[{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","issue":"9","type":"journal_article","day":"04","publisher":"American Physical Society","date_updated":"2026-03-23T15:39:34Z","oa_version":"Published Version","year":"2026","has_accepted_license":"1","date_published":"2026-03-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","title":"Learning mixed quantum states in large-scale experiments","_id":"21480","PlanS_conform":"1","citation":{"chicago":"Votto, Matteo, Marko Ljubotina, Cécilia Lancien, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, Lorenzo Piroli, and Benoît Vermersch. “Learning Mixed Quantum States in Large-Scale Experiments.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/rbg2-f61m\">https://doi.org/10.1103/rbg2-f61m</a>.","ista":"Votto M, Ljubotina M, Lancien C, Cirac JI, Zoller P, Serbyn M, Piroli L, Vermersch B. 2026. Learning mixed quantum states in large-scale experiments. Physical Review Letters. 136(9), 090801.","ama":"Votto M, Ljubotina M, Lancien C, et al. Learning mixed quantum states in large-scale experiments. <i>Physical Review Letters</i>. 2026;136(9). doi:<a href=\"https://doi.org/10.1103/rbg2-f61m\">10.1103/rbg2-f61m</a>","apa":"Votto, M., Ljubotina, M., Lancien, C., Cirac, J. I., Zoller, P., Serbyn, M., … Vermersch, B. (2026). Learning mixed quantum states in large-scale experiments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/rbg2-f61m\">https://doi.org/10.1103/rbg2-f61m</a>","ieee":"M. Votto <i>et al.</i>, “Learning mixed quantum states in large-scale experiments,” <i>Physical Review Letters</i>, vol. 136, no. 9. American Physical Society, 2026.","short":"M. Votto, M. Ljubotina, C. Lancien, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, B. Vermersch, Physical Review Letters 136 (2026).","mla":"Votto, Matteo, et al. “Learning Mixed Quantum States in Large-Scale Experiments.” <i>Physical Review Letters</i>, vol. 136, no. 9, 090801, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/rbg2-f61m\">10.1103/rbg2-f61m</a>."},"article_processing_charge":"Yes (in subscription journal)","ddc":["530"],"arxiv":1,"OA_type":"hybrid","article_type":"original","OA_place":"publisher","doi":"10.1103/rbg2-f61m","oa":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"acknowledgement":"We acknowledge insightful discussions with Antoine Browaeys, Mari Carmen Bañuls, Soonwon Choi, Thierry Lahaye, Daniel Stilck-França, Georgios Styliaris, and Xavier Waintal. The experimental data have been collected using the Qiskit library [103], and have been postprocessed using the RandomMeas [104] and ITensor [105] libraries. The work of M. V. and B. V. was funded by the French National Research Agency via the JCJC project QRand (No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (No. ANR-22-\r\nPETQ-0007), QUBITAF (No. ANR-22-PETQ-0004), and HQI (No. ANR-22-PNCQ-0002). We acknowledge the use of IBM Quantum Credits for this work. M. L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868. The work of C. L. was funded by the French National Research Agency via the PRC project ESQuisses (No. ANR-20-CE47-0014-01). J. I. C.\r\nacknowledges funding from the Federal Ministry of Education and Research Germany (BMBF) via the project FermiQP (No. 13N15889). Work at MPQ is part of the Munich Quantum Valley, which is supported by the Bavarian state government with funds from the Hightech Agenda\r\nBayern Plus. P. Z. acknowledges support by the European Union’s Horizon Europe research and innovation program under Grant Agreement No. 101113690 (PASQANS2). The work of L. P. was funded by the European Union (ERC, QUANTHEM, No. 101114881). We acknowledge support\r\nby the Erwin Schrödinger International Institute for Mathematics and Physics (ESI).","file":[{"success":1,"relation":"main_file","access_level":"open_access","date_created":"2026-03-23T15:35:27Z","file_id":"21491","file_name":"2026_PhysicalReviewLetters_Votto.pdf","creator":"dernst","file_size":500041,"content_type":"application/pdf","checksum":"12b16ce2d49c62b2909da95121bfaadb","date_updated":"2026-03-23T15:35:27Z"}],"intvolume":"       136","author":[{"full_name":"Votto, Matteo","last_name":"Votto","first_name":"Matteo"},{"orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko"},{"last_name":"Lancien","full_name":"Lancien, Cécilia","first_name":"Cécilia"},{"full_name":"Cirac, J. Ignacio","last_name":"Cirac","first_name":"J. Ignacio"},{"full_name":"Zoller, Peter","last_name":"Zoller","first_name":"Peter"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Lorenzo","full_name":"Piroli, Lorenzo","last_name":"Piroli"},{"full_name":"Vermersch, Benoît","last_name":"Vermersch","first_name":"Benoît"}],"publication":"Physical Review Letters","file_date_updated":"2026-03-23T15:35:27Z","quality_controlled":"1","volume":136,"article_number":"090801","abstract":[{"text":"We present and test a protocol to learn the matrix-product operator (MPO) representation of an experimentally prepared quantum state. The protocol takes as input classical shadows corresponding to local randomized measurements, and outputs the tensors of an MPO maximizing a suitably defined fidelity with the experimental state. The tensor optimization is carried out sequentially, similarly to the well-known density matrix renormalization group algorithm. Our approach is provably efficient under certain technical conditions expected to be met in short-range correlated states and in typical noisy experimental settings. Under the same conditions, we also provide an efficient scheme to estimate fidelities between the learned and the experimental states. We experimentally demonstrate our protocol by learning entangled quantum states of up to N = 96 qubits in a superconducting quantum processor. Our method upgrades classical shadows to large-scale quantum computation and simulation experiments.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"date_created":"2026-03-23T14:56:32Z","department":[{"_id":"MaSe"}],"external_id":{"arxiv":["2507.12550"]}},{"intvolume":"         8","author":[{"last_name":"Hübl","full_name":"Hübl, Maximilian","first_name":"Maximilian","id":"5eb8629e-15b2-11ec-abd3-e6f3e5e01f32"},{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter"}],"publication":"Physical Review Research","file_date_updated":"2026-03-23T15:53:29Z","oa":1,"publication_identifier":{"eissn":["2643-1564"]},"file":[{"file_size":2680924,"date_created":"2026-03-23T15:53:29Z","file_id":"21493","creator":"dernst","file_name":"2026_PhysicalReviewResearch_Huebl.pdf","date_updated":"2026-03-23T15:53:29Z","checksum":"6d8a68e4a19f8dad5abdf75f72316f3d","content_type":"application/pdf","success":1,"relation":"main_file","access_level":"open_access"}],"DOAJ_listed":"1","acknowledgement":"We thank Maitane Muñoz-Basagoiti for helpful discussions. The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011.","corr_author":"1","language":[{"iso":"eng"}],"date_created":"2026-03-23T14:58:31Z","department":[{"_id":"CaGo"},{"_id":"GradSch"}],"publication_status":"published","article_number":"L012054","abstract":[{"lang":"eng","text":"Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly and is highly relevant in material design and biology. Here, we show that specific but promiscuous short-range binding interactions make it possible to economically assemble linear filaments of user-defined length. Our approach leads to independent control over the mean and width of the filament size distribution and allows us to smoothly explore design trade-offs between assembly quality (spread in size) and cost (number of particle species). We employ a simple hierarchical assembly protocol to minimize assembly times and show that multiple stages of hierarchy make it possible to extend our approach to the assembly of higher-dimensional structures. Our work provides a conceptually simple solution to size control that is applicable to a broad range of systems, from DNA nanoparticles to supramolecular polymers and beyond."}],"quality_controlled":"1","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-03-23T15:59:11Z","year":"2026","oa_version":"Published Version","date_published":"2026-03-05T00:00:00Z","project":[{"grant_number":"FTI23-G-011","_id":"8dd93da8-16d5-11f0-9cad-d2c70200d9a5","name":"Dynamically reconfigurable self-assembly with triangular DNA-origami bricks"}],"has_accepted_license":"1","type":"journal_article","publisher":"American Physical Society","day":"05","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","OA_type":"gold","article_type":"original","doi":"10.1103/68rs-3qgn","OA_place":"publisher","ddc":["530"],"citation":{"ieee":"M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,” <i>Physical Review Research</i>, vol. 8. American Physical Society, 2026.","mla":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>, vol. 8, L012054, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>.","short":"M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026).","ista":"Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments. Physical Review Research. 8, L012054.","chicago":"Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>.","apa":"Hübl, M., &#38; Goodrich, C. P. (2026). Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/68rs-3qgn\">https://doi.org/10.1103/68rs-3qgn</a>","ama":"Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. <i>Physical Review Research</i>. 2026;8. doi:<a href=\"https://doi.org/10.1103/68rs-3qgn\">10.1103/68rs-3qgn</a>"},"article_processing_charge":"Yes","month":"03","title":"Entropic size control of self-assembled filaments","_id":"21482"},{"doi":"10.1016/j.cub.2026.02.023","OA_place":"publisher","OA_type":"hybrid","article_type":"original","ddc":["580"],"citation":{"mla":"Li, Mingyue, et al. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” <i>Current Biology</i>, vol. 36, no. 6, Elsevier, 2026, p. 1468–1480.e6, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">10.1016/j.cub.2026.02.023</a>.","short":"M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, J. Friml, Current Biology 36 (2026) 1468–1480.e6.","ieee":"M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, and J. Friml, “Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization,” <i>Current Biology</i>, vol. 36, no. 6. Elsevier, p. 1468–1480.e6, 2026.","ama":"Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. <i>Current Biology</i>. 2026;36(6):1468-1480.e6. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">10.1016/j.cub.2026.02.023</a>","apa":"Li, M., Rydza, N., Mazur, E., Molnar, G., Nodzyński, T., &#38; Friml, J. (2026). Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">https://doi.org/10.1016/j.cub.2026.02.023</a>","chicago":"Li, Mingyue, Nikola Rydza, Ewa Mazur, Gergely Molnar, Tomasz Nodzyński, and Jiří Friml. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” <i>Current Biology</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.02.023\">https://doi.org/10.1016/j.cub.2026.02.023</a>.","ista":"Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. 2026. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. Current Biology. 36(6), 1468–1480.e6."},"PlanS_conform":"1","article_processing_charge":"Yes (via OA deal)","title":"Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization","month":"03","_id":"21490","page":"1468-1480.e6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2026","oa_version":"Published Version","date_updated":"2026-03-24T08:36:40Z","has_accepted_license":"1","project":[{"_id":"8f347782-16d5-11f0-9cad-8c19706ee739","grant_number":"101142681","name":"Cyclic nucleotides as second messengers in plants"},{"name":"Identification of a novel regulator in auxin canalization","_id":"bd906599-d553-11ed-ba76-abf8547645d7","grant_number":"E271"}],"date_published":"2026-03-23T00:00:00Z","publisher":"Elsevier","type":"journal_article","day":"23","issue":"6","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"corr_author":"1","department":[{"_id":"JiFr"}],"external_id":{"pmid":["41831441"]},"date_created":"2026-03-23T15:11:16Z","publication_status":"published","acknowledged_ssus":[{"_id":"MassSpec"},{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Auxin canalization is a self-organizing process that governs the flexible formation of vasculature by reinforcing the formation of auxin transport channels. A key prerequisite is the feedback between auxin signaling and directional auxin transport, mediated by PIN transporters. Despite the developmental importance of canalization, the molecular components linking auxin perception to the regulation of PIN auxin transporters remain poorly understood. Here, we identify TOW, a novel and essential component of auxin canalization that links intracellular auxin signaling with cell surface auxin perception. TOW is regulated downstream of TIR1/AFB-Aux/IAA-WRKY23 transcriptional auxin signaling. tow mutants exhibit defects in regeneration and de novo vasculature formation, along with impaired formation of polarized, PIN-expressing auxin channels. At the subcellular level, these mutants display disrupted auxin-induced PIN polarization and altered PIN endocytic trafficking dynamics. TOW localizes predominantly to the plasma membrane, where it interacts with receptor-like kinases involved in auxin canalization, including the TMK1 auxin co-receptor and the CAMEL-CANAR complex. TOW promotes PIN interaction with these kinases and stabilizes PINs at the cell surface. Together, our findings identify TOW as a molecular link between intracellular and cell surface auxin signaling mechanisms that converge on PIN trafficking and polarity, providing new insights into how auxin signaling regulates directional auxin transport for the self-organizing formation of vasculature during flexible plant development."}],"quality_controlled":"1","volume":36,"intvolume":"        36","author":[{"full_name":"Li, Mingyue","last_name":"Li","id":"01f96916-0235-11eb-9379-a323192643b7","first_name":"Mingyue"},{"last_name":"Rydza","full_name":"Rydza, Nikola","first_name":"Nikola"},{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"last_name":"Molnar","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"publication":"Current Biology","file_date_updated":"2026-03-24T08:34:37Z","oa":1,"publication_identifier":{"issn":["0960-9822"]},"acknowledgement":"We thank Dr. Z. Ge (ISTA) for providing vectors for the CRISPR-Cas9 system, Dr. Armel Nicolas and Dr. Bella Bruszel for phosphoproteomic analysis, Prof. Michael Wrzaczek (Czech Academy of Sciences, Czechia) for valuable suggestions, and Prof. Maciek Adamowski (University of Gdańsk) for technical assistance. We also acknowledge the support of the Mass Spectrometry and Proteomics Facility, the Imaging & Optics Facility, and the Lab Support Facility at the Institute of Science and Technology Austria. This research was supported by the Scientific Service Units (SSU) of ISTA, utilizing resources provided by the Imaging & Optics Facility (IOF) and the Lab Support Facility (LSF). The work conducted by the Friml group was funded by the European Research Council (ERC) under grant agreement no. 101142681 (CYNIPS) and by the Austrian Science Fund (FWF) under project ESP271. We acknowledge the core facility CELLIM supported by MEYS CR (LM2023050 Czech-BioImaging) and the Plant Sciences Core Facility of CEITEC Masaryk University. E.M. received support from the National Science Centre (NCN), Poland, through the OPUS call within the Weave programme (grant no. 2021/43/I/NZ1/01835). T.N. received support from TowArds Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the ERDF Programme Johannes Amos Comenius.","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":12986894,"file_name":"2026_CurrentBiology_Li.pdf","creator":"dernst","file_id":"21496","date_created":"2026-03-24T08:34:37Z","date_updated":"2026-03-24T08:34:37Z","content_type":"application/pdf","checksum":"fe6c41fdab58a55df5f2a5860c02acdc"}],"pmid":1},{"article_type":"original","OA_type":"hybrid","doi":"10.1093/genetics/iyag042","OA_place":"publisher","article_processing_charge":"Yes (via OA deal)","PlanS_conform":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/medical-genomics-group/familyMC"}]},"citation":{"chicago":"Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” <i>Genetics</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/genetics/iyag042\">https://doi.org/10.1093/genetics/iyag042</a>.","ista":"Krätschmer I, Robinson MR. 2026. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. Genetics., iyag042.","ama":"Krätschmer I, Robinson MR. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. <i>Genetics</i>. 2026. doi:<a href=\"https://doi.org/10.1093/genetics/iyag042\">10.1093/genetics/iyag042</a>","apa":"Krätschmer, I., &#38; Robinson, M. R. (2026). A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyag042\">https://doi.org/10.1093/genetics/iyag042</a>","ieee":"I. Krätschmer and M. R. Robinson, “A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating,” <i>Genetics</i>. Oxford University Press, 2026.","mla":"Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” <i>Genetics</i>, iyag042, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/genetics/iyag042\">10.1093/genetics/iyag042</a>.","short":"I. Krätschmer, M.R. Robinson, Genetics (2026)."},"_id":"21484","month":"02","title":"A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-02-12T00:00:00Z","has_accepted_license":"1","date_updated":"2026-03-24T06:48:10Z","oa_version":"Published Version","year":"2026","day":"12","type":"journal_article","publisher":"Oxford University Press","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-03-23T15:02:54Z","department":[{"_id":"MaRo"}],"external_id":{"pmid":["41677404"]},"corr_author":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","article_number":"iyag042","abstract":[{"text":"An individual's phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents' DNA. Here, we derive how the genetic variance within a population is changed under the influence of indirect maternal, paternal and parent-of-origin effects under random mating. We also consider indirect effects of a sibling, in particular how the genetic variance is altered when looking at the phenotypic difference between two siblings. The calculations are then extended to include assortative mating (AM), which alters the variance by inducing increased homozygosity and correlations within and across loci. AM likely leads to covariance of parental genetic effects, a measure of the similarity of parents in the indirect effects they have on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait AM. Our theory shows how the resemblance among relatives increases under both AM, indirect and parent-of-origin effects. When our model is used to predict correlations among relatives in human height, we find that explaining the patterns observed in real data requires both indirect genetic effects and assortative mating. The degree to which direct, indirect and epigenetic effects shape the phenotypic variance of complex traits remains an open question that requires large-scale family data to be resolved.","lang":"eng"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-5636-9259","first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","last_name":"Krätschmer","full_name":"Krätschmer, Ilse"},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"publication":"Genetics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyag042"}],"pmid":1,"acknowledgement":"We thank members of the Medical Genomics group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria.","oa":1,"publication_identifier":{"issn":["1943-2631"]}},{"date_updated":"2026-03-24T07:14:08Z","year":"2026","oa_version":"Published Version","has_accepted_license":"1","date_published":"2026-03-12T00:00:00Z","project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","day":"12","type":"journal_article","publisher":"Oxford University Press","ddc":["570"],"article_type":"original","OA_type":"gold","doi":"10.1093/evlett/qrag003","OA_place":"publisher","month":"03","title":"Causes and consequences of sex-chromosome turnovers in Diptera","_id":"21486","citation":{"chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>.","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters., qrag003.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. 2026. doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera,” <i>Evolution Letters</i>. Oxford University Press, 2026.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026).","mla":"Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>, qrag003, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>."},"article_processing_charge":"Yes","publication":"Evolution Letters","author":[{"full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297"},{"full_name":"Toups, Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"oa":1,"publication_identifier":{"eissn":["2056-3744"]},"DOAJ_listed":"1","acknowledgement":"This work was supported by a grant from the Austrian Science Fund (FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback on an early version of the manuscript. We are grateful to Kamil Jaron and Julia Gries for helpful discussions and for sharing their unpublished work. Computational resources and support were provided by the Scientific Computing Unit at ISTA.","main_file_link":[{"url":"https://doi.org/10.1093/evlett/qrag003","open_access":"1"}],"publication_status":"epub_ahead","corr_author":"1","language":[{"iso":"eng"}],"date_created":"2026-03-23T15:05:42Z","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"quality_controlled":"1","article_number":"qrag003","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}]},{"file_date_updated":"2026-03-24T07:21:43Z","author":[{"orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash","last_name":"Naik","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","title":"Cell git repository","file_name":"cells-main.zip","creator":"snaik","date_created":"2026-03-16T11:51:10Z","file_id":"21461","file_size":725916,"description":"Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. ","checksum":"5d1fda7e410f24c311fcf6bcf725698f","content_type":"application/zip","date_updated":"2026-03-16T11:51:10Z"},{"date_updated":"2026-03-18T14:52:02Z","checksum":"ee350c8eaed99f3ca348c47c8b190d3c","content_type":"application/x-zip-compressed","file_size":282168895,"creator":"snaik","file_name":"DevBranchDataRepo.zip","date_created":"2026-03-18T14:52:02Z","file_id":"21464","access_level":"open_access","relation":"main_file","success":1},{"file_size":2231,"date_created":"2026-03-18T15:01:32Z","file_id":"21466","creator":"snaik","file_name":"ReadMe.md","date_updated":"2026-03-18T15:01:32Z","content_type":"text/markdown","checksum":"1ecaf2c1a2ce8ff9c75a128cc02d0b8f","success":1,"relation":"main_file","access_level":"open_access"},{"access_level":"open_access","relation":"main_file","success":1,"date_updated":"2026-03-18T15:12:57Z","checksum":"da9a4687e5144b61a64ca341f922046a","content_type":"image/svg+xml","file_size":1951210,"creator":"snaik","file_name":"PaperSchematics.svg","file_id":"21467","date_created":"2026-03-18T15:12:57Z"},{"date_updated":"2026-03-21T03:37:43Z","checksum":"9ac1054b16c212c6f34d402dce2c80e0","content_type":"application/octet-stream","file_size":1897,"file_name":"maxwell_sketch.tex","creator":"snaik","date_created":"2026-03-21T03:37:43Z","file_id":"21468","access_level":"open_access","relation":"main_file","success":1},{"date_updated":"2026-03-24T07:21:43Z","checksum":"7c9ecf78e2593b3830d96fa94baa08df","content_type":"application/x-zip-compressed","file_size":749368723,"file_id":"21495","date_created":"2026-03-24T07:21:43Z","file_name":"DataRepo.zip","creator":"snaik","relation":"main_file","access_level":"open_access","success":1}],"acknowledgement":"We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H.","oa":1,"department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"date_created":"2026-02-04T16:38:02Z","contributor":[{"contributor_type":"researcher","last_name":"Keta","first_name":"Yann-Edwin"},{"contributor_type":"supervisor","last_name":"Henkes","first_name":"Silke "},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","contributor_type":"supervisor"},{"contributor_type":"supervisor","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561"}],"corr_author":"1","license":"https://creativecommons.org/licenses/by-sa/4.0/","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"LifeSc"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"PAT 5044023","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","name":"Keratins in epithelial tissue spreading"},{"_id":"252C3B08-B435-11E9-9278-68D0E5697425","grant_number":"W1250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"}],"date_published":"2026-03-24T00:00:00Z","has_accepted_license":"1","year":"2026","oa_version":"None","date_updated":"2026-03-24T08:32:00Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","status":"public","tmp":{"short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png"},"type":"research_data","publisher":"Institute of Science and Technology Austria","day":"24","OA_place":"repository","doi":"10.15479/AT-ISTA-21137","OA_type":"free access","_id":"21137","title":"Data associated with Keratins coordinate tissue spreading ","month":"3","article_processing_charge":"No","citation":{"ama":"Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>","apa":"Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>","chicago":"Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">https://doi.org/10.15479/AT-ISTA-21137</a>.","ista":"Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","short":"S. Naik, (2026).","mla":"Naik, Suyash. <i>Data Associated with Keratins Coordinate Tissue Spreading </i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21137\">10.15479/AT-ISTA-21137</a>.","ieee":"S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026."}},{"abstract":[{"text":"We study Kirillov algebras attached to minuscule highest weight representations of semisimple Lie algebras. They can be viewed as equivariant cohomology algebras of partial flag varieties. Real structures on the varieties then induce involutions of these algebras. We describe how these involutions act on the spectra of minuscule Kirillov algebras, and model the fixed points via the equivariant cohomology of real partial flag varieties. We then use this model to characterise freeness of the fixed point coordinate ring over the appropriate base. As an application, we recover a q = -1 phenomenon of Stembridge in the minuscule case by geometric means.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"corr_author":"1","date_created":"2026-03-23T15:10:43Z","department":[{"_id":"TaHa"}],"external_id":{"arxiv":["2411.16270"]},"publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1007/s00031-026-09958-y","open_access":"1"}],"publication_identifier":{"eissn":["1531-586X"],"issn":["1083-4362"]},"oa":1,"acknowledgement":"I would like to thank Tamás Hausel for introducing me to this area of mathematics and for his constant guidance. I would also like to thank Jakub Löwit and Miguel González for fruitful discussions and many helpful comments on this paper. This work was done during the author’s PhD studies at the Institute of Science and Technology Austria (ISTA). It was funded by the Austrian Science Fund (FWF) 10.55776/P35847. Open access funding provided by Institute of Science and Technology (IST Austria). ","publication":"Transformation Groups","author":[{"last_name":"Elkner","full_name":"Elkner, Mischa M","first_name":"Mischa M","id":"477faa59-080d-11ed-979a-c693ab7638ab"}],"citation":{"apa":"Elkner, M. M. (2026). On involutions of minuscule Kirillov algebras induced by real structures. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-026-09958-y\">https://doi.org/10.1007/s00031-026-09958-y</a>","ama":"Elkner MM. On involutions of minuscule Kirillov algebras induced by real structures. <i>Transformation Groups</i>. 2026. doi:<a href=\"https://doi.org/10.1007/s00031-026-09958-y\">10.1007/s00031-026-09958-y</a>","ista":"Elkner MM. 2026. On involutions of minuscule Kirillov algebras induced by real structures. Transformation Groups.","chicago":"Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” <i>Transformation Groups</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00031-026-09958-y\">https://doi.org/10.1007/s00031-026-09958-y</a>.","short":"M.M. Elkner, Transformation Groups (2026).","mla":"Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” <i>Transformation Groups</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00031-026-09958-y\">10.1007/s00031-026-09958-y</a>.","ieee":"M. M. Elkner, “On involutions of minuscule Kirillov algebras induced by real structures,” <i>Transformation Groups</i>. Springer Nature, 2026."},"article_processing_charge":"Yes (via OA deal)","month":"03","title":"On involutions of minuscule Kirillov algebras induced by real structures","_id":"21489","doi":"10.1007/s00031-026-09958-y","ddc":["510"],"arxiv":1,"type":"journal_article","publisher":"Springer Nature","day":"14","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-03-24T08:26:10Z","oa_version":"None","year":"2026","date_published":"2026-03-14T00:00:00Z","has_accepted_license":"1","project":[{"name":"Geometry of the tip of the global nilpotent cone","_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3","grant_number":"P35847"}]},{"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-074-9"]},"file":[{"access_level":"open_access","relation":"main_file","success":1,"content_type":"application/pdf","checksum":"cface6dc18152680962b5361575f6e4f","date_updated":"2026-03-04T08:56:15Z","creator":"mdvorak","file_name":"2026_Dvorak_Martin_Thesis.pdf","file_id":"21394","date_created":"2026-03-04T08:56:15Z","file_size":1771231},{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"290ddfacfb7e07fb07e6f0b334e67c90","date_updated":"2026-03-04T09:03:37Z","date_created":"2026-03-04T09:03:37Z","file_id":"21395","creator":"mdvorak","file_name":"2026_Dvorak_Martin_Thesis.docx","file_size":864585}],"file_date_updated":"2026-03-04T09:03:37Z","author":[{"orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin"}],"supervisor":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Blanchette, Jasmin","last_name":"Blanchette","first_name":"Jasmin"}],"abstract":[{"text":"This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion.","lang":"eng"}],"corr_author":"1","language":[{"iso":"eng"}],"date_created":"2026-03-04T09:26:46Z","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","day":"04","type":"dissertation","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","page":"160","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-03-27T12:37:00Z","year":"2026","oa_version":"Published Version","has_accepted_license":"1","date_published":"2026-03-04T00:00:00Z","related_material":{"record":[{"id":"13120","status":"public","relation":"part_of_dissertation"},{"id":"21398","status":"public","relation":"part_of_dissertation"},{"id":"20071","status":"public","relation":"part_of_dissertation"}],"link":[{"url":"https://github.com/madvorak/duality/tree/v3.5.0","relation":"software","description":"Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality)"},{"description":"Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems)","url":"https://github.com/madvorak/vcsp/tree/v8.2.0","relation":"software"},{"description":"Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project)","relation":"software","url":"https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0"},{"relation":"software","url":"https://github.com/madvorak/chomsky/tree/v1.2.0","description":"Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars)"},{"description":"Old version (Lean 3) of the project about grammars","relation":"software","url":"https://github.com/madvorak/grammars"},{"relation":"software","url":"https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean","description":"Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis"}]},"citation":{"ama":"Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>","apa":"Dvorak, M. (2026). <i>Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>","chicago":"Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21393\">https://doi.org/10.15479/AT-ISTA-21393</a>.","ista":"Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.","short":"M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.","mla":"Dvorak, Martin. <i>Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21393\">10.15479/AT-ISTA-21393</a>.","ieee":"M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026."},"article_processing_charge":"No","month":"03","title":"Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids","_id":"21393","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT-ISTA-21393","OA_place":"repository","ddc":["511","000"]},{"volume":7,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Kinetically constrained models were originally introduced to capture slow relaxation in glassy systems, where dynamics are hindered by local constraints instead of energy barriers. Their quantum counterparts have recently drawn attention for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming from chiral symmetry. Yet, the structure and implications of these zero modes remain poorly understood. In this work, we focus on the properties of the zero mode subspace in quantum kinetically constrained models with a U(1) particle-conservation symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric U(1) East-West models to illustrate our two main results. First, we observe that the simultaneous presence of constraints and chiral symmetry generally leads to a parametric increase in the number of zero modes due to the fragmentation of the many-body\r\nHilbert space into disconnected sectors. Second, we generalize the concept of compact localized states from single-particle physics and introduce the notion of collective bound states, a special kind of nonergodic eigenstates that are robust to enlarging the system size. We formulate sufficient criteria for their existence, arguing that the degenerate zero mode subspace plays a central role, and demonstrate bound states in both example models and in a two-dimensional model, the U(1) North-East, and in the pairflip model, a system without particle conservation. Our results motivate a systematic study of bound states and their relation to ergodicity breaking, transport, and other properties of quantum kinetically constrained\r\nmodels. "}],"article_number":"010352","publication_status":"published","department":[{"_id":"MaSe"}],"external_id":{"arxiv":["2504.17627"]},"date_created":"2026-03-28T14:57:56Z","corr_author":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","success":1,"date_updated":"2026-03-30T06:08:07Z","checksum":"d155ffa9e1a8275702149165f4bf963c","content_type":"application/pdf","file_size":1848724,"creator":"dernst","file_name":"2026_PRXQuantum_Nicolau.pdf","date_created":"2026-03-30T06:08:07Z","file_id":"21505"}],"DOAJ_listed":"1","acknowledgement":"The authors acknowledge useful discussions with Berislav Buca. This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research was supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP).","oa":1,"publication_identifier":{"eissn":["2691-3399"]},"scopus_import":"1","publication":"PRX Quantum","author":[{"first_name":"Eulalia","id":"04b4791c-8fd7-11ee-a7df-be2fdc569c48","full_name":"Nicolau Jimenez, Eulalia","last_name":"Nicolau Jimenez"},{"first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","last_name":"Ljubotina","orcid":"0000-0003-0038-7068"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827"}],"file_date_updated":"2026-03-30T06:08:07Z","ec_funded":1,"intvolume":"         7","_id":"21501","title":"Fragmentation, zero modes, and collective bound states in constrained models","month":"03","article_processing_charge":"Yes","citation":{"ama":"Nicolau Jimenez E, Ljubotina M, Serbyn M. Fragmentation, zero modes, and collective bound states in constrained models. <i>PRX Quantum</i>. 2026;7. doi:<a href=\"https://doi.org/10.1103/sl79-1xgb\">10.1103/sl79-1xgb</a>","apa":"Nicolau Jimenez, E., Ljubotina, M., &#38; Serbyn, M. (2026). Fragmentation, zero modes, and collective bound states in constrained models. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/sl79-1xgb\">https://doi.org/10.1103/sl79-1xgb</a>","chicago":"Nicolau Jimenez, Eulalia, Marko Ljubotina, and Maksym Serbyn. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” <i>PRX Quantum</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/sl79-1xgb\">https://doi.org/10.1103/sl79-1xgb</a>.","ista":"Nicolau Jimenez E, Ljubotina M, Serbyn M. 2026. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 7, 010352.","short":"E. Nicolau Jimenez, M. Ljubotina, M. Serbyn, PRX Quantum 7 (2026).","mla":"Nicolau Jimenez, Eulalia, et al. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” <i>PRX Quantum</i>, vol. 7, 010352, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/sl79-1xgb\">10.1103/sl79-1xgb</a>.","ieee":"E. Nicolau Jimenez, M. Ljubotina, and M. Serbyn, “Fragmentation, zero modes, and collective bound states in constrained models,” <i>PRX Quantum</i>, vol. 7. American Physical Society, 2026."},"PlanS_conform":"1","arxiv":1,"ddc":["530"],"OA_place":"publisher","doi":"10.1103/sl79-1xgb","OA_type":"gold","article_type":"original","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"American Physical Society","type":"journal_article","day":"13","has_accepted_license":"1","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"date_published":"2026-03-13T00:00:00Z","oa_version":"Published Version","year":"2026","date_updated":"2026-03-30T06:09:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ddc":["570"],"article_type":"original","OA_type":"hybrid","doi":"10.1038/s41397-026-00399-0","OA_place":"publisher","_id":"21503","month":"03","title":"Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants","article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Hajto J, Piechota M, Krätschmer I, Konowalska P, Boyle GE, Fowler DM, Borczyk M, Korostynski M. 2026. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. Pharmacogenomics Journal. 26(2), 8.","chicago":"Hajto, Jacek, Marcin Piechota, Ilse Krätschmer, Paula Konowalska, Gabriel E. Boyle, Douglas M. Fowler, Malgorzata Borczyk, and Michal Korostynski. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” <i>Pharmacogenomics Journal</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41397-026-00399-0\">https://doi.org/10.1038/s41397-026-00399-0</a>.","apa":"Hajto, J., Piechota, M., Krätschmer, I., Konowalska, P., Boyle, G. E., Fowler, D. M., … Korostynski, M. (2026). Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. <i>Pharmacogenomics Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41397-026-00399-0\">https://doi.org/10.1038/s41397-026-00399-0</a>","ama":"Hajto J, Piechota M, Krätschmer I, et al. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. <i>Pharmacogenomics Journal</i>. 2026;26(2). doi:<a href=\"https://doi.org/10.1038/s41397-026-00399-0\">10.1038/s41397-026-00399-0</a>","ieee":"J. Hajto <i>et al.</i>, “Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants,” <i>Pharmacogenomics Journal</i>, vol. 26, no. 2. Springer Nature, 2026.","short":"J. Hajto, M. Piechota, I. Krätschmer, P. Konowalska, G.E. Boyle, D.M. Fowler, M. Borczyk, M. Korostynski, Pharmacogenomics Journal 26 (2026).","mla":"Hajto, Jacek, et al. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” <i>Pharmacogenomics Journal</i>, vol. 26, no. 2, 8, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41397-026-00399-0\">10.1038/s41397-026-00399-0</a>."},"date_published":"2026-03-09T00:00:00Z","has_accepted_license":"1","date_updated":"2026-03-30T07:10:50Z","year":"2026","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"issue":"2","publisher":"Springer Nature","day":"09","type":"journal_article","publication_status":"published","date_created":"2026-03-29T22:07:08Z","external_id":{"pmid":["41803106"]},"department":[{"_id":"MaRo"}],"language":[{"iso":"eng"}],"volume":26,"quality_controlled":"1","article_number":"8","abstract":[{"text":"Currently, pharmacogenetics relies on partially annotated star alleles, leaving novel variants and complex haplotypes uninterpretable. Computational scoring frameworks could overcome these limitations. Here, we comprehensively evaluated the ability of existing (CADD, FATHMM-XF, PROVEAN, MutationAssessor, SIFT, PhyloP100, APF, APF2) and novel (PharmGScore and PharmMLScore) variant effect predictors to assess pharmacogenetic alleles in multiple scenarios. Altogether we analyzed 541 PharmVar alleles, high‑throughput CYP2C9 and CYP2C19 mutational maps, and 200 642 UK Biobank exomes linked with health records containing antidepressant treatment outcomes. Many evaluated tools, especially ensemble frameworks, matched or exceeded star allele classifications (ROC‑AUC up to 0.85 for allele definitions, 0.95 in vitro; TPR up to 0.99 for exomes) and accurately predicted severe antidepressant adverse events for carriers of deleterious variants in CYP2C19 (OR 1.20–1.35). Our findings show that computational predictors deliver star allele accuracy while overcoming their limitations. With additional validation, computational tools could enhance clinical decision frameworks by enabling continuous scoring, incorporating previously unknown variants, and providing genome-wide applicability.","lang":"eng"}],"file_date_updated":"2026-03-30T07:04:08Z","publication":"Pharmacogenomics Journal","scopus_import":"1","author":[{"first_name":"Jacek","last_name":"Hajto","full_name":"Hajto, Jacek"},{"first_name":"Marcin","full_name":"Piechota, Marcin","last_name":"Piechota"},{"orcid":"0000-0002-5636-9259","last_name":"Krätschmer","full_name":"Krätschmer, Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","first_name":"Ilse"},{"first_name":"Paula","last_name":"Konowalska","full_name":"Konowalska, Paula"},{"last_name":"Boyle","full_name":"Boyle, Gabriel E.","first_name":"Gabriel E."},{"last_name":"Fowler","full_name":"Fowler, Douglas M.","first_name":"Douglas M."},{"last_name":"Borczyk","full_name":"Borczyk, Malgorzata","first_name":"Malgorzata"},{"first_name":"Michal","last_name":"Korostynski","full_name":"Korostynski, Michal"}],"intvolume":"        26","pmid":1,"acknowledgement":"This research has been conducted using the UK Biobank Resource under Application Number 62979. We are grateful to the UK Biobank and all its voluntary participants. This work used data provided by patients and collected by the NHS as part of their care and support.\r\n\r\nThis study was funded by the National Science Center, Poland: PRELUDIUM BIS-3 grant no. 2021/43/O/NZ7/01187 (development and benchmarking of variant scores) and SONATINA 5 grant 2021/40/C/NZ2/00218 (UKB analyses). Additional support came from the statutory funds of the Maj Institute of Pharmacology PAS. We gratefully acknowledge Poland’s high-performance Infrastructure PLGrid ACK Cyfronet AGH, for providing computer facilities and support within computational grant no PLG/2022/015861. DMF and GEB were funded by NIH grants NIH R35GM152106 and UM1HG011969.","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_name":"2026_PharmacogenomicsJour_Hajto.pdf","creator":"dernst","file_id":"21506","date_created":"2026-03-30T07:04:08Z","file_size":2618963,"content_type":"application/pdf","checksum":"2fd3d7e48b779ac24245f6c35449b89a","date_updated":"2026-03-30T07:04:08Z"}],"publication_identifier":{"issn":[" 1470-269X"],"eissn":["1473-1150"]},"oa":1},{"date_published":"2026-02-19T00:00:00Z","has_accepted_license":"1","oa_version":"Published Version","year":"2026","date_updated":"2026-03-30T12:09:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"625-639.e8","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Elsevier","day":"19","type":"journal_article","issue":"4","ddc":["570"],"OA_place":"publisher","doi":"10.1016/j.molcel.2026.01.021","article_type":"original","OA_type":"hybrid","_id":"21509","title":"The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2","month":"02","article_processing_charge":"Yes (in subscription journal)","citation":{"ieee":"J. Weiss <i>et al.</i>, “The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2,” <i>Molecular Cell</i>, vol. 86, no. 4. Elsevier, p. 625–639.e8, 2026.","mla":"Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>, vol. 86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>.","short":"J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R. Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi, U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular Cell 86 (2026) 625–639.e8.","chicago":"Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev, Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” <i>Molecular Cell</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>.","ista":"Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 86(4), 625–639.e8.","ama":"Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. 2026;86(4):625-639.e8. doi:<a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">10.1016/j.molcel.2026.01.021</a>","apa":"Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G., … Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2026.01.021\">https://doi.org/10.1016/j.molcel.2026.01.021</a>"},"PlanS_conform":"1","scopus_import":"1","author":[{"first_name":"Joscha","full_name":"Weiss, Joscha","last_name":"Weiss"},{"first_name":"Luca","full_name":"Vecchia, Luca","last_name":"Vecchia"},{"full_name":"Domjan, David","last_name":"Domjan","first_name":"David"},{"first_name":"Simone","last_name":"Cavadini","full_name":"Cavadini, Simone"},{"first_name":"Anton","last_name":"Sabantsev","full_name":"Sabantsev, Anton"},{"first_name":"Georg","last_name":"Kempf","full_name":"Kempf, Georg"},{"full_name":"Pathare, Ganesh R.","last_name":"Pathare","first_name":"Ganesh R."},{"first_name":"Klaus","last_name":"Brackmann","full_name":"Brackmann, Klaus"},{"orcid":"0000-0002-6080-839X","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","first_name":"Alicia","full_name":"Michael, Alicia","last_name":"Michael"},{"last_name":"Kater","full_name":"Kater, Lukas","first_name":"Lukas"},{"last_name":"Hietter-Pfeiffer","full_name":"Hietter-Pfeiffer, Eric","first_name":"Eric"},{"full_name":"Haddawi, Mina","last_name":"Haddawi","first_name":"Mina"},{"first_name":"Urja P.","full_name":"Kuber, Urja P.","last_name":"Kuber"},{"last_name":"Mühlhäusser","full_name":"Mühlhäusser, Sandra","first_name":"Sandra"},{"last_name":"Grand","full_name":"Grand, Ralph S.","first_name":"Ralph S."},{"full_name":"Stadler, Michael B.","last_name":"Stadler","first_name":"Michael B."},{"first_name":"Sebastian","full_name":"Deindl, Sebastian","last_name":"Deindl"},{"first_name":"Nicolas H.","last_name":"Thomä","full_name":"Thomä, Nicolas H."}],"publication":"Molecular Cell","file_date_updated":"2026-03-30T12:04:38Z","intvolume":"        86","acknowledgement":"We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada, D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance for critical discussions; and members of the Thomä lab for helpful feedback. Support for this work was provided to N.H.T. by the European Research Council under the European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852, and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS, no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden (25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported by an EMBO fellowship (ALTF 549-2021).","file":[{"file_id":"21510","date_created":"2026-03-30T12:04:38Z","file_name":"2026_MolecularCell_Weiss.pdf","creator":"dernst","file_size":9786677,"checksum":"e16a7315b64a706184b177ea1621523c","content_type":"application/pdf","date_updated":"2026-03-30T12:04:38Z","success":1,"relation":"main_file","access_level":"open_access"}],"pmid":1,"oa":1,"publication_identifier":{"issn":["1097-2765"]},"publication_status":"published","external_id":{"pmid":["41679301"]},"department":[{"_id":"AlMi"}],"date_created":"2026-03-30T11:58:48Z","language":[{"iso":"eng"}],"volume":86,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes."}]},{"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"oa":1,"acknowledgement":"The authors would like to acknowledge the many colleagues whose valuable contributions to the field could not be included in this review due to space limitations and reference constraints. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ.","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.71072"}],"publication":"New Phytologist","author":[{"id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David","full_name":"Babic, David","last_name":"Babic"},{"full_name":"Zupunski, Milan","last_name":"Zupunski","first_name":"Milan","id":"f6a21fce-573e-11f0-a150-a8d96aee2539"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical–basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical–basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development."}],"article_number":"nph.71072","publication_status":"epub_ahead","language":[{"iso":"eng"}],"corr_author":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"}],"external_id":{"pmid":["41808651"]},"date_created":"2026-03-23T14:59:06Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","day":"11","publisher":"Wiley","oa_version":"Published Version","year":"2026","date_updated":"2026-03-30T05:58:35Z","date_published":"2026-03-11T00:00:00Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Imaging and genetic toolbox to study Arabidopsis embryogenesis","month":"03","_id":"21483","citation":{"ama":"Babic D, Zupunski M, Friml J. Imaging and genetic toolbox to study Arabidopsis embryogenesis. <i>New Phytologist</i>. 2026. doi:<a href=\"https://doi.org/10.1111/nph.71072\">10.1111/nph.71072</a>","apa":"Babic, D., Zupunski, M., &#38; Friml, J. (2026). Imaging and genetic toolbox to study Arabidopsis embryogenesis. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.71072\">https://doi.org/10.1111/nph.71072</a>","chicago":"Babic, David, Milan Zupunski, and Jiří Friml. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” <i>New Phytologist</i>. Wiley, 2026. <a href=\"https://doi.org/10.1111/nph.71072\">https://doi.org/10.1111/nph.71072</a>.","ista":"Babic D, Zupunski M, Friml J. 2026. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist., nph. 71072.","short":"D. Babic, M. Zupunski, J. Friml, New Phytologist (2026).","mla":"Babic, David, et al. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” <i>New Phytologist</i>, nph. 71072, Wiley, 2026, doi:<a href=\"https://doi.org/10.1111/nph.71072\">10.1111/nph.71072</a>.","ieee":"D. Babic, M. Zupunski, and J. Friml, “Imaging and genetic toolbox to study Arabidopsis embryogenesis,” <i>New Phytologist</i>. Wiley, 2026."},"PlanS_conform":"1","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","doi":"10.1111/nph.71072","OA_type":"hybrid","article_type":"original"},{"citation":{"chicago":"Akther, Sonam, Ashley Bomin Lee, Ayumu Konno, Antonis Asiminas, Marta Vittani, Tsuneko Mishima, Hirokazu Hirai, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” <i>IScience</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.isci.2026.115192\">https://doi.org/10.1016/j.isci.2026.115192</a>.","ista":"Akther S, Lee AB, Konno A, Asiminas A, Vittani M, Mishima T, Hirai H, Meehan CF, Duran J, Guinovart J, Ashida H, Morita T, Baba O, Shigemoto R, Nedergaard M, Hirase H. 2026. Distribution and functional significance of rodent cerebellar glycogen. iScience. 29(4), 115192.","ama":"Akther S, Lee AB, Konno A, et al. Distribution and functional significance of rodent cerebellar glycogen. <i>iScience</i>. 2026;29(4). doi:<a href=\"https://doi.org/10.1016/j.isci.2026.115192\">10.1016/j.isci.2026.115192</a>","apa":"Akther, S., Lee, A. B., Konno, A., Asiminas, A., Vittani, M., Mishima, T., … Hirase, H. (2026). Distribution and functional significance of rodent cerebellar glycogen. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2026.115192\">https://doi.org/10.1016/j.isci.2026.115192</a>","ieee":"S. Akther <i>et al.</i>, “Distribution and functional significance of rodent cerebellar glycogen,” <i>iScience</i>, vol. 29, no. 4. Elsevier, 2026.","mla":"Akther, Sonam, et al. “Distribution and Functional Significance of Rodent Cerebellar Glycogen.” <i>IScience</i>, vol. 29, no. 4, 115192, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.isci.2026.115192\">10.1016/j.isci.2026.115192</a>.","short":"S. Akther, A.B. Lee, A. Konno, A. Asiminas, M. Vittani, T. Mishima, H. Hirai, C.F. Meehan, J. Duran, J. Guinovart, H. Ashida, T. Morita, O. Baba, R. Shigemoto, M. Nedergaard, H. Hirase, IScience 29 (2026)."},"article_processing_charge":"Yes","month":"03","title":"Distribution and functional significance of rodent cerebellar glycogen","_id":"21502","article_type":"original","OA_type":"gold","doi":"10.1016/j.isci.2026.115192","OA_place":"publisher","issue":"4","type":"journal_article","day":"17","publisher":"Elsevier","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-03-30T06:20:06Z","oa_version":"Published Version","year":"2026","date_published":"2026-03-17T00:00:00Z","article_number":"115192","abstract":[{"text":"The mammalian brain stores glucose, the main circulating energy substrate, as glycogen. In rodents, the cerebellum contains relatively high glycogen levels, yet its cellular and subcellular distribution remains poorly defined. Using monoclonal antibodies against glycogen, we examined its distribution in the mouse cerebellar cortex. Glycogen was predominantly localized to Bergmann glia (BG) processes in the molecular layer and was also detected in Purkinje cells (PCs), the principal cerebellar neurons. To assess the functional significance of cerebellar glycogen, we analyzed behavior in mice lacking glycogen synthase 1 (Gys1) in BG or PCs using a floxed Gys1 line. Gys1 deficiency in either PCs or GFAP-positive cells reduced anxiety-like behavior, whereas combined deletion caused PC degeneration and ataxia. These findings reveal a critical role for glycogen metabolism in both astrocytes and neurons in cerebellar function.","lang":"eng"}],"quality_controlled":"1","volume":29,"language":[{"iso":"eng"}],"date_created":"2026-03-29T22:07:07Z","external_id":{"pmid":["41890976"]},"department":[{"_id":"RySh"}],"publication_status":"epub_ahead","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.isci.2026.115192"}],"publication_identifier":{"eissn":["2589-0042"]},"oa":1,"pmid":1,"DOAJ_listed":"1","acknowledgement":"This work was supported by the Novo Nordisk Foundation (NNFOC0058058, H. Hirase), the Danmarks Frie Forskningsfond (0134-00107B and 5283-00069A, H.Hirase), the Lundbeck Foundation, Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) program (22K06454/24H01221, A.K.; 23K27482, H.Hirai), the Japan Agency for Medical Research and Development (AMED) Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS) (JP21dm0207111, H. Hirai), AMED Brain/MINDS 2.0 (JP23wm0625001 and JP24wm0625103, H. Hirai), and grants from the Spanish Ministerio de Ciencia e Innovación (MCIU/FEDER/AEI) (PID2020-118699 GB-100, J.D.) and the Fundación Ramón Areces (J.D.). Sonam Akther has been supported by the RIKEN IPA fellowship. We are thankful to Dr. Yuki Oe for his support in the initial stage of this study and to Dan Xue for his help with the graphical abstract. We thank Dr. Pia Weikop for providing CTN research infrastructure. The authors declare no competing financial interests.","intvolume":"        29","author":[{"last_name":"Akther","full_name":"Akther, Sonam","first_name":"Sonam"},{"first_name":"Ashley Bomin","last_name":"Lee","full_name":"Lee, Ashley Bomin"},{"last_name":"Konno","full_name":"Konno, Ayumu","first_name":"Ayumu"},{"first_name":"Antonis","last_name":"Asiminas","full_name":"Asiminas, Antonis"},{"full_name":"Vittani, Marta","last_name":"Vittani","first_name":"Marta"},{"first_name":"Tsuneko","last_name":"Mishima","full_name":"Mishima, Tsuneko"},{"first_name":"Hirokazu","full_name":"Hirai, Hirokazu","last_name":"Hirai"},{"first_name":"Claire Francesca","full_name":"Meehan, Claire Francesca","last_name":"Meehan"},{"first_name":"Jordi","last_name":"Duran","full_name":"Duran, Jordi"},{"first_name":"Joan","last_name":"Guinovart","full_name":"Guinovart, Joan"},{"full_name":"Ashida, Hitoshi","last_name":"Ashida","first_name":"Hitoshi"},{"full_name":"Morita, Tsuyoshi","last_name":"Morita","first_name":"Tsuyoshi"},{"full_name":"Baba, Otto","last_name":"Baba","first_name":"Otto"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Maiken","last_name":"Nedergaard","full_name":"Nedergaard, Maiken"},{"last_name":"Hirase","full_name":"Hirase, Hajime","first_name":"Hajime"}],"scopus_import":"1","publication":"iScience"},{"scopus_import":"1","publication":"Mathematical Models and Methods in Applied Sciences","author":[{"first_name":"Gennaro","last_name":"Auricchio","full_name":"Auricchio, Gennaro"},{"first_name":"Giovanni","id":"63ff57e8-1fbb-11ee-88f2-f558ffc59cf1","full_name":"Brigati, Giovanni","last_name":"Brigati"},{"full_name":"Giudici, Paolo","last_name":"Giudici","first_name":"Paolo"},{"first_name":"Giuseppe","last_name":"Toscani","full_name":"Toscani, Giuseppe"}],"ec_funded":1,"acknowledgement":"This work has been written within the activities of GNCS and GNFM groups of INdAM (Italian\r\nNational Institute of High Mathematics). G.B. has been funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413. P.G. has been funded by the European Union - NextGenerationEU, in the framework of the GRINSGrowing Resilient, INclusive and Sustainable (GRINS PE00000018).","publication_identifier":{"eissn":["1793-6314"],"issn":["0218-2025"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2507.11387"}],"publication_status":"epub_ahead","date_created":"2026-03-29T22:07:08Z","department":[{"_id":"JaMa"}],"external_id":{"arxiv":["2507.11387"]},"language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Selecting an appropriate divergence measure is a critical aspect of machine learning, as it directly impacts model performance. Among the most widely used, we find the Kullback–Leibler (KL) divergence, originally introduced in kinetic theory as a measure of relative entropy between probability distributions. Just as in machine learning, the ability to quantify the proximity of probability distributions plays a central role in kinetic theory. In this paper, we present a comparative review of divergence measures rooted in kinetic theory, highlighting their theoretical foundations and exploring their potential applications in machine learning and artificial intelligence."}],"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"date_published":"2026-03-14T00:00:00Z","date_updated":"2026-03-30T06:56:35Z","year":"2026","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","day":"14","type":"journal_article","publisher":"World Scientific Publishing","arxiv":1,"OA_type":"green","article_type":"original","doi":"10.1142/S0218202526410010","OA_place":"repository","_id":"21504","month":"03","title":"From kinetic theory to AI: A rediscovery of high-dimensional divergences and their properties","article_processing_charge":"No","citation":{"chicago":"Auricchio, Gennaro, Giovanni Brigati, Paolo Giudici, and Giuseppe Toscani. “From Kinetic Theory to AI: A Rediscovery of High-Dimensional Divergences and Their Properties.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing, 2026. <a href=\"https://doi.org/10.1142/S0218202526410010\">https://doi.org/10.1142/S0218202526410010</a>.","ista":"Auricchio G, Brigati G, Giudici P, Toscani G. 2026. From kinetic theory to AI: A rediscovery of high-dimensional divergences and their properties. Mathematical Models and Methods in Applied Sciences.","ama":"Auricchio G, Brigati G, Giudici P, Toscani G. From kinetic theory to AI: A rediscovery of high-dimensional divergences and their properties. <i>Mathematical Models and Methods in Applied Sciences</i>. 2026. doi:<a href=\"https://doi.org/10.1142/S0218202526410010\">10.1142/S0218202526410010</a>","apa":"Auricchio, G., Brigati, G., Giudici, P., &#38; Toscani, G. (2026). From kinetic theory to AI: A rediscovery of high-dimensional divergences and their properties. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218202526410010\">https://doi.org/10.1142/S0218202526410010</a>","ieee":"G. Auricchio, G. Brigati, P. Giudici, and G. Toscani, “From kinetic theory to AI: A rediscovery of high-dimensional divergences and their properties,” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing, 2026.","mla":"Auricchio, Gennaro, et al. “From Kinetic Theory to AI: A Rediscovery of High-Dimensional Divergences and Their Properties.” <i>Mathematical Models and Methods in Applied Sciences</i>, World Scientific Publishing, 2026, doi:<a href=\"https://doi.org/10.1142/S0218202526410010\">10.1142/S0218202526410010</a>.","short":"G. Auricchio, G. Brigati, P. Giudici, G. Toscani, Mathematical Models and Methods in Applied Sciences (2026)."}},{"publication_status":"published","language":[{"iso":"eng"}],"corr_author":"1","date_created":"2025-12-29T12:06:26Z","department":[{"_id":"JaMa"}],"external_id":{"arxiv":["2403.07803"]},"quality_controlled":"1","volume":65,"article_number":"23","abstract":[{"lang":"eng","text":"We prove the convergence of a modified Jordan–Kinderlehrer–Otto scheme to a solution\r\nto the Fokker–Planck equation in Ω e R^d with general—strictly positive and temporally\r\nconstant—Dirichlet boundary conditions. We work under mild assumptions on the domain,\r\nthe drift, and the initial datum. In the special case where Ω is an interval in R1, we prove\r\nthat such a solution is a gradient flow—curve of maximal slope—within a suitable space of\r\nmeasures, endowed with a modified Wasserstein distance. Our discrete scheme and modified\r\ndistance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures\r\nAppl. 94, (2010), pp. 107–130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41–88]\r\non an optimal-transport approach to evolution equations with Dirichlet boundary conditions.\r\nSimilarly to these works, we allow the mass to flow from/to the boundary ∂Ω throughout\r\nthe evolution. However, our leading idea is to also keep track of the mass at the boundary\r\nby working with measures defined on the whole closure Ω . The driving functional is a\r\nmodification of the classical relative entropy that also makes use of the information at the\r\nboundary. As an intermediate result, when Ω is an interval in R1, we find a formula for the\r\ndescending slope of this geodesically nonconvex functional."}],"intvolume":"        65","file_date_updated":"2026-01-05T12:36:39Z","author":[{"last_name":"Quattrocchi","full_name":"Quattrocchi, Filippo","first_name":"Filippo","id":"3ebd6ba8-edfb-11eb-afb5-91a9745ba308","orcid":"0009-0000-9773-1931"}],"scopus_import":"1","publication":"Calculus of Variations and Partial Differential Equations","oa":1,"publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"acknowledgement":"The author would like to thank Jan Maas for suggesting this project and for many helpful comments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, Oliver Tse for pointing out the reference [10], and the anonymous reviewer for carefully reading this manuscript and providing valuable suggestions. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.Open access funding provided by Institute of Science and Technology (IST Austria).","file":[{"success":1,"relation":"main_file","access_level":"open_access","file_size":958382,"file_id":"20945","date_created":"2026-01-05T12:36:39Z","creator":"dernst","file_name":"2026_CalculusVariations_Quattrocchi.pdf","date_updated":"2026-01-05T12:36:39Z","checksum":"635370d64abaf444f50f5cca60bba1be","content_type":"application/pdf"}],"ddc":["510"],"arxiv":1,"article_type":"original","OA_type":"hybrid","OA_place":"publisher","doi":"10.1007/s00526-025-03193-1","month":"01","title":"Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions","_id":"20865","related_material":{"record":[{"id":"20571","status":"public","relation":"earlier_version"}]},"PlanS_conform":"1","citation":{"ama":"Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>Calculus of Variations and Partial Differential Equations</i>. 2026;65(1). doi:<a href=\"https://doi.org/10.1007/s00526-025-03193-1\">10.1007/s00526-025-03193-1</a>","apa":"Quattrocchi, F. (2026). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-025-03193-1\">https://doi.org/10.1007/s00526-025-03193-1</a>","chicago":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s00526-025-03193-1\">https://doi.org/10.1007/s00526-025-03193-1</a>.","ista":"Quattrocchi F. 2026. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. Calculus of Variations and Partial Differential Equations. 65(1), 23.","short":"F. Quattrocchi, Calculus of Variations and Partial Differential Equations 65 (2026).","mla":"Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 1, 23, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s00526-025-03193-1\">10.1007/s00526-025-03193-1</a>.","ieee":"F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 65, no. 1. Springer Nature, 2026."},"article_processing_charge":"Yes (via OA deal)","date_updated":"2026-04-07T08:37:46Z","year":"2026","oa_version":"Published Version","date_published":"2026-01-01T00:00:00Z","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","issue":"1","publisher":"Springer Nature","day":"01","type":"journal_article"},{"citation":{"ista":"Liagre BRB, Desai AA, Einramhof L, Bugnet LA. 2026. Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description to data fitting. Astronomy and Astrophysics. 707, A321.","chicago":"Liagre, Bastien Raymond Bernard, Aayush A Desai, Lukas Einramhof, and Lisa Annabelle Bugnet. “Near-Degeneracy Effects in Quadrupolar Mixed Modes: From an Asymptotic Description to Data Fitting.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202558023\">https://doi.org/10.1051/0004-6361/202558023</a>.","apa":"Liagre, B. R. B., Desai, A. A., Einramhof, L., &#38; Bugnet, L. A. (2026). Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description to data fitting. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202558023\">https://doi.org/10.1051/0004-6361/202558023</a>","ama":"Liagre BRB, Desai AA, Einramhof L, Bugnet LA. Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description to data fitting. <i>Astronomy and Astrophysics</i>. 2026;707. doi:<a href=\"https://doi.org/10.1051/0004-6361/202558023\">10.1051/0004-6361/202558023</a>","ieee":"B. R. B. Liagre, A. A. Desai, L. Einramhof, and L. A. Bugnet, “Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description to data fitting,” <i>Astronomy and Astrophysics</i>, vol. 707. EDP Sciences, 2026.","short":"B.R.B. Liagre, A.A. Desai, L. Einramhof, L.A. Bugnet, Astronomy and Astrophysics 707 (2026).","mla":"Liagre, Bastien Raymond Bernard, et al. “Near-Degeneracy Effects in Quadrupolar Mixed Modes: From an Asymptotic Description to Data Fitting.” <i>Astronomy and Astrophysics</i>, vol. 707, A321, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202558023\">10.1051/0004-6361/202558023</a>."},"PlanS_conform":"1","article_processing_charge":"No","title":"Near-degeneracy effects in quadrupolar mixed modes: From an asymptotic description to data fitting","month":"03","_id":"21658","doi":"10.1051/0004-6361/202558023","OA_place":"publisher","OA_type":"diamond","article_type":"original","arxiv":1,"ddc":["520"],"type":"journal_article","publisher":"EDP Sciences","day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2026","date_updated":"2026-04-07T09:01:44Z","has_accepted_license":"1","date_published":"2026-03-01T00:00:00Z","abstract":[{"lang":"eng","text":"Dipolar (ℓ = 1) mixed modes have revealed a surprisingly weak differential rotation between the core and the envelope of evolved solar-like stars. Quadrupolar (ℓ = 2) mixed modes also contain information regarding internal dynamics but are very rarely characterised due to their low amplitude and the challenging identification of adjacent or overlapping rotationally split multiplets affected by near-degeneracy effects. We aim to extend the broadly used asymptotic seismic diagnostics beyond ℓ = 1 mixed modes by developing an analogue asymptotic description of ℓ = 2 mixed modes while explicitly accounting for near-degeneracy effects that distort their rotational multiplets. We have derived a new asymptotic formulation of near-degenerate mixed ℓ = 2 modes that describes off-diagonal terms representing the interaction between modes of adjacent radial orders. This formalism, expressed directly in the mixed-mode basis, provides analytical expressions for the near-degeneracy effects. We implemented the formalism within a global Bayesian mode-fitting framework for a direct fit of all ℓ = 0, 1, 2 modes in the power spectrum density. We were able to asymptotically model the asymmetric rotational splitting present in various radial orders of ℓ = 2 modes observed in young red giant stars without the need for any numerical stellar modelling. We applied our formalism to the Kepler target KIC 7341231, and it yielded core and envelope rotation rates consistent with previous numerical modelling while providing improved constraints from the global and model-independent approach. We also characterised the new target, KIC 8179973, measuring its rotation rate and mixed-mode parameters for the first time. As our framework relies on a direct global fit, it allows for much better precision on the asteroseismic parameters and rotation rate estimates than standard methods, yielding better constraints for rotation inversions. We have placed the first observational constraints on the asymptotic ℓ = 2 mixed-mode parameters (ΔΠ2, q2, and εg, 2), thus paving the way towards the use of asymptotic seismology beyond ℓ = 1 mixed modes."}],"article_number":"A321","quality_controlled":"1","volume":707,"language":[{"iso":"eng"}],"corr_author":"1","department":[{"_id":"LiBu"},{"_id":"IlCa"},{"_id":"GradSch"}],"external_id":{"arxiv":["2511.05314 "]},"date_created":"2026-04-05T22:01:32Z","publication_status":"published","oa":1,"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"acknowledgement":"We thank the referee for their careful and constructive report, which has substantially enhanced both the quality and clarity of the manuscript. L. Bugnet and L. Einramhof gratefully acknowledge support from the European Research Council (ERC) under the Horizon Europe programme (Calcifer; Starting Grant agreement N°101165631). While partially funded by the European Union, views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. The authors acknowledge the great support and feedback provided during the redaction of this article by Pr. Rafael García and Pr. Savita Mathur. We would also like to thank Dr. Emily Hatt for her insights on uncertainty estimates. The authors also thank the members of the Asteroseismology and Stellar Dynamics group of the Institute of Science and Technology Austria (ISTA) for very useful discussions: L. Barrault, S.B. Das, K. Smith. This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. Software: AstroPy (Astropy Collaboration 2013, 2018), Matplotlib (Hunter 2007), NumPy (Harris et al. 2020), SciPy (Virtanen et al. 2020), emcee (Foreman-Mackey et al. 2013), celerite (Foreman-Mackey et al. 2017), slepc4py (Dalcin et al. 2011; Hernandez et al. 2005), KADACS (García et al. 2011), sloscillations (Kuszlewicz et al. 2019, 2023).","file":[{"content_type":"application/pdf","checksum":"560cac19dc70184626b85e71a26ee22e","date_updated":"2026-04-07T09:00:50Z","creator":"dernst","file_name":"2026_AstronomyAstrophysics_Liagre.pdf","date_created":"2026-04-07T09:00:50Z","file_id":"21664","file_size":12287607,"access_level":"open_access","relation":"main_file","success":1}],"DOAJ_listed":"1","intvolume":"       707","file_date_updated":"2026-04-07T09:00:50Z","author":[{"last_name":"Liagre","full_name":"Liagre, Bastien Raymond Bernard","id":"662f1873-cab4-11f0-a719-8087d302868d","first_name":"Bastien Raymond Bernard"},{"id":"502cfd30-32c1-11ee-a9a4-d8dad5c6739e","first_name":"Aayush A","full_name":"Desai, Aayush A","last_name":"Desai"},{"full_name":"Einramhof, Lukas","last_name":"Einramhof","first_name":"Lukas","id":"f1497a1a-72ef-11ef-b75a-fd877bbf6e8c"},{"last_name":"Bugnet","full_name":"Bugnet, Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000"}],"scopus_import":"1","publication":"Astronomy and Astrophysics"},{"quality_controlled":"1","volume":18,"article_number":"e2025MS005343","abstract":[{"text":"We compare three global kilometer-scale models (ICON, IFS and NICAM) to clarify the advantages and challenges of high-resolution global weather and climate modeling, using different approaches to represent convection, from fully parameterized to fully explicit. Our analysis focuses on tropical precipitation characteristics spanning a wide range of spatio-temporal scales—including the diurnal cycle, extreme precipitation, convective organization, and the Madden-Julian Oscillation (MJO)—along with interactions between convection and the thermodynamic environment. All three models commonly show weaker convective organization with smaller precipitation cells than observed, though the strength of the bias varies by model. This diversity is introduced by differences in the representation of (a) convective initiation affected by the convective sensitivity to moisture and (b) tropospheric moistening associated with deep convection. Models with stronger thermodynamic-convection coupling increase environmental moisture near convection, thereby enhancing convective organization. This has important upscale effects on the MJO; while IFS and NICAM capture its eastward propagation well, ICON has difficulty reproducing it. The amplitudes and phases of precipitation diurnal cycles over land show much greater disagreement among the models than over ocean, influenced by how convection is initiated. Biases in rain evaporation and cold pool formation hinder the propagation of mesoscale convection, leading to errors such as the misrepresentation of nocturnal convection moving off the coast of Sumatra in IFS and ICON. These results highlight the importance of thermodynamic-convection coupling in realistically simulating tropical convection across scales. To improve this coupling, kilometer-scale models require better representation of the interaction between resolved convection and three-dimensional turbulent mixing.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"corr_author":"1","date_created":"2026-04-05T22:01:31Z","department":[{"_id":"CaMu"}],"publication_identifier":{"eissn":["1942-2466"]},"oa":1,"DOAJ_listed":"1","acknowledgement":"We thank Peter Bechtold, Lukas Brunner, Peter Dueben, Richard Forbes, Estibaliz Gascon, and Benoit Vanniere for providing insightful comments on the present study. We also thank Sebastian Milinski, Xabier Pedruzo and Thomas Rackow for their contributions to setting up IFS-FESOM for nextGEMS. We are also grateful to Dr. Walter Hannah and an anonymous reviewer for their constructive comments, which improved the original version of the manuscript. D. Takasuka was supported by JSPS KAKENHI Grants 20H05728 and 24K22893 and by JSPS Core-to-Core Program, “International Core-to-Core Project on Global Storm Resolving Analysis” (Grant Number: JPJSCCA20220001). T. Becker was supported by the Horizon 2020 project nextGEMS under grant agreement number 101003470. J. Bao acknowledges funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement No 101034413). The ICON and IFS simulations were performed with supercomputing resources of the German Climate Computing Centre (Deutsches Klimarechenzentrum, DKRZ) granted by its Scientific Steering Committee (WLA) under project ID 1235. The NICAM simulation was performed on the supercomputer Fugaku (proposal numbers hp220132, hp230078, hp230108, hp230278, and hp240267).","file":[{"file_size":3854313,"date_created":"2026-04-07T09:11:23Z","file_id":"21665","file_name":"2026_JAMES_Takasuka.pdf","creator":"dernst","date_updated":"2026-04-07T09:11:23Z","content_type":"application/pdf","checksum":"ca7dac4bab31348d0640ed22580c6dce","success":1,"relation":"main_file","access_level":"open_access"}],"intvolume":"        18","ec_funded":1,"author":[{"first_name":"Daisuke","full_name":"Takasuka, Daisuke","last_name":"Takasuka"},{"first_name":"Tobias","full_name":"Becker, Tobias","last_name":"Becker"},{"last_name":"Bao","full_name":"Bao, Jiawei","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"}],"scopus_import":"1","file_date_updated":"2026-04-07T09:11:23Z","publication":"Journal of Advances in Modeling Earth Systems","month":"03","title":"Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations","_id":"21657","citation":{"short":"D. Takasuka, T. Becker, J. Bao, Journal of Advances in Modeling Earth Systems 18 (2026).","mla":"Takasuka, Daisuke, et al. “Precipitation Characteristics and Thermodynamic-Convection Coupling in Global Kilometer-Scale Simulations.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 18, no. 3, e2025MS005343, Wiley, 2026, doi:<a href=\"https://doi.org/10.1029/2025MS005343\">10.1029/2025MS005343</a>.","ieee":"D. Takasuka, T. Becker, and J. Bao, “Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 18, no. 3. Wiley, 2026.","apa":"Takasuka, D., Becker, T., &#38; Bao, J. (2026). Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2025MS005343\">https://doi.org/10.1029/2025MS005343</a>","ama":"Takasuka D, Becker T, Bao J. Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations. <i>Journal of Advances in Modeling Earth Systems</i>. 2026;18(3). doi:<a href=\"https://doi.org/10.1029/2025MS005343\">10.1029/2025MS005343</a>","ista":"Takasuka D, Becker T, Bao J. 2026. Precipitation characteristics and thermodynamic-convection coupling in global kilometer-scale simulations. Journal of Advances in Modeling Earth Systems. 18(3), e2025MS005343.","chicago":"Takasuka, Daisuke, Tobias Becker, and Jiawei Bao. “Precipitation Characteristics and Thermodynamic-Convection Coupling in Global Kilometer-Scale Simulations.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2026. <a href=\"https://doi.org/10.1029/2025MS005343\">https://doi.org/10.1029/2025MS005343</a>."},"article_processing_charge":"Yes","ddc":["550"],"article_type":"original","OA_type":"gold","OA_place":"publisher","doi":"10.1029/2025MS005343","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","issue":"3","type":"journal_article","publisher":"Wiley","day":"01","date_updated":"2026-04-07T09:14:51Z","oa_version":"None","year":"2026","has_accepted_license":"1","date_published":"2026-03-01T00:00:00Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":707,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The recent detection of solar equatorial Rossby waves has renewed interest in the study of gravito-inertial waves propagating in the convective envelope of solar-type stars. In particular, the ability of these envelope gravito-inertial modes to couple with those trapped in the radiative interior could open up new opportunities for probing the deep-layer dynamics of solar-type stars. The possibility for such a coupling to occur is particularly favoured among pre-main-sequence (PMS) solar-type stars. Indeed, due to the contraction of the protostellar object, they are able to reach high rotation frequencies before nuclear reactions are ignited and magnetic braking becomes the driving mechanism for their rotational evolution. In this work, we studied the coupling between the envelope inertial waves and the radiative interior g modes in PMS stars, focussing on the case of prograde dipolar modes. We considered the cases of 0.5 M⊙ and 1 M⊙ PMS models, each with three different scenarios of rotational evolution. We show that for stars that have formed with a sufficient amount of angular momentum, this coupling can occur in frequency ranges that are accessible to space-borne photometry, creating inertial dips in the period spacing pattern. Using an asymptotic analysis, we characterised the shape of these inertial dips to show that they depend on rotation and on the stiffness of the convective-radiative interface."}],"article_number":"L16","publication_status":"published","department":[{"_id":"LiBu"}],"external_id":{"arxiv":["2603.01979"]},"date_created":"2026-04-05T22:01:32Z","language":[{"iso":"eng"}],"acknowledgement":"The authors want to thank the anonymous referee for useful comments. SNB acknowledges support from PLATO ASI-INAF agreement no. 2022-28-HH.0 “PLATO Fase D”. SNB and AFL acknowledge support from the INAF grant MASTODINT. CP thanks the Belgian Federal Science Policy Office (BELSPO) for the financial support in the framework of the PRODEX Program of the European Space Agency (ESA) under contract number 4000141194. S.M acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp. LB and SM gratefully acknowledge support from the European Research Council (ERC) under the Horizon Europe programme (LB: Calcifer; Starting Grant agreement N°101165631; SM: 4D-STAR; Synergy Grant agreement N°101071505). While partially funded by the European Union, views and opinions expressed are, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. The authors acknowledge G. Buldgen, H. Dhouib, and M.A. Dupret for fruitful discussions.","file":[{"access_level":"open_access","relation":"main_file","success":1,"checksum":"a7fd798bf450d67d4166fdf54ff2c70c","content_type":"application/pdf","date_updated":"2026-04-07T09:20:02Z","file_name":"2026_AstronomyAstrophysics_Breton.pdf","creator":"dernst","date_created":"2026-04-07T09:20:02Z","file_id":"21666","file_size":1535506}],"DOAJ_listed":"1","oa":1,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"file_date_updated":"2026-04-07T09:20:02Z","scopus_import":"1","publication":"Astronomy & Astrophysics","author":[{"full_name":"Breton, S. N.","last_name":"Breton","first_name":"S. N."},{"first_name":"C.","full_name":"Pezzotti, C.","last_name":"Pezzotti"},{"first_name":"S.","full_name":"Mathis, S.","last_name":"Mathis"},{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000"},{"first_name":"M. P.","full_name":"Di Mauro, M. P.","last_name":"Di Mauro"},{"first_name":"J.","full_name":"Joergensen, J.","last_name":"Joergensen"},{"first_name":"K.","full_name":"Zwintz, K.","last_name":"Zwintz"},{"first_name":"A. F.","last_name":"Lanza","full_name":"Lanza, A. F."}],"intvolume":"       707","_id":"21659","title":"Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type stars","month":"03","article_processing_charge":"No","citation":{"chicago":"Breton, S. N., C. Pezzotti, S. Mathis, Lisa Annabelle Bugnet, M. P. Di Mauro, J. Joergensen, K. Zwintz, and A. F. Lanza. “Core-Envelope Coupling of Gravito-Inertial Waves in Pre-Main-Sequence Solar-Type Stars.” <i>Astronomy &#38; Astrophysics</i>. Wiley, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202659309\">https://doi.org/10.1051/0004-6361/202659309</a>.","ista":"Breton SN, Pezzotti C, Mathis S, Bugnet LA, Di Mauro MP, Joergensen J, Zwintz K, Lanza AF. 2026. Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type stars. Astronomy &#38; Astrophysics. 707, L16.","ama":"Breton SN, Pezzotti C, Mathis S, et al. Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type stars. <i>Astronomy &#38; Astrophysics</i>. 2026;707. doi:<a href=\"https://doi.org/10.1051/0004-6361/202659309\">10.1051/0004-6361/202659309</a>","apa":"Breton, S. N., Pezzotti, C., Mathis, S., Bugnet, L. A., Di Mauro, M. P., Joergensen, J., … Lanza, A. F. (2026). Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type stars. <i>Astronomy &#38; Astrophysics</i>. Wiley. <a href=\"https://doi.org/10.1051/0004-6361/202659309\">https://doi.org/10.1051/0004-6361/202659309</a>","ieee":"S. N. Breton <i>et al.</i>, “Core-envelope coupling of gravito-inertial waves in pre-main-sequence solar-type stars,” <i>Astronomy &#38; Astrophysics</i>, vol. 707. Wiley, 2026.","mla":"Breton, S. N., et al. “Core-Envelope Coupling of Gravito-Inertial Waves in Pre-Main-Sequence Solar-Type Stars.” <i>Astronomy &#38; Astrophysics</i>, vol. 707, L16, Wiley, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202659309\">10.1051/0004-6361/202659309</a>.","short":"S.N. Breton, C. Pezzotti, S. Mathis, L.A. Bugnet, M.P. Di Mauro, J. Joergensen, K. Zwintz, A.F. Lanza, Astronomy &#38; Astrophysics 707 (2026)."},"PlanS_conform":"1","arxiv":1,"ddc":["520"],"doi":"10.1051/0004-6361/202659309","OA_place":"publisher","OA_type":"diamond","article_type":"letter_editor","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Wiley","type":"journal_article","day":"01","project":[{"_id":"914d8549-16d5-11f0-9cad-bbe6324c93a9","grant_number":"101165631","name":"Unveiling the mysteries of stellar dynamics: a pioneering journey in magnetoasteroseismology"}],"has_accepted_license":"1","date_published":"2026-03-01T00:00:00Z","year":"2026","oa_version":"Published Version","date_updated":"2026-04-07T09:23:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_type":"original","OA_type":"gold","OA_place":"publisher","doi":"10.1103/rdsn-stlq","ddc":["530"],"arxiv":1,"article_processing_charge":"Yes","PlanS_conform":"1","citation":{"short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 8 (2026).","mla":"Becker, A., et al. “Two-Body Kapitza-Dirac Scattering of One-Dimensional Ultracold Atoms.” <i>Physical Review Research</i>, vol. 8, 013297, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/rdsn-stlq\">10.1103/rdsn-stlq</a>.","ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms,” <i>Physical Review Research</i>, vol. 8. American Physical Society, 2026.","ama":"Becker A, Koutentakis G, Schmelcher P. Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms. <i>Physical Review Research</i>. 2026;8. doi:<a href=\"https://doi.org/10.1103/rdsn-stlq\">10.1103/rdsn-stlq</a>","apa":"Becker, A., Koutentakis, G., &#38; Schmelcher, P. (2026). Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/rdsn-stlq\">https://doi.org/10.1103/rdsn-stlq</a>","chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Two-Body Kapitza-Dirac Scattering of One-Dimensional Ultracold Atoms.” <i>Physical Review Research</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/rdsn-stlq\">https://doi.org/10.1103/rdsn-stlq</a>.","ista":"Becker A, Koutentakis G, Schmelcher P. 2026. Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms. Physical Review Research. 8, 013297."},"_id":"21660","month":"03","title":"Two-body Kapitza-Dirac scattering of one-dimensional ultracold atoms","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-03-18T00:00:00Z","has_accepted_license":"1","project":[{"name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","grant_number":"F100403"}],"date_updated":"2026-04-07T09:37:57Z","oa_version":"Published Version","year":"2026","type":"journal_article","day":"18","publisher":"American Physical Society","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-04-05T22:01:32Z","external_id":{"arxiv":["2512.15260"]},"department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"corr_author":"1","publication_status":"published","article_number":"013297","abstract":[{"lang":"eng","text":"Kapitza-Dirac scattering, the diffraction of matter waves from a standing light field, is widely utilized in ultracold gases, but its behavior in the strongly interacting regime is an open question. Here, we develop a numerically exact two-body description of Kapitza-Dirac scattering for two contact-interacting atoms in a one-dimensional harmonic trap subjected to a pulsed optical lattice, enabling us to obtain the numerically exact dynamics. We map how interaction strength, lattice depth, lattice wave number, and pulse duration reshape the diffraction pattern, leading to an interaction-dependent population redistribution in real and momentum space. By comparing the exact dynamics to an impulsive sudden-approximation description, we delineate the parameter regimes where it remains accurate and those, notably at strong attraction and small lattice wave number, where it fails. Our results provide a controlled few-body benchmark for interacting Kapitza-Dirac scattering and quantitative guidance for Kapitza-Dirac-based probes of ultracold atomic systems."}],"volume":8,"quality_controlled":"1","file_date_updated":"2026-04-07T09:34:31Z","author":[{"last_name":"Becker","full_name":"Becker, A.","first_name":"A."},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis","full_name":"Koutentakis, Georgios"},{"full_name":"Schmelcher, P.","last_name":"Schmelcher","first_name":"P."}],"publication":"Physical Review Research","scopus_import":"1","intvolume":"         8","acknowledgement":"We thank Max Hachmann, Andreas Hemmerich, and Yann Kiefer for valuable discussions. This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994. G.M.K. has received funding by the Austrian Science Fund (FWF) 10.55776/F1004.","DOAJ_listed":"1","file":[{"date_updated":"2026-04-07T09:34:31Z","content_type":"application/pdf","checksum":"339bff9d13486a8028049404988b9b0b","file_size":2131627,"file_id":"21667","date_created":"2026-04-07T09:34:31Z","file_name":"2026_PhysicalReviewResearch_Becker.pdf","creator":"dernst","relation":"main_file","access_level":"open_access","success":1}],"publication_identifier":{"issn":["2643-1564"]},"oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2026","date_updated":"2026-04-07T09:52:54Z","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"has_accepted_license":"1","date_published":"2026-03-09T00:00:00Z","type":"journal_article","day":"09","publisher":"Springer Nature","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1007/s10009-026-00848-y","OA_place":"publisher","OA_type":"hybrid","article_type":"original","ddc":["000"],"citation":{"ieee":"A. Hartmanns, S. Junges, T. Quatmann, and M. Weininger, “The revised practitioner’s guide to MDP model checking algorithms,” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2026.","short":"A. Hartmanns, S. Junges, T. Quatmann, M. Weininger, International Journal on Software Tools for Technology Transfer (2026).","mla":"Hartmanns, Arnd, et al. “The Revised Practitioner’s Guide to MDP Model Checking Algorithms.” <i>International Journal on Software Tools for Technology Transfer</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s10009-026-00848-y\">10.1007/s10009-026-00848-y</a>.","ista":"Hartmanns A, Junges S, Quatmann T, Weininger M. 2026. The revised practitioner’s guide to MDP model checking algorithms. International Journal on Software Tools for Technology Transfer.","chicago":"Hartmanns, Arnd, Sebastian Junges, Tim Quatmann, and Maximilian Weininger. “The Revised Practitioner’s Guide to MDP Model Checking Algorithms.” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s10009-026-00848-y\">https://doi.org/10.1007/s10009-026-00848-y</a>.","apa":"Hartmanns, A., Junges, S., Quatmann, T., &#38; Weininger, M. (2026). The revised practitioner’s guide to MDP model checking algorithms. <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-026-00848-y\">https://doi.org/10.1007/s10009-026-00848-y</a>","ama":"Hartmanns A, Junges S, Quatmann T, Weininger M. The revised practitioner’s guide to MDP model checking algorithms. <i>International Journal on Software Tools for Technology Transfer</i>. 2026. doi:<a href=\"https://doi.org/10.1007/s10009-026-00848-y\">10.1007/s10009-026-00848-y</a>"},"related_material":{"record":[{"id":"21668","relation":"software","status":"public"}]},"article_processing_charge":"Yes (in subscription journal)","title":"The revised practitioner’s guide to MDP model checking algorithms","month":"03","_id":"21661","ec_funded":1,"scopus_import":"1","author":[{"last_name":"Hartmanns","full_name":"Hartmanns, Arnd","first_name":"Arnd"},{"first_name":"Sebastian","full_name":"Junges, Sebastian","last_name":"Junges"},{"first_name":"Tim","last_name":"Quatmann","full_name":"Quatmann, Tim"},{"orcid":"0000-0002-0163-2152","first_name":"Maximilian","id":"02ab0197-cc70-11ed-ab61-918e71f56881","last_name":"Weininger","full_name":"Weininger, Maximilian"}],"keyword":["Quantitative model checking","Markov decision process","Linear programming","Value iteration","Policy iteration"],"publication":"International Journal on Software Tools for Technology Transfer","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10009-026-00848-y"}],"oa":1,"publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"acknowledgement":"This research was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreements 101008233 (MISSION)\r\nand 101034413 (IST-BRIDGE), by the Interreg North Sea project STORM_SAFE, by a KI-Starter grant from the Ministerium für Kultur und Wissenschaft NRW, by NWO VENI grant no. 639.021.754, and by NWO VIDI grant VI.Vidi.223.110 (TruSTy). Experiments were performed with computing resources granted by RWTH Aachen University under project rwth1632.","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"date_created":"2026-04-05T22:01:32Z","publication_status":"epub_ahead","abstract":[{"lang":"eng","text":"Model checking undiscounted reachability and expected-reward properties on Markov decision processes (MDPs) are key for the verification of systems that act under uncertainty. Popular algorithms are policy iteration and variants of value iteration; in tool competitions, most participants rely on the latter. These algorithms generally need worst-case exponential time. However, the problem can equally be formulated as a linear programme, solvable in polynomial time. In this paper, we give a detailed overview of today’s state-of-the-art algorithms for MDP model checking with a focus on performance and correctness. We highlight their fundamental differences, and describe various optimizations and implementation variants. We experimentally compare floating-point and exact-arithmetic implementations of all algorithms on three benchmark sets using two probabilistic model checkers. Our results show that (optimistic) value iteration is a sensible default, but other algorithms are preferable in specific settings. This paper thereby provides a guide for MDP verification practitioners—tool builders and users alike."}],"quality_controlled":"1"}]