[{"OA_type":"green","file_date_updated":"2026-10-20T14:00:27Z","title":"Machine unlearning using forgetting neural networks","das_tickbox":"0","doi":"10.5220/0014326500004052","keyword":["Machine Unlearning","Neuroscience-Inspired Machine Learning","Membership Inference Attacks"],"date_published":"2026-04-01T00:00:00Z","author":[{"first_name":"Amartya","last_name":"Hatua","full_name":"Hatua, Amartya"},{"full_name":"Nguyen, Trung T.","last_name":"Nguyen","first_name":"Trung T."},{"full_name":"Cano Cordoba, Filip","orcid":"0000-0002-0783-904X","last_name":"Cano Cordoba","id":"708cad98-e86a-11ef-8098-bdae2d7c6af1","first_name":"Filip"},{"full_name":"Sung, Andrew H.","last_name":"Sung","first_name":"Andrew H."}],"file":[{"success":1,"date_created":"2026-10-20T14:00:27Z","creator":"dernst","date_updated":"2026-10-20T14:00:27Z","checksum":"d0f5212846c8f3129509b081648465cb","relation":"main_file","content_type":"application/pdf","file_size":779692,"file_id":"23178","access_level":"open_access","file_name":"2026_CAART_Hatua.pdf"}],"publication_status":"published","page":"1536-1546","status":"public","department":[{"_id":"ToHe"}],"citation":{"chicago":"Hatua, Amartya, Trung T. Nguyen, Filip Cano Cordoba, and Andrew H. Sung. “Machine Unlearning Using Forgetting Neural Networks.” In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, 2:1536–46. Science and Technology Publications, 2026. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>.","apa":"Hatua, A., Nguyen, T. T., Cano Cordoba, F., &#38; Sung, A. H. (2026). Machine unlearning using forgetting neural networks. In <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i> (Vol. 2, pp. 1536–1546). Marbella, Spain: Science and Technology Publications. <a href=\"https://doi.org/10.5220/0014326500004052\">https://doi.org/10.5220/0014326500004052</a>","short":"A. Hatua, T.T. Nguyen, F. Cano Cordoba, A.H. Sung, in:, Proceedings of the 18th International Conference on Agents and Artificial Intelligence, Science and Technology Publications, 2026, pp. 1536–1546.","ista":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. 2026. Machine unlearning using forgetting neural networks. Proceedings of the 18th International Conference on Agents and Artificial Intelligence. ICAART: International Conference on Agents and Artificial Intelligence vol. 2, 1536–1546.","ama":"Hatua A, Nguyen TT, Cano Cordoba F, Sung AH. Machine unlearning using forgetting neural networks. In: <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>. Vol 2. Science and Technology Publications; 2026:1536-1546. doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>","mla":"Hatua, Amartya, et al. “Machine Unlearning Using Forgetting Neural Networks.” <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, vol. 2, Science and Technology Publications, 2026, pp. 1536–46, doi:<a href=\"https://doi.org/10.5220/0014326500004052\">10.5220/0014326500004052</a>.","ieee":"A. Hatua, T. T. Nguyen, F. Cano Cordoba, and A. H. Sung, “Machine unlearning using forgetting neural networks,” in <i>Proceedings of the 18th International Conference on Agents and Artificial Intelligence</i>, Marbella, Spain, 2026, vol. 2, pp. 1536–1546."},"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"date_updated":"2026-10-20T14:05:02Z","_id":"22104","intvolume":"         2","researchdata_availability":"no","date_created":"2026-06-21T22:03:01Z","supplementarymaterial":"no","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","conference":{"start_date":"2026-03-05","end_date":"2026-03-08","name":"ICAART: International Conference on Agents and Artificial Intelligence","location":"Marbella, Spain"},"fulldoi":"https://doi.org/10.5220/0014326500004052","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"year":"2026","type":"conference","publication":"Proceedings of the 18th International Conference on Agents and Artificial Intelligence","external_id":{"arxiv":["2410.22374"]},"OA_place":"repository","oa":1,"arxiv":1,"article_processing_charge":"No","month":"04","day":"01","volume":2,"publication_identifier":{"isbn":["9789897587962"],"eissn":["2184-433X"],"issn":["2184-3589"]},"scopus_import":"1","abstract":[{"lang":"eng","text":" Modern computer systems store vast amounts of personal data, enabling advances in AI and ML but risking user privacy and trust. For privacy reasons, it is sometimes desired for an ML model to forget part of the data it was trained on. In this paper, we introduce a novel unlearning approach based on Forgetting Neural Networks (FNNs), a neuroscience-inspired architecture that explicitly encodes forgetting through multiplicative decay factors. While FNNs had previously been studied as a theoretical construct, we provide the first concrete implementation and demonstrate their effectiveness for targeted unlearning. We propose several variants with per-neuron forgetting factors, including rank-based assignments guided by activation levels, and evaluate them on MNIST and Fashion-MNIST benchmarks. Our method systematically removes information associated with forget sets while preserving performance on retained data. Membership inference attacks confirm the effectiveness of FNN-based unlearning in erasing information about the training data from the neural network. These results establish FNNs as a promising foundation for efficient and interpretable unlearning."}],"publisher":"Science and Technology Publications","acknowledgement":"This work has been supported by the European Research\r\nCouncil under Grant No.: ERC-2020-AdG\r\n101020093. We thank Brian Subirana for the original\r\nideation of the concept of forgetting neural networks\r\nand his belief in their potential.","ddc":["000"],"has_accepted_license":"1"},{"citation":{"ieee":"J. Lee and L. Erdös, “Mesoscopic eigenvalue statistics for correlated random matrices,” <i>arXiv</i>. .","ama":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>","ista":"Lee J, Erdös L. Mesoscopic eigenvalue statistics for correlated random matrices. arXiv, 2607.05848.","mla":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, 2607.05848, doi:<a href=\"https://doi.org/10.48550/arXiv.2607.05848\">10.48550/arXiv.2607.05848</a>.","short":"J. Lee, L. Erdös, ArXiv (n.d.).","chicago":"Lee, Jaehun, and László Erdös. “Mesoscopic Eigenvalue Statistics for Correlated Random Matrices.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>.","apa":"Lee, J., &#38; Erdös, L. (n.d.). Mesoscopic eigenvalue statistics for correlated random matrices. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2607.05848\">https://doi.org/10.48550/arXiv.2607.05848</a>"},"department":[{"_id":"LaEr"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2607.05848"}],"status":"public","oa_version":"Preprint","ec_funded":1,"language":[{"iso":"eng"}],"date_created":"2026-07-18T08:59:02Z","_id":"22359","date_updated":"2026-10-20T10:06:12Z","article_number":"2607.05848","OA_type":"green","doi":"10.48550/arXiv.2607.05848","title":"Mesoscopic eigenvalue statistics for correlated random matrices","das_tickbox":"1","author":[{"id":"96155047-f36a-11ef-b766-8b5ae7cecd49","last_name":"Lee","first_name":"Jaehun","full_name":"Lee, Jaehun"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"}],"publication_status":"submitted","date_published":"2026-07-07T00:00:00Z","keyword":["Central limit theorem","universality","matrix Dyson equation","multi-resolvent local law"],"arxiv":1,"article_processing_charge":"No","oa":1,"external_id":{"arxiv":["2607.05848"]},"OA_place":"repository","publication":"arXiv","month":"07","abstract":[{"text":"We prove a mesoscopic central limit theorem for linear eigenvalue statistics of correlated Hermitian random matrices. The class considered here includes Wigner and Wigner-type matrices, as well as models whose entry correlations decay polynomially in the distance between index pairs. The proof combines a multivariate cumulant expansion with multi-resolvent local laws and a detailed analysis of the resulting variance kernel on the operator-level.","lang":"eng"}],"day":"07","acknowledgement":"Supported by ERC Advanced Grant “RMTBeyond” No. 101020331","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","fulldoi":"https://doi.org/10.48550/arXiv.2607.05848","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"type":"preprint"},{"file":[{"content_type":"application/pdf","file_size":3286905,"relation":"main_file","checksum":"95c1695f3c7183b2ad9d58167500b18d","date_updated":"2026-07-21T12:20:49Z","creator":"dernst","date_created":"2026-07-21T12:20:49Z","success":1,"file_name":"2026_AstronomyAstrophysics_Marcel.pdf","access_level":"open_access","file_id":"22382"}],"publication_status":"published","date_published":"2026-06-01T00:00:00Z","author":[{"first_name":"G.","last_name":"Marcel","full_name":"Marcel, G."},{"last_name":"Turner","first_name":"S. G. D.","full_name":"Turner, S. G. D."},{"last_name":"Ricketts","first_name":"B. J.","full_name":"Ricketts, B. J."},{"full_name":"López-Barquero, V.","last_name":"López-Barquero","first_name":"V."},{"last_name":"Buisson","first_name":"D. J. K.","full_name":"Buisson, D. J. K."},{"last_name":"Vincentelli","first_name":"F.","full_name":"Vincentelli, F."},{"full_name":"Middleton, M.","last_name":"Middleton","first_name":"M."},{"last_name":"Reynolds","first_name":"C.S.","full_name":"Reynolds, C.S."},{"last_name":"Avara","id":"c9b42585-7787-11f0-9bdd-bf7d947cf79d","first_name":"Mark","full_name":"Avara, Mark"}],"file_date_updated":"2026-07-21T12:20:49Z","title":"Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations","das_tickbox":"0","doi":"10.1051/0004-6361/202558103","OA_type":"diamond","intvolume":"       710","date_created":"2026-07-21T10:29:36Z","researchdata_availability":"no","quality_controlled":"1","article_number":"A387","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"22381","date_updated":"2026-10-21T06:33:09Z","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"ZoHa"}],"citation":{"ama":"Marcel G, Turner SGD, Ricketts BJ, et al. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. 2026;710. doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>","ista":"Marcel G, Turner SGD, Ricketts BJ, López-Barquero V, Buisson DJK, Vincentelli F, Middleton M, Reynolds CS, Avara M. 2026. Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. Astronomy &#38; Astrophysics. 710, A387.","mla":"Marcel, G., et al. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>, vol. 710, A387, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202558103\">10.1051/0004-6361/202558103</a>.","ieee":"G. Marcel <i>et al.</i>, “Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations,” <i>Astronomy &#38; Astrophysics</i>, vol. 710. EDP Sciences, 2026.","chicago":"Marcel, G., S. G. D. Turner, B. J. Ricketts, V. López-Barquero, D. J. K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, and Mark Avara. “Disk Warping and Black Hole X-Ray Binaries: I. Tentative Unification of Low-Frequency Quasi-Periodic Oscillations.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>.","apa":"Marcel, G., Turner, S. G. D., Ricketts, B. J., López-Barquero, V., Buisson, D. J. K., Vincentelli, F., … Avara, M. (2026). Disk warping and black hole X-ray binaries: I. Tentative unification of low-frequency quasi-periodic oscillations. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202558103\">https://doi.org/10.1051/0004-6361/202558103</a>","short":"G. Marcel, S.G.D. Turner, B.J. Ricketts, V. López-Barquero, D.J.K. Buisson, F. Vincentelli, M. Middleton, C.S. Reynolds, M. Avara, Astronomy &#38; Astrophysics 710 (2026)."},"status":"public","article_type":"original","type":"journal_article","PlanS_conform":"1","fulldoi":"https://doi.org/10.1051/0004-6361/202558103","year":"2026","supplementarymaterial":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"GM acknowledges support from the Polish National Science Center grant 2023/48/Q/ST9/00138 and the Academy of Finland grant 355672. The authors thank the Editor for their insightful comments and effective stewardship of the review process. SGDT acknowledges support under\r\nSTFC Grant ST/X001113/1. This work made use of the python packages\r\nMatplotlib (Hunter 2007), NumPy (Harris et al. 2020), and Stingray v2.2\r\n(Huppenkothen et al. 2019; Bachetti et al. 2024b,a).","has_accepted_license":"1","ddc":["520"],"publisher":"EDP Sciences","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"abstract":[{"text":"Context. X-ray binaries exhibit complex variability patterns studied in the power spectrum. These include the broadband noise (BBN)\r\ncomponents and various types of narrow components called quasi-periodic oscillations (QPOs). There is currently no consensus about\r\nwhat determines the presence or absence of the BBN or what generates the QPOs. Many believe that QPO generation is due to framedragging effects caused by Lense–Thirring torques.\r\nAims. We investigated the potential impact of frame-dragging effects on the accretion disk itself. In particular, we focused on its\r\nimpact on the observed variability and on the presence (and types) of associated QPOs.\r\nMethods. We made analytical estimates to assess the potential presence of a geometric warp in the inner accretion disk during state\r\ntransitions.\r\nResults. We show that the presence of a warp can modify the spectral-timing properties in a way that matches the observed transition\r\nbetween QPO types during outbursts. We also discuss the peculiar case of Cyg X-1, as well as how the hard-to-soft transition could\r\nbe driven by the warp itself.\r\nConclusions. The (expected) emergence of a warp provides a consistent explanation for the evolution of both the BBN and the QPO\r\nproperties during state transitions. This offers a first path toward unifying the variability of black hole X-ray binaries.","lang":"eng"}],"scopus_import":"1","day":"01","volume":710,"month":"06","oa":1,"article_processing_charge":"No","arxiv":1,"external_id":{"arxiv":["2511.10474"]},"OA_place":"publisher","publication":"Astronomy & Astrophysics"},{"date_updated":"2026-10-21T07:47:08Z","_id":"22399","date_created":"2026-07-25T13:08:32Z","alternative_title":["ISTA Master’s Thesis"],"degree_awarded":"MS","status":"public","citation":{"ieee":"A. Spasić, “Studying the evolutionary systems biology of the lac operon,” Institute of Science and Technology Austria, 2026.","mla":"Spasić, Aleksa. <i>Studying the Evolutionary Systems Biology of the Lac Operon</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>.","ista":"Spasić A. 2026. Studying the evolutionary systems biology of the lac operon. Institute of Science and Technology Austria.","ama":"Spasić A. Studying the evolutionary systems biology of the lac operon. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22399\">10.15479/AT-ISTA-22399</a>","short":"A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute of Science and Technology Austria, 2026.","apa":"Spasić, A. (2026). <i>Studying the evolutionary systems biology of the lac operon</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>","chicago":"Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22399\">https://doi.org/10.15479/AT-ISTA-22399</a>."},"department":[{"_id":"GradSch"},{"_id":"GaTk"},{"_id":"CaGu"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.15479/AT-ISTA-22399","das_tickbox":"0","title":"Studying the evolutionary systems biology of the lac operon","file_date_updated":"2026-10-20T08:47:40Z","page":"32","date_published":"2026-07-27T00:00:00Z","author":[{"id":"ecee9d38-4040-11ef-8843-b941efb445d6","last_name":"Spasić","first_name":"Aleksa","full_name":"Spasić, Aleksa"}],"file":[{"creator":"aspasic","date_created":"2026-07-27T13:00:07Z","relation":"main_file","checksum":"c29880dd71fcc37f23ac6e2843066ede","embargo_to":"open_access","date_updated":"2026-10-20T08:47:40Z","file_size":1986078,"content_type":"application/pdf","embargo":"2027-07-30","file_id":"22588","access_level":"closed","file_name":"Aleksa_Spasic_Thesis_final.pdf"},{"file_name":"Thesis_final.docx","file_id":"22589","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":1868853,"date_created":"2026-07-27T13:00:22Z","creator":"aspasic","date_updated":"2026-07-27T13:07:23Z","checksum":"4ebe3bd2d833d913c0756343cca5e5f0","relation":"source_file"}],"publication_status":"published","day":"27","publication_identifier":{"issn":["2791-4585"]},"corr_author":"1","publisher":"Institute of Science and Technology Austria","ddc":["576"],"has_accepted_license":"1","OA_place":"publisher","article_processing_charge":"No","doi_confirm":"1","month":"07","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2026","fulldoi":"https://doi.org/10.15479/AT-ISTA-22399","supervisor":[{"full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}]},{"title":"Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks","file_date_updated":"2026-07-20T11:29:38Z","doi":"10.15479/AT-ISTA-22281","date_published":"2026-07-13T00:00:00Z","author":[{"first_name":"Antoine","last_name":"El-Hayek","orcid":"0000-0003-4268-7368","id":"888a098e-fcac-11ee-aff7-d347be57b725","full_name":"El-Hayek, Antoine"}],"file":[{"file_size":5465973,"content_type":"application/pdf","creator":"aelhayek","success":1,"date_created":"2026-07-17T11:39:47Z","relation":"main_file","date_updated":"2026-07-17T11:39:47Z","checksum":"923e4ca769c9ef2f6b0b005444faf462","file_name":"2026_El-Hayek_Antoine_Thesis.pdf","file_id":"22356","access_level":"open_access"},{"file_name":"2026_El-Hayek_Antoine_Thesis.zip","access_level":"closed","file_id":"22357","content_type":"application/x-zip-compressed","file_size":9116107,"checksum":"262689f9df27dd6c2c7c7861f1de7329","date_updated":"2026-07-20T11:29:38Z","relation":"source_file","date_created":"2026-07-17T11:40:34Z","creator":"aelhayek"}],"publication_status":"published","page":"244","date_created":"2026-07-13T09:39:59Z","date_updated":"2026-10-21T08:05:35Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"22281","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"MoHe"}],"citation":{"short":"A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks, Institute of Science and Technology Austria, 2026.","apa":"El-Hayek, A. (2026). <i>Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>","chicago":"El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22281\">https://doi.org/10.15479/AT-ISTA-22281</a>.","ieee":"A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks,” Institute of Science and Technology Austria, 2026.","ama":"El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>","ista":"El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms and distributed computing on dynamic networks. Institute of Science and Technology Austria.","mla":"El-Hayek, Antoine. <i>Handling Updates and Failures: Dynamic Graph Algorithms and Distributed Computing on Dynamic Networks</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22281\">10.15479/AT-ISTA-22281</a>."},"status":"public","degree_awarded":"PhD","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"type":"dissertation","publisher_comment":"Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are All Rights Reserved.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-22281","supervisor":[{"full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"year":"2026","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"In this thesis, we took a look at networks, and more specifically, at networks that change over time, whether those are networks in the distributed algorithms sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms, we looked at two main problems. First, the broadcast problem: given n agents, each agent is tasked to forward a (unique) message to every other agent. Agents collaborate and can copy and forward all messages they have received up until that point. Broadcast is achieved when one agent has successfully broadcast its message to everyone else. We studied the case where the communication network is controlled by an adversary, under the condition that the graph is rooted in every round of communication. We show that the adversary can delay broadcast for at most  l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$ previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the $\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the stochastic version of the problem: here, the adversary -- parametrized by $k$ where $k=0$ signifies that the adversary has no control,  and $k=n$ that the adversary has full control -- can choose parts of the graph, and the graph is then completed stochastically. Here, we are able to look at a stronger version of broadcast: instead of having $n$ messages trying to be broadcast in parallel, we can assume that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols: given a population of $n$ agents, where each initially holds an opinion among $k$ different ones. In each round, two agents are chosen uniformly at random, and can interact. If they have different opinions, they forget their opinions and become undecided. If one of them is undecided while the other has an opinion, they undecided agent copies they opinion of the decided one. The question is then, how many interactions does it take for the whole population to share the same opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound  for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally, in dynamic algorithms, we study the minimum cut problem: we are given a graph, whose vertex set we want to partition into two subsets such that the number of edges crossing from one subset to the other is minimized. Then, the graph can be updated via edge insertions or deletions, and we must update the solution without recomputing everything from scratch. We present an exact fully-dynamic minimum cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are able to extend this to all values of the minimum cut in weighted graphs, at the cost of a $(1+o(1))$-approximation ratio.","lang":"eng"}],"day":"13","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982 \"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for a Reactive Network Layer\".\r\n","ddc":["000"],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","corr_author":"1","oa":1,"doi_confirm":"1","article_processing_charge":"No","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"20051"},{"id":"19982","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"21720"},{"relation":"part_of_dissertation","status":"public","id":"22374"},{"relation":"part_of_dissertation","status":"public","id":"22373"},{"relation":"part_of_dissertation","status":"public","id":"18557"}]},"month":"07"},{"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","year":"2026","fulldoi":"https://doi.org/10.15479/AT-ISTA-20991","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"}],"day":"16","abstract":[{"text":"Rapid local adaptation to new environments is critical for species persistence, especially in introduced populations. The evolutionary success of these populations is fundamentally dictated by the organization of genetic variation—the genomic architecture—in the face of severe demographic constraints, such as the founder effects and genetic bottlenecks that frequently accompany colonization. A central question in evolutionary biology is whether rapid adaptation relies on major-effect loci, such as chromosomal inversions, or on many small-effect loci dispersed across the genome. Furthermore, the genomic architecture strongly influences the extent to which evolutionary outcomes are predictable. Using introduced populations of the marine snail, Littorina saxatilis, as a model, this thesis investigates how genetic variation and genomic structure drive adaptation following introduction. We employed a population genomics approach on experimentally and accidentally introduced populations to dissect the specific genomic features that underpin divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the predictability of local adaptation through an uncommon 30-year transplant experiment in nature. By distinguishing allele and chromosomal inversion frequency changes from neutral expectations, we found that evolutionary change was highly predictable at the macro-scale (phenotypes and chromosomal inversions), but less robust at the level of individual collinear loci. This result demonstrates that evolution can be predictable when a population possesses sufficient standing genetic variation (SGV), with chromosomal inversions acting as key integrated units that facilitate a rapid response to selection. Building on this, Chapter 3 applied whole-genome sequencing to three accidentally introduced populations (Venice, San Francisco, and Redwood City) to investigate their likely source and genomic patterns of divergence. We identified genomic regions of remarkable divergence potentially associated with local adaptation, and likely fuelled by SGV, while explicitly acknowledging the difficulty in disentangling selection signals from the genome-wide effects of demographic processes. Furthermore, we found that the divergence patterns relied extensively on the collinear genome in these introduced populations, and less clearly on the chromosomal inversions. This observation contrasts with local adaptation observed in the experimental system that relied on both collinear loci and highly selected chromosomal inversions, highlighting how demographic history and genomic architecture influence the detectable signature of local adaptation.\r\n\r\nA major limitation to conducting large-scale comparative evolutionary studies is the lack of data standardization, which prevents the integration of community knowledge and high-resolution environmental and genetic data. Chapter 4 addresses this by developing a community database for the Littorina system. This platform implements standardized protocols for the integration of diverse phenotypic and environmental data from multiple Littorina species. Likewise, the platform also centralizes the availability of associated genomic data through links to external repositories. This database represents a crucial tool to test complex, large-scale evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces the fundamental importance of SGV as the raw material for successful local adaptation, a conclusion supported by evidence in both experimental and accidental introductions. Furthermore, this work highlights the critical role of the genomic architecture—specifically chromosomal inversions—in driving the predictability and effectiveness of adaptive responses. Our findings underscore how the interplay between SGV and genomic architecture dictates the trajectory and detectability of evolution in colonizing populations, while simultaneously providing a necessary tool to advance comparative evolutionary genomics in emerging model organisms.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-077-0"]},"corr_author":"1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","ddc":["576"],"acknowledgement":"I acknowledge the funding agencies 1Norwegian Research Council RCN project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\", funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory, Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science, RTI2018-101274-J-I00)","OA_place":"publisher","article_processing_charge":"No","oa":1,"month":"01","related_material":{"record":[{"id":"18498","relation":"research_data","status":"public"},{"id":"18491","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT-ISTA-20991","title":"The genomic architecture of local adaptation in introduced populations","file_date_updated":"2026-01-16T13:08:59Z","page":"199","publication_status":"published","author":[{"full_name":"Garcia Castillo, Diego Fernando","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo"}],"date_published":"2026-01-16T00:00:00Z","file":[{"file_id":"20996","access_level":"closed","file_name":"2026_Garcia_Diego_Thesis.docx","date_created":"2026-01-16T12:25:13Z","creator":"dgarciac","checksum":"841f1bc073d667125729b2a017f8c37a","date_updated":"2026-01-16T12:25:13Z","relation":"source_file","file_size":22456421,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"access_level":"open_access","file_id":"20997","file_name":"2026_Garcia_Diego_Thesis.pdf","date_updated":"2026-01-16T12:25:13Z","checksum":"a1f33d4f183ce7072eee42a6ccf5340b","relation":"main_file","date_created":"2026-01-16T12:25:13Z","success":1,"creator":"dgarciac","content_type":"application/pdf","file_size":9556719},{"file_size":54491433,"content_type":"application/x-compressed","description":"Source code of the PostgreSQL database, front-end and back-end of the LittorinaDB web application developed as a product of the 4th chapter of the thesis.","relation":"supplementary_material","date_updated":"2026-01-16T13:08:14Z","checksum":"98a80691067174c30fe53f38ce7344e6","creator":"dgarciac","date_created":"2026-01-16T13:08:14Z","file_name":"2026_DiegoGarcia_LittorinaDB Source Code and Protocols.rar","access_level":"closed","file_id":"20998"},{"checksum":"99a3cab2fa36666b9a92eefc27d586da","date_updated":"2026-01-16T13:08:14Z","relation":"supplementary_material","date_created":"2026-01-16T13:08:14Z","creator":"dgarciac","content_type":"application/x-compressed","file_size":7982811,"access_level":"open_access","file_id":"20999","file_name":"2026_DiegoGarcia_Thesis-Supplementary_Material.rar"},{"file_size":732,"content_type":"text/plain","checksum":"255fdf56b2932c46bf27c63aa6106a4f","date_updated":"2026-01-16T13:08:59Z","relation":"supplementary_material","date_created":"2026-01-16T13:08:59Z","creator":"dgarciac","file_name":"README.txt","access_level":"open_access","file_id":"21000"}],"_id":"20991","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)"},"date_updated":"2026-10-21T08:18:21Z","date_created":"2026-01-16T09:47:59Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","status":"public","citation":{"ieee":"D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced populations,” Institute of Science and Technology Austria, 2026.","ama":"Garcia Castillo DF. The genomic architecture of local adaptation in introduced populations. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>","ista":"Garcia Castillo DF. 2026. The genomic architecture of local adaptation in introduced populations. Institute of Science and Technology Austria.","mla":"Garcia Castillo, Diego Fernando. <i>The Genomic Architecture of Local Adaptation in Introduced Populations</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20991\">10.15479/AT-ISTA-20991</a>.","short":"D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced Populations, Institute of Science and Technology Austria, 2026.","apa":"Garcia Castillo, D. F. (2026). <i>The genomic architecture of local adaptation in introduced populations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>","chicago":"Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation in Introduced Populations.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20991\">https://doi.org/10.15479/AT-ISTA-20991</a>."},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"related_material":{"record":[{"id":"20481","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12109"},{"id":"19278","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17373"}]},"month":"08","oa":1,"article_processing_charge":"No","doi_confirm":"1","OA_place":"publisher","acknowledgement":"This project has received financing from the European Research Council grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and innovation programme.\r\nThis research was supported by the Scientific Service Units of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility, the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina Strugaru for help with testing the device for Young’s modulus measurements.\r\n","ddc":["530"],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_identifier":{"isbn":["978-3-99078-083-1"],"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Contact electrification (CE) is a simple yet elusive phenomenon that occurs when two materials come into contact and separate, leaving behind net electrical charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In this thesis, we investigate CE from three complementary perspectives: developing a quantitative method to measure charge at the nanoscale, exploring the dynamic behavior of charge on insulating surfaces, and uncovering the role of mechanical history in forming a triboelectric series.\r\n\r\nIn the first part, we establish a rigorous framework for converting qualitative Kelvin probe force microscopy (KPFM) voltage maps into quantitative charge density distributions. Using finite element method (FEM) simulations, we determine the point-spread function of the KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed by numerical deconvolution. This procedure enables the recovery of both the magnitude and sign of charge density with high fidelity, resolving nanoscale features that are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces, we show that existing analytical approximations, such as parallel plate or spherical models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM approach therefore provides a fast and general method to convert qualitative KPFM signals into quantitative charge data, enabling nanoscale charge mapping under realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal stability of CE-induced charges and identify the key material factors that determine whether KPFM can capture meaningful charge patterns. Through time-resolved experiments combining a custom-built transfer system with both microscopic and macroscopic measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve CE charge long enough for stationary imaging. For less conductive polymers, such as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction. Using a simple capacitor-based model, we reproduce the observed decay dynamics and confirm that the transferred charge decays characteristic to the sample's bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn the third part, we address the question: can we form a triboelectric series with identical materials? Using controlled repetitive contact experiments, we show that nominally identical materials can progressively order themselves into a triboelectric series, where surfaces with more contact history charge negatively relative to fresher ones. By constructing a minimal model based on this ``contact bias'', we replicate the evolution from random to ordered charging observed in experiments. Supporting surface analyses, including atomic force microscopy, reveal that repeated contact induces nanoscale morphological changes, suggesting a mechanism tightly coupled to mechanical strain. These results highlight the crucial role of surface history and nanoscale mechanics in dictating charge transfer, motivating further exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric polarization."}],"day":"12","fulldoi":"https://doi.org/10.15479/AT-ISTA-22684","project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"}],"supervisor":[{"last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"year":"2026","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"type":"dissertation","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"ScWa"}],"citation":{"apa":"Pertl, F. (2026). <i>Experimental probing of nanoscale charge features and surface morphology changes during tribocharging</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>","chicago":"Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22684\">https://doi.org/10.15479/AT-ISTA-22684</a>.","short":"F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging, Institute of Science and Technology Austria, 2026.","mla":"Pertl, Felix. <i>Experimental Probing of Nanoscale Charge Features and Surface Morphology Changes during Tribocharging</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>.","ista":"Pertl F. 2026. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. Institute of Science and Technology Austria.","ama":"Pertl F. Experimental probing of nanoscale charge features and surface morphology changes during tribocharging. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22684\">10.15479/AT-ISTA-22684</a>","ieee":"F. Pertl, “Experimental probing of nanoscale charge features and surface morphology changes during tribocharging,” Institute of Science and Technology Austria, 2026."},"status":"public","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"date_created":"2026-08-12T09:44:40Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-21T08:39:24Z","_id":"22684","author":[{"full_name":"Pertl, Felix","first_name":"Felix","last_name":"Pertl","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"}],"file":[{"checksum":"0a4f5a941c40b921447e72291d72bc6f","date_updated":"2026-08-12T13:04:21Z","relation":"source_file","date_created":"2026-08-12T13:04:21Z","creator":"fpertl","file_size":31192621,"content_type":"application/x-zip-compressed","access_level":"closed","file_id":"22690","file_name":"2026_Pertl_Felix_Thesis.zip"},{"file_name":"2026_Pertl_Felix_Thesis.pdf","access_level":"open_access","file_id":"22691","file_size":27882509,"content_type":"application/pdf","date_updated":"2026-08-12T13:04:21Z","checksum":"ae60dcdb363222138886b2857643d4e3","relation":"main_file","date_created":"2026-08-12T13:04:21Z","creator":"fpertl"}],"date_published":"2026-08-12T00:00:00Z","publication_status":"published","page":"107","file_date_updated":"2026-08-12T13:04:21Z","title":"Experimental probing of nanoscale charge features and surface morphology changes during tribocharging","doi":"10.15479/AT-ISTA-22684"},{"supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"fulldoi":"https://doi.org/10.1007/s00031-024-09873-0","year":"2026","PlanS_conform":"1","type":"journal_article","dataavailabilitystatement":"Not applicable.","article_type":"original","oa":1,"article_processing_charge":"Yes (via OA deal)","publication":"Transformation Groups","OA_place":"publisher","external_id":{"isi":["001287455300001"]},"month":"03","publication_identifier":{"eissn":["1531-586X"],"issn":["1083-4362"]},"abstract":[{"lang":"eng","text":"We prove that the zero-fiber of the moment map of a totally negative quiver has rational singularities. Our proof consists in generalizing dimension bounds on jet spaces of this fiber, which were introduced by Budur. We also transfer the rational singularities property to other moduli spaces of objects in 2-Calabi-Yau categories, based on recent work of Davison. This has interesting arithmetic applications on quiver moment maps and moduli spaces of objects in 2-Calabi-Yau categories. First, we generalize results of Wyss on the asymptotic behaviour of counts of jets of quiver moment maps over finite fields. Moreover, we interpret the limit of counts of jets on a given moduli space as its p-adic volume under a canonical measure analogous to the measure built by Carocci, Orecchia and Wyss on certain moduli spaces of coherent sheaves."}],"scopus_import":"1","day":"01","volume":31,"acknowledgement":"I would like to warmly thank Dimitri Wyss for his guidance and supervision and Nero Budur for helpful discussions and answering all my questions on his previous works. I would also like to thank Francesca Carocci, Ben Davison, Lucien Hennecart and Olivier Schiffmann for helpful remarks and discussions during the writing of this paper. Finally, I would like to thank the anonymous referees for their careful reading and suggesting improvements in the exposition.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). This work was supported by the Swiss National Science Foundation [No. 196960]. This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","has_accepted_license":"1","ddc":["510"],"corr_author":"1","publisher":"Springer Nature","OA_type":"hybrid","isi":1,"title":"Rational singularities for moment maps of totally negative quivers","file_date_updated":"2026-07-23T05:50:09Z","das_tickbox":"1","doi":"10.1007/s00031-024-09873-0","publication_status":"published","file":[{"file_size":912029,"content_type":"application/pdf","creator":"dernst","date_created":"2026-07-23T05:50:09Z","success":1,"relation":"main_file","date_updated":"2026-07-23T05:50:09Z","checksum":"8985b4154b730284d3412ddc9e55d965","file_name":"2026_TransformationGroups_Vernet.pdf","file_id":"22385","access_level":"open_access"}],"date_published":"2026-03-01T00:00:00Z","author":[{"first_name":"Tanguy","last_name":"Vernet","id":"19f1e3bf-c59a-11ee-a1af-ed269948817b","full_name":"Vernet, Tanguy"}],"page":"1047-1083","department":[{"_id":"TaHa"}],"citation":{"apa":"Vernet, T. (2026). Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>","chicago":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00031-024-09873-0\">https://doi.org/10.1007/s00031-024-09873-0</a>.","short":"T. Vernet, Transformation Groups 31 (2026) 1047–1083.","ama":"Vernet T. Rational singularities for moment maps of totally negative quivers. <i>Transformation Groups</i>. 2026;31:1047-1083. doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>","ista":"Vernet T. 2026. Rational singularities for moment maps of totally negative quivers. Transformation Groups. 31, 1047–1083.","mla":"Vernet, Tanguy. “Rational Singularities for Moment Maps of Totally Negative Quivers.” <i>Transformation Groups</i>, vol. 31, Springer Nature, 2026, pp. 1047–83, doi:<a href=\"https://doi.org/10.1007/s00031-024-09873-0\">10.1007/s00031-024-09873-0</a>.","ieee":"T. Vernet, “Rational singularities for moment maps of totally negative quivers,” <i>Transformation Groups</i>, vol. 31. Springer Nature, pp. 1047–1083, 2026."},"status":"public","mathsc":["14B05","14D23","14G20","16G20"],"ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"        31","date_created":"2024-08-18T22:01:04Z","researchdata_availability":"not applicable","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-21T10:55:21Z","_id":"17437"},{"doi":"10.1145/3779121","title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","file_date_updated":"2026-07-06T09:03:02Z","das_tickbox":"0","file":[{"file_id":"22252","access_level":"open_access","file_name":"2026_TransactionsGraphics_Filakovsky.pdf","success":1,"date_created":"2026-07-06T09:03:02Z","creator":"dernst","date_updated":"2026-07-06T09:03:02Z","checksum":"0399ab94085878fc810084845eabd627","relation":"main_file","content_type":"application/pdf","file_size":941518}],"date_published":"2026-05-04T00:00:00Z","publication_status":"published","author":[{"full_name":"Filakovský, Marek","first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský"},{"full_name":"Nakajima, Tamio Vesa","last_name":"Nakajima","first_name":"Tamio Vesa"},{"full_name":"Opršal, Jakub","first_name":"Jakub","last_name":"Opršal","orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242"},{"first_name":"Gianluca","last_name":"Tasinato","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"keyword":["Constraint satisfaction problem","hypergraph colouring","promise problem","topological methods"],"OA_type":"gold","date_created":"2026-07-05T22:01:37Z","researchdata_availability":"no","intvolume":"        18","_id":"22247","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-21T13:23:55Z","quality_controlled":"1","article_number":"10","citation":{"ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” <i>ACM Transactions on Computation Theory</i>, vol. 18, no. 2. Association for Computing Machinery, 2026.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” <i>ACM Transactions on Computation Theory</i>, vol. 18, no. 2, 10, Association for Computing Machinery, 2026, doi:<a href=\"https://doi.org/10.1145/3779121\">10.1145/3779121</a>.","ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. <i>ACM Transactions on Computation Theory</i>. 2026;18(2). doi:<a href=\"https://doi.org/10.1145/3779121\">10.1145/3779121</a>","ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2026. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. ACM Transactions on Computation Theory. 18(2), 10.","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, ACM Transactions on Computation Theory 18 (2026).","chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” <i>ACM Transactions on Computation Theory</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3779121\">https://doi.org/10.1145/3779121</a>.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., &#38; Wagner, U. (2026). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. <i>ACM Transactions on Computation Theory</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3779121\">https://doi.org/10.1145/3779121</a>"},"department":[{"_id":"UlWa"}],"status":"public","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"type":"journal_article","PlanS_conform":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","supplementarymaterial":"no","year":"2026","project":[{"grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"fulldoi":"https://doi.org/10.1145/3779121","abstract":[{"lang":"eng","text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, …, k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring).\r\nHere, we investigate the complexity of approximating the “linearly ordered chromatic number” of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023)."}],"scopus_import":"1","publication_identifier":{"eissn":["1942-3462"],"issn":["1942-3454"]},"volume":18,"day":"04","has_accepted_license":"1","ddc":["500"],"acknowledgement":"This research was supported by the Charles University project PRIMUS/21/SCI/014, by the Ministry of Education, Youth\r\nand Sports of the Czech Republic under the project MSCAfellow5_MUNI (CZ.02.01.01/00/22_010/0003229), and by the\r\nAustrian Science Fund (FWF project P31312-N35). This research was funded by UKRI EP/X024431/1 and by a Clarendon\r\nFund Scholarship. This project has received funding from the European Union’s Horizon 2020 research and innovation\r\nprogramme under the Marie Skłodowska-Curie Grant Agreement No 101034413.\r\n","corr_author":"1","publisher":"Association for Computing Machinery","arxiv":1,"article_processing_charge":"Yes","oa":1,"external_id":{"arxiv":["2312.12981"]},"OA_place":"publisher","publication":"ACM Transactions on Computation Theory","month":"05","related_material":{"record":[{"id":"15168","relation":"earlier_version","status":"public"}]}},{"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"scopus_import":"1","abstract":[{"text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in R^3\r\n consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in R^3 admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument. We prove the following variant of this result: any mass distribution (or point set) in R^3 admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction. Moreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in R^3 (with prescribed normal direction of one of the planes) in time O(n^7/3). A preliminary version of this work appeared in SoCG’24 (Aronov et al., 40th International Symposium on Computational Geometry, 2024).","lang":"eng"}],"day":"01","volume":75,"acknowledgement":"Work by BA was supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship. Research of BA also partially supported by ERC grant no. 882971, “GeoScape,” and by the Erdős Center. Work by AB was supported by Australian Research Council grant DP220102212. Work by IR was supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551. BA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work. Open Access funding enabled and organized by CAUL and its Member Institutions.","has_accepted_license":"1","ddc":["500"],"publisher":"Springer Nature","oa":1,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","external_id":{"isi":["001506904300001"],"arxiv":["2403.02627"]},"publication":"Discrete & Computational Geometry","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20339"},{"status":"public","relation":"earlier_version","id":"18917"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s00454-025-00759-w"}]},"month":"06","type":"journal_article","PlanS_conform":"1","article_type":"original","supplementarymaterial":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/s00454-025-00739-0","year":"2026","intvolume":"        75","researchdata_availability":"no","date_created":"2025-06-22T22:02:07Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-21T13:38:17Z","_id":"19860","department":[{"_id":"UlWa"}],"citation":{"ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” <i>Discrete &#38; Computational Geometry</i>, vol. 75. Springer Nature, pp. 1331–1355, 2026.","ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2026. Eight-partitioning points in 3D, and efficiently too. Discrete &#38; Computational Geometry. 75, 1331–1355.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. 2026;75:1331-1355. doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>, vol. 75, Springer Nature, 2026, pp. 1331–55, doi:<a href=\"https://doi.org/10.1007/s00454-025-00739-0\">10.1007/s00454-025-00739-0</a>.","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, Discrete &#38; Computational Geometry 75 (2026) 1331–1355.","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>.","apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2026). Eight-partitioning points in 3D, and efficiently too. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-025-00739-0\">https://doi.org/10.1007/s00454-025-00739-0</a>"},"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2026-07-23T11:14:05Z","das_tickbox":"0","isi":1,"title":"Eight-partitioning points in 3D, and efficiently too","doi":"10.1007/s00454-025-00739-0","file":[{"file_name":"2026_DiscreteCompGeom_Aronov.pdf","file_id":"22395","access_level":"open_access","file_size":525281,"content_type":"application/pdf","date_created":"2026-07-23T11:14:05Z","success":1,"creator":"dernst","date_updated":"2026-07-23T11:14:05Z","checksum":"a32774a0d14f46cafbd77bfb9d9ac4b6","relation":"main_file"}],"publication_status":"published","author":[{"last_name":"Aronov","first_name":"Boris","full_name":"Aronov, Boris"},{"full_name":"Basit, Abdul","last_name":"Basit","first_name":"Abdul"},{"first_name":"Indu","last_name":"Ramesh","full_name":"Ramesh, Indu"},{"id":"0433290C-AF8F-11E9-A4C7-F729E6697425","last_name":"Tasinato","first_name":"Gianluca","full_name":"Tasinato, Gianluca"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"date_published":"2026-06-01T00:00:00Z","page":"1331-1355","OA_type":"hybrid"},{"publication":"Science","OA_place":"repository","external_id":{"pmid":["41990180"]},"article_processing_charge":"No","oa":1,"month":"04","related_material":{"record":[{"id":"23145","status":"public","relation":"dissertation_contains"}]},"volume":392,"day":"16","abstract":[{"lang":"eng","text":"Reactive oxygen species (ROS) have been implicated in multiple signaling processes in plants, but the underlying mechanisms and roles remain enigmatic. In this study, we developed a method of live imaging of apoplastic ROS at the root surface. Distinct signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts. Genetic and optogenetic manipulations of Arabidopsis identified calcium transients as necessary and sufficient for ROS bursts through activation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS bursts are not required, but they do limit gravity-induced root bending. Root bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH oxidase activation. The resulting ROS production stiffens cell walls to facilitate soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility and stiffness to navigate soil."}],"scopus_import":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"corr_author":"1","publisher":"AAAS","ddc":["580"],"has_accepted_license":"1","acknowledgement":"We gratefully acknowledge the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility (University of Nottingham) for support with imaging and the Growth Facility (IPMB) for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing of Arabidopsis mini-soil columns.\r\nThis project received funding from the European Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B). I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030 and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government through its “Investments for the Future” program and also by the projects “Mecha-Nuc” ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université Paris-Saclay. Phytohormonal analysis was performed using the service laboratory funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This research was funded in whole or in part by the Austrian Science Fund (P 37051-B) and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required, the author will make the Author Accepted Manuscript (AAM) version available under a CC BY public copyright license.","issue":"6795","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","project":[{"grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","name":"Cyclic nucleotides as second messengers in plants"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"fulldoi":"https://doi.org/10.1126/science.adu8197","type":"journal_article","article_type":"original","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"status":"public","citation":{"ieee":"I. Kulich <i>et al.</i>, “Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation,” <i>Science</i>, vol. 392, no. 6795. AAAS, pp. 296–300, 2026.","ama":"Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. 2026;392(6795):296-300. doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>","ista":"Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ, Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. Science. 392(6795), 296–300.","mla":"Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>, vol. 392, no. 6795, AAAS, 2026, pp. 296–300, doi:<a href=\"https://doi.org/10.1126/science.adu8197\">10.1126/science.adu8197</a>.","short":"I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad, G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma, M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300.","apa":"Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad, K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>","chicago":"Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.adu8197\">https://doi.org/10.1126/science.adu8197</a>."},"department":[{"_id":"JiFr"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"oa_version":"Accepted Version","date_updated":"2026-10-22T09:15:44Z","_id":"21763","quality_controlled":"1","date_created":"2026-04-26T22:01:47Z","intvolume":"       392","OA_type":"green","doi":"10.1126/science.adu8197","file_date_updated":"2026-05-07T05:54:43Z","title":"Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals for soil navigation","page":"296-300","date_published":"2026-04-16T00:00:00Z","file":[{"creator":"dernst","success":1,"date_created":"2026-05-07T05:54:43Z","relation":"main_file","date_updated":"2026-05-07T05:54:43Z","checksum":"eb5b29247832ecdc53c8146da0509bbe","file_size":6150733,"content_type":"application/pdf","file_id":"21832","access_level":"open_access","file_name":"2026_Science_Kulich_accepted.pdf"}],"author":[{"full_name":"Kulich, Ivan","last_name":"Kulich","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan"},{"full_name":"Vladimirtsev, Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","first_name":"Dmitrii"},{"first_name":"Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"full_name":"Gao, Shiqiang","first_name":"Shiqiang","last_name":"Gao"},{"first_name":"Matteo","last_name":"Citterico","full_name":"Citterico, Matteo"},{"first_name":"Kai R.","last_name":"Konrad","full_name":"Konrad, Kai R."},{"first_name":"Georg","last_name":"Nagel","full_name":"Nagel, Georg"},{"full_name":"Wrzaczek, Michael","first_name":"Michael","last_name":"Wrzaczek"},{"last_name":"Cascaro","first_name":"Léa","full_name":"Cascaro, Léa"},{"first_name":"Pauline","last_name":"Vinet","full_name":"Vinet, Pauline"},{"full_name":"Durand, Pauline","last_name":"Durand","first_name":"Pauline"},{"first_name":"Atef","last_name":"Asnacios","full_name":"Asnacios, Atef"},{"first_name":"Lokesh","last_name":"Verma","full_name":"Verma, Lokesh"},{"full_name":"Bennett, Malcolm J.","last_name":"Bennett","first_name":"Malcolm J."},{"full_name":"Pandey, Bipin K.","last_name":"Pandey","first_name":"Bipin K."},{"full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"publication_status":"published"},{"publication_identifier":{"issn":["2663-337X"]},"day":"18","acknowledgement":"European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 ","ddc":["580"],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","corr_author":"1","doi_confirm":"1","article_processing_charge":"No","OA_place":"publisher","related_material":{"record":[{"id":"12291","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"21763"},{"status":"public","relation":"part_of_dissertation","id":"23175"},{"status":"public","relation":"part_of_dissertation","id":"23174"},{"id":"20656","status":"public","relation":"part_of_dissertation"}]},"month":"10","type":"dissertation","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"},{"_id":"Bio"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.15479/AT-ISTA-23145","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"project":[{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051"},{"name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739","grant_number":"101142681"}],"year":"2026","date_created":"2026-10-16T17:14:40Z","_id":"23145","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"date_updated":"2026-10-22T09:15:44Z","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"citation":{"short":"M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.","chicago":"Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>.","apa":"Randuch, M. (2026). <i>Fast growth responses in plants: Growth regulation and phospho-proteomic </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-23145\">https://doi.org/10.15479/AT-ISTA-23145</a>","ieee":"M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.","mla":"Randuch, Marek. <i>Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>.","ama":"Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-23145\">10.15479/AT-ISTA-23145</a>","ista":"Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria."},"degree_awarded":"PhD","status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2026-10-20T11:48:37Z","title":"Fast growth responses in plants: Growth regulation and phospho-proteomic ","doi":"10.15479/AT-ISTA-23145","date_published":"2026-10-18T00:00:00Z","file":[{"file_name":"2026_Marek_Randuch_Thesis.docx","file_id":"23176","access_level":"closed","file_size":89544771,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2026-10-20T09:17:28Z","creator":"mranduch","checksum":"4ace20ba4f1bb0f8dcc3f8eb45eb68fa","date_updated":"2026-10-20T11:48:37Z","relation":"source_file"},{"date_created":"2026-10-20T09:17:20Z","creator":"mranduch","checksum":"fc630c7e8d795e7f13000cbb428424b3","date_updated":"2026-10-20T11:48:37Z","embargo_to":"open_access","relation":"main_file","content_type":"application/pdf","file_size":28321059,"embargo":"2027-10-20","file_id":"23177","access_level":"closed","file_name":"2026_Marek_Randuch_Thesis.pdf"}],"author":[{"full_name":"Randuch, Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"}],"publication_status":"published","page":"289"},{"OA_place":"repository","publication":"bioRxiv","external_id":{"biorxivid":["10.1101/2025.10.04.680446"]},"oa":1,"article_processing_charge":"No","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"23145"}]},"month":"08","day":"26","abstract":[{"lang":"eng","text":"Plants must continually balance growth with arrest, especially under stress. Auxin signaling acts as a central regulatory hub in this process, yet the mechanisms that dynamically tune early auxin signalling in real time remain unknown. Here, we used the light-gated, Ca2+-permeable Channelrhodopsin 2 variant XXM2.0 to optogenetically impose defined Ca2+ signatures on Arabidopsis root cells. Repetitive light activation triggered cytosolic Ca2+ signals that in turn suppressed auxin-induced membrane depolarization and Ca2+ transients. Moreover, prolonged optogenetic Ca2+ stimulation affects auxin-responsive transcriptional reprogramming. As phenotypic output, reversible inhibition of root growth by suppressing cell division and elongation was observed. We further identify a candidate CaM7–CNGC14 module that likely mediates Ca2+-dependent gating of early auxin signalling. Our study thus introduces a synthetic biology approach to decompose calcium–auxin crosstalk in plant cells, and demonstrates that optogenetically imposed cytosolic Ca2+ signals act as dynamic regulators of auxin susceptibility in roots."}],"corr_author":"1","acknowledgement":"We would like to thank Dirk Becker (University of Wuerzburg) for his help in making the optogenetic constructs and for his comments on the manuscript. We also appreciate Rob Roelfsema (University of Wuerzburg) for his feedback on the manuscript. We sincerely thank the anonymous reviewers for the thoughtful and inspiring suggestions that helped broaden the discussion and identify important future research directions. Funding\r\nNational Key R&D Program of China, 2025YFA0923400 (RH)\r\n\r\nNational Natural Science Foundation of China (NSFC), W2531024 (RH); 32271501(NL)\r\n\r\nNSFC-Excellent Young Scientists Fund Program (overseas) (SH)\r\n\r\nNSFC-RFIS, ZB2025101410702 (RH)\r\n\r\nGuangdong Pearl River Talents Program, 2023ZT10N033\r\n\r\nChina Scholarship Council no. 202306510063 (HS)\r\n\r\nThe European Research Council grant 101142681 CYNIPS (JF)\r\n\r\nAustrian Science Fund grant FWF; P 37051-B (JF)\r\n\r\nGerman Research Foundation grant CRC 1644 (512328399; 512328399) (KK, ZH)\r\n\r\nERC Synergy project STARMORPH, reg. no. 101166880 (AP, ON)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1101/2025.10.04.680446","project":[{"grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6"}],"year":"2026","type":"preprint","status":"public","department":[{"_id":"JiFr"}],"main_file_link":[{"url":"https://doi.org/10.1101/2025.10.04.680446","open_access":"1"}],"citation":{"ieee":"H. Song <i>et al.</i>, “Ca2+ signature gates early auxin signaling in Arabidopsis roots,” <i>bioRxiv</i>. .","ama":"Song H, Baudon A, Freund M, et al. Ca2+ signature gates early auxin signaling in Arabidopsis roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>","ista":"Song H, Baudon A, Freund M, Randuch M, Pěnčík A, Ondřej N, He Z, Kaufmann K, Li N, Gilliham M, Friml J, Hedrich R, Huang S. Ca2+ signature gates early auxin signaling in Arabidopsis roots. bioRxiv, <a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>.","mla":"Song, Huifang, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.10.04.680446\">10.1101/2025.10.04.680446</a>.","short":"H. Song, A. Baudon, M. Freund, M. Randuch, A. Pěnčík, N. Ondřej, Z. He, K. Kaufmann, N. Li, M. Gilliham, J. Friml, R. Hedrich, S. Huang, BioRxiv (n.d.).","chicago":"Song, Huifang, Angel Baudon, Matthias Freund, Marek Randuch, Aleš Pěnčík, Novák Ondřej, Zhaohui He, et al. “Ca2+ Signature Gates Early Auxin Signaling in Arabidopsis Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.10.04.680446\">https://doi.org/10.1101/2025.10.04.680446</a>.","apa":"Song, H., Baudon, A., Freund, M., Randuch, M., Pěnčík, A., Ondřej, N., … Huang, S. (n.d.). Ca2+ signature gates early auxin signaling in Arabidopsis roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.10.04.680446\">https://doi.org/10.1101/2025.10.04.680446</a>"},"language":[{"iso":"eng"}],"oa_version":"Preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"_id":"23175","date_updated":"2026-10-22T09:15:44Z","date_created":"2026-10-19T11:51:47Z","biorxivid":1,"OA_type":"green","title":"Ca2+ signature gates early auxin signaling in Arabidopsis roots","doi":"10.1101/2025.10.04.680446","date_published":"2026-08-26T00:00:00Z","publication_status":"draft","author":[{"first_name":"Huifang","last_name":"Song","full_name":"Song, Huifang"},{"first_name":"Angel","last_name":"Baudon","full_name":"Baudon, Angel"},{"first_name":"Matthias","last_name":"Freund","full_name":"Freund, Matthias"},{"first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","full_name":"Randuch, Marek"},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"full_name":"Ondřej, Novák","last_name":"Ondřej","first_name":"Novák"},{"last_name":"He","first_name":"Zhaohui","full_name":"He, Zhaohui"},{"full_name":"Kaufmann, Kerstin","last_name":"Kaufmann","first_name":"Kerstin"},{"full_name":"Li, Nan","last_name":"Li","first_name":"Nan"},{"full_name":"Gilliham, Matthew","first_name":"Matthew","last_name":"Gilliham"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Hedrich","first_name":"Rainer","full_name":"Hedrich, Rainer"},{"full_name":"Huang, Shouguang","first_name":"Shouguang","last_name":"Huang"}]},{"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2026-05-06","name":"CLEO: Fundamental Science","location":"Long Beach, CA, United States","start_date":"2026-05-02"},"fulldoi":"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4","year":"2026","publication_identifier":{"isbn":["9781957171586"]},"abstract":[{"text":"We develop a quantum theory of light-matter interactions in 229Th nanophotonic resonators pumped via the optonuclear quadrupolar effect, predicting detectable photon fluxes with realistic platforms and revealing how collective dynamics shape the future nuclear clock performance.","lang":"eng"}],"scopus_import":"1","day":"15","corr_author":"1","publisher":"Optica Publishing Group","article_processing_charge":"No","publication":"CLEO Fundamental Science Proceedings","month":"05","title":"Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators","doi":"10.1364/CLEO_FS.2026.FTU1B.4","author":[{"first_name":"Karen","id":"d21e88e4-b0a3-11f1-8f28-b033c1af3b5a","last_name":"Mamian","full_name":"Mamian, Karen"},{"last_name":"De Haan","first_name":"Jan","full_name":"De Haan, Jan"},{"first_name":"Toby","last_name":"Bi","full_name":"Bi, Toby"},{"full_name":"Dubey, Swadheen","last_name":"Dubey","first_name":"Swadheen"},{"first_name":"Georgy A.","last_name":"Kazakov","full_name":"Kazakov, Georgy A."},{"first_name":"Kjeld","last_name":"Beeks","full_name":"Beeks, Kjeld"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"first_name":"Sandro","last_name":"Kraemer","full_name":"Kraemer, Sandro"},{"full_name":"Pereira, Lino M.C.","last_name":"Pereira","first_name":"Lino M.C."},{"full_name":"Del’Haye, Pascal","last_name":"Del’Haye","first_name":"Pascal"},{"first_name":"Kasper","last_name":"Van Gasse","full_name":"Van Gasse, Kasper"},{"full_name":"Schumm, Thorsten","first_name":"Thorsten","last_name":"Schumm"},{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes","first_name":"Charles","full_name":"Roques-Carmes, Charles"}],"publication_status":"published","date_published":"2026-05-15T00:00:00Z","OA_type":"closed access","date_created":"2026-10-25T23:02:24Z","quality_controlled":"1","article_number":"FTU1B.4","_id":"23197","date_updated":"2026-10-27T10:53:59Z","alternative_title":["Technical Digest Series"],"department":[{"_id":"ChRo"}],"citation":{"ieee":"K. Mamian <i>et al.</i>, “Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators,” in <i>CLEO Fundamental Science Proceedings</i>, Long Beach, CA, United States, 2026.","ama":"Mamian K, De Haan J, Bi T, et al. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In: <i>CLEO Fundamental Science Proceedings</i>. Optica Publishing Group; 2026. doi:<a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">10.1364/CLEO_FS.2026.FTU1B.4</a>","ista":"Mamian K, De Haan J, Bi T, Dubey S, Kazakov GA, Beeks K, Marquardt C, Kraemer S, Pereira LMC, Del’Haye P, Van Gasse K, Schumm T, Roques-Carmes C. 2026. Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. CLEO Fundamental Science Proceedings. CLEO: Fundamental Science, Technical Digest Series, , FTU1B.4.","mla":"Mamian, Karen, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” <i>CLEO Fundamental Science Proceedings</i>, FTU1B.4, Optica Publishing Group, 2026, doi:<a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">10.1364/CLEO_FS.2026.FTU1B.4</a>.","short":"K. Mamian, J. De Haan, T. Bi, S. Dubey, G.A. Kazakov, K. Beeks, C. Marquardt, S. Kraemer, L.M.C. Pereira, P. Del’Haye, K. Van Gasse, T. Schumm, C. Roques-Carmes, in:, CLEO Fundamental Science Proceedings, Optica Publishing Group, 2026.","apa":"Mamian, K., De Haan, J., Bi, T., Dubey, S., Kazakov, G. A., Beeks, K., … Roques-Carmes, C. (2026). Collective optonuclear cavity quantum electrodynamics in 229Th nanophotonic resonators. In <i>CLEO Fundamental Science Proceedings</i>. Long Beach, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4</a>","chicago":"Mamian, Karen, Jan De Haan, Toby Bi, Swadheen Dubey, Georgy A. Kazakov, Kjeld Beeks, Christoph Marquardt, et al. “Collective Optonuclear Cavity Quantum Electrodynamics in 229Th Nanophotonic Resonators.” In <i>CLEO Fundamental Science Proceedings</i>. Optica Publishing Group, 2026. <a href=\"https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4\">https://doi.org/10.1364/CLEO_FS.2026.FTU1B.4</a>."},"status":"public","oa_version":"None","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1016/j.gde.2026.102483","year":"2026","PlanS_conform":"1","type":"journal_article","article_type":"original","oa":1,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2601.19681"]},"publication":"Current Opinion in Genetics & Development","OA_place":"publisher","month":"05","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"abstract":[{"text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype–phenotype map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the first of a two-part series, we briefly review the pertinent modeling and simulation efforts for a unique system that enables close, quantitative, and mechanistic links between biophysics, as well as systems, synthetic, and evolutionary biology.","lang":"eng"}],"scopus_import":"1","day":"09","volume":99,"acknowledgement":"We thank Nick Barton and Noa Ottilie Borst for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA).\r\nThis study was supported by the European Molecular Biology Laboratory (J.C.); the European Molecular Biology Laboratory Interdisciplinary Postdoc Programme (EIPOD) under the Marie Skłodowska-Curie Actions cofund (S.H.A.).","has_accepted_license":"1","ddc":["570"],"corr_author":"1","publisher":"Elsevier","OA_type":"hybrid","title":"Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps","doi":"10.1016/j.gde.2026.102483","author":[{"id":"776a6ed0-a053-11f0-8635-80b95e0e0d53","orcid":"0000-0003-2977-7844","last_name":"Mascolo","first_name":"Elia","full_name":"Mascolo, Elia"},{"full_name":"Körei, Reka E","first_name":"Reka E","last_name":"Körei","id":"50FDE43E-AA30-11E9-A72B-8A12E6697425"},{"full_name":"Herrera-Álvarez, Santiago","last_name":"Herrera-Álvarez","first_name":"Santiago"},{"full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"first_name":"Justin","last_name":"Crocker","full_name":"Crocker, Justin"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"publication_status":"epub_ahead","date_published":"2026-05-09T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.gde.2026.102483","open_access":"1"}],"department":[{"_id":"GradSch"},{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"apa":"Mascolo, E., Körei, R. E., Herrera-Álvarez, S., Guet, C. C., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>","chicago":"Mascolo, Elia, Reka E Körei, Santiago Herrera-Álvarez, Calin C Guet, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102483\">https://doi.org/10.1016/j.gde.2026.102483</a>.","short":"E. Mascolo, R.E. Körei, S. Herrera-Álvarez, C.C. Guet, J. Crocker, G. Tkačik, Current Opinion in Genetics &#38; Development 99 (2026).","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 1: Simulations on Global, Biophysically-Realistic Genotype–Phenotype Maps.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99, 102483, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>.","ista":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. Current Opinion in Genetics &#38; Development. 99, 102483.","ama":"Mascolo E, Körei RE, Herrera-Álvarez S, Guet CC, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps. <i>Current Opinion in Genetics &#38; Development</i>. 2026;99. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102483\">10.1016/j.gde.2026.102483</a>","ieee":"E. Mascolo, R. E. Körei, S. Herrera-Álvarez, C. C. Guet, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 1: Simulations on global, biophysically-realistic genotype–phenotype maps,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 99. Elsevier, 2026."},"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"        99","date_created":"2026-06-10T07:37:12Z","quality_controlled":"1","article_number":"102483","_id":"21983","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-27T13:12:27Z"},{"DOAJ_listed":"1","oa":1,"article_processing_charge":"Yes","external_id":{"pmid":["42869904"]},"publication":"Nature Communications","OA_place":"publisher","month":"10","publication_identifier":{"eissn":["2041-1723"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) are widespread across diverse flowering plant species and play important roles regulating reproduction and environmental responses. However, how sRNAs exert their function is largely unknown, likely due to their typical origin in non-genic regions, the lack of distinct gene targets, and the sparse characterization of their associated Argonaute (AGO) effector proteins. Here we show that Arabidopsis male reproductive sRNAs associate with AGO4, 5, 6 and 9, all of which are enriched in meiocytes along with RNA Polymerase V (Pol V). This enables these sRNAs to methylate loci with imperfect sequence homology. AGO4, AGO6 and AGO9 predominantly load 24-nucleotide (nt) Pol IV-derived sRNAs and mediate DNA methylation in meiocytes in a dosage-dependent manner. Despite closer homology to microRNA-associated AGO1 and AGO10, AGO5 primarily binds CLSY3- and Pol IV-derived 21-24 nt sRNAs. Transcriptomic and methylomic analyses of meiocytes from single and compound ago mutants demonstrate distinct yet complementary roles of AGO4/6/9 and AGO5 in regulating protein-coding genes and silencing transposons in the germline. These molecular disruptions are accompanied by significant meiotic defects. Together, our findings reveal how AGO4/6/9-mediated DNA methylation and AGO5, likely acting through post-transcriptional gene silencing, work together to promote male germline development."}],"day":"14","volume":17,"acknowledgement":"We thank Michael J. Axtell for generously sharing ago4-4 ago6-2, ago6-2 ago9-1 double and ago4-4 ago6-2 ago9-1 triple mutants. We thank the John Innes Centre Bioimaging Facility and ISTA Imaging and Optics Facility for their assistance with the confocal microscopy, and the ISTA Scientific Computing Facility for high performance computing resources. This work was funded by a Marie Curie Postdoctoral Fellowship (101153710; C.Y.), a European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (ISTA Bridge Fellowship) (S.X.), a DFG grant (FOR 5235 CSCS; A.S.), a European Research Council (ERC) Starting Grant (804981; X.F) and an ERC Consolidator Grant (101126201; C.Y. and XF).","has_accepted_license":"1","ddc":["580"],"corr_author":"1","publisher":"Springer Nature","supplementarymaterial":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"8e917275-16d5-11f0-9cad-fee255fa62e0","name":"The moleculaR mEchAnismS Of dNa methylatIon reprogrammiNg in Arabidopsis sexual lineaGe","grant_number":"101153710"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"grant_number":"804981","call_identifier":"H2020","_id":"bdb51a6e-d553-11ed-ba76-c2025f3d5725","name":"Establishment, modulation and inheritance of sexual lineage specific DNA methylation in plants"},{"name":"Mechanisms and biological functions of H3K27me3 reprogramming in plant microspores","_id":"7c012eb8-9f16-11ee-852c-dc2b6371d5a0","grant_number":"101126201"}],"fulldoi":"https://doi.org/10.1038/s41467-026-77326-1","year":"2026","PlanS_conform":"1","type":"journal_article","dataavailabilitystatement":"Illumina sequencing data (RIP-seq, BS-seq, and RNA-seq) generated in this study have been deposited in the NCBI BioProject and are accessible under accession number PRJNA1192978. Published BS-seq data of Arabidopsis meiocyte used in this study for Fig. 4a are available in the NCBI GEO database under accession code GSE161625. All custom codes are available via the request to the corresponding author.","article_type":"original","department":[{"_id":"XiFe"}],"citation":{"ama":"Long J, Yang C, Xu S, et al. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-77326-1\">10.1038/s41467-026-77326-1</a>","ista":"Long J, Yang C, Xu S, De Jaeger-Braet JG, She W, Ono S, Walker J, de Souza Vieira Y, Schnittger A, Feng X. 2026. Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. Nature Communications. 17, 10758.","mla":"Long, Jincheng, et al. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” <i>Nature Communications</i>, vol. 17, 10758, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-77326-1\">10.1038/s41467-026-77326-1</a>.","ieee":"J. Long <i>et al.</i>, “Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","chicago":"Long, Jincheng, Chao Yang, Shujuan Xu, Joke G De Jaeger-Braet, Wenjing She, Seijiro Ono, James Walker, Ygor de Souza Vieira, Arp Schnittger, and Xiaoqi Feng. “Multiple Argonaute Complexes Orchestrate Epigenetic Silencing in the Arabidopsis Germline.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-77326-1\">https://doi.org/10.1038/s41467-026-77326-1</a>.","apa":"Long, J., Yang, C., Xu, S., De Jaeger-Braet, J. G., She, W., Ono, S., … Feng, X. (2026). Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-77326-1\">https://doi.org/10.1038/s41467-026-77326-1</a>","short":"J. Long, C. Yang, S. Xu, J.G. De Jaeger-Braet, W. She, S. Ono, J. Walker, Y. de Souza Vieira, A. Schnittger, X. Feng, Nature Communications 17 (2026)."},"status":"public","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"        17","researchdata_availability":"yes","date_created":"2026-10-27T10:38:56Z","article_number":"10758","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"23198","date_updated":"2026-10-28T08:43:20Z","OA_type":"gold","das_tickbox":"1","title":"Multiple Argonaute complexes orchestrate epigenetic silencing in the Arabidopsis germline","file_date_updated":"2026-10-28T08:41:06Z","doi":"10.1038/s41467-026-77326-1","file":[{"success":1,"date_created":"2026-10-28T08:41:06Z","creator":"dernst","checksum":"f24efcba89d880d48fef04b780923780","date_updated":"2026-10-28T08:41:06Z","relation":"main_file","content_type":"application/pdf","file_size":4220128,"file_id":"23204","access_level":"open_access","file_name":"2026_NatureComm_Long.pdf"}],"pmid":1,"author":[{"full_name":"Long, Jincheng","last_name":"Long","first_name":"Jincheng"},{"first_name":"Chao","id":"082e3e6e-8069-11ed-8390-c8cce7b1aaca","last_name":"Yang","full_name":"Yang, Chao"},{"full_name":"Xu, Shujuan","first_name":"Shujuan","id":"9724dd9d-f591-11ee-bd51-e97ed0652286","last_name":"Xu"},{"id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","last_name":"De Jaeger-Braet","first_name":"Joke G","full_name":"De Jaeger-Braet, Joke G"},{"first_name":"Wenjing","last_name":"She","full_name":"She, Wenjing"},{"full_name":"Ono, Seijiro","last_name":"Ono","first_name":"Seijiro"},{"last_name":"Walker","first_name":"James","full_name":"Walker, James"},{"full_name":"de Souza Vieira, Ygor","first_name":"Ygor","last_name":"de Souza Vieira","id":"af019b77-d2a9-11f1-9e65-c47a5932b764"},{"full_name":"Schnittger, Arp","last_name":"Schnittger","first_name":"Arp"},{"full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"publication_status":"published","date_published":"2026-10-14T00:00:00Z"},{"OA_type":"gold","publication_status":"published","file":[{"file_name":"2026_AstrophysicalJour_Stephenson.pdf","file_id":"23202","access_level":"open_access","file_size":4194012,"content_type":"application/pdf","creator":"dernst","date_created":"2026-10-28T08:02:57Z","success":1,"relation":"main_file","date_updated":"2026-10-28T08:02:57Z","checksum":"6968c85ac6ccc997a30dab818dc04e42"}],"author":[{"full_name":"Stephenson, Mabel G.","last_name":"Stephenson","first_name":"Mabel G."},{"first_name":"John","last_name":"Chisholm","full_name":"Chisholm, John"},{"full_name":"Saldana-Lopez, A.","last_name":"Saldana-Lopez","first_name":"A."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"first_name":"Alaina","last_name":"Henry","full_name":"Henry, Alaina"},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"first_name":"Sophia R.","last_name":"Flury","full_name":"Flury, Sophia R."},{"full_name":"Hutchison, Taylor A.","last_name":"Hutchison","first_name":"Taylor A."},{"first_name":"Steven L.","last_name":"Finkelstein","full_name":"Finkelstein, Steven L."},{"full_name":"Guseva, Natalia G.","first_name":"Natalia G.","last_name":"Guseva"},{"first_name":"Yuri I.","last_name":"Izotov","full_name":"Izotov, Yuri I."},{"first_name":"Rui","last_name":"Marques-Chaves","full_name":"Marques-Chaves, Rui"},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."},{"first_name":"Naveen A.","last_name":"Reddy","full_name":"Reddy, Naveen A."},{"full_name":"Schaerer, Daniel","first_name":"Daniel","last_name":"Schaerer"}],"date_published":"2026-10-15T00:00:00Z","doi":"10.3847/1538-4357/ae9eb7","file_date_updated":"2026-10-28T08:02:57Z","das_tickbox":"0","title":"The evolution of low-ionization electron densities in galaxies across cosmic epochs","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","citation":{"chicago":"Stephenson, Mabel G., John Chisholm, A. Saldana-Lopez, Jorryt J Matthee, Alaina Henry, Rohan P. Naidu, Sophia R. Flury, et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” <i>The Astrophysical Journal</i>. IOP Publishing, 2026. <a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">https://doi.org/10.3847/1538-4357/ae9eb7</a>.","apa":"Stephenson, M. G., Chisholm, J., Saldana-Lopez, A., Matthee, J. J., Henry, A., Naidu, R. P., … Schaerer, D. (2026). The evolution of low-ionization electron densities in galaxies across cosmic epochs. <i>The Astrophysical Journal</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">https://doi.org/10.3847/1538-4357/ae9eb7</a>","short":"M.G. Stephenson, J. Chisholm, A. Saldana-Lopez, J.J. Matthee, A. Henry, R.P. Naidu, S.R. Flury, T.A. Hutchison, S.L. Finkelstein, N.G. Guseva, Y.I. Izotov, R. Marques-Chaves, P.A. Oesch, N.A. Reddy, D. Schaerer, The Astrophysical Journal 1010 (2026).","mla":"Stephenson, Mabel G., et al. “The Evolution of Low-Ionization Electron Densities in Galaxies across Cosmic Epochs.” <i>The Astrophysical Journal</i>, vol. 1010, no. 2, 184, IOP Publishing, 2026, doi:<a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">10.3847/1538-4357/ae9eb7</a>.","ista":"Stephenson MG, Chisholm J, Saldana-Lopez A, Matthee JJ, Henry A, Naidu RP, Flury SR, Hutchison TA, Finkelstein SL, Guseva NG, Izotov YI, Marques-Chaves R, Oesch PA, Reddy NA, Schaerer D. 2026. The evolution of low-ionization electron densities in galaxies across cosmic epochs. The Astrophysical Journal. 1010(2), 184.","ama":"Stephenson MG, Chisholm J, Saldana-Lopez A, et al. The evolution of low-ionization electron densities in galaxies across cosmic epochs. <i>The Astrophysical Journal</i>. 2026;1010(2). doi:<a href=\"https://doi.org/10.3847/1538-4357/ae9eb7\">10.3847/1538-4357/ae9eb7</a>","ieee":"M. G. Stephenson <i>et al.</i>, “The evolution of low-ionization electron densities in galaxies across cosmic epochs,” <i>The Astrophysical Journal</i>, vol. 1010, no. 2. IOP Publishing, 2026."},"department":[{"_id":"JoMa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"23200","date_updated":"2026-10-28T08:05:42Z","quality_controlled":"1","article_number":"184","date_created":"2026-10-27T10:40:40Z","intvolume":"      1010","year":"2026","fulldoi":"https://doi.org/10.3847/1538-4357/ae9eb7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","article_type":"original","type":"journal_article","PlanS_conform":"1","month":"10","external_id":{"arxiv":["2608.23846"]},"OA_place":"publisher","publication":"The Astrophysical Journal","arxiv":1,"article_processing_charge":"Yes","DOAJ_listed":"1","oa":1,"publisher":"IOP Publishing","ddc":["520"],"has_accepted_license":"1","acknowledgement":"We are grateful for the support for programs GO 1871, GO 1895, and GO 3577 provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127. This work is based in part on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with programs GO 1324, GO 1871, GO 1895 and GO 3577. The specific observations analyzed can be accessed via DOI: 10.17909/01dt-fm17.\r\n\r\nA.S.L. acknowledges support from Knut and Alice Wallenberg Foundation. T.A.H. acknowledges support from an appointment to the NASA Postdoctoral Program at the NASA Goddard Space, administered by Oak Ridge Associated Universities under contract with NASA, as well as the University of Maryland Baltimore County and the Center for Space Sciences and Technology. N.G.G. and Y.I.I. and acknowledge support from the joint Ukrainian-Swiss project No. 224866. This work has received funding from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140.\r\n\r\nFacility: JWST (NIRCam - , NIRSpec).\r\n\r\nSoftware: numpy (v.1.24.3; C. R. Harris et al. 2020), scipy (v.1.13.1; P. Virtanen et al. 2020), astropy (Astropy Collaboration et al. 2013, 2018, 2022), pyneb (v.1.1.24; V. Luridiana et al. 2013, 2015; C. Morisset et al. 2020), msaexp (v.0.8.4; G. B. Brammer 2022), msafit (A. de Graaff et al. 2024), grizli (G. Brammer 2018), EAZY (G. B. Brammer et al. 2008), BAGPIPES (A. C. Carnall et al. 2018), Prospector (B. D. Johnson et al. 2019, 2021), pysersic (I. Pasha & T. B. Miller 2023), GALFIT (C. Y. Peng et al. 2002, 2010), kendall (S. R. Flury et al. 2022; S. R. Flury 2023).","volume":1010,"day":"15","abstract":[{"lang":"eng","text":"We investigate the low-ionization electron density in the interstellar medium (ISM) of galaxies across 0 < z < 8,\r\nderived with the [O II] λλ3727, 3730 and [S II] λλ6718, 6733 doublets, using both deep JWST/NIRCam/grism\r\nand NIRSpec/MSA spectroscopy. Along with ancillary density samples from the literature at 0 < z < 6, we\r\nassemble three samples containing a total of 703 galaxies spanning 3.7 < z < 7.8 at 〈z〉 ∼ 5.6; 691 galaxies in the\r\nluminosity-complete NIRCam/grism programs CONGRESS and FRESCO at 〈z〉 ∼ 4.3 and ∼5.3, respectively;\r\nand 12 galaxies with high-resolution NIRSpec/MSA spectra from the GO 1871 and GLASS programs. We find\r\nmedian electron densities of ne[S II] = + 463 203 cm 281 3\r\nfor CONGRESS, ne[S II] = + 301 206 cm 388 3\r\nfor FRESCO, and\r\nne[O II] = + 202 102 cm 145 3\r\nfor the NIRSpec/MSA sample. The median low-ionization ne increases from z = 0 to 4,\r\nin agreement with previous studies and those using JWST observations. However, beyond z ∼ 4 median ne begins\r\nto deviate from a monotonically increasing evolution with z. We find a positive, but shallow, correlation between\r\nO32 (a proxy for the ionization parameter) and ne, while also confirming a positive correlation between O32 and z.\r\nWe suggest that these trends are possibly due to an evolving ISM gas density and ionization structure, and\r\npropose a toy model where the gas clumping evolves with z to explain the observed density and ionization\r\nvariations."}],"scopus_import":"1","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]}},{"dataavailabilitystatement":"The data underlying this article are available from the authors on reasonable request. Furthermore, the data for the simulated radio images from various angles as discussed in Section 2.3 are publicly available as FITS files from https://doi.org/10.5281/zenodo.20140021.","article_type":"original","type":"journal_article","PlanS_conform":"1","year":"2026","fulldoi":"https://doi.org/10.1093/mnras/stag1798","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","has_accepted_license":"1","ddc":["520"],"acknowledgement":"JHM and ELE acknowledge funding from a Royal Society University Research Fellowship (URF\\R1\\221062). AJC acknowledges support from the Oxford Hintze Centre for Astrophysical Surveys, which is funded through generous support from the Hintze Family Charitable Foundation. HW acknowledges funding by the Science and Technology Facilities Council Grant Number ST/W000903/1 and the ISTA-Fellow programme. The authors acknowledge the use of resources provided by the Isambard 3 Tier-2 HPC Facility. Isambard 3 is hosted by the University of Bristol and operated by the GW4 Alliance (https://gw4.ac.uk) and is funded by UK Research and Innovation and the Engineering and Physical Sciences Research Council (EP/X039137/1). The authors would like to acknowledge the use of the University of Oxford Advanced Research Computing (ARC) facility in carrying out this work (https://doi.org/10.5281/zenodo.22558). We are grateful for the use of the following software packages: pluto (A. Mignone et al. 2007) and matplotlib (J. D. Hunter 2007). We are grateful to Dipanjan Mukherjee, Imogen Whittam, Matt Jarvis, Judith Croston and Fraser Cowie for useful discussions. The authors wish to thank the anonymous referee for their helpful and constructive comments which have improved the quality of this manuscript.","publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"The physics governing the morphology of radio-loud active galactic nucleus (AGN) jets is not fully understood. We investigate how magnetization, flickering jet power and the interplay between them affects the morphology of radio galaxies. We present a grid of relativistic magnetohydrodynamic simulations using the pluto code covering constant and variable jets with two levels of magnetization. We find that the constant high-magnetization jets can lead to highly asymmetrical cocoon morphologies, while the variable high-magnetization jet can exhibit a broken morphology, caused by a discontinuous jet beam. Our work highlights the importance of magnetization and variability on the stability and resulting morphology of radio-loud AGN jets, suggesting both are significant factors in addition to jet power or environment. Furthermore, we show that the interaction between magnetization and variability can lead to the development of localized kink instabilities along the jet beam. Finally, we discuss the effects of hydrodynamic mixing in low-magnetization jets and the role of viewing-angle dependence in comparisons between our simulations and observed sources. To facilitate this comparison we present a library of simulated radio images at different times in the simulations and from various viewing angles, which highlight a diverse set of complex morphologies."}],"scopus_import":"1","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"volume":552,"day":"01","month":"11","arxiv":1,"article_processing_charge":"Yes","DOAJ_listed":"1","oa":1,"publication":"Monthly Notices of the Royal Astronomical Society","external_id":{"arxiv":["2605.13469"]},"OA_place":"publisher","date_published":"2026-11-01T00:00:00Z","file":[{"content_type":"application/pdf","file_size":8344810,"relation":"main_file","date_updated":"2026-10-28T08:19:16Z","checksum":"57e15f531d22d18eaeca96d58b2ab911","creator":"dernst","date_created":"2026-10-28T08:19:16Z","success":1,"file_name":"2026_MonthNoticesRAS_Elley.pdf","access_level":"open_access","file_id":"23203"}],"publication_status":"published","author":[{"full_name":"Elley, Emma L","last_name":"Elley","first_name":"Emma L"},{"full_name":"Matthews, James H","first_name":"James H","last_name":"Matthews"},{"full_name":"Whitehead, Henry William","id":"b5363ed7-0345-11f1-8029-eef7ff5d6bfc","orcid":"0009-0006-0716-0965","last_name":"Whitehead","first_name":"Henry William"},{"full_name":"Cooper, Alex J","last_name":"Cooper","first_name":"Alex J"}],"doi":"10.1093/mnras/stag1798","das_tickbox":"1","title":"The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets","file_date_updated":"2026-10-28T08:19:16Z","OA_type":"gold","researchdata_availability":"upon request","date_created":"2026-10-27T10:39:59Z","intvolume":"       552","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-10-28T08:19:37Z","_id":"23199","article_number":"stag1798","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"E. L. Elley, J. H. Matthews, H. W. Whitehead, and A. J. Cooper, “The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 552, no. 4. Oxford University Press, 2026.","mla":"Elley, Emma L., et al. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 552, no. 4, stag1798, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/mnras/stag1798\">10.1093/mnras/stag1798</a>.","ista":"Elley EL, Matthews JH, Whitehead HW, Cooper AJ. 2026. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. Monthly Notices of the Royal Astronomical Society. 552(4), stag1798.","ama":"Elley EL, Matthews JH, Whitehead HW, Cooper AJ. The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. <i>Monthly Notices of the Royal Astronomical Society</i>. 2026;552(4). doi:<a href=\"https://doi.org/10.1093/mnras/stag1798\">10.1093/mnras/stag1798</a>","short":"E.L. Elley, J.H. Matthews, H.W. Whitehead, A.J. Cooper, Monthly Notices of the Royal Astronomical Society 552 (2026).","chicago":"Elley, Emma L, James H Matthews, Henry William Whitehead, and Alex J Cooper. “The Impact of Flickering Variability and Magnetization on the Dynamics, Stability, and Morphology of Radio-Loud AGN Jets.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/mnras/stag1798\">https://doi.org/10.1093/mnras/stag1798</a>.","apa":"Elley, E. L., Matthews, J. H., Whitehead, H. W., &#38; Cooper, A. J. (2026). The impact of flickering variability and magnetization on the dynamics, stability, and morphology of radio-loud AGN jets. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stag1798\">https://doi.org/10.1093/mnras/stag1798</a>"},"department":[{"_id":"ZoHa"}],"status":"public"},{"date_published":"2026-05-15T00:00:00Z","author":[{"last_name":"Mor","first_name":"Paul Alexis","full_name":"Mor, Paul Alexis"},{"full_name":"Kroo, Annie R.","first_name":"Annie R.","last_name":"Kroo"},{"full_name":"Valdez, Carson G.","first_name":"Carson G.","last_name":"Valdez"},{"first_name":"Marko","last_name":"Šimić","full_name":"Šimić, Marko"},{"first_name":"Aviv","last_name":"Karnieli","full_name":"Karnieli, Aviv"},{"full_name":"Cavicchioli, Gabriele","last_name":"Cavicchioli","first_name":"Gabriele"},{"full_name":"Sun, Zhanghao","last_name":"Sun","first_name":"Zhanghao"},{"full_name":"Grimaldi, Vittorio","first_name":"Vittorio","last_name":"Grimaldi"},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"},{"full_name":"Solgaard, Olav","first_name":"Olav","last_name":"Solgaard"},{"last_name":"Miller","first_name":"David A.B.","full_name":"Miller, David A.B."},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","first_name":"Charles","full_name":"Roques-Carmes, Charles"}],"publication_status":"published","doi":"10.1364/CLEO_SI.2026.STU2F.1","title":"Variational processing of partially coherent light in a photonic integrated circuit","type":"conference","year":"2026","fulldoi":"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1","conference":{"name":"CLEO: Conference on Lasers and Electro-Optics","location":"Long Beach, CA, United States","end_date":"2026-05-06","start_date":"2026-05-02"},"OA_type":"closed access","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Technical Digest Series"],"publisher":"Optica Publishing Group","scopus_import":"1","abstract":[{"text":"We introduce an experimental realization of the measurement, processing, and generation of partially coherent light on a photonic chip. This device relies on self-configuring networks optimized sequentially to learn the coherency matrix of input light.","lang":"eng"}],"date_created":"2026-10-25T23:02:24Z","publication_identifier":{"isbn":["9781957171586"]},"_id":"23196","date_updated":"2026-10-28T07:57:55Z","quality_controlled":"1","day":"15","article_number":"STU2F.1","oa_version":"None","language":[{"iso":"eng"}],"month":"05","citation":{"ieee":"P. A. Mor <i>et al.</i>, “Variational processing of partially coherent light in a photonic integrated circuit,” in <i>CLEO Science and Innovations Proceedings</i>, Long Beach, CA, United States, 2026.","ista":"Mor PA, Kroo AR, Valdez CG, Šimić M, Karnieli A, Cavicchioli G, Sun Z, Grimaldi V, Fan S, Solgaard O, Miller DAB, Roques-Carmes C. 2026. Variational processing of partially coherent light in a photonic integrated circuit. CLEO Science and Innovations Proceedings. CLEO: Conference on Lasers and Electro-Optics, Technical Digest Series, , STU2F.1.","ama":"Mor PA, Kroo AR, Valdez CG, et al. Variational processing of partially coherent light in a photonic integrated circuit. In: <i>CLEO Science and Innovations Proceedings</i>. Optica Publishing Group; 2026. doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">10.1364/CLEO_SI.2026.STU2F.1</a>","mla":"Mor, Paul Alexis, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” <i>CLEO Science and Innovations Proceedings</i>, STU2F.1, Optica Publishing Group, 2026, doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">10.1364/CLEO_SI.2026.STU2F.1</a>.","short":"P.A. Mor, A.R. Kroo, C.G. Valdez, M. Šimić, A. Karnieli, G. Cavicchioli, Z. Sun, V. Grimaldi, S. Fan, O. Solgaard, D.A.B. Miller, C. Roques-Carmes, in:, CLEO Science and Innovations Proceedings, Optica Publishing Group, 2026.","chicago":"Mor, Paul Alexis, Annie R. Kroo, Carson G. Valdez, Marko Šimić, Aviv Karnieli, Gabriele Cavicchioli, Zhanghao Sun, et al. “Variational Processing of Partially Coherent Light in a Photonic Integrated Circuit.” In <i>CLEO Science and Innovations Proceedings</i>. Optica Publishing Group, 2026. <a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">https://doi.org/10.1364/CLEO_SI.2026.STU2F.1</a>.","apa":"Mor, P. A., Kroo, A. R., Valdez, C. G., Šimić, M., Karnieli, A., Cavicchioli, G., … Roques-Carmes, C. (2026). Variational processing of partially coherent light in a photonic integrated circuit. In <i>CLEO Science and Innovations Proceedings</i>. Long Beach, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_SI.2026.STU2F.1\">https://doi.org/10.1364/CLEO_SI.2026.STU2F.1</a>"},"article_processing_charge":"No","department":[{"_id":"ChRo"}],"status":"public","publication":"CLEO Science and Innovations Proceedings"},{"date_updated":"2026-11-02T23:31:03Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"18706","quality_controlled":"1","date_created":"2024-12-23T11:03:59Z","researchdata_availability":"no","intvolume":"        37","status":"public","citation":{"short":"L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37 (2026) 614–642.","chicago":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>. Cambridge University Press, 2026. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>.","apa":"Portinale, L., &#38; Quattrocchi, F. (2026). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0956792524000810\">https://doi.org/10.1017/s0956792524000810</a>","ieee":"L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026.","mla":"Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” <i>European Journal of Applied Mathematics</i>, vol. 37, no. 3, Cambridge University Press, 2026, pp. 614–42, doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>.","ama":"Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. <i>European Journal of Applied Mathematics</i>. 2026;37(3):614-642. doi:<a href=\"https://doi.org/10.1017/s0956792524000810\">10.1017/s0956792524000810</a>","ista":"Portinale L, Quattrocchi F. 2026. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 37(3), 614–642."},"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1017/s0956792524000810","isi":1,"das_tickbox":"0","file_date_updated":"2026-07-23T05:55:03Z","title":"Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs","keyword":["optimal transport","discrete-to-continuum","homogenisation","linear growth","gamma-convergence"],"page":"614-642","date_published":"2026-06-01T00:00:00Z","author":[{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"},{"full_name":"Quattrocchi, Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","last_name":"Quattrocchi","orcid":"0009-0000-9773-1931","first_name":"Filippo"}],"file":[{"file_name":"2026_EuropJourAppliedMath_Portinale.pdf","access_level":"open_access","file_id":"22386","file_size":612317,"content_type":"application/pdf","relation":"main_file","date_updated":"2026-07-23T05:55:03Z","checksum":"d038f4d00cbfbde2672c17138eab21c9","creator":"dernst","success":1,"date_created":"2026-07-23T05:55:03Z"}],"publication_status":"published","OA_type":"gold","volume":37,"day":"01","abstract":[{"lang":"eng","text":"We prove discrete-to-continuum convergence for dynamical optimal transport on  Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of  1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations."}],"scopus_import":"1","publication_identifier":{"issn":["0956-7925"],"eissn":["1469-4425"]},"publisher":"Cambridge University Press","has_accepted_license":"1","ddc":["500"],"acknowledgement":"L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.","publication":"European Journal of Applied Mathematics","external_id":{"isi":["001381435800001"]},"OA_place":"publisher","article_processing_charge":"Yes","oa":1,"DOAJ_listed":"1","month":"06","related_material":{"record":[{"id":"20563","status":"public","relation":"dissertation_contains"}]},"PlanS_conform":"1","type":"journal_article","article_type":"original","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","year":"2026","project":[{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"fulldoi":"https://doi.org/10.1017/s0956792524000810"}]