--- OA_place: publisher _id: '20074' abstract: - lang: eng text: "Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Verena full_name: Hübschmann, Verena id: 32B7C918-F248-11E8-B48F-1D18A9856A87 last_name: Hübschmann citation: ama: Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:10.15479/AT-ISTA-20074 apa: Schmied, V. (2025). Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20074 chicago: Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20074. ieee: V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025. ista: Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria. mla: Schmied, Verena. Human Microglia Impact Neuronal Development in Retinal Organoids. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20074. short: V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-07-24T12:37:22Z date_published: 2025-07-24T00:00:00Z date_updated: 2026-08-12T08:45:16Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/AT-ISTA-20074 doi_confirm: '1' file: - access_level: closed checksum: d09f9984002353ad7442358394919bf3 content_type: application/x-zip-compressed creator: vhuebsch date_created: 2025-07-30T08:47:53Z date_updated: 2025-07-30T08:47:53Z file_id: '20086' file_name: PhD_Thesis_Schmied.zip file_size: 43566093 relation: source_file - access_level: open_access checksum: 4833690d7283c587f518ba98eeb2c946 content_type: application/pdf creator: vhuebsch date_created: 2025-07-30T08:47:46Z date_updated: 2025-07-30T09:29:09Z file_id: '20087' file_name: PhD_Thesis_Schmied.pdf file_size: 13120922 relation: main_file file_date_updated: 2025-07-30T09:29:09Z fulldoi: https://doi.org/10.15479/AT-ISTA-20074 has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '151' project: - _id: 9B99D380-BA93-11EA-9121-9846C619BF3A grant_number: SC19-017 name: How human microglia shape developing neurons during health and inflammation publication_identifier: isbn: - 978-3-99078-060-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11478' relation: part_of_dissertation status: public - id: '19593' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: Human microglia impact neuronal development in retinal organoids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20342' abstract: - lang: eng text: Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication. article_number: '13149' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 2025;21(2). doi:10.46298/lmcs-21(2:2)2025 apa: Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. EPI Sciences. https://doi.org/10.46298/lmcs-21(2:2)2025 chicago: Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science. EPI Sciences, 2025. https://doi.org/10.46298/lmcs-21(2:2)2025. ieee: U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” Logical Methods in Computer Science, vol. 21, no. 2. EPI Sciences, 2025. ista: Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149. mla: Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” Logical Methods in Computer Science, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:10.46298/lmcs-21(2:2)2025. short: U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025). corr_author: '1' date_created: 2025-09-11T12:17:52Z date_published: 2025-04-08T00:00:00Z date_updated: 2026-08-12T08:46:05Z day: '08' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.46298/lmcs-21(2:2)2025 ec_funded: 1 external_id: arxiv: - '2307.06016' isi: - '001468887900001' file: - access_level: open_access checksum: 0b4d477bd981379724c35a4de2c176e5 content_type: application/pdf creator: esarac date_created: 2025-09-11T12:17:12Z date_updated: 2025-09-11T12:17:12Z file_id: '20343' file_name: 2307.06016.pdf file_size: 709584 relation: main_file success: 1 file_date_updated: 2025-09-11T12:17:12Z fulldoi: https://doi.org/10.46298/lmcs-21(2:2)2025 has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '2' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: Logical Methods in Computer Science publication_identifier: eissn: - 1860-5974 publication_status: published publisher: EPI Sciences quality_controlled: '1' related_material: record: - id: '13221' relation: earlier_version status: public - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: Safety and liveness of quantitative properties and automata tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2025' ... --- OA_place: publisher _id: '20167' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: "This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hanna full_name: Schön, Hanna id: C8E17EDC-D7AA-11E9-B7B7-45ECE5697425 last_name: Schön citation: ama: Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:10.15479/AT-ISTA-20167 apa: Schön, H. (2025). The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20167 chicago: Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20167. ieee: H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025. ista: Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria. mla: Schön, Hanna. The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20167. short: H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-08-13T11:13:13Z date_published: 2025-08-13T00:00:00Z date_updated: 2026-08-13T13:05:37Z day: '13' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: MaDe doi: 10.15479/AT-ISTA-20167 doi_confirm: '1' file: - access_level: closed checksum: b40c74404b8d9593802dabf57bfdf10f content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hschoen date_created: 2025-09-08T14:33:50Z date_updated: 2025-09-09T08:57:04Z file_id: '20311' file_name: 2025_Schoen_Hanna_Thesis.docx file_size: 78812587 relation: source_file - access_level: closed checksum: 16abc3ff66396ce2457fe07ffa8bed90 content_type: application/pdf creator: hschoen date_created: 2025-09-11T14:20:59Z date_updated: 2026-08-13T13:05:36Z embargo: 2027-03-15 embargo_to: open_access file_id: '20347' file_name: 2025_Schoen_Hanna_Thesis.pdf file_size: 9667057 relation: main_file file_date_updated: 2026-08-13T13:05:36Z fulldoi: https://doi.org/10.15479/AT-ISTA-20167 has_accepted_license: '1' language: - iso: eng month: '08' oa_version: Published Version page: '171' project: - _id: 23870BE8-32DE-11EA-91FC-C7463DDC885E grant_number: 209504/A/17/Z name: Molecular mechanisms of neural circuit function - _id: 23813290-32DE-11EA-91FC-C7463DDC885E grant_number: ALTF 302-2019 name: Control of gene expression at the endoplasmic reticulum publication_identifier: isbn: - 978-3-99078-061-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 title: The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20538' abstract: - lang: eng text: In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70. article_number: '169465' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sonja full_name: Knödlstorfer, Sonja last_name: Knödlstorfer - first_name: Giorgia full_name: Toscano, Giorgia id: 334a5e40-8747-11f0-b671-ba1f5154b4b4 last_name: Toscano - first_name: Aleksandra L. full_name: Ptaszek, Aleksandra L. last_name: Ptaszek - first_name: Georg full_name: Kontaxis, Georg last_name: Kontaxis - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Jakob full_name: Schneider, Jakob id: 64368429-eb97-11eb-a6c2-c980b1f44415 last_name: Schneider - first_name: Katharina full_name: Maier, Katharina last_name: Maier - first_name: Anna full_name: Kapitonova, Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - first_name: Roman J. full_name: Lichtenecker, Roman J. last_name: Lichtenecker - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Robert full_name: Konrat, Robert last_name: Konrat citation: ama: Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 2025;437(23). doi:10.1016/j.jmb.2025.169465 apa: Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2025.169465 chicago: Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology. Elsevier, 2025. https://doi.org/10.1016/j.jmb.2025.169465. ieee: S. Knödlstorfer et al., “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” Journal of Molecular Biology, vol. 437, no. 23. Elsevier, 2025. ista: Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465. mla: Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” Journal of Molecular Biology, vol. 437, no. 23, 169465, Elsevier, 2025, doi:10.1016/j.jmb.2025.169465. short: S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025). date_created: 2025-10-26T23:01:35Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-08-13T14:19:02Z day: '01' ddc: - '540' department: - _id: PaSc - _id: GradSch doi: 10.1016/j.jmb.2025.169465 external_id: pmid: - '41016549' file: - access_level: open_access checksum: feb92f9c79032c261165f4ca573f444a content_type: application/pdf creator: dernst date_created: 2025-12-30T10:29:08Z date_updated: 2025-12-30T10:29:08Z file_id: '20915' file_name: 2025_JourMolecularBiology_Knoedlstorfer.pdf file_size: 3076611 relation: main_file success: 1 file_date_updated: 2025-12-30T10:29:08Z fulldoi: https://doi.org/10.1016/j.jmb.2025.169465 has_accepted_license: '1' intvolume: ' 437' issue: '23' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bdb9578d-d553-11ed-ba76-ed5d39fce6f0 grant_number: I06223 name: Structure and mechanism of the mitochondrial MIM insertase - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Journal of Molecular Biology publication_identifier: eissn: - 1089-8638 issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0 tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 437 year: '2025' ... --- OA_place: publisher _id: '19395' abstract: - lang: eng text: "Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood." acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer citation: ama: 'Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant development. 2025. doi:10.15479/AT-ISTA-19395' apa: 'Monzer, A. (2025). Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19395' chicago: 'Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19395.' ieee: 'A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.' ista: 'Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.' mla: 'Monzer, Aline. Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19395.' short: 'A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-03-12T14:25:42Z date_published: 2025-03-13T00:00:00Z date_updated: 2026-08-14T09:33:46Z day: '13' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-19395 doi_confirm: '1' file: - access_level: open_access checksum: 9a3dd03bb4ec6b9907a325c3c4e8a1d7 content_type: application/pdf creator: amonzer date_created: 2025-03-12T14:14:49Z date_updated: 2025-03-12T14:14:49Z file_id: '19396' file_name: Final Thesis Aline Monzer.pdf file_size: 13119670 relation: main_file success: 1 - access_level: closed checksum: a353ce1ee2eabce37bca35499e76dbf1 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amonzer date_created: 2025-03-12T14:15:19Z date_updated: 2025-04-01T07:55:27Z file_id: '19397' file_name: Thesis Aline.docx file_size: 13774837 relation: source_file file_date_updated: 2025-04-01T07:55:27Z fulldoi: https://doi.org/10.15479/AT-ISTA-19395 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: eisbn: - 978-3-99078-054-1 eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '14826' relation: part_of_dissertation status: public - id: '19399' relation: part_of_dissertation status: public - id: '19398' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Cell-surface auxin signaling: Linking molecular pathways to plant development' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: repository OA_type: green _id: '19398' abstract: - lang: eng text: Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance. article_processing_charge: No author: - first_name: Aline full_name: Monzer, Aline id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425 last_name: Monzer - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Michael full_name: Smejkal, Michael id: 79a5a1be-04a3-11f0-ba18-a1730e0b58e9 last_name: Smejkal - first_name: Ema full_name: Cervenova, Ema id: 9f185b95-04a3-11f0-8245-f5e32eeb470f last_name: Cervenova - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv. doi:10.1101/2025.02.28.640727 apa: Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv. https://doi.org/10.1101/2025.02.28.640727 chicago: Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, n.d. https://doi.org/10.1101/2025.02.28.640727. ieee: A. Monzer et al., “TMK interacting network of receptor like kinases for auxin canalization and beyond,” bioRxiv. . ista: Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, 10.1101/2025.02.28.640727. mla: Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” BioRxiv, doi:10.1101/2025.02.28.640727. short: A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.). corr_author: '1' das_tickbox: '1' date_created: 2025-03-12T14:28:53Z date_published: 2025-03-02T00:00:00Z date_updated: 2026-08-14T09:33:45Z day: '02' ddc: - '580' department: - _id: GradSch - _id: JiFr - _id: EvBe doi: 10.1101/2025.02.28.640727 fulldoi: https://doi.org/10.1101/2025.02.28.640727 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2025.02.28.640727 month: '03' oa: 1 oa_version: Published Version publication: bioRxiv publication_status: draft related_material: record: - id: '19395' relation: dissertation_contains status: public status: public title: TMK interacting network of receptor like kinases for auxin canalization and beyond tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '19684' abstract: - lang: eng text: "The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate." acknowledged_ssus: - _id: ScienComp acknowledgement: "The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 citation: ama: 'Yalniz G. Transition to turbulence: Data-, solution-, and pattern-driven approaches. 2025. doi:10.15479/AT-ISTA-19684' apa: 'Yalniz, G. (2025). Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19684' chicago: 'Yalniz, Gökhan. “Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19684.' ieee: 'G. Yalniz, “Transition to turbulence: Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.' ista: 'Yalniz G. 2025. Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.' mla: 'Yalniz, Gökhan. Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19684.' short: 'G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-05-12T15:12:28Z date_published: 2025-05-13T00:00:00Z date_updated: 2026-09-02T08:16:32Z day: '13' ddc: - '514' - '519' - '532' - '004' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/AT-ISTA-19684 doi_confirm: '1' file: - access_level: open_access checksum: 0e452642b79f13633f1595bde71a67e3 content_type: application/pdf creator: gyalniz date_created: 2025-05-12T15:13:28Z date_updated: 2025-05-12T15:13:28Z file_id: '19685' file_name: Gökhan Yalnız - PhD thesis.pdf file_size: 20058169 relation: main_file success: 1 - access_level: open_access checksum: 921099d76adab2df784ce12ce41cfb22 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:15:59Z date_updated: 2025-05-12T15:43:28Z description: '3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).' file_id: '19686' file_name: Movie 2A.1.mp4 file_size: 37763743 relation: supplementary_material title: Chapter 2 - Movie 2A.1 - access_level: open_access checksum: 0ae5ac7d9896003c0c4207dd746808dc content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:09Z date_updated: 2025-05-12T15:43:28Z description: 'Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19687' file_name: Movie 3A.1.mp4 file_size: 3902655 relation: supplementary_material title: Chapter 3 - Movie 3A.1 - access_level: open_access checksum: ef8d270e066c1a9c3cb5ae46acf945e6 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:21Z date_updated: 2025-05-12T15:43:28Z description: 'Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19688' file_name: Movie 3A.2.mp4 file_size: 7043169 relation: supplementary_material title: Chapter 3 - Movie 3A.2 - access_level: open_access checksum: 7ed871f428100d6827ac9b0e8ca8e985 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:36Z date_updated: 2025-05-12T15:43:28Z description: 'Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19689' file_name: Movie 3A.3.mp4 file_size: 7748659 relation: supplementary_material title: Chapter 3 - Movie 3A.3 - access_level: open_access checksum: dd5a252e1da00c8f303588e22e2baeef content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:16:50Z date_updated: 2025-05-12T15:43:28Z description: 'Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).' file_id: '19690' file_name: Movie 3A.4.mp4 file_size: 5873052 relation: supplementary_material title: Chapter 3 - Movie 3A.4 - access_level: open_access checksum: 5ac58b86810698db28cbfc28f351ff70 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:11Z date_updated: 2025-05-12T15:43:28Z description: Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit. file_id: '19691' file_name: Movie 4A.1.mp4 file_size: 9209327 relation: supplementary_material title: Chapter 4 - Movie 4A.1 - access_level: open_access checksum: ac877f1e1ef39439911bf37cb1793b8e content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:43Z date_updated: 2025-05-12T15:43:28Z description: Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain. file_id: '19692' file_name: Movie 5A.1.mp4 file_size: 5893993 relation: supplementary_material title: Chapter 5 - Movie 5A.1 - access_level: open_access checksum: fd17eabb70129ceaa414e40924d1d2fe content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:49Z date_updated: 2025-05-12T15:43:28Z description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain. file_id: '19693' file_name: Movie 5A.2.mp4 file_size: 3990352 relation: supplementary_material title: Chapter 5 - Movie 5A.2 - access_level: open_access checksum: 32f904497ab0bbee38f0788d96b91454 content_type: video/mp4 creator: gyalniz date_created: 2025-05-12T15:17:58Z date_updated: 2025-05-12T15:43:28Z description: Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is a zoom-in of the full (L_x = L_z) domain. file_id: '19694' file_name: Movie 5A.3.mp4 file_size: 5171009 relation: supplementary_material title: Chapter 5 - Movie 5A.3 - access_level: closed checksum: f313261b9bb12dfb943fead8318954c6 content_type: application/x-zip-compressed creator: gyalniz date_created: 2025-05-12T15:27:10Z date_updated: 2025-05-12T15:43:28Z file_id: '19695' file_name: Gökhan Yalnız - PhD thesis.zip file_size: 18991996 relation: source_file file_date_updated: 2025-05-12T15:43:28Z fulldoi: https://doi.org/10.15479/AT-ISTA-19684 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '155' project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: Revisiting the Turbulence Problem Using Statistical Mechanics publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9558' relation: part_of_dissertation status: public - id: '12105' relation: part_of_dissertation status: public - id: '13274' relation: part_of_dissertation status: public - id: '14466' relation: part_of_dissertation status: public - id: '7563' relation: part_of_dissertation status: public status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: 'Transition to turbulence: Data-, solution-, and pattern-driven approaches' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '19795' abstract: - lang: eng text: Super-resolution microscopy often entails long acquisition times of minutes to hours. Since drifts during the acquisition adversely affect data quality, active sample stabilization is commonly used for some of these techniques to reach their full potential. Although drifts in the lateral plane can often be corrected after acquisition, this is not always possible or may come with drawbacks. Therefore, it is appealing to stabilize sample position in three dimensions (3D) during acquisition. Various schemes for active sample stabilization have been demonstrated previously, with some reaching sub-nanometer stability in 3D. Here, we present a scheme for active drift correction that delivers the nanometer-scale 3D stability demanded by state-of-the-art super-resolution techniques and is straightforward to implement compared to previous schemes capable of reaching this level of stabilization precision. Using a refined algorithm that can handle various types of reference structure, without sparse signal peaks being mandatory, we stabilized sample position to ∼1 nm in 3D using objective lenses both with high and low numerical aperture. Our implementation requires only the addition of a simple widefield imaging path and we provide an open-source control software with graphical user interface to facilitate easy adoption of the module. Finally, we demonstrate how this has the potential to enhance data collection for diffraction-limited and super-resolution imaging techniques using single-molecule localization microscopy and cryo-confocal imaging as showcases. acknowledged_ssus: - _id: M-Shop - _id: EM-Fac - _id: LifeSc acknowledgement: 'We acknowledge expert support by ISTA’s scientific service units, including the Miba Machine Shop, the Electron Microscopy Facility, and the Lab Support Facility. This work has been made possible in part by CZI grant DAF2021-234754 and grant DOI: https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI: https://doi.org/10.13039/100014989) (F.K.M.S. and J.G.D.). We further gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant DK W1232 (M.R.T. and J.G.D.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.L.); ISTA postdoctoral fellowship IST fellow (A.W.); and Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.).' article_number: '100211' article_processing_charge: Yes article_type: original author: - first_name: Jakob full_name: Vorlaufer, Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer orcid: 0009-0000-7590-3501 - first_name: Nikolai full_name: Semenov, Nikolai id: e64d39c7-72ef-11ef-b75a-ee3046860d1b last_name: Semenov - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - first_name: Manjunath full_name: Javoor, Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor orcid: 0000-0003-2311-2112 - first_name: Bettina full_name: Zens, Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens orcid: 0000-0002-9561-1239 - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - first_name: Marek full_name: Suplata, Marek id: EE8452B8-C26A-11E9-B157-E80CE6697425 last_name: Suplata - first_name: Wiebke full_name: Jahr, Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr orcid: 0000-0003-0201-2315 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Andreas full_name: Wartak, Andreas id: 60aaa06c-3de5-11eb-9e53-baa88e955dcb last_name: Wartak - first_name: Florian Km full_name: Schur, Florian Km id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Vorlaufer J, Semenov N, Kreuzinger C, et al. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 2025;5(2). doi:10.1016/j.bpr.2025.100211 apa: Vorlaufer, J., Semenov, N., Kreuzinger, C., Javoor, M., Zens, B., Agudelo Duenas, N., … Danzl, J. G. (2025). Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. Elsevier. https://doi.org/10.1016/j.bpr.2025.100211 chicago: Vorlaufer, Jakob, Nikolai Semenov, Caroline Kreuzinger, Manjunath Javoor, Bettina Zens, Nathalie Agudelo Duenas, Mojtaba Tavakoli, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical Reports. Elsevier, 2025. https://doi.org/10.1016/j.bpr.2025.100211. ieee: J. Vorlaufer et al., “Image-based 3D active sample stabilization on the nanometer scale for optical microscopy,” Biophysical Reports, vol. 5, no. 2. Elsevier, 2025. ista: Vorlaufer J, Semenov N, Kreuzinger C, Javoor M, Zens B, Agudelo Duenas N, Tavakoli M, Suplata M, Jahr W, Lyudchik J, Wartak A, Schur FK, Danzl JG. 2025. Image-based 3D active sample stabilization on the nanometer scale for optical microscopy. Biophysical Reports. 5(2), 100211. mla: Vorlaufer, Jakob, et al. “Image-Based 3D Active Sample Stabilization on the Nanometer Scale for Optical Microscopy.” Biophysical Reports, vol. 5, no. 2, 100211, Elsevier, 2025, doi:10.1016/j.bpr.2025.100211. short: J. Vorlaufer, N. Semenov, C. Kreuzinger, M. Javoor, B. Zens, N. Agudelo Duenas, M. Tavakoli, M. Suplata, W. Jahr, J. Lyudchik, A. Wartak, F.K. Schur, J.G. Danzl, Biophysical Reports 5 (2025). corr_author: '1' date_created: 2025-06-08T22:01:22Z date_published: 2025-06-11T00:00:00Z date_updated: 2026-09-03T09:36:24Z day: '11' ddc: - '570' department: - _id: JoDa - _id: GradSch - _id: FlSc - _id: EM-Fac doi: 10.1016/j.bpr.2025.100211 ec_funded: 1 file: - access_level: open_access checksum: 4018c833f25a3ad3b57e3577fed70334 content_type: application/pdf creator: dernst date_created: 2025-06-10T07:24:46Z date_updated: 2025-06-10T07:24:46Z file_id: '19802' file_name: 2025_BiophysicalReports_Vorlaufer.pdf file_size: 7238179 relation: main_file success: 1 file_date_updated: 2025-06-10T07:24:46Z fulldoi: https://doi.org/10.1016/j.bpr.2025.100211 has_accepted_license: '1' intvolume: ' 5' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 62909c6f-2b32-11ec-9570-e1476aab5308 grant_number: CZI01 name: CryoMinflux-guided in-situ molecular census and structure determination - _id: 6285a163-2b32-11ec-9570-8e204ca2dba5 grant_number: '26137' name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 2668BFA0-B435-11E9-9278-68D0E5697425 grant_number: LT00057 name: High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration publication: Biophysical Reports publication_identifier: eissn: - 2667-0747 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '20206' relation: dissertation_contains status: public - id: '22744' relation: dissertation_contains status: public scopus_import: '1' status: public title: Image-based 3D active sample stabilization on the nanometer scale for optical microscopy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2025' ... --- OA_place: publisher OA_type: free access _id: '22825' abstract: - lang: eng text: "The empirical emergence of neural collapse—a surprising symmetry in the feature representations of the training data in the penultimate layer of deep neural\r\nnetworks—has spurred a line of theoretical research aimed at its understanding.\r\nHowever, existing work focuses on data-agnostic models or, when data structure is\r\ntaken into account, it remains limited to multi-layer perceptrons. Our paper fills\r\nboth these gaps by analyzing modern architectures in a data-aware regime: we\r\nprove that global optima of deep regularized transformers and residual networks\r\n(ResNets) with LayerNorm trained with cross entropy or mean squared error loss\r\nare approximately collapsed, and the approximation gets tighter as the depth grows.\r\nMore generally, we formally reduce any end-to-end large-depth ResNet or transformer training into an equivalent unconstrained features model, thus justifying its\r\nwide use in the literature even beyond data-agnostic settings. Our theoretical results\r\nare supported by experiments on computer vision and language datasets showing\r\nthat, as the depth grows, neural collapse indeed becomes more prominent." acknowledged_ssus: - _id: ScienComp acknowledgement: "M. M. and P. S. are funded by the European Union (ERC, INF2\r\n, project number 101161364). Views\r\nand opinions expressed are however those of the author(s) only and do not necessarily reflect those\r\nof the European Union or the European Research Council Executive Agency. Neither the European\r\nUnion nor the granting authority can be held responsible for them. This research was supported\r\nby the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)." alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Peter full_name: Súkeník, Peter id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c last_name: Súkeník - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Súkeník P, Lampert C, Mondelli M. Neural collapse is globally optimal in deep regularized ResNets and transformers. In: 39th Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025:48646-48677. doi:10.52202/085713-1450' apa: 'Súkeník, P., Lampert, C., & Mondelli, M. (2025). Neural collapse is globally optimal in deep regularized ResNets and transformers. In 39th Conference on Neural Information Processing Systems (Vol. 38, pp. 48646–48677). San Diego, CA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/085713-1450' chicago: Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse Is Globally Optimal in Deep Regularized ResNets and Transformers.” In 39th Conference on Neural Information Processing Systems, 38:48646–77. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-1450. ieee: P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse is globally optimal in deep regularized ResNets and transformers,” in 39th Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38, pp. 48646–48677. ista: 'Súkeník P, Lampert C, Mondelli M. 2025. Neural collapse is globally optimal in deep regularized ResNets and transformers. 39th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38, 48646–48677.' mla: Súkeník, Peter, et al. “Neural Collapse Is Globally Optimal in Deep Regularized ResNets and Transformers.” 39th Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025, pp. 48646–77, doi:10.52202/085713-1450. short: P. Súkeník, C. Lampert, M. Mondelli, in:, 39th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025, pp. 48646–48677. conference: end_date: 2025-12-07 location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2025-12-02 corr_author: '1' das_tickbox: '0' date_created: 2026-09-06T22:01:59Z date_published: 2025-12-02T00:00:00Z date_updated: 2026-09-10T08:11:46Z day: '02' ddc: - '000' department: - _id: MaMo - _id: GradSch - _id: ChLa doi: 10.52202/085713-1450 external_id: arxiv: - '2505.15239' fulldoi: https://doi.org/10.52202/085713-1450 intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.52202/085713-1450 month: '12' oa: 1 oa_version: Published Version page: 48646-48677 project: - _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf grant_number: '101161364' name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits' publication: 39th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9798331338275' issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Neural collapse is globally optimal in deep regularized ResNets and transformers type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_place: publisher OA_type: free access _id: '22824' abstract: - lang: eng text: "We present new fast-rate PAC-Bayesian generalization bounds for multi-task and\r\nmeta-learning in the unbalanced setting, i.e. when the tasks have training sets of\r\ndifferent sizes, as is typically the case in real-world scenarios. Previously, only\r\nstandard-rate bounds were known for this situation, while fast-rate bounds were\r\nlimited to the setting where all training sets are of equal size. Our new bounds\r\nare numerically computable as well as interpretable, and we demonstrate their\r\nflexibility in handling a number of cases where they give stronger guarantees\r\nthan previous bounds. Besides the bounds themselves, we also make conceptual\r\ncontributions: we demonstrate that the unbalanced multi-task setting has different\r\nstatistical properties than the balanced situation, specifically that proofs from\r\nthe balanced situation do not carry over to the unbalanced setting. Additionally,\r\nwe shed light on the fact that the unbalanced situation allows two meaningful\r\ndefinitions of multi-task risk, depending on whether all tasks should be considered\r\nequally important or if sample-rich tasks should receive more weight than samplepoor ones." acknowledged_ssus: - _id: ScienComp acknowledgement: This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No author: - first_name: Hossein full_name: Zakerinia, Hossein id: 653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4 last_name: Zakerinia orcid: 0009-0007-3977-6462 - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Zakerinia H, Lampert C. Fast rate bounds for multi-task and meta-learning with different sample sizes. In: 39th Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025:9062-9093. doi:10.52202/085713-0278' apa: 'Zakerinia, H., & Lampert, C. (2025). Fast rate bounds for multi-task and meta-learning with different sample sizes. In 39th Conference on Neural Information Processing Systems (Vol. 38, pp. 9062–9093). San Diego, CA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/085713-0278' chicago: Zakerinia, Hossein, and Christoph Lampert. “Fast Rate Bounds for Multi-Task and Meta-Learning with Different Sample Sizes.” In 39th Conference on Neural Information Processing Systems, 38:9062–93. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-0278. ieee: H. Zakerinia and C. Lampert, “Fast rate bounds for multi-task and meta-learning with different sample sizes,” in 39th Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38, pp. 9062–9093. ista: 'Zakerinia H, Lampert C. 2025. Fast rate bounds for multi-task and meta-learning with different sample sizes. 39th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38, 9062–9093.' mla: Zakerinia, Hossein, and Christoph Lampert. “Fast Rate Bounds for Multi-Task and Meta-Learning with Different Sample Sizes.” 39th Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025, pp. 9062–93, doi:10.52202/085713-0278. short: H. Zakerinia, C. Lampert, in:, 39th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025, pp. 9062–9093. conference: end_date: 2025-12-07 location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2025-12-02 corr_author: '1' das_tickbox: '0' date_created: 2026-09-06T22:01:59Z date_published: 2025-12-02T00:00:00Z date_updated: 2026-09-10T08:37:33Z day: '02' department: - _id: GradSch - _id: ChLa doi: 10.52202/085713-0278 fulldoi: https://doi.org/10.52202/085713-0278 intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.52202/085713-0278 month: '12' oa: 1 oa_version: Published Version page: 9062-9093 publication: 39th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9798331338275' issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: Fast rate bounds for multi-task and meta-learning with different sample sizes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_place: publisher _id: '19903' abstract: - lang: eng text: "Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation.\r\nWith game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take.\r\nIndividuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome.\r\nCooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions." acknowledgement: "The research for this thesis was supported by the European Research Council\r\n(grant agreements No. 863818 and No. 850529), the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie grant agreement No. 754411),\r\nthe Austrian Science Fund (grant DOI 10.55776/COE12), the French Agence Nationale\r\nde la Recherche under the Programme d’investissements d’avenir (project reference 17-\r\nEURE-0010) and the Australian Government through the Australian Research Council\r\n(grant No. SR200100005, “Securing Antarctica’s Environmental Future”)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Valentin full_name: Hübner, Valentin id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910 last_name: Hübner orcid: 0009-0001-5009-4987 citation: ama: Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:10.15479/AT-ISTA-19903 apa: Hübner, V. (2025). Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19903 chicago: Hübner, Valentin. “Reciprocity and Inequality in Social Dilemmas.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19903. ieee: V. Hübner, “Reciprocity and inequality in social dilemmas,” Institute of Science and Technology Austria, 2025. ista: Hübner V. 2025. Reciprocity and inequality in social dilemmas. Institute of Science and Technology Austria. mla: Hübner, Valentin. Reciprocity and Inequality in Social Dilemmas. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19903. short: V. Hübner, Reciprocity and Inequality in Social Dilemmas, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-06-25T13:50:10Z date_published: 2025-06-25T00:00:00Z date_updated: 2026-09-16T06:58:24Z day: '25' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/AT-ISTA-19903 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 794c02f8c82ca59ba6dda3bd7eed871a content_type: application/x-xz creator: vhuebner date_created: 2025-06-25T13:38:07Z date_updated: 2025-06-25T13:38:07Z file_id: '19905' file_name: Thesis Valentin Hübner source.tar.xz file_size: 6192760 relation: source_file - access_level: open_access checksum: ac56063d81c81e40322b6ff5a8c4912e content_type: application/pdf creator: vhuebner date_created: 2025-07-09T13:37:00Z date_updated: 2025-07-09T13:37:00Z file_id: '19976' file_name: Thesis Valentin Hübner.pdf file_size: 4837864 relation: main_file file_date_updated: 2025-07-09T13:37:00Z fulldoi: https://doi.org/10.15479/AT-ISTA-19903 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '06' oa: 1 oa_version: Published Version page: '157' project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 4029cfc7-b034-11f1-9e55-88ab2ff3b6ee grant_number: COE12 name: Bilateral Artificial Intelligence (Chatterjee) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19843' relation: part_of_dissertation status: public - id: '15083' relation: part_of_dissertation status: public - id: '19074' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Reciprocity and inequality in social dilemmas tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20138' abstract: - lang: eng text: "The evolution shapes the world around us.\r\nNot only in biology, where the fittest individuals spread their genes but also in physics and social dynamics, the evolutionary forces determine the development of a state of matter or public opinions.\r\nMany models describe these dynamics.\r\nThis thesis examines the role of the structure in the models of selection.\r\nThe population structure is represented as a graph or a network, and each vertex is occupied by one individual.\r\nEvery individual has a type and fitness that represents the reproductive potential and depends on the type, occupied vertex, and the arrangement of the neighbors.\r\nThe evolution is modeled in discrete steps; in one step, one individual is replaced by a neighbor selected randomly with the influence of fitness.\r\n\r\n\r\n\r\nThe role of the networks is widely examined in the literature.\r\nThe structures that promote the spread of the desired type compared to the structureless case are called amplifiers.\r\nThe existence of amplifiers in various settings is an intensively studied topic, and in some settings, the amplifiers have been identified.\r\nMoreover, there are other important questions about the number of steps until one type spreads over the whole network (fixation time), the computational complexity, and the questions about the robustness of these processes.\r\n\r\n\r\nThis thesis explores the role of structure in evolution from many perspectives.\r\nFirst, it introduces different models and various choices that can be made in the models of evolution.\r\nIt highlights the role of the structure in the real world and how this is reflected in these models.\r\nThen, it describes the previous results and open problems.\r\nSecond, the thesis describes an amplifier for two variants of the Moran process: one with a constant birth rate and the other with a constant death rate.\r\nThis is an important contribution to the robustness of the amplification.\r\nThird, the thesis determines the complexity of spatial games.\r\nThese are processes where the fitness comes from a game, and the strength of selection is high.\r\nIt shows that determining the fate of cooperation in these games is a PSPACE-complete problem.\r\nFourth, the thesis describes the amplifier of cooperation for spatial games.\r\nThis is the first amplifier in this setting.\r\nFifth, the thesis examines the coexistence in the Moran process with environmental heterogeneity.\r\nIn this setting, the fitness depends not only on the type of the individual but also on the occupied vertex.\r\nThe chapter determines the relationship between the interactions of vertices of different types and the coexistence time.\r\nSixth, the thesis examines the social balance on networks and proposes a stochastic dynamic partially aware of the state of the graph, which reaches a balanced position quickly.\r\nFinally, the thesis presents conclusions and outlines the directions for future work.\r\n\r\n\r\n" acknowledgement: "This work was supported by the European Research Council CoG 863818 (ForMSMArt) and Austrian Science Fund 10.55776/COE12.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 citation: ama: Svoboda J. Structural properties of games on graphs. 2025. doi:10.15479/AT-ISTA-20138 apa: Svoboda, J. (2025). Structural properties of games on graphs. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20138 chicago: Svoboda, Jakub. “Structural Properties of Games on Graphs.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20138. ieee: J. Svoboda, “Structural properties of games on graphs,” Institute of Science and Technology Austria, 2025. ista: Svoboda J. 2025. Structural properties of games on graphs. Institute of Science and Technology Austria. mla: Svoboda, Jakub. Structural Properties of Games on Graphs. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20138. short: J. Svoboda, Structural Properties of Games on Graphs, Institute of Science and Technology Austria, 2025. corr_author: '1' das_tickbox: '1' date_created: 2025-08-05T14:33:59Z date_published: 2025-08-05T00:00:00Z date_updated: 2026-09-16T06:59:33Z day: '05' ddc: - '000' - '519' degree_awarded: PhD department: - _id: GradSch - _id: KrCh doi: 10.15479/AT-ISTA-20138 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: c6c4df9777f4537940de7ab392ad57e2 content_type: application/pdf creator: jsvoboda date_created: 2025-08-14T09:54:43Z date_updated: 2025-08-14T09:54:43Z file_id: '20177' file_name: 2025_Svoboda_Jakub_Thesis.pdf file_size: 5927291 relation: main_file success: 1 - access_level: closed checksum: 485e9f9822821bc03666d245d80aaa08 content_type: application/zip creator: jsvoboda date_created: 2025-08-14T09:55:20Z date_updated: 2025-08-21T11:48:39Z file_id: '20178' file_name: 2025_Svoboda_Jakub_Thesis.zip file_size: 6731815 relation: source_file file_date_updated: 2025-08-21T11:48:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-20138 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '08' oa: 1 oa_version: Published Version page: '167' project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 4029cfc7-b034-11f1-9e55-88ab2ff3b6ee grant_number: COE12 name: Bilateral Artificial Intelligence (Chatterjee) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: "Chapter 4 is copyrighted by CC BY-NC-ND\r\n4.0, which prohibits derivatives. Chapter 6 is copyrighted: Copyright (2025) by the American\r\nPhysical Society. For a copy, redistribution, or modification needs to be permitted by the\r\nAmerican Physical Society.\r\n" related_material: record: - id: '12787' relation: part_of_dissertation status: public - id: '12101' relation: part_of_dissertation status: public - id: '12257' relation: part_of_dissertation status: public - id: '15297' relation: part_of_dissertation status: public - id: '18703' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Structural properties of games on graphs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '20299' abstract: - lang: eng text: "Deterministic Markov Decision Processes (DMDPs) are a mathematical framework for decision-making where the outcomes and future possible actions are deterministically determined by the current action taken. DMDPs can be viewed as a finite directed weighted graph, where in each step, the controller chooses an outgoing edge. An objective is a measurable function on runs (or infinite trajectories) of the DMDP, and the value for an objective is the maximal cumulative reward (or weight) that the controller can guarantee. We consider the classical mean-payoff (aka limit-average) objective, which is a basic and fundamental objective.\r\n\r\nHoward's policy iteration algorithm is a popular method for solving DMDPs with mean-payoff objectives. Although Howard's algorithm performs well in practice, as experimental studies suggested, the best known upper bound is exponential and the current known lower bound is as follows: For the input size I, the algorithm requires (math formular) iterations, where (math formular) hides the poly-logarithmic factors, i.e., the current lower bound on iterations is sub-linear with respect to the input size. Our main result is an improved lower bound for this fundamental algorithm where we show that for the input size I, the algorithm requires (math formular) iterations." acknowledgement: "This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant and Austrian Science Fund (FWF) 10.55776/COE12.\r\n" alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Ali full_name: Asadi, Ali id: 02d96aae-000e-11ec-b801-cadd0a5eefbb last_name: Asadi - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jakob full_name: De Raaij, Jakob last_name: De Raaij citation: ama: 'Asadi A, Chatterjee K, De Raaij J. Lower bound on Howard policy iteration for deterministic Markov Decision Processes. In: The 41st Conference on Uncertainty in Artificial Intelligence. Vol 286. ML Research Press; 2025:223-232.' apa: 'Asadi, A., Chatterjee, K., & De Raaij, J. (2025). Lower bound on Howard policy iteration for deterministic Markov Decision Processes. In The 41st Conference on Uncertainty in Artificial Intelligence (Vol. 286, pp. 223–232). Rio de Janeiro, Brazil: ML Research Press.' chicago: Asadi, Ali, Krishnendu Chatterjee, and Jakob De Raaij. “Lower Bound on Howard Policy Iteration for Deterministic Markov Decision Processes.” In The 41st Conference on Uncertainty in Artificial Intelligence, 286:223–32. ML Research Press, 2025. ieee: A. Asadi, K. Chatterjee, and J. De Raaij, “Lower bound on Howard policy iteration for deterministic Markov Decision Processes,” in The 41st Conference on Uncertainty in Artificial Intelligence, Rio de Janeiro, Brazil, 2025, vol. 286, pp. 223–232. ista: 'Asadi A, Chatterjee K, De Raaij J. 2025. Lower bound on Howard policy iteration for deterministic Markov Decision Processes. The 41st Conference on Uncertainty in Artificial Intelligence. UAI: Conference on Uncertainty in Artificial Intelligence, PMLR, vol. 286, 223–232.' mla: Asadi, Ali, et al. “Lower Bound on Howard Policy Iteration for Deterministic Markov Decision Processes.” The 41st Conference on Uncertainty in Artificial Intelligence, vol. 286, ML Research Press, 2025, pp. 223–32. short: A. Asadi, K. Chatterjee, J. De Raaij, in:, The 41st Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2025, pp. 223–232. conference: end_date: 2025-07-25 location: Rio de Janeiro, Brazil name: 'UAI: Conference on Uncertainty in Artificial Intelligence' start_date: 2025-07-21 corr_author: '1' date_created: 2025-09-07T22:01:34Z date_published: 2025-01-01T00:00:00Z date_updated: 2026-09-16T07:01:05Z day: '01' ddc: - '000' department: - _id: KrCh - _id: GradSch ec_funded: 1 external_id: arxiv: - '2506.12254' file: - access_level: open_access checksum: 4180c81bb6ed3b4f5c7a8e48d06520c6 content_type: application/pdf creator: dernst date_created: 2025-09-09T06:27:59Z date_updated: 2025-09-09T06:27:59Z file_id: '20313' file_name: 2025_UAI_Asadi.pdf file_size: 317097 relation: main_file success: 1 file_date_updated: 2025-09-09T06:27:59Z has_accepted_license: '1' intvolume: ' 286' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 223-232 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 4029cfc7-b034-11f1-9e55-88ab2ff3b6ee grant_number: COE12 name: Bilateral Artificial Intelligence (Chatterjee) publication: The 41st Conference on Uncertainty in Artificial Intelligence publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Lower bound on Howard policy iteration for deterministic Markov Decision Processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 286 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '20297' abstract: - lang: eng text: "A standard model that arises in several applications in sequential decision-making is partially observable Markov decision processes (POMDPs) where a decision-making agent interacts with an uncertain environment. A basic objective in POMDPs is the reachability objective, where given a target set of states, the goal is to eventually arrive at one of them.\r\n\r\nThe limit-sure problem asks whether reachability can be ensured with probability arbitrarily close to 1. In general, the limit-sure reachability problem for POMDPs is undecidable. However, in many practical cases, the most relevant question is the existence of policies with a small amount of memory. In this work, we study the limit-sure reachability problem for POMDPs with a fixed amount of memory. We establish that the computational complexity of the problem is NP-complete." acknowledgement: This research was partially supported by Austrian Science Fund (FWF) 10.55776/COE12, the support of the French Agence Nationale de la Recherche (ANR) under reference ANR-21-CE40-0020 (CONVERGENCE project), and the ERC CoG 863818 (ForM-SMArt) grant. alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Ali full_name: Asadi, Ali id: 02d96aae-000e-11ec-b801-cadd0a5eefbb last_name: Asadi - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Raimundo J full_name: Saona Urmeneta, Raimundo J id: BD1DF4C4-D767-11E9-B658-BC13E6697425 last_name: Saona Urmeneta orcid: 0000-0001-5103-038X - first_name: Ali full_name: Shafiee, Ali id: 2783031a-7378-11f0-b2d0-f17f1db2ebad last_name: Shafiee citation: ama: 'Asadi A, Chatterjee K, Saona Urmeneta RJ, Shafiee A. Limit-sure reachability for small memory policies in POMDPs is NP-complete. In: The 41st Conference on Uncertainty in Artificial Intelligence. Vol 286. ML Research Press; 2025:238-247.' apa: 'Asadi, A., Chatterjee, K., Saona Urmeneta, R. J., & Shafiee, A. (2025). Limit-sure reachability for small memory policies in POMDPs is NP-complete. In The 41st Conference on Uncertainty in Artificial Intelligence (Vol. 286, pp. 238–247). Rio de Janeiro, Brazil: ML Research Press.' chicago: Asadi, Ali, Krishnendu Chatterjee, Raimundo J Saona Urmeneta, and Ali Shafiee. “Limit-Sure Reachability for Small Memory Policies in POMDPs Is NP-Complete.” In The 41st Conference on Uncertainty in Artificial Intelligence, 286:238–47. ML Research Press, 2025. ieee: A. Asadi, K. Chatterjee, R. J. Saona Urmeneta, and A. Shafiee, “Limit-sure reachability for small memory policies in POMDPs is NP-complete,” in The 41st Conference on Uncertainty in Artificial Intelligence, Rio de Janeiro, Brazil, 2025, vol. 286, pp. 238–247. ista: 'Asadi A, Chatterjee K, Saona Urmeneta RJ, Shafiee A. 2025. Limit-sure reachability for small memory policies in POMDPs is NP-complete. The 41st Conference on Uncertainty in Artificial Intelligence. UAI: Conference on Uncertainty in Artificial Intelligence, PMLR, vol. 286, 238–247.' mla: Asadi, Ali, et al. “Limit-Sure Reachability for Small Memory Policies in POMDPs Is NP-Complete.” The 41st Conference on Uncertainty in Artificial Intelligence, vol. 286, ML Research Press, 2025, pp. 238–47. short: A. Asadi, K. Chatterjee, R.J. Saona Urmeneta, A. Shafiee, in:, The 41st Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2025, pp. 238–247. conference: end_date: 2025-07-25 location: Rio de Janeiro, Brazil name: 'UAI: Conference on Uncertainty in Artificial Intelligence' start_date: 2025-07-21 corr_author: '1' date_created: 2025-09-07T22:01:34Z date_published: 2025-07-01T00:00:00Z date_updated: 2026-09-16T07:03:02Z day: '01' ddc: - '000' department: - _id: KrCh - _id: GradSch ec_funded: 1 external_id: arxiv: - '2412.00941' file: - access_level: open_access checksum: 1a37ebe7ba73ab6985765bf0d17a0acc content_type: application/pdf creator: dernst date_created: 2025-09-09T08:19:41Z date_updated: 2025-09-09T08:19:41Z file_id: '20315' file_name: 2025_UAI_AsadiAli.pdf file_size: 307458 relation: main_file success: 1 file_date_updated: 2025-09-09T08:19:41Z has_accepted_license: '1' intvolume: ' 286' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 238-247 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 4029cfc7-b034-11f1-9e55-88ab2ff3b6ee grant_number: COE12 name: Bilateral Artificial Intelligence (Chatterjee) publication: The 41st Conference on Uncertainty in Artificial Intelligence publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Limit-sure reachability for small memory policies in POMDPs is NP-complete tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 286 year: '2025' ... --- APC_amount: 3599,50 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '20646' abstract: - lang: eng text: Describing general quantum many-body dynamics is a challenging task due to the exponential growth of the Hilbert space with system size. The time-dependent variational principle (TDVP) provides a powerful tool to tackle this task by projecting quantum evolution onto a classical dynamical system within a variational manifold. In classical systems, periodic orbits play a crucial role in understanding the structure of the phase space and the long-term behavior of the system. However, finding periodic orbits is generally difficult, and their existence and properties in generic TDVP dynamics over matrix product states have remained largely unexplored. In this work, we develop an algorithm to systematically identify and characterize periodic orbits in TDVP dynamics. Applying our method to the periodically kicked Ising model, we uncover both stable and unstable periodic orbits. We characterize the Kolmogorov-Arnold-Moser tori in the vicinity of stable periodic orbits and track the change of the periodic orbits as we modify the Hamiltonian parameters. We observe that periodic orbits exist at any value of the coupling constant of the kicked Ising model between prethermal and fully thermalizing regimes, but their relevance to quantum dynamics and imprint on quantum eigenstates diminishes as the system leaves the prethermal regime. Our results demonstrate that periodic orbits provide valuable insights into the TDVP approximation of quantum many-body evolution and establish a closer connection between quantum and classical chaos. acknowledgement: We acknowledge useful discussions with C. Kollath, A. Green, and D. Huse. E.P., M.L., and M.S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). This research was funded in whole or in part by the Austrian Science Fund (FWF) (Grant No. 10.55776/COE1). For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research was supported in part by National Science Foundation (NSF) Grant No. PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP) and by the Erwin Schrödinger International Institute for Mathematics and Physics (ESI). article_number: '040333' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Elena full_name: Petrova, Elena id: 0ac84990-897b-11ed-a09c-f5abb56a4ede last_name: Petrova - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Petrova E, Ljubotina M, Yalniz G, Serbyn M. Finding periodic orbits in projected quantum many-body dynamics. PRX Quantum. 2025;6(4). doi:10.1103/tldp-kvkd apa: Petrova, E., Ljubotina, M., Yalniz, G., & Serbyn, M. (2025). Finding periodic orbits in projected quantum many-body dynamics. PRX Quantum. American Physical Society. https://doi.org/10.1103/tldp-kvkd chicago: Petrova, Elena, Marko Ljubotina, Gökhan Yalniz, and Maksym Serbyn. “Finding Periodic Orbits in Projected Quantum Many-Body Dynamics.” PRX Quantum. American Physical Society, 2025. https://doi.org/10.1103/tldp-kvkd. ieee: E. Petrova, M. Ljubotina, G. Yalniz, and M. Serbyn, “Finding periodic orbits in projected quantum many-body dynamics,” PRX Quantum, vol. 6, no. 4. American Physical Society, 2025. ista: Petrova E, Ljubotina M, Yalniz G, Serbyn M. 2025. Finding periodic orbits in projected quantum many-body dynamics. PRX Quantum. 6(4), 040333. mla: Petrova, Elena, et al. “Finding Periodic Orbits in Projected Quantum Many-Body Dynamics.” PRX Quantum, vol. 6, no. 4, 040333, American Physical Society, 2025, doi:10.1103/tldp-kvkd. short: E. Petrova, M. Ljubotina, G. Yalniz, M. Serbyn, PRX Quantum 6 (2025). corr_author: '1' date_created: 2025-11-14T09:40:52Z date_published: 2025-11-12T00:00:00Z date_updated: 2026-09-16T07:04:35Z day: '12' ddc: - '539' department: - _id: GradSch - _id: BjHo - _id: MaSe doi: 10.1103/tldp-kvkd ec_funded: 1 external_id: arxiv: - '2504.12472' isi: - '001616473700003' file: - access_level: open_access checksum: 5d6d04ac518b4118405334e1ddc7a56d content_type: application/pdf creator: gyalniz date_created: 2025-11-14T09:44:10Z date_updated: 2025-11-14T09:44:10Z file_id: '20647' file_name: tldp-kvkd.pdf file_size: 2504713 relation: main_file success: 1 file_date_updated: 2025-11-14T09:44:10Z fulldoi: https://doi.org/10.1103/tldp-kvkd has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund - _id: 92c64506-16d5-11f0-9cad-87ce313ee832 grant_number: COE01 name: Quantum Science Austria (Serbyn) publication: PRX Quantum publication_identifier: eissn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/reaching-for-the-quantum-scars/ scopus_import: '1' status: public title: Finding periodic orbits in projected quantum many-body dynamics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2025' ... --- OA_place: publisher _id: '20607' acknowledged_ssus: - _id: Bio - _id: SSU - _id: LifeSc - _id: M-Shop acknowledgement: "I gratefully acknowledge the support of the ISTA Graduate School and the Scientific Service Units of\r\nISTA, whose resources made this work possible—especially the Imaging & Optics Facility, the Lab\r\nSupport Facility, and the Miba Machine Shop. I would like to thank two staff scientists in particular:\r\nRobert Hauschild (Imaging & Optics Facility) and Daniel Balazs (Lab Support Facility), for their\r\nassistance and advice. My PhD was partially funded by the Austrian Science Fund (FWF)\r\n(10.55776/P37169 and 10.55776/COE5)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal citation: ama: 'Mondal S. Oxygen and sulfur redox: Conversion kinetics and phase equilibria. 2025. doi:10.15479/AT-ISTA-20607' apa: 'Mondal, S. (2025). Oxygen and sulfur redox: Conversion kinetics and phase equilibria. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20607' chicago: 'Mondal, Soumyadip. “Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20607.' ieee: 'S. Mondal, “Oxygen and sulfur redox: Conversion kinetics and phase equilibria,” Institute of Science and Technology Austria, 2025.' ista: 'Mondal S. 2025. Oxygen and sulfur redox: Conversion kinetics and phase equilibria. Institute of Science and Technology Austria.' mla: 'Mondal, Soumyadip. Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20607.' short: 'S. Mondal, Oxygen and Sulfur Redox: Conversion Kinetics and Phase Equilibria, Institute of Science and Technology Austria, 2025.' corr_author: '1' das_tickbox: '1' date_created: 2025-11-07T12:40:54Z date_published: 2025-09-19T00:00:00Z date_updated: 2026-09-16T07:07:04Z day: '19' ddc: - '541' - '543' - '542' degree_awarded: PhD department: - _id: GradSch - _id: StFr doi: 10.15479/AT-ISTA-20607 doi_confirm: '1' file: - access_level: closed checksum: b5eed6a3dccb83cd2a8a22e11fd7d867 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: smondal date_created: 2025-11-13T16:47:47Z date_updated: 2025-11-13T16:47:47Z file_id: '20644' file_name: 2025_Mondal_Soumyadip_Thesis.docx file_size: 32589295 relation: source_file - access_level: closed checksum: 89b1529e0a7b524f46624d73ecadf8cb content_type: application/pdf creator: smondal date_created: 2025-11-13T16:47:46Z date_updated: 2025-11-13T16:47:46Z embargo: 2026-11-13 embargo_to: open_access file_id: '20645' file_name: 2025_Mondal_Soumyadip_Thesis.pdf file_size: 5007370 relation: main_file file_date_updated: 2025-11-13T16:47:47Z fulldoi: https://doi.org/10.15479/AT-ISTA-20607 has_accepted_license: '1' language: - iso: eng month: '09' oa_version: Published Version page: '71' project: - _id: 8df062be-16d5-11f0-9cad-f559b6612c7e grant_number: P37169 name: Singlet oxygen in non-aqueous oxygen redox chemistry - _id: 5eaf4378-b033-11f1-b276-f928018a46c1 grant_number: COE05 name: Materials for Energy Conversion and Storage (Freunberger) publication_identifier: isbn: - 978-3-99078-071-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12065' relation: part_of_dissertation status: public - id: '13044' relation: part_of_dissertation status: public - id: '20437' relation: part_of_dissertation status: deleted - id: '14687' relation: part_of_dissertation status: public status: public supervisor: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 title: 'Oxygen and sulfur redox: Conversion kinetics and phase equilibria' 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' ... --- OA_place: publisher OA_type: free access _id: '22828' abstract: - lang: eng text: 'We propose Joint Moment Estimation (JME), a method for continually and privately estimating both the first and second moments of a data stream with reduced noise compared to naive approaches. JME supports the matrix mechanism and exploits a joint sensitivity analysis to identify a privacy regime in which the second-moment estimation incurs no additional privacy cost, thereby improving accuracy while maintaining privacy. We demonstrate JME’s effectiveness in two applications: estimating the running mean and covariance matrix for Gaussian density estimation and model training with DP-Adam.' acknowledgement: "We thank Monika Henzinger for her valuable feedback and insightful discussions on earlier versions\r\nof this draft. We are also grateful to Mher Safaryan for his contributions to discussions on DP-Adam.\r\nAdditionally, we thank Ryan McKenna for suggesting Joint Clipping as a baseline.\r\nJalaj Upadhyay’s research was funded by the Rutgers Decanal Grant no. 302918, NSF CNS 2433628,\r\nGoogle Research Scholar Award, and Google Seed Fund Grant. A part of this work was done while\r\nvisiting the Institute of Science and Technology Austria (ISTA).\r\nNikita Kalinin’s research was funded in part by the Austrian Science Fund (FWF) [10.55776/COE12]" alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No author: - first_name: Nikita full_name: Kalinin, Nikita id: 4b14526e-14d2-11ed-ba64-c14c9553d137 last_name: Kalinin - first_name: Jalaj full_name: Upadhyay, Jalaj last_name: Upadhyay - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kalinin N, Upadhyay J, Lampert C. Continual release moment estimation with differential privacy. In: Advances in Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025:64002-64047. doi:10.52202/085713-1924' apa: 'Kalinin, N., Upadhyay, J., & Lampert, C. (2025). Continual release moment estimation with differential privacy. In Advances in Neural Information Processing Systems (Vol. 38, pp. 64002–64047). San Diego, CA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/085713-1924' chicago: Kalinin, Nikita, Jalaj Upadhyay, and Christoph Lampert. “Continual Release Moment Estimation with Differential Privacy.” In Advances in Neural Information Processing Systems, 38:64002–47. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-1924. ieee: N. Kalinin, J. Upadhyay, and C. Lampert, “Continual release moment estimation with differential privacy,” in Advances in Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38, pp. 64002–64047. ista: 'Kalinin N, Upadhyay J, Lampert C. 2025. Continual release moment estimation with differential privacy. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38, 64002–64047.' mla: Kalinin, Nikita, et al. “Continual Release Moment Estimation with Differential Privacy.” Advances in Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025, pp. 64002–47, doi:10.52202/085713-1924. short: N. Kalinin, J. Upadhyay, C. Lampert, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025, pp. 64002–64047. conference: location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' corr_author: '1' das_tickbox: '0' date_created: 2026-09-06T22:02:00Z date_published: 2025-12-02T00:00:00Z date_updated: 2026-09-16T07:40:56Z day: '02' department: - _id: GradSch - _id: ChLa doi: 10.52202/085713-1924 fulldoi: https://doi.org/10.52202/085713-1924 intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.52202/085713-1924 month: '12' oa: 1 oa_version: Published Version page: 64002-64047 project: - _id: d8f03aaa-b035-11f1-8588-d5147fa879e0 grant_number: COE12 name: Bilateral Artificial Intelligence (Lampert) publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9798331338275' issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Continual release moment estimation with differential privacy type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_place: repository OA_type: green _id: '22827' abstract: - lang: eng text: Quantized training of Large Language Models (LLMs) remains an open challenge, as maintaining accuracy while performing all matrix multiplications in low precision has proven difficult. This is particularly the case when fine-tuning pre-trained models, which can have large weight, activation, and error (output gradient) outlier values that make lower-precision optimization difficult. To address this, we present HALO, a new quantization-aware training approach for Transformers that enables accurate and efficient low-precision training by combining 1) strategic placement of Hadamard rotations in both forward and backward passes, which mitigate outliers, 2) high-performance kernel support, and 3) FSDP integration for low-precision communication. Our approach ensures that all large matrix multiplications during the forward and backward passes are executed in lower precision. Applied to LLaMa models, HALO achieves near-full-precision-equivalent results during fine-tuning on various tasks, while delivering up to 1.41x end-to-end speedup for full fine-tuning on RTX 4090 GPUs. HALO efficiently supports both standard and parameter-efficient fine-tuning (PEFT). Our results demonstrate the first practical approach to fully quantized LLM fine-tuning that maintains accuracy in INT8 and FP6 precision, while delivering performance benefits. acknowledgement: "This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 program (grant agreement PSAP, No. 101002047. This research also obtained\r\nfunding from the “UrbanTwin: An urban digital twin for climate action: Assessing policies and\r\nsolutions for energy, water and infrastructure” project, funded by the ETH-Domain Joint Initiative\r\nprogram in the Strategic Area Energy, Climate and Sustainable Environment." alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Saleh full_name: Ashkboos, Saleh last_name: Ashkboos - first_name: Mahdi full_name: Nikdan, Mahdi id: 66374281-f394-11eb-9cf6-869147deecc0 last_name: Nikdan - first_name: Soroush full_name: Tabesh, Soroush id: 06000900-6068-11ef-8d61-c2472ef2e752 last_name: Tabesh orcid: 0009-0003-4119-6281 - first_name: Roberto full_name: Lopez Castro, Roberto id: 18495c31-fb57-11ef-ba0d-c290e10e394e last_name: Lopez Castro - first_name: Torsten full_name: Hoefler, Torsten last_name: Hoefler - 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: 'Ashkboos S, Nikdan M, Tabesh S, Lopez Castro R, Hoefler T, Alistarh D-A. HALO: Hadamard-assisted lower-precision optimization for LLMs. In: 39th Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025:131755-131780. doi:10.52202/085713-3966' apa: 'Ashkboos, S., Nikdan, M., Tabesh, S., Lopez Castro, R., Hoefler, T., & Alistarh, D.-A. (2025). HALO: Hadamard-assisted lower-precision optimization for LLMs. In 39th Conference on Neural Information Processing Systems (Vol. 38, pp. 131755–131780). San Diego, CA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/085713-3966' chicago: 'Ashkboos, Saleh, Mahdi Nikdan, Soroush Tabesh, Roberto Lopez Castro, Torsten Hoefler, and Dan-Adrian Alistarh. “HALO: Hadamard-Assisted Lower-Precision Optimization for LLMs.” In 39th Conference on Neural Information Processing Systems, 38:131755–80. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-3966.' ieee: 'S. Ashkboos, M. Nikdan, S. Tabesh, R. Lopez Castro, T. Hoefler, and D.-A. Alistarh, “HALO: Hadamard-assisted lower-precision optimization for LLMs,” in 39th Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38, pp. 131755–131780.' ista: 'Ashkboos S, Nikdan M, Tabesh S, Lopez Castro R, Hoefler T, Alistarh D-A. 2025. HALO: Hadamard-assisted lower-precision optimization for LLMs. 39th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38, 131755–131780.' mla: 'Ashkboos, Saleh, et al. “HALO: Hadamard-Assisted Lower-Precision Optimization for LLMs.” 39th Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025, pp. 131755–80, doi:10.52202/085713-3966.' short: S. Ashkboos, M. Nikdan, S. Tabesh, R. Lopez Castro, T. Hoefler, D.-A. Alistarh, in:, 39th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025, pp. 131755–131780. conference: end_date: 2025-12-07 location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2025-12-02 das_tickbox: '0' date_created: 2026-09-06T22:02:00Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-09-17T06:39:18Z day: '01' department: - _id: DaAl - _id: GradSch doi: 10.52202/085713-3966 external_id: arxiv: - '2501.02625' fulldoi: https://doi.org/10.52202/085713-3966 intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2501.02625 month: '12' oa: 1 oa_version: Preprint page: 131755-131780 publication: 39th Conference on Neural Information Processing Systems publication_identifier: eissn: - 1049-5258 isbn: - '9798331338275' publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'HALO: Hadamard-assisted lower-precision optimization for LLMs' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_place: repository OA_type: green _id: '22832' abstract: - lang: eng text: "In many scientific experiments, the data annotating cost constraints the pace\r\nfor testing novel hypotheses. Yet, modern machine learning pipelines offer a\r\npromising solution—provided their predictions yield correct conclusions. We\r\nfocus on Prediction-Powered Causal Inferences (PPCI), i.e., estimating the\r\ntreatment effect in an unlabeled target experiment, relying on training data with\r\nthe same outcome annotated but potentially different treatment or effect modifiers.\r\nWe first show that conditional calibration guarantees valid PPCI at population\r\nlevel. Then, we introduce a sufficient representation constraint transferring validity\r\nacross experiments, which we propose to enforce in practice in Deconfounded\r\nEmpirical Risk Minimization, our new model-agnostic training objective. We\r\nvalidate our method on synthetic and real-world scientific data, solving impossible\r\nproblem instances for Empirical Risk Minimization even with standard invariance\r\nconstraints. In particular, for the first time, we achieve valid causal inference\r\non a scientific experiment with complex recording and no human annotations,\r\nfine-tuning a foundational model on our similar annotated experiment." acknowledgement: "We thank the Causal Learning and Artificial Intelligence group at ISTA for the continuous feedback\r\non the project and valuable discussions. We thank the Social Immunity group at ISTA, particularly\r\nJinook Oh, for the annotation program and Michaela Hoenigsberger for supporting our ecological\r\nexperiment. Riccardo Cadei is supported by a Google Research Scholar Award and a Google Initiated\r\nGift to Francesco Locatello. This research was funded in part by the Austrian Science Fund (FWF)\r\n10.55776/COE12). It was further partially supported by the ISTA Interdisciplinary Project Committee\r\nfor the collaborative project “ALED” between Francesco Locatello and Sylvia Cremer. For open\r\naccess purposes, the author has applied a CC BY public copyright license to any author accepted\r\nmanuscript version arising from this submission.\r\n" alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Riccardo full_name: Cadei, Riccardo id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b last_name: Cadei - first_name: Ilker full_name: Demirel, Ilker last_name: Demirel - first_name: Piersilvio full_name: De Bartolomeis, Piersilvio last_name: De Bartolomeis - first_name: Lukas full_name: Lindorfer, Lukas id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455 last_name: Lindorfer - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Cordelia full_name: Schmid, Cordelia last_name: Schmid - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Cadei R, Demirel I, De Bartolomeis P, et al. Prediction-Powered Causal Inferences. In: 39th Conference on Neural Information Processing Systems. Vol 38. Neural Information Processing Systems Foundation; 2025:82200-82229. doi:10.52202/085713-2479' apa: 'Cadei, R., Demirel, I., De Bartolomeis, P., Lindorfer, L., Cremer, S., Schmid, C., & Locatello, F. (2025). Prediction-Powered Causal Inferences. In 39th Conference on Neural Information Processing Systems (Vol. 38, pp. 82200–82229). San Diego, CA, United States: Neural Information Processing Systems Foundation. https://doi.org/10.52202/085713-2479' chicago: Cadei, Riccardo, Ilker Demirel, Piersilvio De Bartolomeis, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Prediction-Powered Causal Inferences.” In 39th Conference on Neural Information Processing Systems, 38:82200–229. Neural Information Processing Systems Foundation, 2025. https://doi.org/10.52202/085713-2479. ieee: R. Cadei et al., “Prediction-Powered Causal Inferences,” in 39th Conference on Neural Information Processing Systems, San Diego, CA, United States, 2025, vol. 38, pp. 82200–82229. ista: 'Cadei R, Demirel I, De Bartolomeis P, Lindorfer L, Cremer S, Schmid C, Locatello F. 2025. Prediction-Powered Causal Inferences. 39th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 38, 82200–82229.' mla: Cadei, Riccardo, et al. “Prediction-Powered Causal Inferences.” 39th Conference on Neural Information Processing Systems, vol. 38, Neural Information Processing Systems Foundation, 2025, pp. 82200–29, doi:10.52202/085713-2479. short: R. Cadei, I. Demirel, P. De Bartolomeis, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, 39th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2025, pp. 82200–82229. conference: end_date: 2025-12-07 location: San Diego, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2025-12-02 corr_author: '1' das_tickbox: '1' dataavailabilitystatement: "We share all the code implementation in the supplementary material.\r\nOur new experimental ecology dataset preview is anonymously shared on Figshare at\r\nhttps://figshare.com/s/9a490b6f6eeebd73350b. We further rely on ISTAnt dataset publicly\r\navailable at https://doi.org/10.6084/m9.figshare.26484934.v2. The synthetic experiments\r\non CausalMNIST relies on MNIST dataset LeCun [1998], publicly available. Additional\r\nexperimental details are reported in Section 5 and Appendices B-C." date_created: 2026-09-06T22:02:01Z date_published: 2025-12-01T00:00:00Z date_updated: 2026-09-17T06:56:40Z day: '01' department: - _id: FrLo - _id: GradSch - _id: SyCr doi: 10.52202/085713-2479 external_id: arxiv: - '2502.06343' fulldoi: https://doi.org/10.52202/085713-2479 intvolume: ' 38' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2502.06343 month: '12' oa: 1 oa_version: Preprint page: 82200-82229 project: - _id: a392d8f0-b034-11f1-b88e-d3025c6734f6 grant_number: COE12 name: Bilateral Artificial Intelligence (Locatello) publication: 39th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9798331338275' issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Prediction-Powered Causal Inferences type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2025' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '20324' abstract: - lang: eng text: We report relaxation oscillations in a one-dimensional array of Josephson junctions, wherein the array dynamically switches between low-current and high-current states. The oscillations are current-voltage dual to those ordinarily observed in single junctions. The current-voltage dual circuit quantitatively accounts for temporal dynamics of the array, including the dependence on biasing conditions. Injection locking of the oscillations results in well-developed current plateaux. A thermal model explains the self-consistent reduction of the superconducting gap due to overheating of the array in the high-current state. Our work suggests that overheating determines the switching from the high-current state to the low-current state. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: We gratefully acknowledge support from the Miba Machine Shop and the Nanofabrictation Facility at IST Austria. This work was supported by the Austrian FWF under Grant No. P33692-N (S.M., J.S., and A.P.H.), the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS Foundation research grant (A.P.H.). article_number: '014035' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 - first_name: Diego A full_name: Lancheros Naranjo, Diego A id: 6c55e976-15b2-11ec-abd3-d790e8937fde last_name: Lancheros Naranjo - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson-junction array. Physical Review Applied. 2025;24. doi:10.1103/qvls-7s3q apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (2025). Dual relaxation oscillations in a Josephson-junction array. Physical Review Applied. American Physical Society. https://doi.org/10.1103/qvls-7s3q chicago: Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson-Junction Array.” Physical Review Applied. American Physical Society, 2025. https://doi.org/10.1103/qvls-7s3q. ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson-junction array,” Physical Review Applied, vol. 24. American Physical Society, 2025. ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. 2025. Dual relaxation oscillations in a Josephson-junction array. Physical Review Applied. 24, 014035. mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson-Junction Array.” Physical Review Applied, vol. 24, 014035, American Physical Society, 2025, doi:10.1103/qvls-7s3q. short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, Physical Review Applied 24 (2025). corr_author: '1' date_created: 2025-09-10T05:41:30Z date_published: 2025-07-17T00:00:00Z date_updated: 2026-09-24T10:13:38Z day: '17' ddc: - '530' department: - _id: GradSch - _id: AnHi doi: 10.1103/qvls-7s3q ec_funded: 1 external_id: arxiv: - '2408.07829 ' isi: - '001537333100001' file: - access_level: open_access checksum: 6cc3c9beeb7c0a88ee0a072c9a32b78b content_type: application/pdf creator: dernst date_created: 2025-09-10T07:29:06Z date_updated: 2025-09-10T07:29:06Z file_id: '20335' file_name: 2025_PhysReviewAppl_Mukhopadhyay.pdf file_size: 1370466 relation: main_file success: 1 file_date_updated: 2025-09-10T07:29:06Z fulldoi: https://doi.org/10.1103/qvls-7s3q has_accepted_license: '1' intvolume: ' 24' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: Physical Review Applied publication_identifier: issn: - 2331-7019 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '18057' relation: earlier_version status: public scopus_import: '1' status: public title: Dual relaxation oscillations in a Josephson-junction array tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2025' ...