[{"external_id":{"arxiv":["2410.18913"],"pmid":["40344113"],"isi":["001480669300011"]},"citation":{"ista":"Kerschbaumer A, Ljubotina M, Serbyn M, Desaules J-YM. 2025. Quantum many-body scars beyond the PXP model in Rydberg simulators. Physical Review Letters. 134(16), 160401.","chicago":"Kerschbaumer, Aron, Marko Ljubotina, Maksym Serbyn, and Jean-Yves Marc Desaules. “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevLett.134.160401\">https://doi.org/10.1103/PhysRevLett.134.160401</a>.","short":"A. Kerschbaumer, M. Ljubotina, M. Serbyn, J.-Y.M. Desaules, Physical Review Letters 134 (2025).","apa":"Kerschbaumer, A., Ljubotina, M., Serbyn, M., &#38; Desaules, J.-Y. M. (2025). Quantum many-body scars beyond the PXP model in Rydberg simulators. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.134.160401\">https://doi.org/10.1103/PhysRevLett.134.160401</a>","ieee":"A. Kerschbaumer, M. Ljubotina, M. Serbyn, and J.-Y. M. Desaules, “Quantum many-body scars beyond the PXP model in Rydberg simulators,” <i>Physical Review Letters</i>, vol. 134, no. 16. American Physical Society, 2025.","mla":"Kerschbaumer, Aron, et al. “Quantum Many-Body Scars beyond the PXP Model in Rydberg Simulators.” <i>Physical Review Letters</i>, vol. 134, no. 16, 160401, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.160401\">10.1103/PhysRevLett.134.160401</a>.","ama":"Kerschbaumer A, Ljubotina M, Serbyn M, Desaules J-YM. Quantum many-body scars beyond the PXP model in Rydberg simulators. <i>Physical Review Letters</i>. 2025;134(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.134.160401\">10.1103/PhysRevLett.134.160401</a>"},"quality_controlled":"1","status":"public","OA_type":"hybrid","publication":"Physical Review Letters","scopus_import":"1","department":[{"_id":"MaSe"}],"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"acknowledgement":"The authors are grateful to Zlatko Papić, Dolev Bluvstein, Nishad Maskara, Marcello Dalmonte, Thomas Iadecola, and Johannes Feldmeier for insightful discussions. A. K., M. L., and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). J.-Y. D. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","intvolume":"       134","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","issue":"16","article_number":"160401","year":"2025","publisher":"American Physical Society","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"22","_id":"19664","author":[{"orcid":"0009-0002-2370-8661","first_name":"Aron","full_name":"Kerschbaumer, Aron","id":"ade85a9c-3200-11ee-973b-91c1eb240410","last_name":"Kerschbaumer"},{"first_name":"Marko","full_name":"Ljubotina, Marko","orcid":"0000-0003-0038-7068","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","last_name":"Desaules","first_name":"Jean-Yves Marc","full_name":"Desaules, Jean-Yves Marc","orcid":"0000-0002-3749-6375"}],"date_created":"2025-05-11T22:02:38Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"19623"}],"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/a-sky-full-of-quantum-scars/"}]},"volume":134,"oa":1,"abstract":[{"lang":"eng","text":"Persistent revivals recently observed in Rydberg atom simulators have challenged our understanding of thermalization and attracted much interest to the concept of quantum many-body scars (QMBSs). QMBSs are non-thermal highly excited eigenstates that coexist with typical eigenstates in the spectrum of many-body Hamiltonians, and have since been reported in multiple theoretical models, including the so-called PXP model, approximately realized by Rydberg simulators. At the same time, questions of how common QMBSs are and in what models they are physically realized remain open. In this Letter, we demonstrate that QMBSs exist in a broader family of models that includes and generalizes PXP to longer-range constraints and states with different periodicity. We show that in each model, multiple QMBS families can be found. Each of them relies on a different approximate algebra, leading to oscillatory dynamics in all cases. However, in contrast to the PXP model, their observation requires launching dynamics from weakly entangled initial states rather than from a product state. QMBSs reported here may be experimentally probed using Rydberg atom simulator in the regime of longer-range Rydberg blockades."}],"month":"04","file":[{"checksum":"b7f581291e20f152d0efc64727314ca2","access_level":"open_access","file_size":1028993,"relation":"main_file","success":1,"content_type":"application/pdf","file_name":"2025_PhysReviewLetters_Kerschbaumer.pdf","file_id":"19677","date_updated":"2025-05-12T07:33:38Z","date_created":"2025-05-12T07:33:38Z","creator":"dernst"}],"date_updated":"2026-06-10T08:40:51Z","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_type":"original","date_published":"2025-04-22T00:00:00Z","title":"Quantum many-body scars beyond the PXP model in Rydberg simulators","pmid":1,"isi":1,"type":"journal_article","oa_version":"Published Version","arxiv":1,"file_date_updated":"2025-05-12T07:33:38Z","has_accepted_license":"1","doi":"10.1103/PhysRevLett.134.160401","publication_status":"published","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"},{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"ddc":["530"]},{"OA_place":"repository","intvolume":"        39","article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"This work is partly supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093. It is also partially supported by the State Government of Styria, Austria – Department Zukunftsfonds Steiermark.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","publisher":"Association for the Advancement of Artificial Intelligence","issue":"15","OA_type":"green","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","status":"public","quality_controlled":"1","citation":{"ieee":"F. Cano Cordoba, T. A. Henzinger, B. Könighofer, K. Kueffner, and K. Mallik, “Fairness shields: Safeguarding against biased decision makers,” in <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, Philadelphia, PA, United States, 2025, vol. 39, no. 15, pp. 15659–15668.","mla":"Cano Cordoba, Filip, et al. “Fairness Shields: Safeguarding against Biased Decision Makers.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 15, Association for the Advancement of Artificial Intelligence, 2025, pp. 15659–68, doi:<a href=\"https://doi.org/10.1609/aaai.v39i15.33719\">10.1609/aaai.v39i15.33719</a>.","ama":"Cano Cordoba F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. Fairness shields: Safeguarding against biased decision makers. In: <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Vol 39. Association for the Advancement of Artificial Intelligence; 2025:15659-15668. doi:<a href=\"https://doi.org/10.1609/aaai.v39i15.33719\">10.1609/aaai.v39i15.33719</a>","chicago":"Cano Cordoba, Filip, Thomas A Henzinger, Bettina Könighofer, Konstantin Kueffner, and Kaushik Mallik. “Fairness Shields: Safeguarding against Biased Decision Makers.” In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, 39:15659–68. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i15.33719\">https://doi.org/10.1609/aaai.v39i15.33719</a>.","ista":"Cano Cordoba F, Henzinger TA, Könighofer B, Kueffner K, Mallik K. 2025. Fairness shields: Safeguarding against biased decision makers. Proceedings of the 39th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 39, 15659–15668.","apa":"Cano Cordoba, F., Henzinger, T. A., Könighofer, B., Kueffner, K., &#38; Mallik, K. (2025). Fairness shields: Safeguarding against biased decision makers. In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i> (Vol. 39, pp. 15659–15668). Philadelphia, PA, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i15.33719\">https://doi.org/10.1609/aaai.v39i15.33719</a>","short":"F. Cano Cordoba, T.A. Henzinger, B. Könighofer, K. Kueffner, K. Mallik, in:, Proceedings of the 39th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2025, pp. 15659–15668."},"external_id":{"arxiv":["2412.11994"]},"ec_funded":1,"department":[{"_id":"ToHe"}],"scopus_import":"1","date_created":"2025-05-11T22:02:39Z","page":"15659-15668","author":[{"orcid":"0000-0002-0783-904X","full_name":"Cano Cordoba, Filip","first_name":"Filip","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","last_name":"Cano Cordoba"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Könighofer","first_name":"Bettina","full_name":"Könighofer, Bettina"},{"orcid":"0000-0001-8974-2542","first_name":"Konstantin","full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","last_name":"Kueffner"},{"orcid":"0000-0001-9864-7475","first_name":"Kaushik","full_name":"Mallik, Kaushik","last_name":"Mallik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"}],"_id":"19665","volume":39,"day":"11","corr_author":"1","month":"04","title":"Fairness shields: Safeguarding against biased decision makers","date_published":"2025-04-11T00:00:00Z","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"date_updated":"2026-02-16T12:24:30Z","abstract":[{"text":"As AI-based decision-makers increasingly influence human lives, it is a growing concern that their decisions may be unfair or biased with respect to people's protected attributes, such as gender and race. Most existing bias prevention measures provide probabilistic fairness guarantees in the long run, and it is possible that the decisions are biased on any decision sequence of fixed length. We introduce *fairness shielding*, where a symbolic decision-maker---the fairness shield---continuously monitors the sequence of decisions of another deployed black-box decision-maker, and makes interventions so that a given fairness criterion is met while the total intervention costs are minimized. We present four different algorithms for computing fairness shields, among which one guarantees fairness over fixed horizons, and three guarantee fairness periodically after fixed intervals. Given a distribution over future decisions and their intervention costs, our algorithms solve different instances of bounded-horizon optimal control problems with different levels of computational costs and optimality guarantees. Our empirical evaluation demonstrates the effectiveness of these shields in ensuring fairness while maintaining cost efficiency across various scenarios.","lang":"eng"}],"oa":1,"project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"}],"conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2025-02-25","end_date":"2025-03-04","location":"Philadelphia, PA, United States"},"oa_version":"Preprint","type":"conference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.11994"}],"publication_status":"published","doi":"10.1609/aaai.v39i15.33719","arxiv":1},{"issue":"25","year":"2025","publisher":"Association for the Advancement of Artificial Intelligence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101034413,\r\nthe ERC CoG 863818 (ForM-SMArt), and the DFG through the Cluster of Excellence EXC 2050/1 (CeTI, project ID 390696704, as part of Germany’s Excellence Strategy) and the TRR 248 (see https://perspicuous-computing.science, project ID 389792660).","language":[{"iso":"eng"}],"intvolume":"        39","article_processing_charge":"No","OA_place":"repository","scopus_import":"1","department":[{"_id":"KrCh"}],"ec_funded":1,"external_id":{"arxiv":["2412.10185"]},"citation":{"short":"T. Meggendorfer, M. Weininger, P. Wienhöft, in:, Proceedings of the 39th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2025, pp. 26631–26641.","apa":"Meggendorfer, T., Weininger, M., &#38; Wienhöft, P. (2025). Solving robust Markov decision processes: Generic, reliable, efficient. In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i> (Vol. 39, pp. 26631–26641). Philadelphia, PA, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i25.34865\">https://doi.org/10.1609/aaai.v39i25.34865</a>","ista":"Meggendorfer T, Weininger M, Wienhöft P. 2025. Solving robust Markov decision processes: Generic, reliable, efficient. Proceedings of the 39th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 39, 26631–26641.","chicago":"Meggendorfer, Tobias, Maximilian Weininger, and Patrick Wienhöft. “Solving Robust Markov Decision Processes: Generic, Reliable, Efficient.” In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, 39:26631–41. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i25.34865\">https://doi.org/10.1609/aaai.v39i25.34865</a>.","ama":"Meggendorfer T, Weininger M, Wienhöft P. Solving robust Markov decision processes: Generic, reliable, efficient. In: <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Vol 39. Association for the Advancement of Artificial Intelligence; 2025:26631-26641. doi:<a href=\"https://doi.org/10.1609/aaai.v39i25.34865\">10.1609/aaai.v39i25.34865</a>","ieee":"T. Meggendorfer, M. Weininger, and P. Wienhöft, “Solving robust Markov decision processes: Generic, reliable, efficient,” in <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, Philadelphia, PA, United States, 2025, vol. 39, no. 25, pp. 26631–26641.","mla":"Meggendorfer, Tobias, et al. “Solving Robust Markov Decision Processes: Generic, Reliable, Efficient.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 25, Association for the Advancement of Artificial Intelligence, 2025, pp. 26631–41, doi:<a href=\"https://doi.org/10.1609/aaai.v39i25.34865\">10.1609/aaai.v39i25.34865</a>."},"quality_controlled":"1","status":"public","OA_type":"green","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","volume":39,"_id":"19666","page":"26631-26641","author":[{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","first_name":"Tobias","full_name":"Meggendorfer, Tobias"},{"last_name":"Weininger","id":"02ab0197-cc70-11ed-ab61-918e71f56881","orcid":"0000-0002-0163-2152","first_name":"Maximilian","full_name":"Weininger, Maximilian"},{"last_name":"Wienhöft","full_name":"Wienhöft, Patrick","first_name":"Patrick"}],"date_created":"2025-05-11T22:02:39Z","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.14385449","relation":"software"}]},"day":"11","publication_identifier":{"issn":["2159-5399"],"eissn":["2374-3468"]},"date_updated":"2026-02-16T12:25:05Z","date_published":"2025-04-11T00:00:00Z","title":"Solving robust Markov decision processes: Generic, reliable, efficient","month":"04","oa":1,"abstract":[{"lang":"eng","text":"Markov decision processes (MDP) are a well-established model for sequential decision-making in the presence of probabilities. In *robust* MDP (RMDP), every action is associated with an *uncertainty set* of probability distributions, modelling that transition probabilities are not known precisely. Based on the known theoretical connection to stochastic games, we provide a framework for solving RMDPs that is generic, reliable, and efficient. It is *generic* both with respect to the model, allowing for a wide range of uncertainty sets, including but not limited to intervals, L1- or L2-balls, and polytopes; and with respect to the objective, including long-run average reward, undiscounted total reward, and stochastic shortest path. It is *reliable*, as our approach not only converges in the limit, but provides precision guarantees at any time during the computation. It is *efficient* because -- in contrast to state-of-the-art approaches -- it avoids explicitly constructing the underlying stochastic game. Consequently, our prototype implementation outperforms existing tools by several orders of magnitude and can solve RMDPs with a million states in under a minute."}],"conference":{"end_date":"2025-03-04","location":"Philadelphia, PA, United States","name":"AAAI: Conference on Artificial Intelligence","start_date":"2025-02-25"},"project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"doi":"10.1609/aaai.v39i25.34865","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.10185","open_access":"1"}],"type":"conference","oa_version":"Preprint"},{"oa":1,"abstract":[{"lang":"eng","text":"The problem of checking satisfiability of linear real arithmetic (LRA) and non-linear real arithmetic (NRA) formulas has broad applications, in particular, they are at the heart of logic-related applications such as logic for artificial intelligence, program analysis, etc. While there has been much work on checking satisfiability of unquantified LRA and NRA formulas, the problem of checking satisfiability of quantified LRA and NRA formulas remains a significant challenge. The main bottleneck in the existing methods is a computationally expensive quantifier elimination step. In this work, we propose a novel method for efficient quantifier elimination in quantified LRA and NRA formulas. We propose a template-based Skolemization approach, where we automatically synthesize linear/polynomial Skolem functions in order to eliminate quantifiers in the formula. The key technical ingredient in our approach are Positivstellensätze theorems from algebraic geometry, which allow for an efficient manipulation of polynomial inequalities. Our method offers a range of appealing theoretical properties combined with a strong practical performance. On the theory side, our method is sound, semi-complete, and runs in subexponential time and polynomial space, as opposed to existing sound and complete quantifier elimination methods that run in doubly-exponential time and at least exponential space. On the practical side, our experiments show superior performance compared to state of the art SMT solvers in terms of the number of solved instances and runtime, both on LRA and on NRA benchmarks."}],"month":"04","title":"Quantified linear and polynomial arithmetic satisfiability via template-based skolemization","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"date_updated":"2026-02-16T12:24:47Z","date_published":"2025-04-11T00:00:00Z","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.16226","open_access":"1"}],"type":"conference","publication_status":"published","doi":"10.1609/aaai.v39i11.33213","arxiv":1,"project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"conference":{"start_date":"2025-02-25","name":"AAAI: Conference on Artificial Intelligence","location":"Philadelphia, PA, United States","end_date":"2025-03-04"},"quality_controlled":"1","citation":{"apa":"Chatterjee, K., Goharshady, E., Karrabi, M., Motwani, H. J., Seeliger, M., &#38; Zikelic, D. (2025). Quantified linear and polynomial arithmetic satisfiability via template-based skolemization. In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i> (Vol. 39, pp. 11158–11166). Philadelphia, PA, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i11.33213\">https://doi.org/10.1609/aaai.v39i11.33213</a>","short":"K. Chatterjee, E. Goharshady, M. Karrabi, H.J. Motwani, M. Seeliger, D. Zikelic, in:, Proceedings of the 39th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2025, pp. 11158–11166.","ista":"Chatterjee K, Goharshady E, Karrabi M, Motwani HJ, Seeliger M, Zikelic D. 2025. Quantified linear and polynomial arithmetic satisfiability via template-based skolemization. Proceedings of the 39th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 39, 11158–11166.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Mehrdad Karrabi, Harshit J. Motwani, Maximilian Seeliger, and Dorde Zikelic. “Quantified Linear and Polynomial Arithmetic Satisfiability via Template-Based Skolemization.” In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, 39:11158–66. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i11.33213\">https://doi.org/10.1609/aaai.v39i11.33213</a>.","ama":"Chatterjee K, Goharshady E, Karrabi M, Motwani HJ, Seeliger M, Zikelic D. Quantified linear and polynomial arithmetic satisfiability via template-based skolemization. In: <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Vol 39. Association for the Advancement of Artificial Intelligence; 2025:11158-11166. doi:<a href=\"https://doi.org/10.1609/aaai.v39i11.33213\">10.1609/aaai.v39i11.33213</a>","mla":"Chatterjee, Krishnendu, et al. “Quantified Linear and Polynomial Arithmetic Satisfiability via Template-Based Skolemization.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 11, Association for the Advancement of Artificial Intelligence, 2025, pp. 11158–66, doi:<a href=\"https://doi.org/10.1609/aaai.v39i11.33213\">10.1609/aaai.v39i11.33213</a>.","ieee":"K. Chatterjee, E. Goharshady, M. Karrabi, H. J. Motwani, M. Seeliger, and D. Zikelic, “Quantified linear and polynomial arithmetic satisfiability via template-based skolemization,” in <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, Philadelphia, PA, United States, 2025, vol. 39, no. 11, pp. 11158–11166."},"OA_type":"green","status":"public","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","external_id":{"arxiv":["2412.16226"]},"ec_funded":1,"scopus_import":"1","department":[{"_id":"KrCh"}],"OA_place":"repository","intvolume":"        39","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was partially funded by ERC CoG 863818 (ForM-SMArt) and Austrian Science Fund (FWF) 10.55776/COE12.","language":[{"iso":"eng"}],"publisher":"Association for the Advancement of Artificial Intelligence","year":"2025","issue":"11","corr_author":"1","day":"11","date_created":"2025-05-11T22:02:39Z","_id":"19667","page":"11158-11166","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000-0002-8595-0587","full_name":"Kafshdar Goharshadi, Ehsan","first_name":"Ehsan","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","last_name":"Kafshdar Goharshadi"},{"id":"67638922-f394-11eb-9cf6-f20423e08757","last_name":"Karrabi","orcid":"0009-0007-5253-9170","full_name":"Karrabi, Mehrdad","first_name":"Mehrdad"},{"last_name":"Motwani","first_name":"Harshit J.","full_name":"Motwani, Harshit J."},{"full_name":"Seeliger, Maximilian","first_name":"Maximilian","last_name":"Seeliger"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"volume":39},{"type":"conference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.12996"}],"oa_version":"Preprint","arxiv":1,"doi":"10.1609/aaai.v39i25.34840","publication_status":"published","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2025-02-25","end_date":"2025-03-04","location":"Philadelphia, PA, United States"},"abstract":[{"lang":"eng","text":"Learning-based methods provide a promising approach to solving highly non-linear control tasks that are often challenging for classical control methods. To ensure the satisfaction of a safety property, learning-based methods jointly learn a control policy together with a certificate function for the property. Popular examples include barrier functions for safety and Lyapunov functions for asymptotic stability. While there has been significant progress on learning-based control with certificate functions in the white-box setting, where the correctness of the certificate function can be formally verified, there has been little work on ensuring their reliability in the black-box setting where the system dynamics are unknown. In this work, we consider the problems of certifying and repairing neural network control policies and certificate functions in the black-box setting. We propose a novel framework that utilizes runtime monitoring to detect system behaviors that violate the property of interest under some initially trained neural network policy and certificate. These violating behaviors are used to extract new training data, that is used to re-train the neural network policy and the certificate function and to ultimately repair them. We demonstrate the effectiveness of our approach empirically by using it to repair and to boost the safety rate of neural network policies learned by a state-of-the-art method for learning-based control on two autonomous system control tasks."}],"oa":1,"month":"04","date_published":"2025-04-11T00:00:00Z","date_updated":"2025-05-12T09:49:25Z","publication_identifier":{"issn":["2159-5399"],"eissn":["2374-3468"]},"title":"Neural control and certificate repair via runtime monitoring","day":"11","corr_author":"1","author":[{"full_name":"Yu, Zhengqi","first_name":"Zhengqi","id":"20aa2ae8-f2f1-11ed-bbfa-8205053f1342","last_name":"Yu"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"page":"26409-26417","_id":"19668","date_created":"2025-05-11T22:02:40Z","volume":39,"external_id":{"arxiv":["2412.12996"]},"status":"public","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","OA_type":"green","quality_controlled":"1","citation":{"apa":"Yu, E., Zikelic, D., &#38; Henzinger, T. A. (2025). Neural control and certificate repair via runtime monitoring. In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i> (Vol. 39, pp. 26409–26417). Philadelphia, PA, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i25.34840\">https://doi.org/10.1609/aaai.v39i25.34840</a>","short":"E. Yu, D. Zikelic, T.A. Henzinger, in:, Proceedings of the 39th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2025, pp. 26409–26417.","ista":"Yu E, Zikelic D, Henzinger TA. 2025. Neural control and certificate repair via runtime monitoring. Proceedings of the 39th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 39, 26409–26417.","chicago":"Yu, Emily, Dorde Zikelic, and Thomas A Henzinger. “Neural Control and Certificate Repair via Runtime Monitoring.” In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, 39:26409–17. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i25.34840\">https://doi.org/10.1609/aaai.v39i25.34840</a>.","ama":"Yu E, Zikelic D, Henzinger TA. Neural control and certificate repair via runtime monitoring. In: <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Vol 39. Association for the Advancement of Artificial Intelligence; 2025:26409-26417. doi:<a href=\"https://doi.org/10.1609/aaai.v39i25.34840\">10.1609/aaai.v39i25.34840</a>","ieee":"E. Yu, D. Zikelic, and T. A. Henzinger, “Neural control and certificate repair via runtime monitoring,” in <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, Philadelphia, PA, United States, 2025, vol. 39, no. 25, pp. 26409–26417.","mla":"Yu, Emily, et al. “Neural Control and Certificate Repair via Runtime Monitoring.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 25, Association for the Advancement of Artificial Intelligence, 2025, pp. 26409–17, doi:<a href=\"https://doi.org/10.1609/aaai.v39i25.34840\">10.1609/aaai.v39i25.34840</a>."},"department":[{"_id":"ToHe"}],"scopus_import":"1","ec_funded":1,"language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the ERC project ERC2020-AdG 101020093","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","intvolume":"        39","article_processing_charge":"No","issue":"25","publisher":"Association for the Advancement of Artificial Intelligence","year":"2025"},{"volume":39,"date_created":"2025-05-11T22:02:40Z","page":"11150-11157","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Ruichen","full_name":"Luo, Ruichen","id":"b391db08-1ffe-11ee-8b67-d18ddcfb5a14","last_name":"Luo"},{"orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","full_name":"Svoboda, Jakub","first_name":"Jakub","orcid":"0000-0002-1419-3267"}],"_id":"19669","day":"11","corr_author":"1","year":"2025","publisher":"Association for the Advancement of Artificial Intelligence","issue":"11","intvolume":"        39","article_processing_charge":"No","OA_place":"repository","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant and the Austrian Science Fund (FWF) 10.55776/COE12 grant.","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"KrCh"}],"scopus_import":"1","status":"public","OA_type":"green","publication":"Proceedings of the 39th AAAI Conference on Artificial Intelligence","quality_controlled":"1","citation":{"apa":"Chatterjee, K., Luo, R., Saona Urmeneta, R. J., &#38; Svoboda, J. (2025). Linear equations with min and max operators: Computational complexity. In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i> (Vol. 39, pp. 11150–11157). Philadelphia, PA, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v39i11.33212\">https://doi.org/10.1609/aaai.v39i11.33212</a>","short":"K. Chatterjee, R. Luo, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 39th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2025, pp. 11150–11157.","chicago":"Chatterjee, Krishnendu, Ruichen Luo, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Linear Equations with Min and Max Operators: Computational Complexity.” In <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, 39:11150–57. Association for the Advancement of Artificial Intelligence, 2025. <a href=\"https://doi.org/10.1609/aaai.v39i11.33212\">https://doi.org/10.1609/aaai.v39i11.33212</a>.","ista":"Chatterjee K, Luo R, Saona Urmeneta RJ, Svoboda J. 2025. Linear equations with min and max operators: Computational complexity. Proceedings of the 39th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 39, 11150–11157.","ama":"Chatterjee K, Luo R, Saona Urmeneta RJ, Svoboda J. Linear equations with min and max operators: Computational complexity. In: <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>. Vol 39. Association for the Advancement of Artificial Intelligence; 2025:11150-11157. doi:<a href=\"https://doi.org/10.1609/aaai.v39i11.33212\">10.1609/aaai.v39i11.33212</a>","ieee":"K. Chatterjee, R. Luo, R. J. Saona Urmeneta, and J. Svoboda, “Linear equations with min and max operators: Computational complexity,” in <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, Philadelphia, PA, United States, 2025, vol. 39, no. 11, pp. 11150–11157.","mla":"Chatterjee, Krishnendu, et al. “Linear Equations with Min and Max Operators: Computational Complexity.” <i>Proceedings of the 39th AAAI Conference on Artificial Intelligence</i>, vol. 39, no. 11, Association for the Advancement of Artificial Intelligence, 2025, pp. 11150–57, doi:<a href=\"https://doi.org/10.1609/aaai.v39i11.33212\">10.1609/aaai.v39i11.33212</a>."},"external_id":{"arxiv":["2412.12228"]},"conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2025-02-25","location":"Philadelphia, PA, United States","end_date":"2025-03-04"},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"doi":"10.1609/aaai.v39i11.33212","publication_status":"published","arxiv":1,"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.12228","open_access":"1"}],"type":"conference","title":"Linear equations with min and max operators: Computational complexity","date_published":"2025-04-11T00:00:00Z","date_updated":"2025-05-12T09:42:09Z","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"month":"04","abstract":[{"lang":"eng","text":"We consider a class of optimization problems defined by a system of linear equations with min and max operators. This class of optimization problems has been studied under restrictive conditions, such as, (C1) the halting or stability condition; (C2) the non-negative coefficients condition; (C3) the sum upto 1 condition; and (C4) the only min or only max operator condition. Several seminal results in the literature focus on special cases. For example, turn-based stochastic games correspond to conditions C2 and C3; and Markov decision process to conditions C2, C3, and C4. However, the systematic computational complexity study of all the cases has not been explored, which we address in this work. Some highlights of our results are: with conditions C2 and C4, and with conditions C3 and C4, the problem is NP-complete, whereas with condition C1 only, the problem is in UP intersects coUP. Finally, we establish the computational complexity of the decision problem of checking the respective conditions."}],"oa":1},{"issue":"4","article_number":"044122","year":"2025","publisher":"AIP Publishing","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"acknowledgement":"he authors thank Frank Jülicher, for supporting the initiative and stimulating discussions. We thank Tetsuya Spippayashi for enlightening clarifications on the historical origins of Cacio e pepe and Giuseppe Ricchitelli for helping with the construction of the experimental apparatus. We further thank Martina Gaiba, Alessandro Gaiba, John D. Treado, Virginia Lepore, Eleonora Nanu, Julia Kirsch, Lara Koehler, Burak Budanur, Irina Pi-Jaumà, Elizabeth Brückner, M.J. Franco Oñate, Giorgio Nicoletti, and Marco Salvalaglio for their support and for eating up the sample leftovers. Finally, we thank Simone Frau for taking the photograph in Fig. 1(a).","intvolume":"        37","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","department":[{"_id":"EdHa"}],"external_id":{"arxiv":["2501.00536"],"isi":["001482986200001"]},"quality_controlled":"1","citation":{"mla":"Bartolucci, G., et al. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>, vol. 37, no. 4, 044122, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>.","ieee":"G. Bartolucci <i>et al.</i>, “Phase behavior of Cacio e Pepe sauce,” <i>Physics of Fluids</i>, vol. 37, no. 4. AIP Publishing, 2025.","ama":"Bartolucci G, Busiello DM, Ciarchi M, et al. Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>","ista":"Bartolucci G, Busiello DM, Ciarchi M, Corticelli A, Di Terlizzi I, Olmeda F, Revignas D, Schimmenti VM. 2025. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 37(4), 044122.","chicago":"Bartolucci, G., D. M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, Fabrizio Olmeda, D. Revignas, and V. M. Schimmenti. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>.","apa":"Bartolucci, G., Busiello, D. M., Ciarchi, M., Corticelli, A., Di Terlizzi, I., Olmeda, F., … Schimmenti, V. M. (2025). Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>","short":"G. Bartolucci, D.M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, F. Olmeda, D. Revignas, V.M. Schimmenti, Physics of Fluids 37 (2025)."},"publication":"Physics of Fluids","status":"public","OA_type":"hybrid","volume":37,"_id":"19670","author":[{"first_name":"G.","full_name":"Bartolucci, G.","last_name":"Bartolucci"},{"last_name":"Busiello","first_name":"D. M.","full_name":"Busiello, D. M."},{"last_name":"Ciarchi","first_name":"M.","full_name":"Ciarchi, M."},{"full_name":"Corticelli, A.","first_name":"A.","last_name":"Corticelli"},{"first_name":"I.","full_name":"Di Terlizzi, I.","last_name":"Di Terlizzi"},{"last_name":"Olmeda","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio","first_name":"Fabrizio"},{"full_name":"Revignas, D.","first_name":"D.","last_name":"Revignas"},{"first_name":"V. M.","full_name":"Schimmenti, V. M.","last_name":"Schimmenti"}],"date_created":"2025-05-11T22:02:40Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/2025-ig-nobel-prize-for-perfect-pasta-sauce/","description":"News on ISTA","relation":"press_release"}]},"day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-28T13:24:53Z","publication_identifier":{"issn":["1070-6631"],"eissn":["1089-7666"]},"article_type":"original","date_published":"2025-04-01T00:00:00Z","title":"Phase behavior of Cacio e Pepe sauce","month":"04","file":[{"creator":"dernst","date_created":"2025-05-12T09:31:22Z","file_id":"19681","file_name":"2025_PhysicsFluids_Bartolucci.pdf","date_updated":"2025-05-12T09:31:22Z","content_type":"application/pdf","success":1,"relation":"main_file","file_size":4926853,"access_level":"open_access","checksum":"242d05898aa0a2348b9c108747adb5ce"}],"oa":1,"abstract":[{"lang":"eng","text":"“Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish."}],"ddc":["530"],"arxiv":1,"publication_status":"published","doi":"10.1063/5.0255841","has_accepted_license":"1","file_date_updated":"2025-05-12T09:31:22Z","isi":1,"type":"journal_article","oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Silvopastoral use in native forests could impact population dynamics of key tree species, with contrasting effects at different life cycle stages. Prior studies in South American temperate forests have mainly focused on initial stages, lacking a comprehensive understanding of the entire life cycle within productive systems. We assessed the population dynamics of two key species of mixed forests in northern Patagonia (Austrocedrus chilensis and Nothofagus dombeyi) under two silvopastoral use intensities (high vs. low), using demographic techniques and population projection models. Over 3 years, we quantified vital rates (survival, fertility, growth, reversion and stasis) and used matrix models to calculate deterministic population growth rates (λ). High-intensity silvopastoral use had predominantly negative effects on the elements of the projection matrices of A. chilensis, whereas N. dombeyi exhibited mostly positive or no changes. As a result, projections indicated slight population decreases for A. chilensis (mostly λ < 1) at high silvopastoral use levels compared to low levels, while N. dombeyi showed similar projections (λ ≅ 1) between use levels. Decreased λ for A. chilensis resulted mainly from lower adult tree survival, while early life stages had limited influence on λ for these long-lived species. In summary, silvopastoral use affects population dynamics of key tree species of these mixed forests of northern Patagonia, with implications for sustainable management. Our findings highlight the importance of considering the entire life cycle and suggest targeted practices to enhance A. chilensis populations."}],"date_published":"2025-04-01T00:00:00Z","article_type":"original","publication_identifier":{"issn":["1442-9985"],"eissn":["1442-9993"]},"date_updated":"2025-09-30T12:31:04Z","title":"A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia","month":"04","doi":"10.1111/aec.70058","publication_status":"published","type":"journal_article","isi":1,"oa_version":"None","department":[{"_id":"NiBa"}],"scopus_import":"1","external_id":{"isi":["001476761500001"]},"publication":"Austral Ecology","status":"public","OA_type":"closed access","citation":{"apa":"Arpigiani, D., Aschero, V., Soler Schaller, R. M., &#38; Amoroso, M. M. (2025). A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>","short":"D. Arpigiani, V. Aschero, R.M. Soler Schaller, M.M. Amoroso, Austral Ecology 50 (2025).","chicago":"Arpigiani, Daniela, Valeria Aschero, Rosina Matilde Soler Schaller, and Mariano M. Amoroso. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/aec.70058\">https://doi.org/10.1111/aec.70058</a>.","ista":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. 2025. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. Austral Ecology. 50(4), e70058.","ama":"Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia. <i>Austral Ecology</i>. 2025;50(4). doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>","mla":"Arpigiani, Daniela, et al. “A Life-Cycle Approach to Understand Consequences of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” <i>Austral Ecology</i>, vol. 50, no. 4, e70058, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/aec.70058\">10.1111/aec.70058</a>.","ieee":"D. Arpigiani, V. Aschero, R. M. Soler Schaller, and M. M. Amoroso, “A life-cycle approach to understand consequences of silvopastoral use on two native tree species of Northern Patagonia,” <i>Austral Ecology</i>, vol. 50, no. 4. Wiley, 2025."},"quality_controlled":"1","issue":"4","article_number":"e70058","publisher":"Wiley","year":"2025","acknowledgement":"We would like to express our sincere gratitude to the owners of the estates, Lisandro and Oscar Lanfré, Roberto Criado and Yayo Tillería, for allowing us to conduct our research on their properties and for generously sharing their time and knowledge throughout these years. We are also deeply thankful to our field assistants, Matías Scotti, Clara Pissolito, Noel Szudruk, Mariano Varela, Ian Mott, Brisa Guenuleo, Nicolás Bistolfi, Facundo Gómez and Belén Vallerga, who tirelessly collaborated in the arduous tasks of monitoring and data collection, even in challenging weather conditions. We are grateful to CONICET for providing the doctoral scholarship to D. Arpigiani. This study received partial financial support from the Agencia MINCyT (PICT 2015-1692) and the Universidad Nacional de Río Negro (PI 40-B-478), Argentina.","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        50","article_processing_charge":"No","day":"01","volume":50,"author":[{"last_name":"Arpigiani","full_name":"Arpigiani, Daniela","first_name":"Daniela"},{"last_name":"Aschero","first_name":"Valeria","full_name":"Aschero, Valeria"},{"last_name":"Soler Schaller","id":"9e668447-8c32-11ed-b0c7-8dc2d7b80803","full_name":"Soler Schaller, Rosina Matilde","first_name":"Rosina Matilde"},{"full_name":"Amoroso, Mariano M.","first_name":"Mariano M.","last_name":"Amoroso"}],"_id":"19671","date_created":"2025-05-11T22:02:41Z"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","corr_author":"1","date_created":"2025-05-11T22:02:41Z","author":[{"id":"74c777f4-32da-11ee-b498-874db0835561","last_name":"Polesello","full_name":"Polesello, Andrea","first_name":"Andrea"},{"full_name":"Charinti, Giousef Alexandros","first_name":"Giousef Alexandros","id":"7f7cc04c-074c-11ed-af92-eb16afd85c75","last_name":"Charinti"},{"full_name":"Meroni, Agostino Niyonkuru","first_name":"Agostino Niyonkuru","last_name":"Meroni"},{"first_name":"Caroline J","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"},{"first_name":"Claudia","full_name":"Pasquero, Claudia","last_name":"Pasquero"}],"_id":"19672","volume":17,"status":"public","OA_type":"gold","publication":"Journal of Advances in Modeling Earth Systems","quality_controlled":"1","citation":{"mla":"Polesello, Andrea, et al. “Intensity Oscillations of Tropical Cyclones: Surface versus Mid and Upper Tropospheric Processes.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 4, e2024MS004613, Wiley, 2025, doi:<a href=\"https://doi.org/10.1029/2024MS004613\">10.1029/2024MS004613</a>.","ieee":"A. Polesello, G. A. Charinti, A. N. Meroni, C. J. Muller, and C. Pasquero, “Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 17, no. 4. Wiley, 2025.","ama":"Polesello A, Charinti GA, Meroni AN, Muller CJ, Pasquero C. Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. <i>Journal of Advances in Modeling Earth Systems</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1029/2024MS004613\">10.1029/2024MS004613</a>","ista":"Polesello A, Charinti GA, Meroni AN, Muller CJ, Pasquero C. 2025. Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. Journal of Advances in Modeling Earth Systems. 17(4), e2024MS004613.","chicago":"Polesello, Andrea, Giousef Alexandros Charinti, Agostino Niyonkuru Meroni, Caroline J Muller, and Claudia Pasquero. “Intensity Oscillations of Tropical Cyclones: Surface versus Mid and Upper Tropospheric Processes.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2025. <a href=\"https://doi.org/10.1029/2024MS004613\">https://doi.org/10.1029/2024MS004613</a>.","apa":"Polesello, A., Charinti, G. A., Meroni, A. N., Muller, C. J., &#38; Pasquero, C. (2025). Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2024MS004613\">https://doi.org/10.1029/2024MS004613</a>","short":"A. Polesello, G.A. Charinti, A.N. Meroni, C.J. Muller, C. Pasquero, Journal of Advances in Modeling Earth Systems 17 (2025)."},"external_id":{"isi":["001472439600001"]},"ec_funded":1,"department":[{"_id":"CaMu"}],"scopus_import":"1","article_processing_charge":"Yes","intvolume":"        17","OA_place":"publisher","language":[{"iso":"eng"}],"acknowledgement":"The authors acknowledge two anonymous reviewers and the editor who provided insightful remarks and comments that helped to significantly improve the manuscript. AP and CJM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). Part of this work is an outcome of the project MIUR—Dipartimenti di Eccellenza 2023–2027. ANM is supported by HPC-TRES Grant 2023-04.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","publisher":"Wiley","DOAJ_listed":"1","article_number":"e2024MS004613","issue":"4","oa_version":"Published Version","type":"journal_article","isi":1,"has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-05-12T12:17:08Z","doi":"10.1029/2024MS004613","ddc":["550"],"project":[{"call_identifier":"H2020","grant_number":"805041","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"abstract":[{"lang":"eng","text":"Some of the classical models of tropical cyclone intensification predict tropical cyclones to intensify up to a steady intensity, which depends on surface fluxes only, without any relevant role played by convective motions in the troposphere, typically assumed to have a moist adiabatic lapse rate. Simulations performed using the non-hydrostatic, high-resolution model System for Atmosphere Modeling in idealized settings (rotating radiative-convective equilibrium on a doubly periodic domain) show early intensification consistent with these theoretical expectations, but different intensity evolution, with the cyclone undergoing an oscillation in wind speed. This oscillation can be linked to feedbacks between the cyclone intensity and air buoyancy: convective heating, radiative heating, and mixing with warm low stratospheric air warm the mid and upper troposphere of the cyclone stabilizing the air column and thus reducing its intensity. After the intensity decay phase, mid and upper tropospheric cooling, mostly through cold advection from the surroundings, cooled by radiation, rebuilds Convective Available Potential Energy, that peaks just before a new intensification phase. These idealized simulations thus highlight the potentially important interactions between a tropical cyclone, its environment and radiation."}],"oa":1,"file":[{"success":1,"checksum":"2f7c74aceaeea4be1fff4de300791319","relation":"main_file","file_size":942325,"access_level":"open_access","content_type":"application/pdf","file_name":"2025_JAMES_Polesello.pdf","file_id":"19683","date_updated":"2025-05-12T12:17:08Z","creator":"dernst","date_created":"2025-05-12T12:17:08Z"}],"month":"04","title":"Intensity oscillations of tropical cyclones: Surface versus mid and upper tropospheric processes","date_published":"2025-04-01T00:00:00Z","article_type":"original","date_updated":"2025-09-30T12:30:29Z","publication_identifier":{"eissn":["1942-2466"]}},{"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"corr_author":"1","day":"23","_id":"19673","page":"1-26","author":[{"last_name":"Wang","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","full_name":"Wang, Victor","first_name":"Victor","orcid":"0000-0002-0704-7026"}],"date_created":"2025-05-11T22:02:41Z","volume":3,"external_id":{"arxiv":["2304.08674"]},"citation":{"short":"V. Wang, Journal of the Association for Mathematical Research 3 (2025) 1–26.","apa":"Wang, V. (2025). Prime Hasse principles via diophantine second moments. <i>Journal of the Association for Mathematical Research</i>. Association for Mathematical Research. <a href=\"https://doi.org/10.56994/JAMR.003.001.001\">https://doi.org/10.56994/JAMR.003.001.001</a>","ista":"Wang V. 2025. Prime Hasse principles via diophantine second moments. Journal of the Association for Mathematical Research. 3(1), 1–26.","chicago":"Wang, Victor. “Prime Hasse Principles via Diophantine Second Moments.” <i>Journal of the Association for Mathematical Research</i>. Association for Mathematical Research, 2025. <a href=\"https://doi.org/10.56994/JAMR.003.001.001\">https://doi.org/10.56994/JAMR.003.001.001</a>.","ama":"Wang V. Prime Hasse principles via diophantine second moments. <i>Journal of the Association for Mathematical Research</i>. 2025;3(1):1-26. doi:<a href=\"https://doi.org/10.56994/JAMR.003.001.001\">10.56994/JAMR.003.001.001</a>","mla":"Wang, Victor. “Prime Hasse Principles via Diophantine Second Moments.” <i>Journal of the Association for Mathematical Research</i>, vol. 3, no. 1, Association for Mathematical Research, 2025, pp. 1–26, doi:<a href=\"https://doi.org/10.56994/JAMR.003.001.001\">10.56994/JAMR.003.001.001</a>.","ieee":"V. Wang, “Prime Hasse principles via diophantine second moments,” <i>Journal of the Association for Mathematical Research</i>, vol. 3, no. 1. Association for Mathematical Research, pp. 1–26, 2025."},"quality_controlled":"1","publication":"Journal of the Association for Mathematical Research","status":"public","OA_type":"diamond","scopus_import":"1","department":[{"_id":"TiBr"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was partially supported by the European Union’s Horizon 2020 research and innovation program under the MarieSkłodowska-Curie Grant Agreement No. 101034413","language":[{"iso":"eng"}],"intvolume":"         3","article_processing_charge":"No","OA_place":"publisher","issue":"1","publisher":"Association for Mathematical Research","year":"2025","type":"journal_article","oa_version":"Published Version","arxiv":1,"has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-05-12T10:23:26Z","doi":"10.56994/JAMR.003.001.001","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"ddc":["510"],"oa":1,"abstract":[{"text":"We show that almost all primes p =\\= ± 4 mod9 are sums of three cubes, assuming a conjecture due to Hooley, Manin, et al. on cubic fourfolds. This conjecture is approachable under standard statistical hypotheses on geometric families of L-functions.","lang":"eng"}],"month":"01","file":[{"date_created":"2025-05-12T10:23:26Z","creator":"dernst","file_name":"2025_JAMR_Wang.pdf","date_updated":"2025-05-12T10:23:26Z","content_type":"application/pdf","file_id":"19682","success":1,"checksum":"f9a1057d146632890466a7dc33bf625e","access_level":"open_access","relation":"main_file","file_size":1094167}],"date_updated":"2025-05-12T10:26:00Z","publication_identifier":{"eissn":["2998-4114"]},"article_type":"original","date_published":"2025-01-23T00:00:00Z","title":"Prime Hasse principles via diophantine second moments"},{"article_processing_charge":"No","OA_place":"repository","language":[{"iso":"eng"}],"acknowledgement":"The authors gratefully acknowledge Volkan Cevher for an insightful discussion about sparse recovery algorithms, Alex Smola for valuable feedback on the experiments, and Marco Baroni for an engaging conversation on the phenomenon of head specialization in NLP.\r\n","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","year":"2025","title":"ResiDual transformer alignment with spectral decomposition","date_published":"2025-04-14T00:00:00Z","article_number":"2411.00246","date_updated":"2025-05-19T07:03:16Z","status":"public","publication":"arXiv","OA_type":"green","citation":{"ama":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>","ieee":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual transformer alignment with spectral decomposition,” <i>arXiv</i>. .","mla":"Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, 2411.00246, doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>.","apa":"Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., &#38; Locatello, F. (n.d.). ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>","short":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.).","chicago":"Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>.","ista":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246."},"external_id":{"arxiv":["2411.00246"]},"abstract":[{"lang":"eng","text":"When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets)."}],"oa":1,"department":[{"_id":"FrLo"}],"date_created":"2025-05-11T22:02:41Z","author":[{"full_name":"Basile, Lorenzo","first_name":"Lorenzo","last_name":"Basile"},{"last_name":"Maiorca","full_name":"Maiorca, Valentino","first_name":"Valentino"},{"first_name":"Luca","full_name":"Bortolussi, Luca","last_name":"Bortolussi"},{"first_name":"Emanuele","full_name":"Rodolà, Emanuele","last_name":"Rodolà"},{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco"}],"_id":"19674","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2411.00246"}],"type":"preprint","publication_status":"submitted","doi":"10.48550/arXiv.2411.00246","arxiv":1,"day":"14"},{"abstract":[{"lang":"eng","text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate."}],"oa":1,"title":"Transition to turbulence : Data-, solution-, and pattern-driven approaches","date_published":"2025-05-13T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-06-18T19:23:35Z","file":[{"checksum":"0e452642b79f13633f1595bde71a67e3","relation":"main_file","file_size":20058169,"access_level":"open_access","success":1,"file_name":"Gökhan Yalnız - PhD thesis.pdf","content_type":"application/pdf","file_id":"19685","date_updated":"2025-05-12T15:13:28Z","creator":"gyalniz","date_created":"2025-05-12T15:13:28Z"},{"description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","date_created":"2025-05-12T15:15:59Z","creator":"gyalniz","title":"Chapter 2 - Movie 2A.1","content_type":"video/mp4","file_id":"19686","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 2A.1.mp4","checksum":"921099d76adab2df784ce12ce41cfb22","file_size":37763743,"relation":"supplementary_material","access_level":"open_access"},{"date_created":"2025-05-12T15:16:09Z","creator":"gyalniz","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","file_id":"19687","file_name":"Movie 3A.1.mp4","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","title":"Chapter 3 - Movie 3A.1","access_level":"open_access","relation":"supplementary_material","file_size":3902655,"checksum":"0ae5ac7d9896003c0c4207dd746808dc"},{"description":"Turbulent flow (left) in P2K domain and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","creator":"gyalniz","date_created":"2025-05-12T15:16:21Z","file_id":"19688","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_name":"Movie 3A.2.mp4","title":"Chapter 3 - Movie 3A.2","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","file_size":7043169,"access_level":"open_access","relation":"supplementary_material"},{"title":"Chapter 3 - Movie 3A.3","content_type":"video/mp4","file_name":"Movie 3A.3.mp4","date_updated":"2025-05-12T15:43:28Z","file_id":"19689","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","date_created":"2025-05-12T15:16:36Z","creator":"gyalniz","checksum":"7ed871f428100d6827ac9b0e8ca8e985","file_size":7748659,"access_level":"open_access","relation":"supplementary_material"},{"description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","creator":"gyalniz","date_created":"2025-05-12T15:16:50Z","title":"Chapter 3 - Movie 3A.4","content_type":"video/mp4","file_name":"Movie 3A.4.mp4","file_id":"19690","date_updated":"2025-05-12T15:43:28Z","checksum":"dd5a252e1da00c8f303588e22e2baeef","access_level":"open_access","file_size":5873052,"relation":"supplementary_material"},{"checksum":"5ac58b86810698db28cbfc28f351ff70","file_size":9209327,"access_level":"open_access","relation":"supplementary_material","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit.","creator":"gyalniz","date_created":"2025-05-12T15:17:11Z","file_name":"Movie 4A.1.mp4","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_id":"19691","title":"Chapter 4 - Movie 4A.1"},{"checksum":"ac877f1e1ef39439911bf37cb1793b8e","access_level":"open_access","file_size":5893993,"relation":"supplementary_material","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_name":"Movie 5A.1.mp4","file_id":"19692","title":"Chapter 5 - Movie 5A.1","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","date_created":"2025-05-12T15:17:43Z","creator":"gyalniz"},{"access_level":"open_access","file_size":3990352,"relation":"supplementary_material","checksum":"fd17eabb70129ceaa414e40924d1d2fe","creator":"gyalniz","date_created":"2025-05-12T15:17:49Z","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 5A.2.mp4","file_id":"19693","content_type":"video/mp4","title":"Chapter 5 - Movie 5A.2"},{"title":"Chapter 5 - Movie 5A.3","file_id":"19694","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_name":"Movie 5A.3.mp4","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. 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Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>"},"publisher":"Institute of Science and Technology Austria","year":"2025","acknowledged_ssus":[{"_id":"ScienComp"}],"OA_place":"publisher","article_processing_charge":"No","acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"13","corr_author":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9558"},{"status":"public","relation":"part_of_dissertation","id":"12105"},{"id":"13274","status":"public","relation":"part_of_dissertation"},{"id":"14466","relation":"part_of_dissertation","status":"public"},{"id":"7563","status":"public","relation":"part_of_dissertation"}]},"date_created":"2025-05-12T15:12:28Z","author":[{"last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","first_name":"Gökhan","orcid":"0000-0002-8490-9312"}],"page":"155","_id":"19684"},{"date_updated":"2026-06-10T08:33:41Z","date_published":"2025-07-31T00:00:00Z","title":"Dataset for \"Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State\"","year":"2025","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","month":"07","file":[{"success":1,"checksum":"4c2d29404e070bda7d5619f728ec555c","access_level":"open_access","file_size":557878455,"relation":"main_file","file_name":"dataset.zip","content_type":"application/zip","date_updated":"2025-07-31T08:14:40Z","file_id":"20094","creator":"btatman","date_created":"2025-07-31T08:14:40Z"},{"date_created":"2025-07-31T08:14:21Z","creator":"btatman","date_updated":"2025-07-31T08:14:21Z","file_name":"readme.txt","file_id":"20095","content_type":"text/plain","success":1,"checksum":"6cbccd602be0ecb6ddb1f81fdfcadf92","access_level":"open_access","file_size":3514,"relation":"main_file"}],"article_processing_charge":"No","department":[{"_id":"PaSc"}],"oa":1,"contributor":[{"contributor_type":"project_leader","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"last_name":"Sridharan","contributor_type":"researcher","first_name":"Vidhyalakshmi"},{"contributor_type":"researcher","first_name":"Motilal","last_name":"Uttarkabat"},{"last_name":"Jaroniec","contributor_type":"researcher","first_name":"Christopher"},{"contributor_type":"researcher","first_name":"Matthias","last_name":"Ernst"},{"last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","first_name":"Petra","contributor_type":"researcher","orcid":"0000-0001-8729-7326"}],"citation":{"mla":"Tatman, Benjamin. <i>Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>.","ieee":"B. Tatman, “Dataset for ‘Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.’” Institute of Science and Technology Austria, 2025.","ama":"Tatman B. Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.” 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>","chicago":"Tatman, Benjamin. “Dataset for ‘Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">https://doi.org/10.15479/AT-ISTA-19696</a>.","ista":"Tatman B. 2025. Dataset for ‘Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">10.15479/AT-ISTA-19696</a>.","short":"B. Tatman, (2025).","apa":"Tatman, B. (2025). Dataset for “Bumps on the Road: The Way to Clean Relaxation Dispersion in the Solid State.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19696\">https://doi.org/10.15479/AT-ISTA-19696</a>"},"status":"public","_id":"19696","author":[{"first_name":"Benjamin","full_name":"Tatman, Benjamin","last_name":"Tatman","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"}],"date_created":"2025-05-14T10:46:07Z","related_material":{"record":[{"id":"20321","status":"public","relation":"research_data"}],"link":[{"url":"http.//doi.org/10.1021/jacs.5c09057","relation":"research_paper","description":"Paper to which the dataset corresponds."}]},"corr_author":"1","day":"31","file_date_updated":"2025-07-31T08:14:40Z","doi":"10.15479/AT-ISTA-19696","has_accepted_license":"1","type":"research_data","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"oa_version":"Published Version"},{"external_id":{"isi":["001483889000001"],"arxiv":["2410.03830"]},"publication":"The Astrophysical Journal","OA_type":"gold","status":"public","citation":{"mla":"Tiede, Christopher, et al. “Suppressed Accretion onto Massive Black Hole Binaries Surrounded by Thin Disks.” <i>The Astrophysical Journal</i>, vol. 984, no. 2, 144, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/adc727\">10.3847/1538-4357/adc727</a>.","ieee":"C. Tiede, J. Zrake, A. Macfadyen, and Z. Haiman, “Suppressed accretion onto massive black hole binaries surrounded by thin disks,” <i>The Astrophysical Journal</i>, vol. 984, no. 2. IOP Publishing, 2025.","ama":"Tiede C, Zrake J, Macfadyen A, Haiman Z. Suppressed accretion onto massive black hole binaries surrounded by thin disks. <i>The Astrophysical Journal</i>. 2025;984(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/adc727\">10.3847/1538-4357/adc727</a>","chicago":"Tiede, Christopher, Jonathan Zrake, Andrew Macfadyen, and Zoltán Haiman. “Suppressed Accretion onto Massive Black Hole Binaries Surrounded by Thin Disks.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/adc727\">https://doi.org/10.3847/1538-4357/adc727</a>.","ista":"Tiede C, Zrake J, Macfadyen A, Haiman Z. 2025. Suppressed accretion onto massive black hole binaries surrounded by thin disks. The Astrophysical Journal. 984(2), 144.","short":"C. Tiede, J. Zrake, A. Macfadyen, Z. Haiman, The Astrophysical Journal 984 (2025).","apa":"Tiede, C., Zrake, J., Macfadyen, A., &#38; Haiman, Z. (2025). Suppressed accretion onto massive black hole binaries surrounded by thin disks. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/adc727\">https://doi.org/10.3847/1538-4357/adc727</a>"},"quality_controlled":"1","department":[{"_id":"ZoHa"}],"scopus_import":"1","acknowledgement":"C.T. sincerely thanks Daniel J. D'Orazio for useful and illuminating discussions. This work was supported by the European Union's Horizon 2023 research and innovation program under Marie Sklodowska-Curie grant agreement No. 101148364, by Sapere Aude Starting grant No. 121587 through the Danish Independent Research Fund, by the LISA Preparatory Science Program (LPS) through NASA grant 80NSSC24K0440, and by NASA Astrophysics Theory Program (ATP) grant 80NSSC22K0822. Computation time for this work was supported through the NYU IT High Performance Computing resources as well as the Tycho supercomputer hosted at the SCIENCE HPC center at the University of Copenhagen.","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","intvolume":"       984","article_processing_charge":"Yes","article_number":"144","issue":"2","publisher":"IOP Publishing","year":"2025","DOAJ_listed":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"09","author":[{"last_name":"Tiede","first_name":"Christopher","full_name":"Tiede, Christopher"},{"first_name":"Jonathan","full_name":"Zrake, Jonathan","last_name":"Zrake"},{"last_name":"Macfadyen","first_name":"Andrew","full_name":"Macfadyen, Andrew"},{"id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36","last_name":"Haiman","orcid":"0000-0003-3633-5403","first_name":"Zoltán","full_name":"Haiman, Zoltán"}],"_id":"19699","date_created":"2025-05-18T22:02:49Z","volume":984,"abstract":[{"text":"We demonstrate that gas disks around binary systems might deliver gas to the binary components only when the circumbinary disk is relatively warm. We present new grid-based hydrodynamics simulations, performed with the binary on the grid and a locally isothermal equation of state, in which the binary is seen to functionally \"stop accreting\" if the orbital Mach number in the disk exceeds a threshold value of about 40. Above this threshold, the disk continues to extract angular momentum from the binary orbit, but it delivers very little mass to the black holes and instead piles up mass in a ring surrounding the binary. This ring will eventually become viscously relaxed and deliver mass to the binary at the large-scale inflow rate. However, we show that the timescale for such relaxation can far exceed the implied binary lifetime. We demonstrate that the ability of a binary–disk system to equilibrate is dependent on the efficiency at which accretion streams deposit mass onto the binary, which, in turn is highly sensitive to the thermodynamic conditions of the inner disk. If disks around massive black hole binaries do operate in such nonaccreting regimes, it suggests these systems may be dimmer than their single black hole counterparts but could exhibit dramatic rebrightening after the black holes inspiral and merge. This dimming begins in the UV/optical and could completely choke high-energy emission, such that these systems would likely be intrinsically X-ray weak with reddened continua, potentially resembling the spectra of \"little red dots\" recently identified in JWST observations.","lang":"eng"}],"oa":1,"file":[{"file_name":"2025_AstrophysicalJour_Tiede.pdf","content_type":"application/pdf","file_id":"19708","date_updated":"2025-05-19T07:20:30Z","creator":"dernst","date_created":"2025-05-19T07:20:30Z","file_size":1058601,"access_level":"open_access","relation":"main_file","checksum":"0d4c57ee944599c0789f3db467c5ca2f","success":1}],"month":"05","article_type":"original","date_published":"2025-05-09T00:00:00Z","date_updated":"2026-02-16T12:42:56Z","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"title":"Suppressed accretion onto massive black hole binaries surrounded by thin disks","type":"journal_article","isi":1,"oa_version":"Published Version","arxiv":1,"file_date_updated":"2025-05-19T07:20:30Z","doi":"10.3847/1538-4357/adc727","has_accepted_license":"1","publication_status":"published","ddc":["520"]},{"oa_version":"Published Version","isi":1,"type":"journal_article","has_accepted_license":"1","doi":"10.3847/1538-4357/adc1ca","file_date_updated":"2025-05-19T07:08:39Z","publication_status":"published","arxiv":1,"ddc":["520"],"abstract":[{"text":"The JWST discovery of \"little red dots\" (LRDs) is reshaping our picture of the early Universe, yet the physical mechanisms driving their compact size and UV-optical colors remain elusive. Here, we report an unusually bright LRD (zspec = 3.1) observed as part of the RUBIES program. This LRD exhibits broad emission lines (FWHM ∼ 4000 km s−1), a blue UV continuum, a clear Balmer break, and a red continuum sampled out to rest-frame 4 μm with MIRI. We develop a new joint galaxy and active galactic nucleus (AGN) model within the Prospector Bayesian inference framework and perform spectrophotometric modeling using NIRCam, MIRI, and NIRSpec/Prism observations. Our fiducial model reveals a M* ∼ 109 M⊙ galaxy alongside a dust-reddened AGN driving the optical emission. Explaining the rest-frame optical color as a reddened AGN requires AV ≳ 3, suggesting that a great majority of the accretion disk energy is reradiated as dust emission. Yet, despite clear AGN signatures, we find a surprising lack of hot torus emission, which implies that either the dust emission in this object must be cold, or the red continuum must instead be driven by a massive, evolved stellar population of the host galaxy—seemingly inconsistent with the high-EW broad lines (Hα rest-frame EW ∼ 800 Å). The widths and luminosities of Pa-β, Pa-δ, Pa-γ, and Hα imply a modest black hole mass of MBH ∼ 108 M⊙. Additionally, we identify a narrow blueshifted He i λ 1.083 μm absorption feature in NIRSpec/G395M spectra, signaling an ionized outflow with kinetic energy up to ∼1% the luminosity of the AGN. The low redshift of RUBIES-BLAGN-1, combined with the depth and richness of the JWST imaging and spectroscopic observations, provides a unique opportunity to build a physical model for these so-far mysterious LRDs, which may prove to be a crucial phase in the early formation of massive galaxies and their supermassive black holes.","lang":"eng"}],"oa":1,"file":[{"relation":"main_file","access_level":"open_access","file_size":3522072,"checksum":"1a9ff4516d11808bc6947744473c9fc2","success":1,"file_id":"19707","file_name":"2025_AstrophysicalJour_Wang.pdf","date_updated":"2025-05-19T07:08:39Z","content_type":"application/pdf","creator":"dernst","date_created":"2025-05-19T07:08:39Z"}],"month":"05","title":"RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow","date_published":"2025-05-09T00:00:00Z","article_type":"original","date_updated":"2026-02-16T12:42:43Z","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"09","date_created":"2025-05-18T22:02:49Z","author":[{"last_name":"Wang","first_name":"Bingjie","full_name":"Wang, Bingjie"},{"first_name":"Anna","full_name":"De Graaff, Anna","last_name":"De Graaff"},{"last_name":"Davies","full_name":"Davies, Rebecca L.","first_name":"Rebecca L."},{"last_name":"Greene","first_name":"Jenny E.","full_name":"Greene, Jenny E."},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"first_name":"Gabriel B.","full_name":"Brammer, Gabriel B.","last_name":"Brammer"},{"first_name":"Andy D.","full_name":"Goulding, Andy D.","last_name":"Goulding"},{"full_name":"Miller, Tim B.","first_name":"Tim B.","last_name":"Miller"},{"last_name":"Suess","full_name":"Suess, Katherine A.","first_name":"Katherine A."},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"full_name":"Williams, Christina C.","first_name":"Christina C.","last_name":"Williams"},{"full_name":"Bezanson, Rachel","first_name":"Rachel","last_name":"Bezanson"},{"full_name":"Boogaard, Leindert A.","first_name":"Leindert A.","last_name":"Boogaard"},{"last_name":"Cleri","full_name":"Cleri, Nikko J.","first_name":"Nikko J."},{"last_name":"Hirschmann","first_name":"Michaela","full_name":"Hirschmann, Michaela"},{"first_name":"Harley","full_name":"Katz, Harley","last_name":"Katz"},{"first_name":"Ivo","full_name":"Labbé, Ivo","last_name":"Labbé"},{"full_name":"Maseda, Michael V.","first_name":"Michael V.","last_name":"Maseda"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"last_name":"Mcconachie","first_name":"Ian","full_name":"Mcconachie, Ian"},{"last_name":"Naidu","full_name":"Naidu, Rohan P.","first_name":"Rohan P."},{"first_name":"Pascal A.","full_name":"Oesch, Pascal A.","last_name":"Oesch"},{"last_name":"Rix","full_name":"Rix, Hans Walter","first_name":"Hans Walter"},{"first_name":"David J.","full_name":"Setton, David J.","last_name":"Setton"},{"first_name":"Katherine E.","full_name":"Whitaker, Katherine E.","last_name":"Whitaker"}],"_id":"19700","volume":984,"publication":"The Astrophysical Journal","OA_type":"gold","status":"public","citation":{"ieee":"B. Wang <i>et al.</i>, “RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow,” <i>The Astrophysical Journal</i>, vol. 984, no. 2. IOP Publishing, 2025.","mla":"Wang, Bingjie, et al. “RUBIES: JWST/NIRSpec Confirmation of an Infrared-Luminous, Broad-Line Little Red Dot with an Ionized Outflow.” <i>The Astrophysical Journal</i>, vol. 984, no. 2, 121, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">10.3847/1538-4357/adc1ca</a>.","ama":"Wang B, De Graaff A, Davies RL, et al. RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. <i>The Astrophysical Journal</i>. 2025;984(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">10.3847/1538-4357/adc1ca</a>","ista":"Wang B, De Graaff A, Davies RL, Greene JE, Leja J, Brammer GB, Goulding AD, Miller TB, Suess KA, Weibel A, Williams CC, Bezanson R, Boogaard LA, Cleri NJ, Hirschmann M, Katz H, Labbé I, Maseda MV, Matthee JJ, Mcconachie I, Naidu RP, Oesch PA, Rix HW, Setton DJ, Whitaker KE. 2025. RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. The Astrophysical Journal. 984(2), 121.","chicago":"Wang, Bingjie, Anna De Graaff, Rebecca L. Davies, Jenny E. Greene, Joel Leja, Gabriel B. Brammer, Andy D. Goulding, et al. “RUBIES: JWST/NIRSpec Confirmation of an Infrared-Luminous, Broad-Line Little Red Dot with an Ionized Outflow.” <i>The Astrophysical Journal</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">https://doi.org/10.3847/1538-4357/adc1ca</a>.","short":"B. Wang, A. De Graaff, R.L. Davies, J.E. Greene, J. Leja, G.B. Brammer, A.D. Goulding, T.B. Miller, K.A. Suess, A. Weibel, C.C. Williams, R. Bezanson, L.A. Boogaard, N.J. Cleri, M. Hirschmann, H. Katz, I. Labbé, M.V. Maseda, J.J. Matthee, I. Mcconachie, R.P. Naidu, P.A. Oesch, H.W. Rix, D.J. Setton, K.E. Whitaker, The Astrophysical Journal 984 (2025).","apa":"Wang, B., De Graaff, A., Davies, R. L., Greene, J. E., Leja, J., Brammer, G. B., … Whitaker, K. E. (2025). RUBIES: JWST/NIRSpec confirmation of an infrared-luminous, broad-line Little Red Dot with an ionized outflow. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/adc1ca\">https://doi.org/10.3847/1538-4357/adc1ca</a>"},"quality_controlled":"1","external_id":{"isi":["001481589300001"],"arxiv":["2403.02304"]},"department":[{"_id":"JoMa"}],"scopus_import":"1","intvolume":"       984","OA_place":"publisher","article_processing_charge":"Yes","language":[{"iso":"eng"}],"acknowledgement":"B.W. and J.L. acknowledge support from JWST-GO-04233.009-A. R.L.D. is supported by the Australian Research Council through the Discovery Early Career Researcher Award (DECRA) Fellowship DE240100136 funded by the Australian Government. T.B.M. was supported by a CIERA postdoctoral fellowship. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). The JWST data presented in this article were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed here can be accessed via DOI:10.17909/c3t4-9p39. Computations for this research were performed on the Pennsylvania State University's Institute for Computational and Data Sciences' Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2025","publisher":"IOP Publishing","DOAJ_listed":"1","article_number":"121","issue":"2"},{"project":[{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"},{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","grant_number":"101118866"}],"ddc":["570"],"doi":"10.1146/annurev-biophys-060524-102720","has_accepted_license":"1","publication_status":"published","file_date_updated":"2025-05-19T07:55:51Z","isi":1,"type":"journal_article","oa_version":"Published Version","date_updated":"2025-09-30T12:33:33Z","publication_identifier":{"eissn":["1936-1238"]},"article_type":"original","date_published":"2025-05-01T00:00:00Z","title":"Information processing in biochemical networks","pmid":1,"month":"05","file":[{"relation":"main_file","file_size":317925,"access_level":"open_access","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","success":1,"date_updated":"2025-05-19T07:55:51Z","content_type":"application/pdf","file_id":"19710","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","date_created":"2025-05-19T07:55:51Z","creator":"dernst"}],"oa":1,"abstract":[{"text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","lang":"eng"}],"volume":54,"_id":"19701","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Wolde, Pieter Rein Ten","first_name":"Pieter Rein Ten","last_name":"Wolde"}],"page":"249-274","date_created":"2025-05-18T22:02:50Z","corr_author":"1","day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Annual Reviews","year":"2025","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","article_processing_charge":"Yes (in subscription journal)","OA_place":"publisher","intvolume":"        54","scopus_import":"1","department":[{"_id":"GaTk"}],"external_id":{"pmid":["39929539"],"isi":["001488641500013"]},"quality_controlled":"1","citation":{"apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual review of biophysics. 54, 249–274.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual review of biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual review of biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>."},"publication":"Annual review of biophysics","status":"public","OA_type":"hybrid"},{"month":"05","file":[{"access_level":"open_access","file_size":6805943,"relation":"main_file","checksum":"73e35151eebd5064972c5a07ffdf2b69","success":1,"creator":"dernst","date_created":"2025-05-19T07:45:31Z","file_name":"2025_PloSCompBio_Kopfova.pdf","date_updated":"2025-05-19T07:45:31Z","content_type":"application/pdf","file_id":"19709"}],"title":"Colonization times in Moran process on graphs","publication_identifier":{"eissn":["1553-7358"]},"date_updated":"2025-09-30T12:34:03Z","date_published":"2025-05-01T00:00:00Z","article_type":"original","oa":1,"abstract":[{"lang":"eng","text":"Moran Birth-death process is a standard stochastic process that is used to model natural selection in spatially structured populations. A newly occurring mutation that invades a population of residents can either fixate on the whole population or it can go extinct due to random drift. The duration of the process depends not only on the total population size n, but also on the spatial structure of the population. In this work, we consider the Moran process with a single type of individuals who invade and colonize an otherwise empty environment. Mathematically, this corresponds to the setting where the residents have zero reproduction rate, thus they never reproduce. The spatial structure is represented by a graph. We present two main contributions. First, in contrast to the Moran process in which residents do reproduce, we show that the colonization time is always at most a polynomial function of the population size n. Namely, we show that colonization always takes at most 1/2n^3 - 1/2n^2 expected steps, and for each n, we identify the slowest graph where it takes exactly that many steps. Moreover, we establish a stronger bound of roughly n^2.5 steps for undirected graphs and an even stronger bound of roughly n^2 steps for so-called regular graphs. Second, we discuss various complications that one faces when attempting to measure fixation times and colonization times in spatially structured populations, and we propose to measure the real duration of the process, rather than counting the steps of the classic Moran process."}],"ddc":["000"],"oa_version":"Published Version","type":"journal_article","isi":1,"doi":"10.1371/journal.pcbi.1012868","file_date_updated":"2025-05-19T07:45:31Z","publication_status":"published","has_accepted_license":"1","arxiv":1,"OA_place":"publisher","article_processing_charge":"Yes","intvolume":"        21","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"DOAJ_listed":"1","year":"2025","publisher":"Public Library of Science","issue":"5","quality_controlled":"1","citation":{"apa":"Kopfová, L., &#38; Tkadlec, J. (2025). Colonization times in Moran process on graphs. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>","short":"L. Kopfová, J. Tkadlec, PLoS Computational Biology 21 (2025) e1012868.","ista":"Kopfová L, Tkadlec J. 2025. Colonization times in Moran process on graphs. PLoS computational biology. 21(5), e1012868.","chicago":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>. Public Library of Science, 2025. <a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">https://doi.org/10.1371/journal.pcbi.1012868</a>.","ama":"Kopfová L, Tkadlec J. Colonization times in Moran process on graphs. <i>PLoS computational biology</i>. 2025;21(5):e1012868. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>","ieee":"L. Kopfová and J. Tkadlec, “Colonization times in Moran process on graphs,” <i>PLoS computational biology</i>, vol. 21, no. 5. Public Library of Science, p. e1012868, 2025.","mla":"Kopfová, Lenka, and Josef Tkadlec. “Colonization Times in Moran Process on Graphs.” <i>PLoS Computational Biology</i>, vol. 21, no. 5, Public Library of Science, 2025, p. e1012868, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012868\">10.1371/journal.pcbi.1012868</a>."},"status":"public","publication":"PLoS computational biology","OA_type":"gold","external_id":{"isi":["001481670600002"],"arxiv":["2410.09476"]},"scopus_import":"1","department":[{"_id":"GradSch"}],"date_created":"2025-05-18T22:02:50Z","_id":"19702","page":"e1012868","author":[{"first_name":"Lenka","full_name":"Kopfová, Lenka","id":"17691681-50b9-11ef-ad56-edf4cacb21b0","last_name":"Kopfová"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"}],"volume":21,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01"},{"language":[{"iso":"eng"}],"acknowledgement":"We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum, I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi, and Xiong labs for technical assistance and constructive feedback. We thank Ryan Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.; an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an ERC Starting Grant (851288) to E.H.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        60","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","issue":"17","year":"2025","publisher":"Elsevier","external_id":{"pmid":["40347948"],"isi":["001570502100005"]},"publication":"Developmental Cell","status":"public","OA_type":"hybrid","citation":{"chicago":"Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel, Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>.","ista":"Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. Developmental Cell. 60(17), 2237–2247.e4.","apa":"Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla, S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>","short":"S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla, K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.","ieee":"S. B. P. Mclaren <i>et al.</i>, “Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord,” <i>Developmental Cell</i>, vol. 60, no. 17. Elsevier, p. 2237–2247.e4, 2025.","mla":"Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>, vol. 60, no. 17, Elsevier, 2025, p. 2237–2247.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>.","ama":"Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. 2025;60(17):2237-2247.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>"},"quality_controlled":"1","department":[{"_id":"EdHa"}],"scopus_import":"1","ec_funded":1,"page":"2237-2247.e4","author":[{"last_name":"Mclaren","first_name":"Susannah B.P.","full_name":"Mclaren, Susannah B.P."},{"full_name":"Xue, Shi-lei","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue"},{"last_name":"Ding","first_name":"Siyuan","full_name":"Ding, Siyuan"},{"first_name":"Alexander K.","full_name":"Winkel, Alexander K.","last_name":"Winkel"},{"full_name":"Baldwin, Oscar","first_name":"Oscar","last_name":"Baldwin"},{"last_name":"Dwarakacherla","first_name":"Shreya","full_name":"Dwarakacherla, Shreya"},{"full_name":"Franze, Kristian","first_name":"Kristian","last_name":"Franze"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fengzhu","full_name":"Xiong, Fengzhu","last_name":"Xiong"}],"_id":"19703","date_created":"2025-05-18T22:02:50Z","volume":60,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"08","file":[{"date_updated":"2025-12-29T13:45:05Z","file_name":"2025_DevelopmentalCell_McLaren.pdf","file_id":"20872","content_type":"application/pdf","creator":"dernst","date_created":"2025-12-29T13:45:05Z","file_size":12564806,"relation":"main_file","access_level":"open_access","checksum":"1ca6f0822c1cbd430686d5e2a4f96401","success":1}],"month":"09","date_published":"2025-09-08T00:00:00Z","article_type":"original","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_updated":"2025-12-29T14:58:14Z","pmid":1,"title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","abstract":[{"text":"An enlarged brain underlies the complex central nervous system of vertebrates. The dramatic expansion of the brain that diverges its shape from the spinal cord follows neural tube closure during embryonic development. Here, we show that this differential deformation is encoded by a pre-pattern of tissue material properties in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting in a thinning versus a resisting response to increasing lumen pressure, respectively. The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain cells to the spinal cord can locally create an expanded brain-like morphology in some cases. Our findings raise questions in vertebrate head evolution and suggest a general role of mechanical pre-patterning in sculpting epithelial tubes.","lang":"eng"}],"oa":1,"project":[{"grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"ddc":["570"],"type":"journal_article","isi":1,"oa_version":"Published Version","PlanS_conform":"1","publication_status":"published","file_date_updated":"2025-12-29T13:45:05Z","doi":"10.1016/j.devcel.2025.04.010","has_accepted_license":"1"},{"acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","intvolume":"       642","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"year":"2025","external_id":{"pmid":["40335689"],"isi":["001483477000001"]},"publication":"Nature","status":"public","OA_type":"hybrid","quality_controlled":"1","citation":{"ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>."},"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"scopus_import":"1","ec_funded":1,"author":[{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"last_name":"Januszewski","full_name":"Januszewski, Michał","first_name":"Michał"},{"full_name":"Vistunou, Vitali","first_name":"Vitali","last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","full_name":"Vorlaufer, Jakob","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bárbara","full_name":"Oliveira, Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","full_name":"Cenameri, Alban","first_name":"Alban"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"last_name":"Jain","first_name":"Viren","full_name":"Jain, Viren"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"page":"398-410","_id":"19704","related_material":{"link":[{"url":"https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/","description":"News on ISTA website","relation":"press_release"}],"record":[{"status":"public","relation":"earlier_version","id":"18677"},{"id":"18697","relation":"research_data","status":"public"}]},"date_created":"2025-05-18T22:02:51Z","volume":642,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"12","corr_author":"1","file":[{"creator":"dernst","date_created":"2025-07-03T06:55:20Z","content_type":"application/pdf","file_name":"2025_Nature_Tavakoli.pdf","file_id":"19959","date_updated":"2025-07-03T06:55:20Z","checksum":"ebc99d7108e728f46db0a009292675ef","access_level":"open_access","relation":"main_file","file_size":133201290,"success":1}],"month":"06","article_type":"original","date_published":"2025-06-12T00:00:00Z","date_updated":"2026-04-28T13:33:34Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"pmid":1,"title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner."}],"oa":1,"project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24"}],"ddc":["570"],"isi":1,"type":"journal_article","oa_version":"Published Version","PlanS_conform":"1","publication_status":"published","has_accepted_license":"1","file_date_updated":"2025-07-03T06:55:20Z","doi":"10.1038/s41586-025-08985-1"},{"ec_funded":1,"department":[{"_id":"RoSe"}],"scopus_import":"1","status":"public","publication":"Reviews in Mathematical Physics","OA_type":"hybrid","quality_controlled":"1","citation":{"ama":"Fialova M, Krejčiřík D. Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. <i>Reviews in Mathematical Physics</i>. 2025;37(6). doi:<a href=\"https://doi.org/10.1142/S0129055X25500114\">10.1142/S0129055X25500114</a>","ieee":"M. Fialova and D. Krejčiřík, “Virtual bound states of the Pauli operator with an Aharonov–Bohm potential,” <i>Reviews in Mathematical Physics</i>, vol. 37, no. 6. World Scientific Publishing, 2025.","mla":"Fialova, Marie, and David Krejčiřík. “Virtual Bound States of the Pauli Operator with an Aharonov–Bohm Potential.” <i>Reviews in Mathematical Physics</i>, vol. 37, no. 6, 2550011, World Scientific Publishing, 2025, doi:<a href=\"https://doi.org/10.1142/S0129055X25500114\">10.1142/S0129055X25500114</a>.","short":"M. Fialova, D. Krejčiřík, Reviews in Mathematical Physics 37 (2025).","apa":"Fialova, M., &#38; Krejčiřík, D. (2025). Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X25500114\">https://doi.org/10.1142/S0129055X25500114</a>","ista":"Fialova M, Krejčiřík D. 2025. Virtual bound states of the Pauli operator with an Aharonov–Bohm potential. Reviews in Mathematical Physics. 37(6), 2550011.","chicago":"Fialova, Marie, and David Krejčiřík. “Virtual Bound States of the Pauli Operator with an Aharonov–Bohm Potential.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2025. <a href=\"https://doi.org/10.1142/S0129055X25500114\">https://doi.org/10.1142/S0129055X25500114</a>."},"external_id":{"isi":["001481012500001"],"arxiv":["2501.17029"]},"publisher":"World Scientific Publishing","year":"2025","article_number":"2550011","issue":"6","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","intvolume":"        37","language":[{"iso":"eng"}],"acknowledgement":"Thanks belong to Johannes Ageskov and Matˇej Tuˇsek for helpful discussions on some technical details. M. F. would further like to acknowledge support for research on this paper from the European Unions Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413 as well as support by funding from Villum Fonden through the QMATH Centreof Excellence Grant No. 10059. D. K. was supported by the EXPRO Grant No.20-17749X of the Czech Science Foundation (GACR).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":37,"date_created":"2025-05-18T22:02:51Z","author":[{"id":"e9c9844d-9e21-11ec-b482-f96fc09f7c4d","last_name":"Fialova","full_name":"Fialova, Marie","first_name":"Marie"},{"full_name":"Krejčiřík, David","first_name":"David","last_name":"Krejčiřík"}],"_id":"19705","abstract":[{"lang":"eng","text":"A maximal realization of the two-dimensional Pauli operator, subject to Aharonov–Bohm magnetic field, is investigated. Contrary to the case of the Pauli operator with regular magnetic potentials, it is shown that both components of the Pauli operator are critical. Asymptotics of the weakly coupled eigenvalues, generated by electric (not necessarily self-adjoint) perturbations, are derived."}],"oa":1,"title":"Virtual bound states of the Pauli operator with an Aharonov–Bohm potential","date_published":"2025-07-01T00:00:00Z","article_type":"original","date_updated":"2026-05-06T13:03:25Z","publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"file":[{"checksum":"559d97ee2da28bf0bd2c6af507f3a914","file_size":484646,"access_level":"open_access","relation":"main_file","success":1,"file_name":"2025_ReviewsMathPhysics_Fialova.pdf","date_updated":"2025-12-30T08:23:12Z","file_id":"20893","content_type":"application/pdf","date_created":"2025-12-30T08:23:12Z","creator":"dernst"}],"month":"07","has_accepted_license":"1","file_date_updated":"2025-12-30T08:23:12Z","doi":"10.1142/S0129055X25500114","publication_status":"published","PlanS_conform":"1","arxiv":1,"APC_amount":"2320,48 EUR","oa_version":"Published Version","isi":1,"type":"journal_article","ddc":["530","510"],"project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}]}]