum: 0a096f0af6ccc3a8329d5bb8797ad533 content_type: application/pdf creator: mkojic date_created: 2025-12-10T13:09:38Z date_updated: 2025-12-10T13:09:38Z file_id: '20775' file_name: 2025_marko_kojic_thesis.pdf file_size: 8597045 relation: main_file success: 1 file_date_updated: 2025-12-10T13:09:58Z fulldoi: https://doi.org/10.15479/AT-ISTA-20741 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication_identifier: isbn: - 978-3-99078-073-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '15118' relation: part_of_dissertation status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Towards understanding the assembly mechanisms of the Z-ring in Archaea and Bacteria 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 OA_type: gold _id: '22120' article_number: EGU25-17446 article_processing_charge: No author: - first_name: José M full_name: Muñoz Hermosilla, José M id: e1037a6d-646e-11ef-b402-e0ed9ab0901e last_name: Muñoz Hermosilla orcid: 0000-0002-1990-8508 - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Florian full_name: Hardmeier, Florian last_name: Hardmeier - first_name: Juan Vicente full_name: Melo Velasco, Juan Vicente id: 2611dec0-b9c6-11ed-9bea-a81c2b17a549 last_name: Melo Velasco - first_name: Guillaume full_name: Jouvet, Guillaume last_name: Jouvet - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Muñoz Hermosilla JM, Miles E, McCarthy M, et al. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In: EGU General Assembly 2025. European Geosciences Union; 2025. doi:10.5194/egusphere-egu25-17446' apa: 'Muñoz Hermosilla, J. M., Miles, E., McCarthy, M., Hardmeier, F., Melo Velasco, J. V., Jouvet, G., & Pellicciotti, F. (2025). Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. In EGU General Assembly 2025. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu25-17446' chicago: Muñoz Hermosilla, José M, Evan Miles, Michael McCarthy, Florian Hardmeier, Juan Vicente Melo Velasco, Guillaume Jouvet, and Francesca Pellicciotti. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” In EGU General Assembly 2025. European Geosciences Union, 2025. https://doi.org/10.5194/egusphere-egu25-17446. ieee: J. M. Muñoz Hermosilla et al., “Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier,” in EGU General Assembly 2025, Vienna, Austria & Virtual, 2025. ista: Muñoz Hermosilla JM, Miles E, McCarthy M, Hardmeier F, Melo Velasco JV, Jouvet G, Pellicciotti F. 2025. Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier. EGU General Assembly 2025. EGU General Assembly, EGU25-17446. mla: Muñoz Hermosilla, José M., et al. “Towards Reconstructing Debris Supply to Reproduce the Historic Changes in Debris Extent at a Swiss Glacier.” EGU General Assembly 2025, EGU25-17446, European Geosciences Union, 2025, doi:10.5194/egusphere-egu25-17446. short: J.M. Muñoz Hermosilla, E. Miles, M. McCarthy, F. Hardmeier, J.V. Melo Velasco, G. Jouvet, F. Pellicciotti, in:, EGU General Assembly 2025, European Geosciences Union, 2025. conference: end_date: 2025-05-02 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2025-04-27 date_created: 2026-06-22T12:17:47Z date_published: 2025-05-14T00:00:00Z date_updated: 2026-07-02T06:41:43Z day: '14' ddc: - '550' department: - _id: FrPe - _id: GradSch doi: 10.5194/egusphere-egu25-17446 fulldoi: https://doi.org/10.5194/egusphere-egu25-17446 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.5194/egusphere-egu25-17446 month: '05' oa: 1 oa_version: Published Version publication: EGU General Assembly 2025 publication_status: published publisher: European Geosciences Union status: public title: Towards reconstructing debris supply to reproduce the historic changes in debris extent at a Swiss glacier 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_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20441' abstract: - lang: eng text: "Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:10.15479/AT-ISTA-20441 apa: Naik, S. (2025). Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20441 chicago: Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20441. ieee: S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025. ista: Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria. mla: Naik, Suyash. Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20441. short: S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-10T14:58:30Z date_published: 2025-10-12T00:00:00Z date_updated: 2026-07-06T12:51:41Z day: '12' ddc: - '596' - '597' - '532' degree_awarded: PhD department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-20441 file: - access_level: open_access checksum: 2892f04d4a5c18677871c3e06ac1244a content_type: application/pdf creator: snaik date_created: 2025-10-28T13:10:08Z date_updated: 2025-10-28T13:10:08Z file_id: '20567' file_name: Thesis_PDFA_.pdf file_size: 6846189 relation: main_file success: 1 - access_level: open_access checksum: 15934d4465cd0e9b7c32678da9a33a2f content_type: application/zip creator: snaik date_created: 2025-10-28T13:10:26Z date_updated: 2025-10-28T13:10:26Z file_id: '20568' file_name: Thesis.zip file_size: 8839300 relation: source_file file_date_updated: 2025-10-28T13:10:26Z fulldoi: https://doi.org/10.15479/AT-ISTA-20441 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa: 1 oa_version: Published Version page: '105' project: - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 25AA5F24-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W 1250-B20 name: Nano-Analytics of Cellular Systems publication_identifier: isbn: - 978-3-99078-069-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20465' relation: part_of_dissertation status: public status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 title: Keratins act as global coordinators of tissue spreading through mechanosensitive feedback tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20920' abstract: - lang: eng text: "Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified in time much less than T.\r\n\r\nWe first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.\r\n\r\nTogether, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 citation: ama: Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:10.15479/AT-ISTA-20920 apa: Hoffmann, C. (2025). Theory and applications of verifiable delay functions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20920 chicago: Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20920. ieee: C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute of Science and Technology Austria, 2025. ista: Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute of Science and Technology Austria. mla: Hoffmann, Charlotte. Theory and Applications of Verifiable Delay Functions. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20920. short: C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2026-01-02T10:46:47Z date_published: 2025-12-31T00:00:00Z date_updated: 2026-07-06T13:15:27Z day: '31' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/AT-ISTA-20920 file: - access_level: closed checksum: 8a099fbf54963bd0be38f7ce73658682 content_type: application/x-zip-compressed creator: choffman date_created: 2026-01-02T10:39:16Z date_updated: 2026-01-02T10:39:16Z file_id: '20921' file_name: 2025_Hoffmann_Charlotte_Source.zip file_size: 8355494 relation: source_file - access_level: open_access checksum: 9521c07bfb2bb5b14a49c09fcfc96474 content_type: application/pdf creator: choffman date_created: 2026-01-02T10:39:26Z date_updated: 2026-01-02T10:39:26Z file_id: '20922' file_name: 2025_Hoffmann_Charlotte_Thesis.pdf file_size: 2258804 relation: main_file success: 1 file_date_updated: 2026-01-02T10:39:26Z fulldoi: https://doi.org/10.15479/AT-ISTA-20920 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '116' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13143' relation: part_of_dissertation status: public - id: '12176' relation: part_of_dissertation status: public - id: '20556' relation: earlier_version status: public - id: '19778' relation: part_of_dissertation status: public - id: '20701' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Theory and applications of verifiable delay functions tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20556' abstract: - lang: eng text: "Verifiable Delay Functions (VDFs) introduced by Boneh et al. (CRYPTO'18) are functions that require a prescribed number of sequential steps T to evaluate, yet their output can be verified in time much faster than T. Since their introduction, VDFs have gained a lot of attention due to their applications in blockchain protocols, randomness beacons, timestamping and deniability. This thesis explores the theory and applications of VDFs, focusing on enhancing their soundness, efficiency and practicality.\r\n\r\nThe only practical VDFs known to date are based on repeated squaring in hidden order groups. Consider the function VDF(x,T)=x^(2^T).\r\nThe iterated squaring assumption states that, for a random group element x, the result of VDF cannot be computed significantly faster than performing T sequential squarings if the group order is unknown. To make the result verifiable a prover can compute a proof of exponentiation (PoE) \\pi. Given \\pi, the output of VDF can be verified in time much less than T.\r\n\r\nWe first present new constructions of statistically sound proofs of exponentiation, which are an important building block in the construction of SNARKs (Succinct Non-Interactive Argument of Knowledge). Statistical soundness means that the proofs remain secure against computationally unbounded adversaries, in particular, it remains secure even when the group order is known. We thereby address limitations in previous PoE protocols which either required (non-standard) hardness assumptions or a lot of parallel repetitions. Our construction significantly reduces the proof size of statistically sound PoEs that allow for a structured exponent, which leads to better efficiency of SNARKs and other applications.\r\n\r\nSecondly, we introduce improved batching techniques for PoEs, which allow multiple proofs to be aggregated and verified with minimal overhead. These protocols optimize communication and computation complexity in large-scale blockchain environments and enable scalable remote benchmarking of parallel computation resources.\r\n\r\nWe then construct VDFs with enhanced properties such as zero-knowledge and watermarkability. It was shown by Arun, Bonneau and Clark (ASIACRYPT'22) that these features enable new cryptographic primitives called short-lived proofs and signatures. The validity of such proofs and signatures expires after a predefined amount of time T, i.e., they are deniable after time T. Our constructions improve upon the constructions by Arun, Bonneau and Clark in several dimensions (faster forging times, arguably weaker assumptions).\r\n\r\nFinally, we apply PoEs in the realm of primality testing, providing cryptographically sound proofs of non-primality for large Proth numbers. This work gives a surprising application of VDFs in the area of computational number theory.\r\n\r\nTogether, our contributions advance both the theoretical foundations and the real-world usability of VDFs in general and in particular of PoEs, making them more adaptable and secure for current and emerging cryptographic applications." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Charlotte full_name: Hoffmann, Charlotte id: 0f78d746-dc7d-11ea-9b2f-83f92091afe7 last_name: Hoffmann orcid: 0000-0003-2027-5549 citation: ama: Hoffmann C. Theory and applications of verifiable delay functions. 2025. doi:10.15479/AT-ISTA-20556 apa: Hoffmann, C. (2025). Theory and applications of verifiable delay functions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20556 chicago: Hoffmann, Charlotte. “Theory and Applications of Verifiable Delay Functions.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20556. ieee: C. Hoffmann, “Theory and applications of verifiable delay functions,” Institute of Science and Technology Austria, 2025. ista: Hoffmann C. 2025. Theory and applications of verifiable delay functions. Institute of Science and Technology Austria. mla: Hoffmann, Charlotte. Theory and Applications of Verifiable Delay Functions. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20556. short: C. Hoffmann, Theory and Applications of Verifiable Delay Functions, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-27T14:16:56Z date_published: 2025-10-31T00:00:00Z date_updated: 2026-07-06T13:15:27Z day: '31' ddc: - '004' degree_awarded: PhD department: - _id: GradSch - _id: KrPi doi: 10.15479/AT-ISTA-20556 file: - access_level: closed checksum: 1fffa4e2c33dd0b9f883d615504a2858 content_type: application/pdf creator: choffman date_created: 2025-10-28T14:33:03Z date_updated: 2026-01-08T14:11:39Z file_id: '20573' file_name: 2025_Hoffmann_Charlotte_Thesis.pdf file_size: 2259304 relation: main_file - access_level: closed checksum: 076ea98a1f0a86c3bbc990b6b9460dc2 content_type: application/x-zip-compressed creator: choffman date_created: 2025-10-28T14:35:06Z date_updated: 2025-11-11T09:34:54Z file_id: '20574' file_name: 2025_Hoffmann_Charlotte_Source.zip file_size: 9987633 relation: source_file file_date_updated: 2026-01-08T14:11:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-20556 has_accepted_license: '1' language: - iso: eng month: '10' oa_version: Published Version page: '116' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13143' relation: part_of_dissertation status: public - id: '12176' relation: part_of_dissertation status: public - id: '20920' relation: later_version status: public - id: '19778' relation: part_of_dissertation status: public - id: '20701' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Theory and applications of verifiable delay functions tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '20101' abstract: - lang: eng text: 'Evading imminent threat from predators is critical for animal survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours remains poorly understood1,2,3,4. Here we find that two sister species of deer mice (genus Peromyscus)5 show different responses to the same looming stimulus: Peromyscus maniculatus, which occupies densely vegetated habitats, predominantly escapes, whereas the open field specialist, Peromyscus polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal grey (dPAG) in driving behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus, and their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain.' acknowledgement: The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J. Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice on optogenetic experiments; A. Calzoni for help aligning histological sections to a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with the electrophysiology analysis; I. Vlaemick for help with whole cell experiments; R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan Brockman Williamson Fellowship. This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute, of which H.E.H. was an Investigator. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Felix full_name: Baier, Felix last_name: Baier - first_name: Katja full_name: Reinhard, Katja last_name: Reinhard - first_name: Bram full_name: Nuttin, Bram last_name: Nuttin - first_name: Arnau full_name: Sans-Dublanc, Arnau last_name: Sans-Dublanc - first_name: Chen full_name: Liu, Chen last_name: Liu - first_name: Victoria full_name: Tong, Victoria last_name: Tong - first_name: Julie Stefanie full_name: Murmann, Julie Stefanie id: 1d390868-f128-11eb-9611-a0ca5f7833b5 last_name: Murmann - first_name: Keimpe full_name: Wierda, Keimpe last_name: Wierda - first_name: Karl full_name: Farrow, Karl last_name: Farrow - first_name: Hopi E. full_name: Hoekstra, Hopi E. last_name: Hoekstra citation: ama: Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. 2025;645:439-447. doi:10.1038/s41586-025-09241-2 apa: Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09241-2 chicago: Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E. Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-09241-2. ieee: F. Baier et al., “The neural basis of species-specific defensive behaviour in Peromyscus mice,” Nature, vol. 645. Springer Nature, pp. 439–447, 2025. ista: Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice. Nature. 645, 439–447. mla: Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” Nature, vol. 645, Springer Nature, 2025, pp. 439–47, doi:10.1038/s41586-025-09241-2. short: F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447. date_created: 2025-08-03T22:01:31Z date_published: 2025-07-23T00:00:00Z date_updated: 2026-07-22T06:20:09Z day: '23' ddc: - '570' department: - _id: GradSch doi: 10.1038/s41586-025-09241-2 external_id: pmid: - '40702175' file: - access_level: open_access checksum: 7ea846a7a49b3b2a248f6a27ab13d591 content_type: application/pdf creator: dernst date_created: 2025-12-30T07:39:45Z date_updated: 2025-12-30T07:39:45Z file_id: '20884' file_name: 2025_Nature_Baier.pdf file_size: 53301589 relation: main_file success: 1 file_date_updated: 2025-12-30T07:39:45Z fulldoi: https://doi.org/10.1038/s41586-025-09241-2 has_accepted_license: '1' intvolume: ' 645' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 439-447 pmid: 1 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20883' relation: research_data status: public scopus_import: '1' status: public title: The neural basis of species-specific defensive behaviour in Peromyscus mice 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: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 645 year: '2025' ... --- OA_place: repository OA_type: hybrid _id: '20883' abstract: - lang: eng text: 'Evading imminent predator threat is critical for survival. Effective defensive strategies can vary, even between closely related species. However, the neural basis of such species-specific behaviours is still poorly understood. Here we find that two sister species of deer mice (genus Peromyscus) show different responses to the same looming stimulus: P. maniculatus, which occupies densely vegetated habitats, predominantly escapes, while the open field specialist, P. polionotus, briefly freezes. This difference arises from species-specific escape thresholds, is largely context-independent, and can be triggered by both visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological recordings, we find that although visual threat activates the superior colliculus in both species, the role of the dorsal periaqueductal gray (dPAG) in driving behaviour differs. While dPAG activity scales with running speed in P. maniculatus, neural activity in the dPAG of P. polionotus correlates poorly with movement, including during visually triggered escape. Moreover, optogenetic activation of dPAG neurons elicits acceleration in P. maniculatus but not P. polionotus, while their chemogenetic inhibition during a looming stimulus delays escape onset in P. maniculatus to match that of P. polionotus. Together, we trace species-specific escape thresholds to a central circuit node, downstream of peripheral sensory neurons, localizing an ecologically relevant behavioural difference to a specific region of the mammalian brain.' article_processing_charge: No author: - first_name: Baier full_name: Felix, Baier last_name: Felix - first_name: Katja full_name: Reinhard, Katja last_name: Reinhard - first_name: Bram full_name: Nuttin, Bram last_name: Nuttin - first_name: Arnau full_name: Sans Dublanc, Arnau last_name: Sans Dublanc - first_name: Chen full_name: Liu, Chen last_name: Liu - first_name: Victoria full_name: Tong, Victoria last_name: Tong - first_name: Julie Stefanie full_name: Murmann, Julie Stefanie id: 1d390868-f128-11eb-9611-a0ca5f7833b5 last_name: Murmann - first_name: Keimpe full_name: Wierda, Keimpe last_name: Wierda - first_name: Karl full_name: Farrow, Karl last_name: Farrow - first_name: Hopi full_name: Hoekstra, Hopi last_name: Hoekstra citation: ama: Felix B, Reinhard K, Nuttin B, et al. The neural basis of species-specific defensive behaviour in Peromyscus mice. 2025. doi:10.5061/DRYAD.Q2BVQ83XC apa: Felix, B., Reinhard, K., Nuttin, B., Sans Dublanc, A., Liu, C., Tong, V., … Hoekstra, H. (2025). The neural basis of species-specific defensive behaviour in Peromyscus mice. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83XC chicago: Felix, Baier, Katja Reinhard, Bram Nuttin, Arnau Sans Dublanc, Chen Liu, Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice.” Dryad, 2025. https://doi.org/10.5061/DRYAD.Q2BVQ83XC. ieee: B. Felix et al., “The neural basis of species-specific defensive behaviour in Peromyscus mice.” Dryad, 2025. ista: Felix B, Reinhard K, Nuttin B, Sans Dublanc A, Liu C, Tong V, Murmann JS, Wierda K, Farrow K, Hoekstra H. 2025. The neural basis of species-specific defensive behaviour in Peromyscus mice, Dryad, 10.5061/DRYAD.Q2BVQ83XC. mla: Felix, Baier, et al. The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus Mice. Dryad, 2025, doi:10.5061/DRYAD.Q2BVQ83XC. short: B. Felix, K. Reinhard, B. Nuttin, A. Sans Dublanc, C. Liu, V. Tong, J.S. Murmann, K. Wierda, K. Farrow, H. Hoekstra, (2025). date_created: 2025-12-30T07:36:29Z date_published: 2025-06-23T00:00:00Z date_updated: 2026-07-22T06:20:09Z day: '23' department: - _id: GradSch doi: 10.5061/DRYAD.Q2BVQ83XC fulldoi: https://doi.org/10.5061/DRYAD.Q2BVQ83XC main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.q2bvq83xc month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '20101' relation: used_in_publication status: public status: public title: The neural basis of species-specific defensive behaviour in Peromyscus mice type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '21399' abstract: - lang: eng text: We report on the Equational Theories Project (ETP), an online collaborative pilot project to explore new ways to collaborate in mathematics with machine assistance. The project successfully determined all 22 028 942 edges of the implication graph between the 4694 simplest equational laws on magmas, by a combination of human-generated and automated proofs, all validated by the formal proof assistant language Lean. As a result of this project, several new constructions of magmas satisfying specific laws were discovered, and several auxiliary questions were also addressed, such as the effect of restricting attention to finite magmas. article_number: '2512.07087' article_processing_charge: No arxiv: 1 author: - first_name: Matthew full_name: Bolan, Matthew last_name: Bolan - first_name: Joachim full_name: Breitner, Joachim last_name: Breitner - first_name: Jose full_name: Brox, Jose last_name: Brox - first_name: Nicholas full_name: Carlini, Nicholas last_name: Carlini - first_name: Mario full_name: Carneiro, Mario last_name: Carneiro - first_name: Floris van full_name: Doorn, Floris van last_name: Doorn - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Andrés full_name: Goens, Andrés last_name: Goens - first_name: Aaron full_name: Hill, Aaron last_name: Hill - first_name: Harald full_name: Husum, Harald last_name: Husum - first_name: Hernán Ibarra full_name: Mejia, Hernán Ibarra last_name: Mejia - first_name: Zoltan A. full_name: Kocsis, Zoltan A. last_name: Kocsis - first_name: Bruno Le full_name: Floch, Bruno Le last_name: Floch - first_name: Amir full_name: Bar-on, Amir last_name: Bar-on - first_name: Lorenzo full_name: Luccioli, Lorenzo last_name: Luccioli - first_name: Douglas full_name: McNeil, Douglas last_name: McNeil - first_name: Alex full_name: Meiburg, Alex last_name: Meiburg - first_name: Pietro full_name: Monticone, Pietro last_name: Monticone - first_name: Pace P. full_name: Nielsen, Pace P. last_name: Nielsen - first_name: Emmanuel Osalotioman full_name: Osazuwa, Emmanuel Osalotioman last_name: Osazuwa - first_name: Giovanni full_name: Paolini, Giovanni last_name: Paolini - first_name: Marco full_name: Petracci, Marco last_name: Petracci - first_name: Bernhard full_name: Reinke, Bernhard last_name: Reinke - first_name: David full_name: Renshaw, David last_name: Renshaw - first_name: Marcus full_name: Rossel, Marcus last_name: Rossel - first_name: Cody full_name: Roux, Cody last_name: Roux - first_name: Jérémy full_name: Scanvic, Jérémy last_name: Scanvic - first_name: Shreyas full_name: Srinivas, Shreyas last_name: Srinivas - first_name: Anand Rao full_name: Tadipatri, Anand Rao last_name: Tadipatri - first_name: Terence full_name: Tao, Terence last_name: Tao - first_name: Vlad full_name: Tsyrklevich, Vlad last_name: Tsyrklevich - first_name: Fernando full_name: Vaquerizo-Villar, Fernando last_name: Vaquerizo-Villar - first_name: Daniel full_name: Weber, Daniel last_name: Weber - first_name: Fan full_name: Zheng, Fan last_name: Zheng citation: ama: 'Bolan M, Breitner J, Brox J, et al. The equational theories project: Advancing collaborative mathematical research at scale. arXiv. doi:10.48550/arXiv.2512.07087' apa: 'Bolan, M., Breitner, J., Brox, J., Carlini, N., Carneiro, M., Doorn, F. van, … Zheng, F. (n.d.). The equational theories project: Advancing collaborative mathematical research at scale. arXiv. https://doi.org/10.48550/arXiv.2512.07087' chicago: 'Bolan, Matthew, Joachim Breitner, Jose Brox, Nicholas Carlini, Mario Carneiro, Floris van Doorn, Martin Dvorak, et al. “The Equational Theories Project: Advancing Collaborative Mathematical Research at Scale.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2512.07087.' ieee: 'M. Bolan et al., “The equational theories project: Advancing collaborative mathematical research at scale,” arXiv. .' ista: 'Bolan M, Breitner J, Brox J, Carlini N, Carneiro M, Doorn F van, Dvorak M, Goens A, Hill A, Husum H, Mejia HI, Kocsis ZA, Floch BL, Bar-on A, Luccioli L, McNeil D, Meiburg A, Monticone P, Nielsen PP, Osazuwa EO, Paolini G, Petracci M, Reinke B, Renshaw D, Rossel M, Roux C, Scanvic J, Srinivas S, Tadipatri AR, Tao T, Tsyrklevich V, Vaquerizo-Villar F, Weber D, Zheng F. The equational theories project: Advancing collaborative mathematical research at scale. arXiv, 2512.07087.' mla: 'Bolan, Matthew, et al. “The Equational Theories Project: Advancing Collaborative Mathematical Research at Scale.” ArXiv, 2512.07087, doi:10.48550/arXiv.2512.07087.' short: M. Bolan, J. Breitner, J. Brox, N. Carlini, M. Carneiro, F. van Doorn, M. Dvorak, A. Goens, A. Hill, H. Husum, H.I. Mejia, Z.A. Kocsis, B.L. Floch, A. Bar-on, L. Luccioli, D. McNeil, A. Meiburg, P. Monticone, P.P. Nielsen, E.O. Osazuwa, G. Paolini, M. Petracci, B. Reinke, D. Renshaw, M. Rossel, C. Roux, J. Scanvic, S. Srinivas, A.R. Tadipatri, T. Tao, V. Tsyrklevich, F. Vaquerizo-Villar, D. Weber, F. Zheng, ArXiv (n.d.). das_tickbox: '1' date_created: 2026-03-04T12:00:16Z date_published: 2025-12-16T00:00:00Z date_updated: 2026-07-22T06:35:39Z day: '16' department: - _id: GradSch - _id: VlKo doi: 10.48550/arXiv.2512.07087 external_id: arxiv: - '2512.07087' fulldoi: https://doi.org/10.48550/arXiv.2512.07087 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2512.07087 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'The equational theories project: Advancing collaborative mathematical research at scale' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: repository OA_type: green _id: '21858' abstract: - lang: eng text: "The recent surge in high-quality open-source Generative AI text models (colloquially: LLMs), as well as efficient finetuning techniques, have opened the possibility of creating high-quality personalized models that generate text attuned to a specific individual’s needs and are capable of credibly imitating their writing style by refining an open-source model with that person’s own data. The technology to create such models is accessible to private individuals, and training and running such models can be done cheaply on consumer-grade hardware. While these advancements are a huge gain for usability and privacy, this position paper argues that the practical feasibility of impersonating specific individuals also introduces novel safety risks. For instance, this technology enables the creation of phishing emails\r\nor fraudulent social media accounts, based on small amounts of publicly available text, or by the individuals themselves to escape AI text detection. We further argue that these risks are complementary to—and distinct from—the much-discussed risks of other impersonation attacks such as image, voice, or video deepfakes, and are not adequately addressed by the larger research community, or the current generation of open- and closed-source models." acknowledgement: "This research was supported by the Scientific Service Units (SSU) of IST Austria through resources\r\nprovided by Scientific Computing (SciComp). EI was supported in part by the FWF DK VGSCO,\r\ngrant agreement number W1260-N35. AJ was supported in part by ERC Proof-of-Concept Grant\r\nFastML, grant agreement 101158077." article_processing_charge: No arxiv: 1 author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Andrej full_name: Jovanovic, Andrej last_name: Jovanovic - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Iofinova EB, Jovanovic A, Alistarh D-A. Position: It’s time to act on the risk of efficient personalized text generation. arXiv. doi:10.48550/arXiv.2502.06560' apa: 'Iofinova, E. B., Jovanovic, A., & Alistarh, D.-A. (n.d.). Position: It’s time to act on the risk of efficient personalized text generation. arXiv. https://doi.org/10.48550/arXiv.2502.06560' chicago: 'Iofinova, Eugenia B, Andrej Jovanovic, and Dan-Adrian Alistarh. “Position: It’s Time to Act on the Risk of Efficient Personalized Text Generation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2502.06560.' ieee: 'E. B. Iofinova, A. Jovanovic, and D.-A. Alistarh, “Position: It’s time to act on the risk of efficient personalized text generation,” arXiv. .' ista: 'Iofinova EB, Jovanovic A, Alistarh D-A. Position: It’s time to act on the risk of efficient personalized text generation. arXiv, 10.48550/arXiv.2502.06560.' mla: 'Iofinova, Eugenia B., et al. “Position: It’s Time to Act on the Risk of Efficient Personalized Text Generation.” ArXiv, doi:10.48550/arXiv.2502.06560.' short: E.B. Iofinova, A. Jovanovic, D.-A. Alistarh, ArXiv (n.d.). corr_author: '1' date_created: 2026-05-11T08:55:23Z date_published: 2025-06-02T00:00:00Z date_updated: 2026-07-27T12:50:03Z day: '02' department: - _id: GradSch - _id: DaAl doi: 10.48550/arXiv.2502.06560 external_id: arxiv: - '2502.06560' fulldoi: https://doi.org/10.48550/arXiv.2502.06560 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2502.06560 month: '06' oa: 1 oa_version: Preprint project: - _id: 8e35c14b-16d5-11f0-9cad-a3fc35339161 grant_number: '101158077' name: 'FastML: Efficient and Cost-Effective Distributed Machine Learning' - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication: arXiv publication_status: draft related_material: record: - id: '21854' relation: dissertation_contains status: public status: public title: 'Position: It''s time to act on the risk of efficient personalized text generation' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '21144' abstract: - lang: eng text: 'This paper deals with the algorithmic aspects of solving feasibility problems of semidefinite programming (SDP), aka linear matrix inequalities (LMIs). Since in some SDP instances all feasible solutions have irrational entries, numerical solvers that work with rational numbers can only find an approximate solution. We study the following question: Is it possible to certify feasibility of a given SDP using an approximate solution that is sufficiently close to some exact solution? Existing approaches make the assumption that there exist rational feasible solutions (and use techniques such as rounding and lattice reduction algorithms). We propose an alternative approach that does not need this assumption. More specifically, we show how to construct a system of polynomial equations whose set of real solutions is guaranteed to have an isolated correct solution (assuming that the target exact solution is maximum-rank). This allows, in particular, for us to use algorithms from real algebraic geometry for solving systems of polynomial equations, yielding a hybrid (or symbolic-numerical) method for SDPs. We experimentally compare it with a pure symbolic method in [D. Henrion, S. Naldi, and M. Safey El Din, SIAM J. Optim., 26 (2016), pp. 2512–2539]; the hybrid method was able to certify feasibility of many SDP instances on which the aforementioned paper failed. Our approach may have further applications, such as refining an approximate solution using methods of numerical algebraic geometry for systems of polynomial equations.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Simone full_name: Naldi, Simone last_name: Naldi - first_name: Jeferson full_name: Zapata, Jeferson id: 00223538-AF8F-11E9-A4C7-F729E6697425 last_name: Zapata citation: ama: Kolmogorov V, Naldi S, Zapata J. Certifying solutions of degenerate semidefinite programs. SIAM Journal on Optimization. 2025;35(3):1630-1654. doi:10.1137/24m1664691 apa: Kolmogorov, V., Naldi, S., & Zapata, J. (2025). Certifying solutions of degenerate semidefinite programs. SIAM Journal on Optimization. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/24m1664691 chicago: Kolmogorov, Vladimir, Simone Naldi, and Jeferson Zapata. “Certifying Solutions of Degenerate Semidefinite Programs.” SIAM Journal on Optimization. Society for Industrial and Applied Mathematics, 2025. https://doi.org/10.1137/24m1664691. ieee: V. Kolmogorov, S. Naldi, and J. Zapata, “Certifying solutions of degenerate semidefinite programs,” SIAM Journal on Optimization, vol. 35, no. 3. Society for Industrial and Applied Mathematics, pp. 1630–1654, 2025. ista: Kolmogorov V, Naldi S, Zapata J. 2025. Certifying solutions of degenerate semidefinite programs. SIAM Journal on Optimization. 35(3), 1630–1654. mla: Kolmogorov, Vladimir, et al. “Certifying Solutions of Degenerate Semidefinite Programs.” SIAM Journal on Optimization, vol. 35, no. 3, Society for Industrial and Applied Mathematics, 2025, pp. 1630–54, doi:10.1137/24m1664691. short: V. Kolmogorov, S. Naldi, J. Zapata, SIAM Journal on Optimization 35 (2025) 1630–1654. date_created: 2026-02-05T13:33:05Z date_published: 2025-09-01T00:00:00Z date_updated: 2026-07-27T14:30:41Z day: '01' department: - _id: VlKo - _id: GradSch doi: 10.1137/24m1664691 external_id: arxiv: - '2405.13625' fulldoi: https://doi.org/10.1137/24m1664691 intvolume: ' 35' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.13625 month: '09' oa: 1 oa_version: Preprint page: 1630-1654 publication: SIAM Journal on Optimization publication_identifier: eissn: - 1095-7189 issn: - 1052-6234 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '21957' relation: dissertation_contains status: public status: public title: Certifying solutions of degenerate semidefinite programs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 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: 2026-07-29T08:59:30Z day: '13' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: MiLe doi: 10.15479/AT-ISTA-19393 file: - access_level: open_access checksum: d3ab25782c7ea38ce9910e57d25f6733 content_type: application/pdf creator: vkarle date_created: 2025-03-12T12:56:46Z date_updated: 2025-03-12T12:56:46Z file_id: '19394' file_name: thesis_final.pdf file_size: 10625143 relation: main_file success: 1 - access_level: closed checksum: 3ccfb0aeba4d860d71e18347913034e4 content_type: application/zip creator: vkarle date_created: 2025-03-13T13:15:10Z date_updated: 2025-03-20T08:02:35Z file_id: '19400' file_name: thesis.zip file_size: 23119202 relation: source_file file_date_updated: 2025-03-20T08:02:35Z fulldoi: https://doi.org/10.15479/AT-ISTA-19393 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '192' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14851' relation: part_of_dissertation status: public - id: '12788' relation: part_of_dissertation status: public - id: '9903' relation: part_of_dissertation status: public - id: '15004' relation: part_of_dissertation status: public - id: '19425' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Non-equilibrium topological phases with periodically driven molecules and quantum rotors tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '20735' abstract: - lang: eng text: "Left–right alternation is a defining feature of spinal locomotor circuits, yet the level of neuronal\r\ndetail required to generate and maintain this pattern remains unclear. This thesis investigates how\r\nmodels spanning multiple levels of abstraction—from biophysically detailed Hodgkin–Huxley (HH)\r\nneurons to adaptive integrate–and–fire (I&F) formulations and synfire-chain modules—can account\r\nfor the generation of fictive swimming in the spinal cord of the Xenopus laevis tadpole. The guiding\r\nhypothesis is that a small set of neuronal mechanisms is sufficient to reproduce the essential features\r\nof rhythmic alternation, and that moving between modeling scales helps distinguish core principles\r\nfrom biological detail.\r\nA minimal bilateral HH network comprising only four canonical neuron classes—excitatory\r\ndescending interneurons (dINs), inhibitory commissural interneurons (cINs), ipsilateral inhibitory\r\ninterneurons (aINs) and motoneurons—served as a biophysical proof of concept. Tuned to reproduce\r\nexperimentally observed firing modes, the model demonstrated that rebound-prone dIN excitability,\r\ncontralateral inhibition and modest electrical coupling are sufficient to generate stable alternating\r\nactivity, even in very small networks. These results motivated the transition to simpler models\r\ncapable of efficient analysis and scaling.\r\nAdaptive exponential I&F (AdEx) neurons were calibrated to physiological recordings using\r\nsimulation-based inference, yielding tonic and phasic/rebound templates that preserved the key\r\ndynamical signatures of the HH model. Phase-plane analysis clarified the mechanisms underlying\r\nsingle-spike responses and rebound firing in dINs. At network level, the I&F models robustly\r\nreproduced left–right alternation, while highlighting constraints on synaptic kinetics and adaptation\r\nneeded to avoid multi-spike responses.\r\nFinally, a synfire-chain framework provided a complementary, timing-centric perspective, demonstrating how precise spike synchrony, synaptic delays and minimal inhibitory coupling can generate\r\nalternating left–right sequences in a feedforward setting. Together, these approaches converge on a\r\ncommon conclusion: rebound-prone ipsilateral excitation combined with precisely timed contralateral inhibition constitutes a sufficient substrate for alternating spinal rhythms.\r\nBy integrating bottom-up and top-down modeling strategies, this thesis provides a unified, extensible framework for studying spinal pattern generation. The results show that essential locomotor\r\ndynamics can be captured across multiple abstraction levels, offering both mechanistic insight and\r\npractical tools for future data-driven investigations of spinal circuit development, robustness and\r\nmodulation." alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Alexia C full_name: Wilson, Alexia C id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d last_name: Wilson orcid: 0000-0001-6191-1367 citation: ama: 'Wilson AC. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. 2025. doi:10.15479/AT-ISTA-20735' apa: 'Wilson, A. C. (2025). Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20735' chicago: 'Wilson, Alexia C. “Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20735.' ieee: 'A. C. Wilson, “Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog,” Institute of Science and Technology Austria, 2025.' ista: 'Wilson AC. 2025. Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog. Institute of Science and Technology Austria.' mla: 'Wilson, Alexia C. Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20735.' short: 'A.C. Wilson, Modelling the Spinal Cord of a Tadpole: Exploring Different Ways to Model the Spinal Cord in the Xenopus Frog, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-12-08T09:49:41Z date_published: 2025-12-09T00:00:00Z date_updated: 2026-07-29T12:55:12Z day: '09' ddc: - '570' - '596' - '005' degree_awarded: MS department: - _id: GradSch - _id: TiVo - _id: LoSw doi: 10.15479/AT-ISTA-20735 doi_confirm: '1' file: - access_level: closed checksum: 9e3b6b73f8cbec2c3687d17fe8e30410 content_type: application/zip creator: awilson date_created: 2026-01-01T17:26:30Z date_updated: 2026-01-02T13:05:07Z file_id: '20919' file_name: tadpoleAdEx.zip file_size: 566072368 relation: source_file - access_level: open_access checksum: 13f4c0d33923e9d5c9d56731345cf21d content_type: application/pdf creator: awilson date_created: 2026-01-04T12:58:49Z date_updated: 2026-01-04T12:58:49Z file_id: '20923' file_name: Masters_Thesis_Alexia_Wilson_FINAL_pdfA.pdf file_size: 7170097 relation: main_file success: 1 file_date_updated: 2026-01-04T12:58:49Z fulldoi: https://doi.org/10.15479/AT-ISTA-20735 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '110' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13097' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 title: 'Modelling the spinal cord of a tadpole: Exploring different ways to model the spinal cord in the Xenopus frog' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '21398' abstract: - lang: eng text: Seymour's decomposition theorem is a hallmark result in matroid theory presenting a structural characterization of the class of regular matroids. Formalization of matroid theory faces many challenges, most importantly that only a limited number of notions and results have been implemented so far. In this work, we formalize the proof of the forward (composition) direction of Seymour's theorem for regular matroids. To this end, we develop a library in Lean 4 that implements definitions and results about totally unimodular matrices, vector matroids, their standard representations, regular matroids, and 1-, 2-, and 3-sums of matrices and binary matroids given by their standard representations. Using this framework, we formally state Seymour's decomposition theorem and implement a formally verified proof of the composition direction in the setting where the matroids have finite rank and may have infinite ground sets. acknowledgement: "We would like to dedicate the paper to the memory of Klaus Truemper, whose monograph Matroid Decomposition [12]\r\nlaid the foundation for our entire work." article_number: '2509.20539' article_processing_charge: No arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Tristan full_name: Figueroa-Reid, Tristan last_name: Figueroa-Reid - first_name: Rida full_name: Hamadani, Rida last_name: Hamadani - first_name: Byung-Hak full_name: Hwang, Byung-Hak last_name: Hwang - first_name: Evgenia full_name: Karunus, Evgenia last_name: Karunus - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Alexander full_name: Meiburg, Alexander last_name: Meiburg - first_name: Alexander full_name: Nelson, Alexander last_name: Nelson - first_name: Peter full_name: Nelson, Peter last_name: Nelson - first_name: Mark full_name: Sandey, Mark last_name: Sandey - first_name: Ivan full_name: Sergeev, Ivan id: ca3c9187-9a72-11ee-a009-8af825d896b0 last_name: Sergeev orcid: 0009-0004-9145-8785 citation: ama: Dvorak M, Figueroa-Reid T, Hamadani R, et al. Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv. doi:10.48550/arXiv.2509.20539 apa: Dvorak, M., Figueroa-Reid, T., Hamadani, R., Hwang, B.-H., Karunus, E., Kolmogorov, V., … Sergeev, I. (n.d.). Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv. https://doi.org/10.48550/arXiv.2509.20539 chicago: Dvorak, Martin, Tristan Figueroa-Reid, Rida Hamadani, Byung-Hak Hwang, Evgenia Karunus, Vladimir Kolmogorov, Alexander Meiburg, et al. “Composition Direction of Seymour’s Theorem for Regular Matroids — Formally Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2509.20539. ieee: M. Dvorak et al., “Composition direction of Seymour’s theorem for regular matroids — Formally verified,” arXiv. . ista: Dvorak M, Figueroa-Reid T, Hamadani R, Hwang B-H, Karunus E, Kolmogorov V, Meiburg A, Nelson A, Nelson P, Sandey M, Sergeev I. Composition direction of Seymour’s theorem for regular matroids — Formally verified. arXiv, 2509.20539. mla: Dvorak, Martin, et al. “Composition Direction of Seymour’s Theorem for Regular Matroids — Formally Verified.” ArXiv, 2509.20539, doi:10.48550/arXiv.2509.20539. short: M. Dvorak, T. Figueroa-Reid, R. Hamadani, B.-H. Hwang, E. Karunus, V. Kolmogorov, A. Meiburg, A. Nelson, P. Nelson, M. Sandey, I. Sergeev, ArXiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2026-03-04T11:56:29Z date_published: 2025-09-23T00:00:00Z date_updated: 2026-07-29T12:56:51Z day: '23' department: - _id: GradSch - _id: VlKo doi: 10.48550/arXiv.2509.20539 external_id: arxiv: - '2509.20539' fulldoi: https://doi.org/10.48550/arXiv.2509.20539 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2509.20539 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '21393' relation: dissertation_contains status: public status: public title: Composition direction of Seymour's theorem for regular matroids — Formally verified type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20203' abstract: - lang: eng text: Tribocharging, or contact electrification, is the phenomenon in which two initially neutral materials exchange electric charge through contact and subsequent separation. While it is widely observed in everyday life and crucial to numerous natural processes, even the most basic aspects of tribocharging are still a mystery—what are the charge carriers involved and what drives their exchange? This work spans three separate projects that address different aspects of tribocharging. First, we introduce a novel strategy combining Finite Element Method (FEM) simulations with Kelvin Probe Force Microscopy (KPFM) to quantitatively extract surface charge density from surface voltage maps. Second, we present a simple theoretical model that allows for the existence of triboelectric cycles, under the assumption that multiple charge carrying species are involved. Third, we present experimental evidence that identical materials can spontaneously evolve into a triboelectric series, driven by contact history. Modeling this behavior enables the replication of experimental results with simulations, and even experimentally forcing the appearance of a pre-designed series by manipulating contact history. Together, the findings from these projects challenge traditional views on tribocharging, provide new tools for probing it, and open up new avenues of research—all with the hopes of bringing us closer to understanding this puzzling phenomenon. acknowledged_ssus: - _id: M-Shop - _id: NanoFab - _id: EM-Fac - _id: LifeSc - _id: ScienComp acknowledgement: "The project in Chapter 2 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 3 has received funding from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120).\r\nThe project in Chapter 4 has received financing from the European Research Council grant\r\nagreement No. 949120 under the European Union’s Horizon 2020 research and innovation\r\nprogramme. The Analytical Instrumentation Center of the TU Wien acknowledges support by\r\nthe FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state\r\nof Lower Austria and the European Regional Development Fund under grant no. WST3-F542638/004-2021.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Juan Carlos A full_name: Sobarzo Ponce, Juan Carlos A id: 4B807D68-AE37-11E9-AC72-31CAE5697425 last_name: Sobarzo Ponce citation: ama: 'Sobarzo Ponce JCA. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. 2025. doi:10.15479/AT-ISTA-20203' apa: 'Sobarzo Ponce, J. C. A. (2025). Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20203' chicago: 'Sobarzo Ponce, Juan Carlos A. “Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20203.' ieee: 'J. C. A. Sobarzo Ponce, “Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges,” Institute of Science and Technology Austria, 2025.' ista: 'Sobarzo Ponce JCA. 2025. Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges. Institute of Science and Technology Austria.' mla: 'Sobarzo Ponce, Juan Carlos A. Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20203.' short: 'J.C.A. Sobarzo Ponce, Tribocharging of Identical Insulators: Triboelectric Series, Triboelectric Cycles and Surface Charges, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-08-21T11:42:59Z date_published: 2025-08-27T00:00:00Z date_updated: 2026-07-29T13:11:25Z day: '27' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: ScWa doi: 10.15479/AT-ISTA-20203 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 661b9d3786cfc985be811befc3262bf5 content_type: application/pdf creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-27T14:50:32Z file_id: '20237' file_name: 2025_Sobarzo_JuanCarlos_Thesis.pdf file_size: 12667200 relation: main_file success: 1 - access_level: closed checksum: ca2f24e6c3b55912982521707552a0f5 content_type: application/x-zip-compressed creator: jsobarzo date_created: 2025-08-27T14:50:32Z date_updated: 2025-08-28T08:19:07Z file_id: '20238' file_name: 2025_Sobarzo_JuanCarlos_Thesis.zip file_size: 18940521 relation: source_file file_date_updated: 2025-08-28T08:19:07Z fulldoi: https://doi.org/10.15479/AT-ISTA-20203 has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '96' project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication_identifier: isbn: - 978-3-99078-062-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12109' relation: part_of_dissertation status: public - id: '15322' relation: part_of_dissertation status: public - id: '19278' relation: part_of_dissertation status: public status: public supervisor: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 title: 'Tribocharging of identical insulators: Triboelectric series, triboelectric cycles and surface charges' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20371' abstract: - lang: eng text: "Quantum mechanics reveals a world that defies classical determinism, where uncertainty, superposition, and fluctuations are fundamental aspects. Engineering devices that harness these quantum features requires not only precision, but also a deep understanding of how they interact with their surrounding environment. Superconducting circuits, which exploit\r\nmacroscopic quantum coherence in low-loss superconducting materials, provide a scalable platform for implementing such systems. Among the critical elements in these circuits, superinductors—high-impedance, dissipation-free inductive components—play a central role by suppressing charge fluctuations. They allow quantum states to be delocalized in phase space, protect qubits from environmental noise, and facilitate access to phenomena such as dual Josephson physics and ultra-strong coupling regimes. \r\nThis thesis explores two complementary implementations of high-impedance circuits: geometric superinductors, demonstrating that high impedance can be achieved beyond kinetic inductance,\r\nand Josephson junction chains, used to investigate both microwave mode properties and DC transport across the superconductor-to-insulator transition. \r\nPart I addresses geometric superinductors. Contrary to the common belief that high-impedance superconducting circuits require kinetic inductance, we demonstrate that purely geometric designs can achieve characteristic impedance exceeding the resistance quantum. By exploiting mutual coupling between adjacent turns, coil-based inductors achieve enhanced self-inductance, creating a reliable platform for qubits and resonators. Modeling, simulation, fabrication, and\r\ncharacterization confirm that these elements behave as superinductor. With low loss, high linearity, and minimal stray capacitance, these elements are reproducible, free of uncontrolled tunneling events, and capable of strong magnetic coupling. This establishes geometric superinductors as robust, single-wave-function superconducting devices suitable for hardware protected qubits and hybrid systems.\r\nPart II presents classical numerical simulations of a Quantum Phase Slip circuit to study dual Shapiro steps. The circuit consists of an ideal Quantum Phase Slip element embedded in a resistive-inductive environment with a parasitic capacitance.\r\nPart III extends the investigation of high characteristic-impedance circuit elements to one-dimensional Josephson junction chains, which act as a quantum simulator for many-body physics and the superconductor–insulator transition. Different devices are realized on both sides of the DC phase transition, showing either a supercurrent branch or Coulomb blockade at zero bias. The effect of the crossover on microwave modes, however, remains insufficiently investigated. Studying these modes provides insight into the interplay between disorder and phase-slip events. Small differences in circuit component sizes determine which side of the transition a device falls on, making these results relevant not only for fundamental understanding but also for the design of quantum devices, emphasizing the crucial role of the\r\nelectromagnetic environment in stabilizing and controlling fragile quantum states. \r\nTogether, these results illustrate how carefully engineered high characteristic-impedance elements provide a link between macroscopic circuits and the inherently uncertain quantum world, enabling experiments that probe, control, and ultimately exploit quantum fluctuations for applications in quantum information, metrology, solid state physics and beyond.\r\n\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "I also gratefully acknowledge the generous support of the NOMIS Foundation Project \"Protected\r\nStates of Quantum Matter\" and the grant from the Beyond-C consortium. Their funding\r\nmade this research possible and gave me the freedom to ask ambitious questions, and try to\r\nanswer them.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni citation: ama: 'Trioni A. High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. 2025. doi:10.15479/AT-ISTA-20371' apa: 'Trioni, A. (2025). High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20371' chicago: 'Trioni, Andrea. “High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20371.' ieee: 'A. Trioni, “High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains,” Institute of Science and Technology Austria, 2025.' ista: 'Trioni A. 2025. High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains. Institute of Science and Technology Austria.' mla: 'Trioni, Andrea. High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20371.' short: 'A. Trioni, High-Impedance Quantum Circuits for Mesoscopic Physics: Geometric Superinductors and Insulating Josephson Chains, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-23T09:57:57Z date_published: 2025-09-23T00:00:00Z date_updated: 2026-07-29T13:12:10Z day: '23' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-20371 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 6fb925648dfa5f4384814c552ee2f099 content_type: application/pdf creator: atrioni date_created: 2025-09-25T07:15:05Z date_updated: 2025-09-25T14:25:31Z file_id: '20392' file_name: 2025_Trioni_Andrea_Thesis.pdf file_size: 22351676 relation: main_file - access_level: closed checksum: 619dc614bdfbf3999b76ac8890b2cebd content_type: application/x-zip-compressed creator: atrioni date_created: 2025-09-25T14:45:43Z date_updated: 2025-09-26T07:20:48Z file_id: '20396' file_name: 2025_Trioni_Andrea_Thesis.zip file_size: 60079009 relation: source_file file_date_updated: 2025-09-26T07:20:48Z fulldoi: https://doi.org/10.15479/AT-ISTA-20371 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '202' project: - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: isbn: - 978-3-99078-067-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8755' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: 'High-impedance quantum circuits for mesoscopic physics: Geometric superinductors and insulating Josephson Chains' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20339' abstract: - lang: eng text: "This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights.\r\n\r\nWe first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations.\r\n\r\nIn the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gianluca full_name: Tasinato, Gianluca id: 0433290C-AF8F-11E9-A4C7-F729E6697425 last_name: Tasinato citation: ama: 'Tasinato G. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. 2025. doi:10.15479/AT-ISTA-20339' apa: 'Tasinato, G. (2025). Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20339' chicago: 'Tasinato, Gianluca. “Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20339.' ieee: 'G. Tasinato, “Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems,” Institute of Science and Technology Austria, 2025.' ista: 'Tasinato G. 2025. Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems. Institute of Science and Technology Austria.' mla: 'Tasinato, Gianluca. Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20339.' short: 'G. Tasinato, Topological Methods in Discrete Geometry and Theoretical Computer Science: Measure Partitioning and Constraint Satisfaction Problems, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-09-10T12:17:55Z date_published: 2025-09-10T00:00:00Z date_updated: 2026-07-29T13:13:18Z day: '10' ddc: - '516' degree_awarded: PhD department: - _id: GradSch - _id: UlWa doi: 10.15479/AT-ISTA-20339 doi_confirm: '1' file: - access_level: closed checksum: ae097a515b9bb4d4b025ca854ae2ed76 content_type: application/x-zip-compressed creator: gtasinat date_created: 2025-09-11T12:24:12Z date_updated: 2025-09-11T12:24:12Z file_id: '20344' file_name: thesis-source.zip file_size: 2218562 relation: source_file - access_level: open_access checksum: 04b2e016409e52167ce42b0eef839fbf content_type: application/pdf creator: gtasinat date_created: 2025-09-11T12:26:14Z date_updated: 2025-09-11T12:26:14Z file_id: '20345' file_name: 2025_Tasinato_Gianluca_Thesis.pdf file_size: 10071982 relation: main_file success: 1 file_date_updated: 2025-09-11T12:26:14Z fulldoi: https://doi.org/10.15479/AT-ISTA-20339 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '106' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '20008' relation: part_of_dissertation status: public - id: '15168' relation: part_of_dissertation status: public - id: '19860' relation: part_of_dissertation status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 title: 'Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- _id: '20641' abstract: - lang: eng text: 'Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ' acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: "We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011." article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Schanda P. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2025. doi:10.15479/AT-ISTA-20641 apa: Becker, L. M., & Schanda, P. (2025). Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20641 chicago: Becker, Lea Marie, and Paul Schanda. “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20641. ieee: L. M. Becker and P. Schanda, “Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2025. ista: Becker LM, Schanda P. 2025. Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20641. mla: Becker, Lea Marie, and Paul Schanda. Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20641. short: L.M. Becker, P. Schanda, (2025). contributor: - contributor_type: researcher first_name: 'Haohao ' last_name: Fu - contributor_type: researcher first_name: Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - contributor_type: researcher first_name: Matthias last_name: Dreydoppel - contributor_type: researcher first_name: Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - contributor_type: researcher first_name: Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - contributor_type: researcher first_name: Ulrich last_name: Weininger - contributor_type: researcher first_name: Sylvain last_name: Engilberge - contributor_type: researcher first_name: Christophe last_name: Chipot corr_author: '1' date_created: 2025-11-13T09:29:58Z date_published: 2025-11-18T00:00:00Z date_updated: 2026-08-04T09:32:44Z day: '18' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-20641 file: - access_level: open_access checksum: a73a0550c644957e7f62241e239d3a1d content_type: application/zip creator: lbecker date_created: 2025-11-13T09:38:35Z date_updated: 2026-02-17T10:16:57Z file_id: '20643' file_name: Research_Data.zip file_size: 1806589513 relation: main_file - access_level: open_access checksum: 7176b257f753c213a0460ee06f802363 content_type: application/pdf creator: lbecker date_created: 2025-11-17T11:54:17Z date_updated: 2026-02-17T10:16:57Z file_id: '20652' file_name: README.pdf file_size: 191376 relation: table_of_contents file_date_updated: 2026-02-17T10:16:57Z fulldoi: https://doi.org/10.15479/AT-ISTA-20641 has_accepted_license: '1' month: '11' oa: 1 oa_version: Published Version project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publisher: Institute of Science and Technology Austria related_material: record: - id: '21145' relation: later_version status: public - id: '22105' relation: used_in_publication status: public status: public title: Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- OA_place: repository OA_type: green _id: '20926' abstract: - lang: eng text: Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs. acknowledgement: Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating discussions. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Dongjin full_name: Kim, Dongjin last_name: Kim - first_name: Xiaoyu full_name: Wang, Xiaoyu id: 8dff9c62-32b0-11ee-9fa8-fc73025e10f3 last_name: Wang - first_name: Santiago full_name: Vargas, Santiago last_name: Vargas - first_name: Peichen full_name: Zhong, Peichen last_name: Zhong - first_name: Daniel S. full_name: King, Daniel S. last_name: King - first_name: Theo Jaffrelot full_name: Inizan, Theo Jaffrelot last_name: Inizan - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 2025;21(24):12709-12724. doi:10.1021/acs.jctc.5c01400 apa: Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., & Cheng, B. (2025). A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.5c01400 chicago: Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King, Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation. American Chemical Society, 2025. https://doi.org/10.1021/acs.jctc.5c01400. ieee: D. Kim et al., “A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials,” Journal of Chemical Theory and Computation, vol. 21, no. 24. American Chemical Society, pp. 12709–12724, 2025. ista: Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724. mla: Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” Journal of Chemical Theory and Computation, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24, doi:10.1021/acs.jctc.5c01400. short: D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 12709–12724. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The training sets, training scripts, and trained potentials are available at https://github.com/ChengUCB/les_fit. The LES library is publicly available at https://github.com/ChengUCB/les. The CACE package with the LES implementation is available at https://github.com/BingqingCheng/cace. The MACE package with the LES implementation is available at https://github.com/ACEsuit/mace. The NequIP and Allegro LES extension package is available at https://github.com/ChengUCB/NequIP-LES. The MatGL package with the LES implementation is available at https://github.com/ChengUCB/matgl. The UMA package with the LES implementation is available at https://github.com/santi921/fairchem/tree/les_branch. date_created: 2026-01-04T23:01:33Z date_published: 2025-12-10T00:00:00Z date_updated: 2026-08-07T09:35:25Z day: '10' department: - _id: GradSch - _id: BiCh doi: 10.1021/acs.jctc.5c01400 external_id: arxiv: - '2507.14302' pmid: - '41368735 ' fulldoi: https://doi.org/10.1021/acs.jctc.5c01400 intvolume: ' 21' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2507.14302 month: '12' oa: 1 oa_version: Preprint page: 12709-12724 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 21 year: '2025' ... --- OA_place: publisher _id: '20074' abstract: - lang: eng text: "Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann citation: ama: Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074 apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074 chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074. ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025. ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074. short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-24T12:37:22Z date_published: 2025-07-24T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20074 doi_confirm: '1' file: - access_level: closed checksum: d09f9984002353ad7442358394919bf3 content_type: application/x-zip-compressed creator: vhuebsch date_created: 2025-07-30T08:47:53Z date_updated: 2025-07-30T08:47:53Z file_id: '20086' file_name: PhD_Thesis_Schmied.zip file_size: 43566093 relation: source_file - access_level: open_access checksum: 4833690d7283c587f518ba98eeb2c946 content_type: application/pdf creator: vhuebsch date_created: 2025-07-30T08:47:46Z date_updated: 2025-07-30T09:29:09Z file_id: '20087' file_name: PhD_Thesis_Schmied.pdf file_size: 13120922 relation: main_file file_date_updated: 2025-07-30T09:29:09Z fulldoi: https://doi.org/10.15479/AT-ISTA-20074 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '151' project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation publication_identifier: isbn: - 978-3-99078-060-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11478' relation: part_of_dissertation status: public - id: '19593' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Human microglia impact neuronal development in retinal organoids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ...