--- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21721' abstract: - lang: eng text: 'Swimming bacteria move through a fluid by actuating their moving body parts. They are force-free and can be described as hydrodynamic force dipoles: pushers or pullers. This modelling description is broadly used in biological physics and active matter research, and it has successfully predicted, for example, the superfluid behaviour of suspensions of pushers or the bend instability and emergence of turbulent flows in active nematics. However, this description accounts only for the translational motion of the swimming body and neglects the effects of hydrodynamic torque dipoles, which are relevant to bacteria with rotary motor-driven flagella, such as swimming Escherichia coli. Here we show that the torque dipole of confined swimming E. coli can power the persistent rotation of symmetric discs. The torque dipole leads to a traction force on the discs, an additive mechanism that is both contactless and independent of the orientation of the bacteria. Our results indicate that the torque dipole of swimming E. coli is notable in confined geometries, which is relevant to bacterial transport through porous materials, biofilms and the development of chiral fluids.' acknowledged_ssus: - _id: NanoFab - _id: EM-Fac acknowledgement: We thank E. Krasnopeeva for help with the bacterial culture, motility and genetic engineering. We thank Q. Martinet for help with the experimental design, F. Pertl for atomic force microscopy measurements and S. Hajek for the scanning electron microscopy imaging. This project has received funding from the European Research Council under the European Union’s Horizon Europe research and innovation programme (VULCAN, 101086998). The views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. J.P. thanks the Nanofabrication and Electron Microscopy Shared Scientific Units of ISTA for support. Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Daniel B full_name: Grober, Daniel B id: c692f879-718d-11ee-81f0-da7caa79c783 last_name: Grober - first_name: Tanumoy full_name: Dhar, Tanumoy last_name: Dhar - first_name: David full_name: Saintillan, David last_name: Saintillan - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Grober DB, Dhar T, Saintillan D, Palacci JA. The hydrodynamic torque dipole from rotary bacterial flagella powers symmetric discs. Nature Physics. 2026;22:620-627. doi:10.1038/s41567-026-03189-4 apa: Grober, D. B., Dhar, T., Saintillan, D., & Palacci, J. A. (2026). The hydrodynamic torque dipole from rotary bacterial flagella powers symmetric discs. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-026-03189-4 chicago: Grober, Daniel B, Tanumoy Dhar, David Saintillan, and Jérémie A Palacci. “The Hydrodynamic Torque Dipole from Rotary Bacterial Flagella Powers Symmetric Discs.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-026-03189-4. ieee: D. B. Grober, T. Dhar, D. Saintillan, and J. A. Palacci, “The hydrodynamic torque dipole from rotary bacterial flagella powers symmetric discs,” Nature Physics, vol. 22. Springer Nature, pp. 620–627, 2026. ista: Grober DB, Dhar T, Saintillan D, Palacci JA. 2026. The hydrodynamic torque dipole from rotary bacterial flagella powers symmetric discs. Nature Physics. 22, 620–627. mla: Grober, Daniel B., et al. “The Hydrodynamic Torque Dipole from Rotary Bacterial Flagella Powers Symmetric Discs.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 620–27, doi:10.1038/s41567-026-03189-4. short: D.B. Grober, T. Dhar, D. Saintillan, J.A. Palacci, Nature Physics 22 (2026) 620–627. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The datasets generated and analysed during the current study are openly available via Zenodo at https://doi.org/10.5281/zenodo.15236674 (ref. 32). All data are released under the CC-BY 4.0 licence. For any further questions about data access or reuse, please contact the corresponding author. date_created: 2026-04-12T22:01:51Z date_published: 2026-04-01T00:00:00Z date_updated: 2026-07-27T12:29:45Z day: '01' ddc: - '570' - '530' department: - _id: JePa doi: 10.1038/s41567-026-03189-4 external_id: pmid: - '42006933' file: - access_level: open_access checksum: bb28ed456cdd288d97854b084dd4b2e1 content_type: application/pdf creator: dernst date_created: 2026-07-27T12:28:27Z date_updated: 2026-07-27T12:28:27Z file_id: '22429' file_name: 2026_NaturePhysics_Grober.pdf file_size: 2960392 relation: main_file success: 1 file_date_updated: 2026-07-27T12:28:27Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '04' oa: 1 oa_version: Published Version page: 620-627 pmid: 1 project: - _id: bdac72da-d553-11ed-ba76-eae56e802b74 grant_number: '101086998' name: 'VULCAN: matter, powered from within' publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: The hydrodynamic torque dipole from rotary bacterial flagella powers symmetric discs 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: 22 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21716' abstract: - lang: eng text: Male germline development in plants is highly sensitive to heat stress, with elevated temperatures frequently impairing male fertility and consequently reducing seed production. Indeed, recent global warming has decreased major crop yields, emphasizing the urgent need to elucidate the molecular and cellular mechanisms underlying heat-induced male sterility. This review synthesizes current knowledge on how heat stress disrupts microsporogenesis and microgametogenesis, and how plants counteract these stresses through diverse thermotolerance mechanisms. We emphasize temperature-sensitive processes, including meiotic progression in male germ cells, programmed cell death of somatic tapetal nurse cells, and post-meiotic pollen tube development. We further discuss how epigenetic regulators enhance thermotolerance by reprogramming DNA methylation landscapes and modulating histone variant distribution. Finally, we propose future directions aimed at understanding the mechanisms of reproductive thermotolerance from the epigenetic perspective. acknowledgement: This work was supported by JSPS KAKENHI (grant number JP22J01430) and the Osamu Hayaishi Memorial Scholarship for Study Abroad for H.N. article_number: '102881' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Hiroki full_name: Nagai, Hiroki id: 608df3e6-e2ab-11ed-8890-c9318cec7da4 last_name: Nagai orcid: 0000-0003-1671-9434 - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: NAGAI H, Feng X. Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. 2026;91(6). doi:10.1016/j.pbi.2026.102881 apa: NAGAI, H., & Feng, X. (2026). Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2026.102881 chicago: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying Male Reproductive Thermotolerance.” Current Opinion in Plant Biology. Elsevier, 2026. https://doi.org/10.1016/j.pbi.2026.102881. ieee: H. NAGAI and X. Feng, “Genetic and epigenetic mechanisms underlying male reproductive thermotolerance,” Current Opinion in Plant Biology, vol. 91, no. 6. Elsevier, 2026. ista: NAGAI H, Feng X. 2026. Genetic and epigenetic mechanisms underlying male reproductive thermotolerance. Current Opinion in Plant Biology. 91(6), 102881. mla: NAGAI, HIROKI, and Xiaoqi Feng. “Genetic and Epigenetic Mechanisms Underlying Male Reproductive Thermotolerance.” Current Opinion in Plant Biology, vol. 91, no. 6, 102881, Elsevier, 2026, doi:10.1016/j.pbi.2026.102881. short: H. NAGAI, X. Feng, Current Opinion in Plant Biology 91 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: No data was used for the research described in the article. date_created: 2026-04-12T22:01:50Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T12:26:03Z day: '01' ddc: - '580' department: - _id: XiFe doi: 10.1016/j.pbi.2026.102881 external_id: pmid: - '41955759' file: - access_level: open_access checksum: 929e801eb8f2aef08cf9d9f97be2b2af content_type: application/pdf creator: dernst date_created: 2026-07-27T12:20:55Z date_updated: 2026-07-27T12:20:55Z file_id: '22428' file_name: 2026_CurrentOpinionPlantBiology_Nagai.pdf file_size: 2255022 relation: main_file success: 1 file_date_updated: 2026-07-27T12:20:55Z has_accepted_license: '1' intvolume: ' 91' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Current Opinion in Plant Biology publication_identifier: eissn: - 1879-0356 issn: - 1369-5266 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Genetic and epigenetic mechanisms underlying male reproductive thermotolerance 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: 91 year: '2026' ... --- OA_place: repository OA_type: green _id: '21726' abstract: - lang: eng text: Quantum control of the many-body wavefunction is a central challenge in quantum materials research, as it could yield a precise control knob to manipulate emergent phenomena. Floquet engineering, the coherent dressing of quantum states with periodic non-resonant optical fields, has become an important strategy for quantum control. Most applications to solid-state systems have targeted weakly interacting or single-ion states, leaving the manipulation of many-body wavefunctions largely unexplored. Here we use Floquet engineering to achieve quantum control of a strongly correlated Hubbard exciton in the one-dimensional Mott insulator Sr2CuO3. A non-resonant mid-infrared optical field coherently dresses the exciton wavefunction, driving its rotation between bright and dark states. We use resonant third-harmonic generation to quantify ultrafast π/2 rotations on the Bloch sphere spanned by these exciton states. Our work advances the quest towards programmable control of correlated states and exciton-based quantum sensing. acknowledgement: We thank K. Burch, M. Buzzi, P. Cappellaro, A. Cavalleri, E. Demler, M. Eckstein, T. Giamarchi, D. Hsieh, H. Okamoto, D. Reis, T. Tohyama, P. Werner and A. Yacoby for insightful discussions. We thank B. Baxley for assistance with graphics. This work was primarily supported by the US Department of Energy, Office of Basic Energy Sciences, Early Career Award Program, under award no. DE-SC0022883 (D.R.B., F.G., T.M. and M.M.) and award no. DE-SC0024494 (D.C. and M.C.). D.C. and P.B.M.D.O. acknowledge funding from the NSF GRFP under grant nos. DGE-1845298 and DGE 2140743, respectively. The work performed at Brookhaven National Laboratory was supported by the US Department of Energy, Division of Materials Science, under contract no. DE-SC0012704. We acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 531215165 (Research Unit “OPTIMAL’). This work was supported by the Cluster of Excellence ‘Advanced Imaging of Matter’ (AIM) and the Max Planck-New York City Center for Non-Equilibrium Quantum Phenomena. The Flatiron Institute is a division of the Simons Foundation. Simulations were performed with computing resources granted by RWTH Aachen University under projects rwth0752 and rwth1258. We acknowledge computing time on the supercomputer JURECA52 at Forschungszentrum Jülich under the project ID enhancerg. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva orcid: 0000-0002-7438-1139 - first_name: Deven full_name: Carmichael, Deven last_name: Carmichael - first_name: Clara S. full_name: Weber, Clara S. last_name: Weber - first_name: I. Te full_name: Lu, I. Te last_name: Lu - first_name: Filippo full_name: Glerean, Filippo last_name: Glerean - first_name: Tepie full_name: Meng, Tepie last_name: Meng - first_name: Pedro B.M. full_name: De Oliveira, Pedro B.M. last_name: De Oliveira - first_name: Christopher C. full_name: Homes, Christopher C. last_name: Homes - first_name: Igor A. full_name: Zaliznyak, Igor A. last_name: Zaliznyak - first_name: G. D. full_name: Gu, G. D. last_name: Gu - first_name: Mark P.M. full_name: Dean, Mark P.M. last_name: Dean - first_name: Angel full_name: Rubio, Angel last_name: Rubio - first_name: Dante M. full_name: Kennes, Dante M. last_name: Kennes - first_name: Martin full_name: Claassen, Martin last_name: Claassen - first_name: Matteo full_name: Mitrano, Matteo last_name: Mitrano citation: ama: Baykusheva DR, Carmichael D, Weber CS, et al. Quantum control of Hubbard excitons. Nature Materials. 2026;25:937-943. doi:10.1038/s41563-026-02517-6 apa: Baykusheva, D. R., Carmichael, D., Weber, C. S., Lu, I. T., Glerean, F., Meng, T., … Mitrano, M. (2026). Quantum control of Hubbard excitons. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-026-02517-6 chicago: Baykusheva, Denitsa Rangelova, Deven Carmichael, Clara S. Weber, I. Te Lu, Filippo Glerean, Tepie Meng, Pedro B.M. De Oliveira, et al. “Quantum Control of Hubbard Excitons.” Nature Materials. Springer Nature, 2026. https://doi.org/10.1038/s41563-026-02517-6. ieee: D. R. Baykusheva et al., “Quantum control of Hubbard excitons,” Nature Materials, vol. 25. Springer Nature, pp. 937–943, 2026. ista: Baykusheva DR, Carmichael D, Weber CS, Lu IT, Glerean F, Meng T, De Oliveira PBM, Homes CC, Zaliznyak IA, Gu GD, Dean MPM, Rubio A, Kennes DM, Claassen M, Mitrano M. 2026. Quantum control of Hubbard excitons. Nature Materials. 25, 937–943. mla: Baykusheva, Denitsa Rangelova, et al. “Quantum Control of Hubbard Excitons.” Nature Materials, vol. 25, Springer Nature, 2026, pp. 937–43, doi:10.1038/s41563-026-02517-6. short: D.R. Baykusheva, D. Carmichael, C.S. Weber, I.T. Lu, F. Glerean, T. Meng, P.B.M. De Oliveira, C.C. Homes, I.A. Zaliznyak, G.D. Gu, M.P.M. Dean, A. Rubio, D.M. Kennes, M. Claassen, M. Mitrano, Nature Materials 25 (2026) 937–943. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The data that support the findings of this study are present in the Article and its Supplementary Information. Source data for Figs. 1–4 are available via Figshare at https://doi.org/10.6084/m9.figshare.31146367 (ref. 51). Any additional data are available from the corresponding authors upon request. date_created: 2026-04-12T22:01:53Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T12:32:56Z day: '01' department: - _id: DeBa doi: 10.1038/s41563-026-02517-6 external_id: arxiv: - '2601.20695 ' intvolume: ' 25' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2601.20695 month: '06' oa: 1 oa_version: Preprint page: 937-943 publication: Nature Materials publication_identifier: eissn: - 1476-4660 issn: - 1476-1122 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41563-026-02697-1 researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: Quantum control of Hubbard excitons type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2026' ... --- OA_type: closed access _id: '21730' abstract: - lang: eng text: Hydrogen peroxide (H2O2) is a crucial member of the reactive oxygen species (ROS) family, playing roles in cellular signalling and immune responses in human health. Moreover, it is a potential biomarker of diabetes when present in aberrant concentrations. Therefore, monitoring trace levels of H2O2 has become a research hotspot for analytical and sensor chemists. In this context, we report a rhodamine-based fluorescent probe (RN), which shows excellent fluorescent enhancement at 555 nm upon the addition of H2O2 along with a low limit of detection (LOD) of 0.67 ppm and fast response (∼2 min). The probe is highly selective for H2O2, showing no fluorescence enhancement with other ROS. RN is synthesised in a one-pot chemical reaction using rhodamine 6G (R6G) and 4,7,10-trioxa-1,13-tridecanediamine (TTDA). H2O2 detection in pre-treated milk samples proves its real-world viability. We found that RN shows low cytotoxicity, which allowed us to successfully explore its potential to monitor H2O2 generation in a diabetic L929 skin cell line and diabetic mice liver tissue. This result demonstrates promising features for assessing early diabetic progression through fluorescence imaging. acknowledged_ssus: - _id: LifeSc acknowledgement: "MM acknowledges the Government of India for DST-INSPIRE\r\nfellowship [IF200389] and Federal Ministry of Education, Science and Research (BMBWF) and the OeAD – Austria’s Agency for Education and Internationalisation for an Ernst Mach Grant, weltweit (grant number MPC-2024-01518) for research internship at ISTA. The Scientific Service Units of ISTA supported this research through resources provided by the Lab Support Facility. PG acknowledges the ANRF, India, for his NPDF fellowship (File no. PDF/2022/001960). PB acknowledges ANRF, India, for the SERB-CRG sponsored project GAP-240712 (vide reference no. CRG/2022/001679)." article_processing_charge: No article_type: original author: - first_name: Moumita full_name: Mondal, Moumita last_name: Mondal - first_name: Pravat full_name: Ghorai, Pravat last_name: Ghorai - first_name: Asmita full_name: Samadder, Asmita last_name: Samadder - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Priyabrata full_name: Banerjee, Priyabrata last_name: Banerjee citation: ama: Mondal M, Ghorai P, Samadder A, Freunberger SA, Banerjee P. H2O2 responsive rhodamine-based probe for monitoring early-stage diabetes diagnosis. Journal of Materials Chemistry B. 2026;14(17):5314-5322. doi:10.1039/d5tb02687c apa: Mondal, M., Ghorai, P., Samadder, A., Freunberger, S. A., & Banerjee, P. (2026). H2O2 responsive rhodamine-based probe for monitoring early-stage diabetes diagnosis. Journal of Materials Chemistry B. Royal Society of Chemistry. https://doi.org/10.1039/d5tb02687c chicago: Mondal, Moumita, Pravat Ghorai, Asmita Samadder, Stefan Alexander Freunberger, and Priyabrata Banerjee. “H2O2 Responsive Rhodamine-Based Probe for Monitoring Early-Stage Diabetes Diagnosis.” Journal of Materials Chemistry B. Royal Society of Chemistry, 2026. https://doi.org/10.1039/d5tb02687c. ieee: M. Mondal, P. Ghorai, A. Samadder, S. A. Freunberger, and P. Banerjee, “H2O2 responsive rhodamine-based probe for monitoring early-stage diabetes diagnosis,” Journal of Materials Chemistry B, vol. 14, no. 17. Royal Society of Chemistry, pp. 5314–5322, 2026. ista: Mondal M, Ghorai P, Samadder A, Freunberger SA, Banerjee P. 2026. H2O2 responsive rhodamine-based probe for monitoring early-stage diabetes diagnosis. Journal of Materials Chemistry B. 14(17), 5314–5322. mla: Mondal, Moumita, et al. “H2O2 Responsive Rhodamine-Based Probe for Monitoring Early-Stage Diabetes Diagnosis.” Journal of Materials Chemistry B, vol. 14, no. 17, Royal Society of Chemistry, 2026, pp. 5314–22, doi:10.1039/d5tb02687c. short: M. Mondal, P. Ghorai, A. Samadder, S.A. Freunberger, P. Banerjee, Journal of Materials Chemistry B 14 (2026) 5314–5322. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: 'The data supporting this article have been included as part of the supplementary information (SI). The supplementary information includes all spectral profiles, plots and tabulated data. See DOI: https://doi.org/10.1039/d5tb02687c.' date_created: 2026-04-13T07:45:26Z date_published: 2026-05-06T00:00:00Z date_updated: 2026-07-27T12:36:05Z day: '06' department: - _id: StFr doi: 10.1039/d5tb02687c external_id: pmid: - '41958432' intvolume: ' 14' issue: '17' language: - iso: eng month: '05' oa_version: None page: 5314-5322 pmid: 1 publication: Journal of Materials Chemistry B publication_identifier: eissn: - 2050-7518 issn: - 2050-750X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: H2O2 responsive rhodamine-based probe for monitoring early-stage diabetes diagnosis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2026' ... --- OA_place: publisher _id: '21854' abstract: - lang: eng text: "As neural-network-based models grow both in size and popularity, interest has grown in making the models smaller and more efficient to train. To that end, many methods have been proposed to prune models by reducing their number of nonzero parameters. Additionally, parameter-efficient fine-tuning, in which a much smaller number of parameters than the total contained in the model is updated during training, has become very popular, especially in the space of Large Language Models. At the same time, the increasingly routine deployment of machine learning in real-world applications has spurred a drive to make them more trustworthy - in the sense of, among other things, being unbiased, interpretable, and editable. In this thesis, we examine the interplay between efficiency and trustworthiness.\r\n\r\nFirst, we analyze the effects of model pruning on bias in computer vision models, demonstrating that increased sparsity leads to greater bias, largely as a function of increased model uncertainty in marginal cases. Based on this observation, we propose several bias mitigation techniques. Then, we demonstrate that example-specific model pruning can improve model interpretation methods while improving pruning efficiency to make example-specific model pruning feasible in real time. Then, we investigate the effectiveness of parameter-efficient and data-efficient model personalization via fine-tuning, demonstrating that it is highly feasible with very small computational and data resources. Finally, we consider efficiency in editing model knowledge using a custom synthetic data framework, demonstrating that parameter-efficient, low-rank fine-tuning frequently outperforms full-rank fine-tuning, and, additionally, that restricting which model blocks are fine-tuned frequently improves results. Together, the results in this thesis provide new insights and techniques for combining trustworthiness and efficiency during neural network inference and training.\r\n\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: "The research in this Ph.D. was funded in whole\r\nor in part by the Austrian Science Fund (FWF) W1260-N35 (Vienna Graduate School for\r\nComputational Optimization). For open access purposes the author has applied a CC BY\r\npublic copyright license to any author accepted manuscript version arising from this submission\r\nwherever possible. Additionally, I am grateful to Alois Schlögl, Waleed Khalid, and the rest of\r\nthe ISTA Scientific Computing team for building and maintaining the infrastructure I used\r\nto run experiments. I’m also deeply grateful to the Alistarh group’s administrative assistant,\r\nChristine Francois, who always deals with our nonsense with common sense and a smile.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 citation: ama: Iofinova EB. On the utility and effects of efficiency in artificial neural networks. 2026. doi:10.15479/AT-ISTA-21854 apa: Iofinova, E. B. (2026). On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21854 chicago: Iofinova, Eugenia B. “On the Utility and Effects of Efficiency in Artificial Neural Networks.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21854. ieee: E. B. Iofinova, “On the utility and effects of efficiency in artificial neural networks,” Institute of Science and Technology Austria, 2026. ista: Iofinova EB. 2026. On the utility and effects of efficiency in artificial neural networks. Institute of Science and Technology Austria. mla: Iofinova, Eugenia B. On the Utility and Effects of Efficiency in Artificial Neural Networks. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21854. short: E.B. Iofinova, On the Utility and Effects of Efficiency in Artificial Neural Networks, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '1' date_created: 2026-05-11T08:43:22Z date_published: 2026-05-11T00:00:00Z date_updated: 2026-07-27T12:50:04Z day: '11' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/AT-ISTA-21854 doi_confirm: '1' file: - access_level: closed checksum: 2e148dad920e3f9b7c32796e0ba2e5f7 content_type: application/zip creator: eiofinov date_created: 2026-05-11T08:36:01Z date_updated: 2026-05-11T08:36:01Z file_id: '21856' file_name: EIofinova_thesis_FinalVersion.zip file_size: 28479571 relation: source_file - access_level: open_access checksum: b10c2933f386f532b2dbf28b19c5525c content_type: application/pdf creator: eiofinov date_created: 2026-05-13T13:10:48Z date_updated: 2026-05-13T13:10:48Z file_id: '21877' file_name: 2026_Iofinova_Eugenia_Thesis.pdf file_size: 18137757 relation: main_file success: 1 file_date_updated: 2026-05-13T13:10:48Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '237' project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publisher_comment: In reference to IEEE copyrighted material which is used with permission in this thesis, the IEEE does not endorse any of ISTA's products or services. Internal or personal use of this material is permitted. If interested in reprinting/republishing IEEE copyrighted material for advertising or promotional purposes or for creating new collective works for resale or redistribution, please go to http://www.ieee.org/publications_standards/publications/rights/rights_link.html to learn how to obtain a License from RightsLink. If applicable, University Microfilms and/or ProQuest Library, or the Archives of Canada may supply single copies of the dissertation. related_material: record: - id: '14771' relation: part_of_dissertation status: public - id: '18121' relation: part_of_dissertation status: public - id: '21858' relation: part_of_dissertation status: public - id: '21859' relation: part_of_dissertation status: public - id: '21857' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: On the utility and effects of efficiency in artificial neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: green _id: '21857' abstract: - lang: eng text: "The availability of powerful open-source large language models (LLMs) opens exciting use cases, such as using personal data to fine-tune these models to imitate a user’s unique writing style. Two key requirements for this functionality are personalization–in the sense that the output should recognizably reflect the user’s own writing style—and privacy–users may justifiably be wary of uploading extremely personal data, such as their email archive, to a third-party service. In this paper, we demonstrate the feasibility of training and running such an assistant, which we call Panza, on commodity hardware, for the specific use case of email generation. Panza’s personalization features are based on a combination of parameter-efficient fine-tuning using a variant of the Reverse Instructions technique [1] and Retrieval-Augmented Generation (RAG) [2]. We demonstrate that this combination allows us to fine-tune an LLM to reflect a user’s writing style using limited data, while executing on extremely limited resources, e.g. on a free Google Colab instance. Our key methodological contribution is the first detailed study of evaluation metrics for this task, and\r\nof how different choices of system components–the use of RAG and of different fine-tuning approaches–impact the system’s performance. Additionally, we demonstrate that very little data - under 100 email samples - are sufficient to create models that convincingly imitate humans, showcasing a previously unknown attack vector in language models. We are releasing the full Panza code as well as three new email datasets licensed for research use." article_number: '81' article_processing_charge: No author: - first_name: Armand full_name: Nicolicioiu, Armand last_name: Nicolicioiu - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Andrej full_name: Jovanovic, Andrej last_name: Jovanovic - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Mahdi full_name: Nikdan, Mahdi id: 66374281-f394-11eb-9cf6-869147deecc0 last_name: Nikdan - first_name: Andrei full_name: Panferov, Andrei id: 2c18daae-4dbe-11ef-8491-98ce2d960f09 last_name: Panferov - first_name: Ilia full_name: Markov, Ilia id: D0CF4148-C985-11E9-8066-0BDEE5697425 last_name: Markov - first_name: Nir full_name: Shavit, Nir last_name: Shavit - 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: 'Nicolicioiu A, Iofinova EB, Jovanovic A, et al. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. OpenReview; 2026.' apa: 'Nicolicioiu, A., Iofinova, E. B., Jovanovic, A., Kurtic, E., Nikdan, M., Panferov, A., … Alistarh, D.-A. (2026). Panza: Investigating the feasibility of fully-local personalized text generation. Third Conference on Parsimony and Learning (Proceedings Track). Tübíngen, Germany: OpenReview.' chicago: 'Nicolicioiu, Armand, Eugenia B Iofinova, Andrej Jovanovic, Eldar Kurtic, Mahdi Nikdan, Andrei Panferov, Ilia Markov, Nir Shavit, and Dan-Adrian Alistarh. Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation. Third Conference on Parsimony and Learning (Proceedings Track). OpenReview, 2026.' ieee: 'A. Nicolicioiu et al., Panza: Investigating the feasibility of fully-local personalized text generation. OpenReview, 2026.' ista: 'Nicolicioiu A, Iofinova EB, Jovanovic A, Kurtic E, Nikdan M, Panferov A, Markov I, Shavit N, Alistarh D-A. 2026. Panza: Investigating the feasibility of fully-local personalized text generation, OpenReview,p.' mla: 'Nicolicioiu, Armand, et al. “Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation.” Third Conference on Parsimony and Learning (Proceedings Track), 81, OpenReview, 2026.' short: 'A. Nicolicioiu, E.B. Iofinova, A. Jovanovic, E. Kurtic, M. Nikdan, A. Panferov, I. Markov, N. Shavit, D.-A. Alistarh, Panza: Investigating the Feasibility of Fully-Local Personalized Text Generation, OpenReview, 2026.' conference: end_date: 2026-03-26 location: Tübíngen, Germany name: 'CPAL: Conference on Parsimony and Learning' start_date: 2026-03-23 corr_author: '1' date_created: 2026-05-11T08:50:28Z date_published: 2026-03-06T00:00:00Z date_updated: 2026-07-27T12:50:03Z day: '06' department: - _id: GradSch - _id: DaAl keyword: - LLMs - PEFT - LoRA - personalization - efficient ML language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/pdf?id=soFWnTqd23 month: '03' oa: 1 oa_version: Accepted Version publication: Third Conference on Parsimony and Learning (Proceedings Track) publication_status: published publisher: OpenReview quality_controlled: '1' related_material: record: - id: '21854' relation: dissertation_contains status: public status: public title: 'Panza: Investigating the feasibility of fully-local personalized text generation' 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_poster user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository OA_type: green _id: '21859' abstract: - lang: eng text: As artificial neural networks, and specifically large language models, have improved rapidly in capabilities and quality, they have increasingly been deployed in real-world applications, from customer service to Google search, despite the fact that they frequently make factually incorrect or undesirable statements. This trend has inspired practical and academic interest in model editing, that is, in adjusting the weights of the model to modify its likely outputs for queries relating to a specific fact or set of facts. This may be done either to amend a fact or set of facts, for instance, to fix a frequent error in the training data, or to suppress a fact or set of facts entirely, for instance, in case of dangerous knowledge. Multiple methods have been proposed to do such edits. However, at the same time, it has been shown that such model editing can be brittle and incomplete. Moreover the effectiveness of any model editing method necessarily depends on the data on which the model is trained, and, therefore, a good understanding of the interaction of the training data distribution and the way it is stored in the network is necessary and helpful to reliably perform model editing. However, working with large language models trained on real-world data does not allow us to understand this relationship or fully measure the effects of model editing. We therefore propose Behemoth, a fully synthetic data generation framework. To demonstrate the practical insights from the framework, we explore model editing in the context of simple tabular data, demonstrating surprising findings that, in some cases, echo real-world results, for instance, that in some cases restricting the update rank results in a more effective update. acknowledged_ssus: - _id: ScienComp acknowledgement: "EI thanks Weiwei Yang, Janardhan Kulkani, and Kate Lytvynets for their advice and support in\r\ndeveloping an earlier version of the Behemoth library. This research was supported by the Scientific\r\nService Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).\r\nEI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.\r\n" article_processing_charge: No arxiv: 1 author: - first_name: Eugenia B full_name: Iofinova, Eugenia B id: f9a17499-f6e0-11ea-865d-fdf9a3f77117 last_name: Iofinova orcid: 0000-0002-7778-3221 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. doi:10.48550/arXiv.2601.23153' apa: 'Iofinova, E. B., & Alistarh, D.-A. (n.d.). Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv. https://doi.org/10.48550/arXiv.2601.23153' chicago: 'Iofinova, Eugenia B, and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2601.23153.' ieee: 'E. B. Iofinova and D.-A. Alistarh, “Behemoth: Benchmarking unlearning in LLMs using fully synthetic data,” arXiv. .' ista: 'Iofinova EB, Alistarh D-A. Behemoth: Benchmarking unlearning in LLMs using fully synthetic data. arXiv, 10.48550/arXiv.2601.23153.' mla: 'Iofinova, Eugenia B., and Dan-Adrian Alistarh. “Behemoth: Benchmarking Unlearning in LLMs Using Fully Synthetic Data.” ArXiv, doi:10.48550/arXiv.2601.23153.' short: E.B. Iofinova, D.-A. Alistarh, ArXiv (n.d.). corr_author: '1' date_created: 2026-05-11T08:58:07Z date_published: 2026-01-30T00:00:00Z date_updated: 2026-07-27T12:50:03Z day: '30' department: - _id: GradSch - _id: DaAl doi: 10.48550/arXiv.2601.23153 external_id: arxiv: - '2601.23153' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2601.23153 month: '01' oa: 1 oa_version: Preprint project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication: arXiv publication_status: draft related_material: record: - id: '21854' relation: dissertation_contains status: public status: public title: 'Behemoth: Benchmarking unlearning in LLMs using fully synthetic data' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: repository _id: '21422' article_processing_charge: No author: - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 citation: ama: Sunko V. Data underpinning “Magneto-optical Kerr effect in an A-type antiferromagnet.” 2026. doi:10.15479/AT-ISTA-21422 apa: Sunko, V. (2026). Data underpinning “Magneto-optical Kerr effect in an A-type antiferromagnet.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21422 chicago: Sunko, Veronika. “Data Underpinning ‘Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21422. ieee: V. Sunko, “Data underpinning ‘Magneto-optical Kerr effect in an A-type antiferromagnet.’” Institute of Science and Technology Austria, 2026. ista: Sunko V. 2026. Data underpinning ‘Magneto-optical Kerr effect in an A-type antiferromagnet’, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21422. mla: Sunko, Veronika. Data Underpinning “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21422. short: V. Sunko, (2026). corr_author: '1' date_created: 2026-03-11T07:04:26Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-07-27T13:59:27Z day: '11' department: - _id: VeSu doi: 10.15479/AT-ISTA-21422 file: - access_level: open_access checksum: 54db0b68f0cf919009317fd3da8f733b content_type: application/zip creator: vsunko date_created: 2026-03-11T10:28:34Z date_updated: 2026-03-11T10:28:34Z file_id: '21429' file_name: MBT_Data_Paper.zip file_size: 85004 relation: main_file success: 1 - access_level: open_access checksum: df1785b7ada7cd07f76a441ee4f52266 content_type: text/plain creator: vsunko date_created: 2026-03-11T10:28:37Z date_updated: 2026-03-11T10:28:37Z file_id: '21430' file_name: README.txt file_size: 2593 relation: main_file success: 1 file_date_updated: 2026-03-11T10:28:37Z has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '21872' relation: used_in_publication status: public status: public title: Data underpinning "Magneto-optical Kerr effect in an A-type antiferromagnet" 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21759' abstract: - lang: eng text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges.' acknowledgement: "We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.)." article_number: '102472' article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Elia full_name: Mascolo, Elia id: 776a6ed0-a053-11f0-8635-80b95e0e0d53 last_name: Mascolo orcid: 0000-0003-2977-7844 - first_name: Reka E full_name: Körei, Reka E id: 50FDE43E-AA30-11E9-A72B-8A12E6697425 last_name: Körei - first_name: Noa O. full_name: Borst, Noa O. last_name: Borst - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 2026;98. doi:10.1016/j.gde.2026.102472' apa: 'Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., & Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2026.102472' chicago: 'Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development. Elsevier, 2026. https://doi.org/10.1016/j.gde.2026.102472.' ieee: 'E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” Current Opinion in Genetics and Development, vol. 98. Elsevier, 2026.' ista: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 98, 102472.' mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” Current Opinion in Genetics and Development, vol. 98, 102472, Elsevier, 2026, doi:10.1016/j.gde.2026.102472.' short: E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics and Development 98 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: No data were used for the research described in the article. date_created: 2026-04-26T22:01:46Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T13:40:24Z day: '01' ddc: - '570' department: - _id: GaTk - _id: NiBa doi: 10.1016/j.gde.2026.102472 file: - access_level: open_access checksum: ac8bbee61717bfe7116e312cc6825259 content_type: application/pdf creator: dernst date_created: 2026-07-27T13:39:59Z date_updated: 2026-07-27T13:39:59Z file_id: '22590' file_name: 2026_CurrentOpinionGeneticsDev_Mascolo.pdf file_size: 3190001 relation: main_file success: 1 file_date_updated: 2026-07-27T13:39:59Z has_accepted_license: '1' intvolume: ' 98' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication: Current Opinion in Genetics and Development publication_identifier: eissn: - 1879-0380 issn: - 0959-437X publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 'Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges' 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: 98 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21849' abstract: - lang: eng text: The development of complex tissues relies on the precise assignment of cell identity. At the molecular scale, this process depends on the deposition of epigenetic modifications—such as methylation—that are regulated by complex biochemical networks and occur at specific regions on the DNA and chromatin. Here we show that despite the complexity of epigenetic regulation, dynamical scaling and self-similarity of DNA methylation marks emerge in embryonic development. Drawing on single-cell multi-omics experiments, super-resolution microscopy and statistical physics, we demonstrate that these phenomena originate in dynamical feedback between DNA methylation and the formation of nanoscale dynamic chromatin aggregates. These nanoscale processes lead to genome-wide increase in DNA methylation marks following a power law and self-similar correlation functions. Using this framework, we identify methylation patterns that precede gene expression changes in embryonic symmetry breaking. Our work identifies linear sequencing measurements as a laboratory to study mesoscopic biophysical processes in vivo. acknowledgement: We thank all members of the W.R. and S.R. laboratories, F. Piazza, B. D. Simons, and F. Jülicher for helpful discussions. We thank M. Ciarchi for providing annotations for the chromatin compartments. S.R. is a member of the Center for Nano Science (CeNS). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 950349). Research in W.R.’s laboratory was supported by the Biotechnology and Biological Sciences Research Council (BB/K010867/1), Wellcome (095645/Z/11/Z) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (EpiCell lineage 882798). F.O. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 101034413. Open access funding provided by Max Planck Society. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Tim full_name: Lohoff, Tim last_name: Lohoff - first_name: Ioannis full_name: Kafetzopoulos, Ioannis last_name: Kafetzopoulos - first_name: Stephen J. full_name: Clark, Stephen J. last_name: Clark - first_name: Laura full_name: Benson, Laura last_name: Benson - first_name: Fatima full_name: Santos, Fatima last_name: Santos - first_name: Felix full_name: Krueger, Felix last_name: Krueger - first_name: Simon full_name: Walker, Simon last_name: Walker - first_name: Wolf full_name: Reik, Wolf last_name: Reik - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Lohoff T, Kafetzopoulos I, et al. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 2026;22:931-940. doi:10.1038/s41567-026-03263-x apa: Olmeda, F., Lohoff, T., Kafetzopoulos, I., Clark, S. J., Benson, L., Santos, F., … Rulands, S. (2026). Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-026-03263-x chicago: Olmeda, Fabrizio, Tim Lohoff, Ioannis Kafetzopoulos, Stephen J. Clark, Laura Benson, Fatima Santos, Felix Krueger, Simon Walker, Wolf Reik, and Steffen Rulands. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” Nature Physics. Springer Nature, 2026. https://doi.org/10.1038/s41567-026-03263-x. ieee: F. Olmeda et al., “Scaling and self-similarity in the formation of the embryonic epigenome,” Nature Physics, vol. 22. Springer Nature, pp. 931–940, 2026. ista: Olmeda F, Lohoff T, Kafetzopoulos I, Clark SJ, Benson L, Santos F, Krueger F, Walker S, Reik W, Rulands S. 2026. Scaling and self-similarity in the formation of the embryonic epigenome. Nature Physics. 22, 931–940. mla: Olmeda, Fabrizio, et al. “Scaling and Self-Similarity in the Formation of the Embryonic Epigenome.” Nature Physics, vol. 22, Springer Nature, 2026, pp. 931–40, doi:10.1038/s41567-026-03263-x. short: F. Olmeda, T. Lohoff, I. Kafetzopoulos, S.J. Clark, L. Benson, F. Santos, F. Krueger, S. Walker, W. Reik, S. Rulands, Nature Physics 22 (2026) 931–940. das_tickbox: '1' dataavailabilitystatement: All sequencing datasets reported in this paper are available on Gene Expression Omnibus (GEO) under accession GSE166226. STORM localization data are available on Zenodo (https://doi.org/10.5281/zenodo.18965309)57. Raw images are available upon request. Code for computing the correlation functions and STORM analysis are available via GitHub at https://github.com/srulands/inference_of_spatio-temporal_processes. date_created: 2026-05-10T22:02:16Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T13:56:09Z day: '01' ddc: - '570' department: - _id: EdHa doi: 10.1038/s41567-026-03263-x ec_funded: 1 external_id: pmid: - '42318073' file: - access_level: open_access checksum: 58e7734f1ebaf6def642140cb489f08f content_type: application/pdf creator: dernst date_created: 2026-07-27T13:54:58Z date_updated: 2026-07-27T13:54:58Z file_id: '22591' file_name: 2026_NaturePhysics_Olmeda.pdf file_size: 7932222 relation: main_file success: 1 file_date_updated: 2026-07-27T13:54:58Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 931-940 pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Scaling and self-similarity in the formation of the embryonic epigenome 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: 22 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21883' abstract: - lang: eng text: Three-dimensional (3D) printing has rapidly developed from a niche hobbyist activity into a widely accessible and indispensable technology across multiple scientific disciplines. Within microscopy, optical engineering laboratories and imaging core facilities, 3D printing enables creating customised solutions for sample holders, optical components and everyday laboratory tools that traditionally required specialised machining. By providing rapid prototyping, low-cost production and reproducibility, 3D printing facilitates innovation and efficiency in facility operations. This article provides a perspective on the possibilities, challenges, and practical aspects of implementing 3D printing within microscopy core facilities. Instead of providing technical review about 3D printing, we focus on service organisation, user engagement, resource management and community-driven repositories for design dissemination. Our aim is to share insights with those considering the implementation of 3D printing as a service for developing add-on components to ease the operation of different aspects of the machine-park driven services and those who are managing advanced instrumentation within research groups. acknowledged_ssus: - _id: Bio - _id: M-Shop acknowledgement: "This work was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Imaging & Optics Facility (IOF) and the MiBa Machine Shop. Specifically; Robert Hauschild (IOF), sharing designs, insights and pioneering 3D printing activities at the Imaging and Optics Facility; Bernhard Hochreiter (IOF), for support and testing of anoxic chamber. We also thank Ana Rita Carvalho Faria and Oliver Biehlmaier (Biozentrum University of Basel, Imaging Core Facility) for sharing the design of the adopted power meter.\r\nOpen Access funding provided by Institute of Science and Technology Austria." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mohammad full_name: Goudarzi, Mohammad id: 3384113A-F248-11E8-B48F-1D18A9856A87 last_name: Goudarzi - first_name: Maximilian full_name: Schuster, Maximilian id: 37e65def-d415-11eb-ae59-a7b67be103db last_name: Schuster - first_name: Arthur full_name: Milberger, Arthur last_name: Milberger - first_name: Manuel full_name: Gunkel, Manuel last_name: Gunkel - first_name: Stefan full_name: Terjung, Stefan last_name: Terjung - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 citation: ama: Goudarzi M, Schuster M, Milberger A, Gunkel M, Terjung S, Krens G. 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. 2026;302(3):382-395. doi:10.1111/jmi.70106 apa: Goudarzi, M., Schuster, M., Milberger, A., Gunkel, M., Terjung, S., & Krens, G. (2026). 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.70106 chicago: Goudarzi, Mohammad, Maximilian Schuster, Arthur Milberger, Manuel Gunkel, Stefan Terjung, and Gabriel Krens. “3D Printing in Core Facilities – Low Pain, High Gain.” Journal of Microscopy. Wiley, 2026. https://doi.org/10.1111/jmi.70106. ieee: M. Goudarzi, M. Schuster, A. Milberger, M. Gunkel, S. Terjung, and G. Krens, “3D printing in core facilities – Low pain, high gain,” Journal of Microscopy, vol. 302, no. 3. Wiley, pp. 382–395, 2026. ista: Goudarzi M, Schuster M, Milberger A, Gunkel M, Terjung S, Krens G. 2026. 3D printing in core facilities – Low pain, high gain. Journal of Microscopy. 302(3), 382–395. mla: Goudarzi, Mohammad, et al. “3D Printing in Core Facilities – Low Pain, High Gain.” Journal of Microscopy, vol. 302, no. 3, Wiley, 2026, pp. 382–95, doi:10.1111/jmi.70106. short: M. Goudarzi, M. Schuster, A. Milberger, M. Gunkel, S. Terjung, G. Krens, Journal of Microscopy 302 (2026) 382–395. corr_author: '1' das_tickbox: '0' date_created: 2026-05-17T22:02:11Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T14:02:46Z day: '01' ddc: - '600' department: - _id: Bio doi: 10.1111/jmi.70106 external_id: pmid: - '42104760' file: - access_level: open_access checksum: 06dfad92b1465ed614a1201b4129960a content_type: application/pdf creator: dernst date_created: 2026-07-27T14:01:34Z date_updated: 2026-07-27T14:01:34Z file_id: '22593' file_name: 2026_JourMicroscopy_Goudarzi.pdf file_size: 4625767 relation: main_file success: 1 file_date_updated: 2026-07-27T14:01:34Z has_accepted_license: '1' intvolume: ' 302' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 382-395 pmid: 1 publication: Journal of Microscopy publication_identifier: eissn: - 1365-2818 issn: - 0022-2720 publication_status: published publisher: Wiley quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: 3D printing in core facilities – Low pain, high gain 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: 302 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21872' abstract: - lang: eng text: Magneto-optic Kerr effect (MOKE) is a powerful probe of broken time-reversal symmetry (T), typically used to study ferromagnets. While MOKE has been observed in some antiferromagnets (AFMs) with vanishing magnetization, it is often associated with structures whose symmetry is lower than basic collinear, bipartite order. In contrast, theory predicts a mechanism for MOKE intrinsic to all AFMs of A-type, i.e. layered AFMs in which ferromagnetic layers are antiferromagnetically aligned. Here we report the experimental confirmation of this mechanism in a bulk AFM. We achieve this by measuring the imaginary component of MOKE as a function of photon energy in MnBi2Te4, an A-type AFM where T is preserved in combination with a translation, and comparing the experimental results with model calculations. Our model suggests that observable MOKE should be expected in all collinear A-type AFMs with out-of-plane spin order, thus enabling optical detection of AFM domains and expanding the scope of MOKE to few-layer AFMs. acknowledgement: We thank Christine Kuntscher for providing optical conductivity and reflectance data published in ref. 33, and Nicola Spaldin, Joel Moore and Bevin Huang for useful discussions. V.S. and J.O. received support from the Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4537 awarded to J.O. at UC Berkeley. Experimental and theoretical work at LBNL and UC Berkeley was funded by the Quantum Materials (KC2202) program under the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Contract No. DE-AC02-05CH11231. Work at the University of Kansas was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, EPSCoR, and Materials Sciences and Engineering Division under Award No. DE-SC0025319. Parts of device fabrication were performed in the KU Nanofabrication Facility, which is supported by the National Institutes of Health NIGMS P30GM145499. Work at ORNL was supported by the U. S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. For the DFT calculations we used resources provided by the Swedish National Infrastructure for Computing (SNIC) at C3SE. We acknowledge support from the US National Science Foundation (NSF) Grant Number 2201516 under the Accelnet program of Office of International Science and Engineering (OISE). This publication is funded in part by a QuantEmX grant from ICAM and the Gordon and Betty Moore Foundation through Grant GBMF9616 to S. K. article_number: '7364' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Veronika full_name: Sunko, Veronika id: 23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3 last_name: Sunko orcid: 0000-0003-2724-3523 - first_name: Salman full_name: Ahsanullah, Salman last_name: Ahsanullah - first_name: Vivek full_name: Jain, Vivek last_name: Jain - first_name: Sophie full_name: Weber, Sophie last_name: Weber - first_name: Sivaloganathan full_name: Kumaran, Sivaloganathan last_name: Kumaran - first_name: Jiaqiang full_name: Yan, Jiaqiang last_name: Yan - first_name: Joseph full_name: Orenstein, Joseph last_name: Orenstein - first_name: Dmitry full_name: Ovchinnikov, Dmitry last_name: Ovchinnikov citation: ama: Sunko V, Ahsanullah S, Jain V, et al. Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. 2026;17. doi:10.1038/s41467-026-72577-4 apa: Sunko, V., Ahsanullah, S., Jain, V., Weber, S., Kumaran, S., Yan, J., … Ovchinnikov, D. (2026). Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-026-72577-4 chicago: Sunko, Veronika, Salman Ahsanullah, Vivek Jain, Sophie Weber, Sivaloganathan Kumaran, Jiaqiang Yan, Joseph Orenstein, and Dmitry Ovchinnikov. “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Nature Communications. Springer Nature, 2026. https://doi.org/10.1038/s41467-026-72577-4. ieee: V. Sunko et al., “Magneto-optical Kerr effect in an A-type antiferromagnet,” Nature Communications, vol. 17. Springer Nature, 2026. ista: Sunko V, Ahsanullah S, Jain V, Weber S, Kumaran S, Yan J, Orenstein J, Ovchinnikov D. 2026. Magneto-optical Kerr effect in an A-type antiferromagnet. Nature Communications. 17, 7364. mla: Sunko, Veronika, et al. “Magneto-Optical Kerr Effect in an A-Type Antiferromagnet.” Nature Communications, vol. 17, 7364, Springer Nature, 2026, doi:10.1038/s41467-026-72577-4. short: V. Sunko, S. Ahsanullah, V. Jain, S. Weber, S. Kumaran, J. Yan, J. Orenstein, D. Ovchinnikov, Nature Communications 17 (2026). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The datasets generated and analyzed during the study of “Magneto-optical Kerr effect in an A-type antiferromagnet" are available in the ISTA REx repository with https://doi.org/10.15479/AT-ISTA-21422. date_created: 2026-05-12T21:31:27Z date_published: 2026-07-27T00:00:00Z date_updated: 2026-07-27T13:59:27Z day: '27' ddc: - '530' department: - _id: VeSu doi: 10.1038/s41467-026-72577-4 external_id: arxiv: - '2504.16167' file: - access_level: open_access checksum: bde19c4342933c05fe801c2bef7dc732 content_type: application/pdf creator: dernst date_created: 2026-07-27T13:58:06Z date_updated: 2026-07-27T13:58:06Z file_id: '22592' file_name: 2026_NatureComm_Sunko.pdf file_size: 1054779 relation: main_file success: 1 file_date_updated: 2026-07-27T13:58:06Z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '21422' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Magneto-optical Kerr effect in an A-type antiferromagnet 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: 17 year: '2026' ... --- OA_type: closed access _id: '21950' abstract: - lang: eng text: One Health initiatives are modern paradigms for research and health care practices in various fields. Concrete definitions of the One Health framework, however, remain heterogeneous, leading to conceptual problems and uncertainties in the application of the framework. This article discusses several approaches to the One Health concept, and their associated consequences, with special focus on animal experimentation. The first issue addressed is how One Health should be defined, as well as what (and who) should be considered within a One Health approach. In order to shed further light on this, we explore the history of animals in biomedical science, highlighting historical milestones in the use of animal models, as well as the development and current state of ethical considerations in the field of animal experimentation. The second issue comes with the inclusion of animal experimentation per se as part of the One Health concept. Therefore, particular attention is paid to bioethical principles and the resulting problems that can arise when applying them to the One Health concept. Arguments such as the idea of inequality between humans and non-human animals, and the premise that all actions are done for the benefit of humans, are raised and then used to explore the question of whether the One Health concept is compatible with existing bioethical principles. Based on the bioethical principles of protecting the environment, the biodiversity and biosphere, this paper seeks an inclusive perspective of the One Health concept. Successful solutions will be based on this concept, which embraces all living beings. The authors conclude that a multispecies ethics approach could help create a more ethical ecosystem that is aligned with the wellbeing of all life on a shared planet. article_processing_charge: No article_type: original author: - first_name: Yesim Isil full_name: Ulman, Yesim Isil last_name: Ulman - first_name: Nikos full_name: Kostomitsopoulos, Nikos last_name: Kostomitsopoulos - first_name: Samuel full_name: Camenzind, Samuel last_name: Camenzind - first_name: Maria full_name: Kitsara, Maria last_name: Kitsara - first_name: Ilja Richard full_name: Pavone, Ilja Richard last_name: Pavone - first_name: Sophie full_name: Schober, Sophie id: 80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8 last_name: Schober citation: ama: 'Ulman YI, Kostomitsopoulos N, Camenzind S, Kitsara M, Pavone IR, Schober S. Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. 2026;54(4):226-235. doi:10.1177/02611929261453330' apa: 'Ulman, Y. I., Kostomitsopoulos, N., Camenzind, S., Kitsara, M., Pavone, I. R., & Schober, S. (2026). Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. SAGE Publications. https://doi.org/10.1177/02611929261453330' chicago: 'Ulman, Yesim Isil, Nikos Kostomitsopoulos, Samuel Camenzind, Maria Kitsara, Ilja Richard Pavone, and Sophie Schober. “Emerging Bioethical Conflicts: One Health and Animal Experimentation.” Alternatives to Laboratory Animals. SAGE Publications, 2026. https://doi.org/10.1177/02611929261453330.' ieee: 'Y. I. Ulman, N. Kostomitsopoulos, S. Camenzind, M. Kitsara, I. R. Pavone, and S. Schober, “Emerging bioethical conflicts: One Health and animal experimentation,” Alternatives to Laboratory Animals, vol. 54, no. 4. SAGE Publications, pp. 226–235, 2026.' ista: 'Ulman YI, Kostomitsopoulos N, Camenzind S, Kitsara M, Pavone IR, Schober S. 2026. Emerging bioethical conflicts: One Health and animal experimentation. Alternatives to Laboratory Animals. 54(4), 226–235.' mla: 'Ulman, Yesim Isil, et al. “Emerging Bioethical Conflicts: One Health and Animal Experimentation.” Alternatives to Laboratory Animals, vol. 54, no. 4, SAGE Publications, 2026, pp. 226–35, doi:10.1177/02611929261453330.' short: Y.I. Ulman, N. Kostomitsopoulos, S. Camenzind, M. Kitsara, I.R. Pavone, S. Schober, Alternatives to Laboratory Animals 54 (2026) 226–235. corr_author: '1' das_tickbox: '1' date_created: 2026-06-07T22:01:36Z date_published: 2026-07-01T00:00:00Z date_updated: 2026-07-27T14:13:17Z day: '01' department: - _id: PreCl doi: 10.1177/02611929261453330 external_id: pmid: - '42185081' intvolume: ' 54' issue: '4' language: - iso: eng month: '07' oa_version: None page: 226-235 pmid: 1 publication: Alternatives to Laboratory Animals publication_identifier: eissn: - 2632-3559 issn: - 0261-1929 publication_status: published publisher: SAGE Publications quality_controlled: '1' scopus_import: '1' status: public title: 'Emerging bioethical conflicts: One Health and animal experimentation' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2026' ... --- OA_type: closed access _id: '21900' abstract: - lang: eng text: Individually silencing 125 fruit fly genes reveals opposing fitness effects of mutations between females and males, as well as between germline and somatic tissues. article_processing_charge: No article_type: comment author: - first_name: Filip full_name: Ruzicka, Filip id: 347955dd-57b0-11ee-9095-c28bdd368f4b last_name: Ruzicka citation: ama: Ruzicka F. Reverse genetics of sexual antagonism. Nature Ecology & Evolution. 2026;10:1035-1036. doi:10.1038/s41559-026-03036-y apa: Ruzicka, F. (2026). Reverse genetics of sexual antagonism. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-026-03036-y chicago: Ruzicka, Filip. “Reverse Genetics of Sexual Antagonism.” Nature Ecology & Evolution. Springer Nature, 2026. https://doi.org/10.1038/s41559-026-03036-y. ieee: F. Ruzicka, “Reverse genetics of sexual antagonism,” Nature Ecology & Evolution, vol. 10. Springer Nature, pp. 1035–1036, 2026. ista: Ruzicka F. 2026. Reverse genetics of sexual antagonism. Nature Ecology & Evolution. 10, 1035–1036. mla: Ruzicka, Filip. “Reverse Genetics of Sexual Antagonism.” Nature Ecology & Evolution, vol. 10, Springer Nature, 2026, pp. 1035–36, doi:10.1038/s41559-026-03036-y. short: F. Ruzicka, Nature Ecology & Evolution 10 (2026) 1035–1036. corr_author: '1' das_tickbox: '0' date_created: 2026-05-20T14:36:45Z date_published: 2026-06-01T00:00:00Z date_updated: 2026-07-27T14:05:02Z day: '01' department: - _id: BeVi doi: 10.1038/s41559-026-03036-y external_id: pmid: - '42067637 ' intvolume: ' 10' language: - iso: eng month: '06' oa_version: None page: 1035-1036 pmid: 1 publication: Nature Ecology & Evolution publication_identifier: eissn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Reverse genetics of sexual antagonism type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2026' ... --- OA_place: publisher _id: '21957' abstract: - lang: eng text: "This thesis investigates algorithmic certification and approximation methods for degenerate semidefinite programs (SDPs) and the singular roots of polynomial systems. In the first part, we present a hybrid symbolic-numeric algorithm for certifying the feasibility of weakly feasible, degenerate SDPs. By reformulating linear matrix inequalities (LMIs) into a structured polynomial system via facial reduction and incidence varieties, we guarantee the existence of an isolated exact solution. This algebraic reduction enables the certification of maximum-rank numerical approximations using methods from algebraic geometry.\r\n\r\nIn the second part, we address the severe ill-conditioning and loss of quadratic convergence that plague standard path-tracking methods near isolated singular roots. To overcome this, we propose tracking algorithms that achieve superlinear convergence without the computational bloat characteristic of classical deflation techniques. By modeling the solution path as a generalized fractional Puiseux series, our approach combines an explicitly derived algebraic predictor with a localized hyperplane desingularization phase during the corrector step. Furthermore, we introduce a continuous path-limit method and an extension of the geometric sequence rule to directly extract exact fractional exponents. This bypasses traditional heuristic trial-and-error methods and explicitly accommodates sparse series expansions. Numerical experiments confirm that our method significantly reduces the cumulative number of matrix inversions while achieving high-accuracy root approximations, even for heavily degenerate systems exhibiting higher coranks." acknowledgement: 'Funding: Vienna Graduate School on Computational Optimization (FWF), grant DOI: 10.55776/W1260.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jeferson full_name: Zapata, Jeferson id: 00223538-AF8F-11E9-A4C7-F729E6697425 last_name: Zapata citation: ama: 'Zapata J. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. 2026. doi:10.15479/AT-ISTA-21957' apa: 'Zapata, J. (2026). Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21957' chicago: 'Zapata, Jeferson. “Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21957.' ieee: 'J. Zapata, “Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames,” Institute of Science and Technology Austria, 2026.' ista: 'Zapata J. 2026. Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames. Institute of Science and Technology Austria.' mla: 'Zapata, Jeferson. Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21957.' short: 'J. Zapata, Overcoming Degeneracy and Singularity: Techniques for Semidefinite Programs and Homotopy Continuation Endgames, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '1' date_created: 2026-06-08T13:29:52Z date_published: 2026-06-09T00:00:00Z date_updated: 2026-07-27T14:30:42Z day: '09' ddc: - '500' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21957 doi_confirm: '1' file: - access_level: closed checksum: b11a959e99d3dcf61040282b5c837141 content_type: application/zip creator: jzapata date_created: 2026-06-08T13:20:02Z date_updated: 2026-06-08T13:20:02Z file_id: '21958' file_name: istaustriathesis_JZapata.zip file_size: 40811933 relation: source_file - access_level: open_access checksum: edf1e5899b2e31505cd1aa3fe8bd4b7f content_type: application/pdf creator: jzapata date_created: 2026-06-10T13:33:25Z date_updated: 2026-06-10T13:33:25Z file_id: '21992' file_name: 4_Final_Thesis_JZapata_REX.pdf file_size: 2207892 relation: main_file success: 1 file_date_updated: 2026-06-10T13:33:25Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '89' project: - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: isbn: - 978-3-99078-079-4 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21144' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: 'Overcoming degeneracy and singularity: Techniques for semidefinite programs and homotopy continuation endgames' 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: '2026' ... --- OA_place: repository _id: '21360' acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21360' apa: 'Riegler, S. (2026). Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21360' chicago: 'Riegler, Stefan. “Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21360.' ieee: 'S. Riegler, “Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species,” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria.' mla: 'Riegler, Stefan. Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21360.' short: 'S. Riegler, Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '1' date_created: 2026-02-27T09:08:14Z date_published: 2026-02-26T00:00:00Z date_updated: 2026-07-27T14:30:08Z day: '26' ddc: - '570' - '575' - '583' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21360 doi_confirm: '1' file: - access_level: closed checksum: 2f1f44e8536c2538f94a440217452c9f content_type: application/x-zip-compressed creator: sriegler date_created: 2026-03-02T10:59:50Z date_updated: 2026-03-02T10:59:50Z file_id: '21386' file_name: 2026_Riegler_Stefan_Thesis.zip file_size: 31430022 relation: source_file - access_level: closed checksum: 2e8dc39640bc26ae5684c944c619719b content_type: application/pdf creator: sriegler date_created: 2026-03-02T10:59:49Z date_updated: 2026-03-02T10:59:49Z embargo: 2027-02-27 embargo_to: open_access file_id: '21387' file_name: 2026_Riegler_Stefan_Thesis.pdf file_size: 11635090 relation: main_file file_date_updated: 2026-03-02T10:59:50Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '02' oa_version: Published Version page: '185' project: - _id: 34afa094-11ca-11ed-8bc3-a375845a59fb grant_number: '101060393' name: Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '21363' relation: research_data status: public status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: 'Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- _id: '21363' abstract: - lang: eng text: The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting. article_processing_charge: No author: - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 citation: ama: 'Riegler S. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:10.15479/AT-ISTA-21363' apa: 'Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21363' chicago: 'Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21363.' ieee: 'S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species.” Institute of Science and Technology Austria, 2026.' ista: 'Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21363.' mla: 'Riegler, Stefan. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21363.' short: S. Riegler, (2026). contributor: - contributor_type: supervisor first_name: Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 corr_author: '1' date_created: 2026-02-27T09:18:41Z date_published: 2026-02-27T00:00:00Z date_updated: 2026-07-27T14:30:07Z day: '27' ddc: - '575' department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-21363 file: - access_level: closed checksum: de9145fa166a28c588b5184a2d3d4fee content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: sriegler date_created: 2026-02-27T09:11:33Z date_updated: 2026-02-27T09:11:33Z embargo: 2027-02-27 embargo_to: open_access file_id: '21364' file_name: SupplementaryTables.xlsx file_size: 63749444 relation: main_file - access_level: closed checksum: ce1f163551c96cee45943a8ea29720b6 content_type: text/plain creator: sriegler date_created: 2026-02-27T09:13:11Z date_updated: 2026-02-27T09:13:11Z embargo: 2027-02-27 embargo_to: open_access file_id: '21365' file_name: ReadMe.txt file_size: 124 relation: main_file file_date_updated: 2026-02-27T09:13:11Z has_accepted_license: '1' month: '02' oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '21360' relation: used_in_publication status: public status: public title: 'Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- OA_place: publisher _id: '22334' abstract: - lang: eng text: "Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters.\r\nFunctionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies.\r\nTaken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function.\r\n" acknowledged_ssus: - _id: LifeSc - _id: NMR acknowledgement: "During the work on this thesis, I was the recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01)." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 citation: ama: Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi:10.15479/AT-ISTA-22334 apa: Becker, L. M. (2026). Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22334 chicago: Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22334. ieee: L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026. ista: Becker LM. 2026. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria. mla: Becker, Lea Marie. Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22334. short: L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026. corr_author: '1' das_tickbox: '1' date_created: 2026-07-14T08:08:51Z date_published: 2026-07-13T00:00:00Z date_updated: 2026-07-28T06:59:15Z day: '13' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: PaSc doi: 10.15479/AT-ISTA-22334 doi_confirm: '1' file: - access_level: closed checksum: 8b85114eff543916c0e1445cd2189555 content_type: application/zip creator: lbecker date_created: 2026-07-16T09:17:08Z date_updated: 2026-07-16T09:17:08Z file_id: '22346' file_name: 2026_Becker_Lea_source_files.zip file_size: 99472908 relation: source_file - access_level: open_access checksum: 6c526862bc6dbd1e4c80ecb34580bc58 content_type: application/pdf creator: lbecker date_created: 2026-07-16T09:17:05Z date_updated: 2026-07-16T09:17:05Z file_id: '22347' file_name: 2026_Becker_Lea_Thesis.pdf file_size: 74647289 relation: main_file success: 1 file_date_updated: 2026-07-16T09:17:08Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '07' oa: 1 oa_version: Published Version page: '205' project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publication_identifier: isbn: - 978-3-99078-084-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12675' relation: part_of_dissertation status: public - id: '21777' relation: part_of_dissertation status: public - id: '12114' relation: part_of_dissertation status: public - id: '22105' relation: part_of_dissertation status: public status: public supervisor: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 title: Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '22105' abstract: - lang: eng text: Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein–protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions. acknowledged_ssus: - _id: NMR - _id: LifeSc acknowledgement: We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged for providing beamtime through its In-House Research programme. We thank S. Falkner for assistance with constructing the structural model of the IgG:GB1 complex. We thank J. Lewandowski for providing feedback on the paper and granting access to backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant number PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272 ‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Haohao full_name: Fu, Haohao last_name: Fu - first_name: Benjamin full_name: Tatman, Benjamin id: 71cda2f3-e604-11ee-a1df-da10587eda3f last_name: Tatman - first_name: Matthias full_name: Dreydoppel, Matthias last_name: Dreydoppel - first_name: Anna full_name: Kapitonova, Anna id: 9fb2a840-89e1-11ee-a8b7-cc5c7ba62471 last_name: Kapitonova - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Ulrich full_name: Weininger, Ulrich last_name: Weininger - first_name: Sylvain full_name: Engilberge, Sylvain last_name: Engilberge - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. 2026;18:1221-1230. doi:10.1038/s41557-026-02155-0 apa: Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs, D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-026-02155-0 chicago: Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot, and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Nature Chemistry. Springer Nature, 2026. https://doi.org/10.1038/s41557-026-02155-0. ieee: L. M. Becker et al., “Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes,” Nature Chemistry, vol. 18. Springer Nature, pp. 1221–1230, 2026. ista: Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. 18, 1221–1230. mla: Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Nature Chemistry, vol. 18, Springer Nature, 2026, pp. 1221–30, doi:10.1038/s41557-026-02155-0. short: L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U. Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry 18 (2026) 1221–1230. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The cryo and room-temperature crystal structures of GB1QDD are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the access code 53330. NMR spectra, analysis scripts and raw data are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files to reproduce the enhanced-sampling MD simulations are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121. date_created: 2026-06-21T22:03:01Z date_published: 2026-07-01T00:00:00Z date_updated: 2026-07-28T06:59:16Z day: '01' ddc: - '540' department: - _id: PaSc - _id: LifeSc doi: 10.1038/s41557-026-02155-0 external_id: pmid: - '42271006' file: - access_level: open_access checksum: 1069fb27949fd2cb641b043b3a96a580 content_type: application/pdf creator: dernst date_created: 2026-07-28T06:58:35Z date_updated: 2026-07-28T06:58:35Z file_id: '22595' file_name: 2026_NatureChemistry_Becker.pdf file_size: 2618184 relation: main_file success: 1 file_date_updated: 2026-07-28T06:58:35Z has_accepted_license: '1' intvolume: ' 18' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1221-1230 pmid: 1 project: - _id: 7be609c4-9f16-11ee-852c-85015ce2b9b0 grant_number: '26777' name: Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches publication: Nature Chemistry publication_identifier: eissn: - '17554349' issn: - '17554330' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20641' relation: research_data status: public - id: '21145' relation: research_data status: public - id: '22334' relation: dissertation_contains status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes 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: 18 year: '2026' ... --- OA_type: closed access _id: '21164' abstract: - lang: eng text: 'Global emission inventories often fail to capture the complexities of vehicular pollution in regions with unique fuel mixes, such as Brazil’s extensive biofuel use, leading to significant uncertainties in atmospheric modeling. This study presents a century-long (1960–2100) bottom-up vehicular emission inventory for Brazil, leveraging locally derived emission factors. Our estimates reveal substantial discrepancies in magnitude, timing, and speciation of non-CO2 pollutants (CO, NMHC, PM2.5) compared to leading global inventories (EDGAR, CEDS, CAMS), highlighting critical inaccuracies in widely used data sets. More critically, future projections under Shared Socioeconomic Pathways (SSPs) uncover a novel positive feedback mechanism: rising temperatures significantly enhance vehicular evaporative nonmethane hydrocarbon (NMHC) emissions. This temperature-dependent increase and subsequent NMHC oxidation to CO2 suggest an overlooked pathway that could amplify climate warming and air pollution globally, particularly after a breakpoint around 2050 (p < 0.05). While historical emissions peaked in the 1990s–2000s, nonexhaust PM becomes increasingly important. Air quality simulations using our inventory in the MUSICA model show good regional PM2.5 agreement but highlight challenges in resolving local primary pollutant peaks. This comprehensive inventory provides crucial data for Brazil and uncovers globally relevant climate–chemistry interactions, urging a re-evaluation of regional specificities in global emission assessments.' acknowledgement: Part of this material is based upon work supported by the NSF National Center for Atmospheric Research, which is a major facility sponsored by the National Science Foundation under Cooperative Agreement No. 1852977. Casallas was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. E. D. Freitas thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 313210/2022–5). Silva gratefully acknowledges the financial support from the National Council for Scientific and Technological Development (CNPq), process number 140512/2021–7. P. Lichtig was supported by base funding from the National Commission for Atomic Energy (CNEA, Arg.) and by NSF NCAR. R.Y. Ynoue thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 406728/2022–4). M. A. Franco thanks the support provided by the National Council for Scientific and Technological Development (CNPq, Process number 407752/2023–4). G. M. Pereira thanks the support by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Process numbers 2018/07848–9, 2016/18438–0, and 2019/01316–80) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES; Process number 88887.103225/2025–00). M.F. Andrade thanks the support by FAPESP (Process number 2016/18438–0) and CNPQ (Klimapolis INCT). article_number: 5c08400 article_processing_charge: No article_type: original author: - first_name: Sergio full_name: Ibarra-Espinosa, Sergio last_name: Ibarra-Espinosa - first_name: Edmilson full_name: Dias de Freitas, Edmilson last_name: Dias de Freitas - first_name: Benjamin full_name: Gaubert, Benjamin last_name: Gaubert - first_name: Pablo full_name: Lichtig, Pablo last_name: Lichtig - first_name: Karl full_name: Ropkins, Karl last_name: Ropkins - first_name: Iara full_name: da Silva, Iara last_name: da Silva - first_name: Guilherme full_name: Martins Pereira, Guilherme last_name: Martins Pereira - first_name: Daniel full_name: Schuch, Daniel last_name: Schuch - first_name: Janaina full_name: Nascimento, Janaina last_name: Nascimento - first_name: Leonardo full_name: Hoinaski, Leonardo last_name: Hoinaski - first_name: Leila Droprinchinski full_name: Martins, Leila Droprinchinski last_name: Martins - first_name: Mario full_name: Gavidia-Calderón, Mario last_name: Gavidia-Calderón - first_name: Angel full_name: Vara-Vela, Angel last_name: Vara-Vela - first_name: Taciana full_name: Toledo de Almeida Albuquerque, Taciana last_name: Toledo de Almeida Albuquerque - first_name: Rita Yuri full_name: Ynoue, Rita Yuri last_name: Ynoue - first_name: Sebastian full_name: Diez, Sebastian last_name: Diez - first_name: Zamir full_name: Mera, Zamir last_name: Mera - first_name: Alejandro full_name: Casallas Garcia, Alejandro id: 92081129-2d75-11ef-a48d-b04dd7a2385a last_name: Casallas Garcia orcid: 0000-0002-1988-5035 - first_name: Fidel full_name: Vallejo, Fidel last_name: Vallejo - first_name: Valeria full_name: Diaz, Valeria last_name: Diaz - first_name: Rizzieri full_name: Pedruzzi, Rizzieri last_name: Pedruzzi - first_name: Rosana full_name: Abrutzky, Rosana last_name: Abrutzky - first_name: Marco A. full_name: Franco, Marco A. last_name: Franco - first_name: Nicolas full_name: Huneeus, Nicolas last_name: Huneeus - first_name: Hector full_name: Jorquera, Hector last_name: Jorquera - first_name: Luis Carlos full_name: Belalcázar-Cerón, Luis Carlos last_name: Belalcázar-Cerón - first_name: Néstor Y. full_name: Rojas, Néstor Y. last_name: Rojas - first_name: Maria full_name: de Fatima Andrade, Maria last_name: de Fatima Andrade - first_name: Louisa full_name: Emmons, Louisa last_name: Emmons - first_name: Guy full_name: Brasseur, Guy last_name: Brasseur citation: ama: 'Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, et al. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology. 2026;60(6). doi:10.1021/acs.est.5c08400' apa: 'Ibarra-Espinosa, S., Dias de Freitas, E., Gaubert, B., Lichtig, P., Ropkins, K., da Silva, I., … Brasseur, G. (2026). A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology. American Chemical Society. https://doi.org/10.1021/acs.est.5c08400' chicago: 'Ibarra-Espinosa, Sergio, Edmilson Dias de Freitas, Benjamin Gaubert, Pablo Lichtig, Karl Ropkins, Iara da Silva, Guilherme Martins Pereira, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science &amp; Technology. American Chemical Society, 2026. https://doi.org/10.1021/acs.est.5c08400.' ieee: 'S. Ibarra-Espinosa et al., “A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality,” Environmental Science &amp; Technology, vol. 60, no. 6. American Chemical Society, 2026.' ista: 'Ibarra-Espinosa S, Dias de Freitas E, Gaubert B, Lichtig P, Ropkins K, da Silva I, Martins Pereira G, Schuch D, Nascimento J, Hoinaski L, Martins LD, Gavidia-Calderón M, Vara-Vela A, Toledo de Almeida Albuquerque T, Ynoue RY, Diez S, Mera Z, Casallas Garcia A, Vallejo F, Diaz V, Pedruzzi R, Abrutzky R, Franco MA, Huneeus N, Jorquera H, Belalcázar-Cerón LC, Rojas NY, de Fatima Andrade M, Emmons L, Brasseur G. 2026. A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality. Environmental Science &amp; Technology. 60(6), 5c08400.' mla: 'Ibarra-Espinosa, Sergio, et al. “A Century of Vehicular Emissions in Brazil: Unveiling the Impacts of Unique Fuel Mix on Air Quality.” Environmental Science &amp; Technology, vol. 60, no. 6, 5c08400, American Chemical Society, 2026, doi:10.1021/acs.est.5c08400.' short: S. Ibarra-Espinosa, E. Dias de Freitas, B. Gaubert, P. Lichtig, K. Ropkins, I. da Silva, G. Martins Pereira, D. Schuch, J. Nascimento, L. Hoinaski, L.D. Martins, M. Gavidia-Calderón, A. Vara-Vela, T. Toledo de Almeida Albuquerque, R.Y. Ynoue, S. Diez, Z. Mera, A. Casallas Garcia, F. Vallejo, V. Diaz, R. Pedruzzi, R. Abrutzky, M.A. Franco, N. Huneeus, H. Jorquera, L.C. Belalcázar-Cerón, N.Y. Rojas, M. de Fatima Andrade, L. Emmons, G. Brasseur, Environmental Science &amp; Technology 60 (2026). das_tickbox: '1' dataavailabilitystatement: Scripts available here https://github.com/ibarraespinosa/musica_vein and here https://github.com/atmoschem/vein. date_created: 2026-02-09T06:54:10Z date_published: 2026-02-17T00:00:00Z date_updated: 2026-07-28T07:03:54Z day: '17' ddc: - '550' department: - _id: CaMu doi: 10.1021/acs.est.5c08400 ec_funded: 1 external_id: pmid: - '41636708' has_accepted_license: '1' intvolume: ' 60' issue: '6' language: - iso: eng month: '02' oa_version: None pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Environmental Science & Technology publication_identifier: eissn: - 1520-5851 issn: - 0013-936X publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: 'A century of vehicular emissions in Brazil: Unveiling the impacts of unique fuel mix on air quality' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2026' ...