[{"publication":"Journal of Physics: Condensed Matter","scopus_import":"1","oa_version":"Published Version","date_created":"2025-08-24T22:01:30Z","type":"journal_article","abstract":[{"lang":"eng","text":"Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner."}],"has_accepted_license":"1","external_id":{"isi":["001550090200001"],"arxiv":["2407.10623"]},"status":"public","citation":{"chicago":"Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>.","ieee":"G. Volpe <i>et al.</i>, “Roadmap for animate matter,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33. IOP Publishing, 2025.","ama":"Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. 2025;37(33). doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>","ista":"Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J, Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal of Physics: Condensed Matter. 37(33), 333501.","apa":"Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>","short":"G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J. Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng, D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth, C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani, T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong, D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong, Journal of Physics: Condensed Matter 37 (2025).","mla":"Volpe, Giorgio, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>."},"article_type":"original","language":[{"iso":"eng"}],"OA_place":"publisher","intvolume":"        37","date_updated":"2026-08-12T14:00:12Z","ddc":["530"],"arxiv":1,"OA_type":"hybrid","author":[{"full_name":"Volpe, Giorgio","first_name":"Giorgio","last_name":"Volpe"},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Guix, Maria","last_name":"Guix","first_name":"Maria"},{"last_name":"Miodownik","first_name":"Mark","full_name":"Miodownik, Mark"},{"full_name":"Martin, Nicolas","first_name":"Nicolas","last_name":"Martin"},{"full_name":"Alvarez, Laura","first_name":"Laura","last_name":"Alvarez"},{"last_name":"Simmchen","first_name":"Juliane","full_name":"Simmchen, Juliane"},{"first_name":"Roberto Di","last_name":"Leonardo","full_name":"Leonardo, Roberto Di"},{"full_name":"Pellicciotta, Nicola","last_name":"Pellicciotta","first_name":"Nicola"},{"last_name":"Martinet","orcid":"0000-0002-2916-6632","first_name":"Quentin","full_name":"Martinet, Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"},{"full_name":"Ng, Wai Kit","last_name":"Ng","first_name":"Wai Kit"},{"last_name":"Saxena","first_name":"Dhruv","full_name":"Saxena, Dhruv"},{"last_name":"Sapienza","first_name":"Riccardo","full_name":"Sapienza, Riccardo"},{"full_name":"Nadine, Sara","first_name":"Sara","last_name":"Nadine"},{"first_name":"João F.","last_name":"Mano","full_name":"Mano, João F."},{"first_name":"Reza","last_name":"Mahdavi","full_name":"Mahdavi, Reza"},{"last_name":"Beck Adiels","first_name":"Caroline","full_name":"Beck Adiels, Caroline"},{"last_name":"Forth","first_name":"Joe","full_name":"Forth, Joe"},{"full_name":"Santangelo, Christian","first_name":"Christian","last_name":"Santangelo"},{"full_name":"Palagi, Stefano","first_name":"Stefano","last_name":"Palagi"},{"full_name":"Seok, Ji Min","first_name":"Ji Min","last_name":"Seok"},{"full_name":"Webster-Wood, Victoria A.","last_name":"Webster-Wood","first_name":"Victoria A."},{"full_name":"Wang, Shuhong","first_name":"Shuhong","last_name":"Wang"},{"full_name":"Yao, Lining","first_name":"Lining","last_name":"Yao"},{"last_name":"Aghakhani","first_name":"Amirreza","full_name":"Aghakhani, Amirreza"},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"full_name":"Kellay, Hamid","first_name":"Hamid","last_name":"Kellay"},{"first_name":"Corentin","last_name":"Coulais","full_name":"Coulais, Corentin"},{"full_name":"Van Hecke, Martin","last_name":"Van Hecke","first_name":"Martin"},{"last_name":"Pierce","first_name":"Christopher J.","full_name":"Pierce, Christopher J."},{"full_name":"Wang, Tianyu","last_name":"Wang","first_name":"Tianyu"},{"first_name":"Baxi","last_name":"Chong","full_name":"Chong, Baxi"},{"last_name":"Goldman","first_name":"Daniel I.","full_name":"Goldman, Daniel I."},{"first_name":"Andreagiovanni","last_name":"Reina","full_name":"Reina, Andreagiovanni"},{"full_name":"Trianni, Vito","first_name":"Vito","last_name":"Trianni"},{"full_name":"Volpe, Giovanni","first_name":"Giovanni","last_name":"Volpe"},{"first_name":"Richard","last_name":"Beckett","full_name":"Beckett, Richard"},{"last_name":"Nair","first_name":"Sean P.","full_name":"Nair, Sean P."},{"full_name":"Armstrong, Rachel","last_name":"Armstrong","first_name":"Rachel"}],"year":"2025","publication_status":"published","file_date_updated":"2025-09-02T07:22:48Z","issue":"33","volume":37,"month":"08","date_published":"2025-08-18T00:00:00Z","_id":"20218","quality_controlled":"1","article_number":"333501","doi":"10.1088/1361-648X/adebd3","acknowledgement":"Living Architecture is Funded by the EU Horizon 2020 Future Emerging Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6 collaborating institutions—Newcastle University, University of Trento, University of the West of England, Spanish National Research Council, Explora Biotech and Liquifer Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE) project is funded by an EU Innovation Award for the development of a bio-digital ‘brick’ prototype, a collaboration between Newcastle University, Translating Nature, and the University of the West of England (2019–2021) under EU Grant Agreement No. 851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy) is Funded by the European Union under Grant Agreement Number 101114746, which is a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton (UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish National Research Council (Spain), and Associated Partners, the University of the West of England (UK) and University of Southampton (UK). Mi-Hy is also supported through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL).","isi":1,"file":[{"file_size":8997829,"checksum":"7309274f78bed785b158bd290337f456","success":1,"date_updated":"2025-09-02T07:22:48Z","file_name":"2025_CondensedMatter_Volpe.pdf","file_id":"20271","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2025-09-02T07:22:48Z","content_type":"application/pdf"}],"publisher":"IOP Publishing","article_processing_charge":"Yes (in subscription journal)","PlanS_conform":"1","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"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)"},"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Roadmap for animate matter","day":"18","department":[{"_id":"JePa"}]},{"publisher":"IOP Publishing","file":[{"file_size":1709516,"success":1,"checksum":"b182856a5a655496e149afa49ec464f3","date_updated":"2025-10-13T06:34:15Z","file_id":"20458","file_name":"2025_JourPhysicsCondMatter_Farooq.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_created":"2025-10-13T06:34:15Z"}],"doi":"10.1088/1361-648X/ae0913","isi":1,"acknowledgement":"We thank Kimberly A. Modic for her support and discussions regarding the technique in the context of a project indirectly related to, but distinct from, the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific discussions not directly related to this study, but whose insights proved helpful. We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain for informal discussions on various aspects of the technique, and to Naoya Iwahara for his thoughtful and constructive feedback. The experimental curve shown in figures 3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for granting access to the laboratory facilities. Je Geun Park provided the crystal used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge. Institutional support from the Institute of Science and Technology Austria (ISTA) is also gratefully acknowledged.","article_number":"405801","_id":"20453","quality_controlled":"1","date_published":"2025-10-06T00:00:00Z","department":[{"_id":"KiMo"}],"day":"06","oa":1,"title":"Non-linear magnetotropic susceptibility in FePS3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"PlanS_conform":"1","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)"},"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","date_updated":"2026-08-12T14:00:34Z","ddc":["530"],"OA_place":"publisher","intvolume":"        37","article_type":"original","citation":{"short":"H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).","mla":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40, 405801, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>.","ieee":"H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40. IOP Publishing, 2025.","ista":"Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. 37(40), 405801.","ama":"Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. 2025;37(40). doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>","apa":"Farooq, H., &#38; Nauman, M. (2025). Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>","chicago":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work."}],"status":"public","external_id":{"isi":["001585824100001"],"pmid":["40967257"]},"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","date_created":"2025-10-12T22:01:26Z","publication":"Journal of Physics: Condensed Matter","corr_author":"1","type":"journal_article","month":"10","issue":"40","volume":37,"file_date_updated":"2025-10-13T06:34:15Z","publication_status":"published","year":"2025","pmid":1,"author":[{"full_name":"Farooq, Hamza","last_name":"Farooq","first_name":"Hamza"},{"full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","orcid":"0000-0002-2111-4846","first_name":"Muhammad"}]},{"publisher":"Royal Society","isi":1,"doi":"10.1098/rsif.2025.0202","acknowledgement":"We acknowledge Prof. Uri Alon for introducing us to the topic of systems biology during the graduate course at the Weizmann Institute of Science, whose insights and teachings have greatly inspired this work.","article_number":"20250202","quality_controlled":"1","_id":"20219","date_published":"2025-08-13T00:00:00Z","department":[{"_id":"SyCr"}],"day":"13","title":"Interplay of asexual and sexual reproduction in bifunctional insects","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"article_processing_charge":"No","OA_type":"closed access","date_updated":"2026-08-12T14:09:20Z","intvolume":"        22","citation":{"chicago":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>.","short":"O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).","mla":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229, 20250202, Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>.","ama":"Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. 2025;22(229). doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>","ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.","ieee":"O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229. Royal Society, 2025.","apa":"Ayalon, O., &#38; Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>"},"article_type":"original","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction."}],"external_id":{"pmid":["40799050"],"isi":["001548084900001"]},"status":"public","oa_version":"None","publication":"Journal of the Royal Society Interface","scopus_import":"1","date_created":"2025-08-24T22:01:30Z","corr_author":"1","type":"journal_article","month":"08","issue":"229","volume":22,"publication_status":"published","year":"2025","pmid":1,"author":[{"full_name":"Ayalon, Oran","first_name":"Oran","last_name":"Ayalon"},{"last_name":"Rajendran","first_name":"Harikrishnan","full_name":"Rajendran, Harikrishnan","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416"}]},{"month":"05","year":"2025","publication_status":"submitted","biorxivid":1,"author":[{"first_name":"Adrián","last_name":"Cárdenas","full_name":"Cárdenas, Adrián"},{"last_name":"Çelik","first_name":"Irem","full_name":"Çelik, Irem"},{"first_name":"Alexandre","last_name":"Espinós","full_name":"Espinós, Alexandre"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"first_name":"Lara","last_name":"López-González","full_name":"López-González, Lara"},{"full_name":"del-Valle-Anton, Lucia","first_name":"Lucia","last_name":"del-Valle-Anton"},{"last_name":"Fernández","first_name":"Virginia","full_name":"Fernández, Virginia"},{"full_name":"Amin, Salma","first_name":"Salma","last_name":"Amin"},{"first_name":"Enrico","last_name":"Negri","full_name":"Negri, Enrico"},{"first_name":"Eduardo Fernández","last_name":"Ortuño","full_name":"Ortuño, Eduardo Fernández"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"last_name":"Borrell","first_name":"Víctor","full_name":"Borrell, Víctor"}],"project":[{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"OA_type":"green","OA_place":"repository","date_updated":"2026-08-13T07:18:38Z","citation":{"mla":"Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","short":"A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton, V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv (n.d.).","apa":"Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton, L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>","ista":"Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","ama":"Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>","ieee":"A. Cárdenas <i>et al.</i>, “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” <i>bioRxiv</i>. .","chicago":"Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>."},"language":[{"iso":"eng"}],"publication":"bioRxiv","oa_version":"Preprint","date_created":"2025-05-29T10:45:55Z","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.22.655488"}],"abstract":[{"lang":"eng","text":"The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process."}],"status":"public","external_id":{"biorxivid":["10.1101/2025.05.22.655488"]},"day":"23","department":[{"_id":"SiHi"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development","article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"doi":"10.1101/2025.05.22.655488","acknowledgement":"We thank A. Iñigo for assistance with imaging, and members of the Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency (AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1) to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship (JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012) to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council (101118729) to V.B., who also acknowledges financial support from AEI through the “Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S).","_id":"19762","date_published":"2025-05-23T00:00:00Z"},{"author":[{"last_name":"Varela-Martínez","first_name":"I","full_name":"Varela-Martínez, I"},{"last_name":"Villalba Requena","orcid":"0000-0002-5615-5277","first_name":"Ana","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247"},{"first_name":"J.","last_name":"Garcia-Marqués","full_name":"Garcia-Marqués, J."},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M.","last_name":"Nieto","full_name":"Nieto, M."}],"article_processing_charge":"No","year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","oa":1,"title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","day":"07","department":[{"_id":"SiHi"}],"month":"05","publication":"bioRxiv","oa_version":"Preprint","date_created":"2025-05-20T10:19:29Z","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.07.652665","open_access":"1"}],"type":"preprint","abstract":[{"text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.","lang":"eng"}],"status":"public","_id":"19717","date_published":"2025-05-07T00:00:00Z","citation":{"chicago":"Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>.","mla":"Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.).","apa":"Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., &#38; Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>","ieee":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” <i>bioRxiv</i>. .","ama":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>","ista":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>."},"language":[{"iso":"eng"}],"OA_place":"repository","date_updated":"2026-08-13T07:16:48Z","doi":"10.1101/2025.05.07.652665","OA_type":"green","acknowledgement":"We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n"},{"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)"},"article_processing_charge":"No","title":"ResiDual transformer alignment with spectral decomposition","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"day":"14","article_number":"2411.00246","_id":"19674","date_published":"2025-04-14T00:00:00Z","doi":"10.48550/arXiv.2411.00246","acknowledgement":"The authors gratefully acknowledge Volkan Cevher for an insightful discussion about sparse recovery algorithms, Alex Smola for valuable feedback on the experiments, and Marco Baroni for an engaging conversation on the phenomenon of head specialization in NLP.\r\n","author":[{"full_name":"Basile, Lorenzo","first_name":"Lorenzo","last_name":"Basile"},{"last_name":"Maiorca","first_name":"Valentino","full_name":"Maiorca, Valentino"},{"last_name":"Bortolussi","first_name":"Luca","full_name":"Bortolussi, Luca"},{"first_name":"Emanuele","last_name":"Rodolà","full_name":"Rodolà, Emanuele"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"publication_status":"submitted","year":"2025","month":"04","external_id":{"arxiv":["2411.00246"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets)."}],"type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.00246","open_access":"1"}],"publication":"arXiv","date_created":"2025-05-11T22:02:41Z","oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"apa":"Basile, L., Maiorca, V., Bortolussi, L., Rodolà, E., &#38; Locatello, F. (n.d.). ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>","ieee":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, and F. Locatello, “ResiDual transformer alignment with spectral decomposition,” <i>arXiv</i>. .","ama":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>","ista":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246.","mla":"Basile, Lorenzo, et al. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, 2411.00246, doi:<a href=\"https://doi.org/10.48550/arXiv.2411.00246\">10.48550/arXiv.2411.00246</a>.","short":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.).","chicago":"Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>."},"ddc":["000"],"arxiv":1,"date_updated":"2026-08-13T07:33:41Z","OA_place":"repository","OA_type":"green"},{"month":"08","publication_status":"published","file_date_updated":"2026-08-13T13:05:36Z","year":"2025","page":"171","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"first_name":"Hanna","last_name":"Schön","id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","full_name":"Schön, Hanna"}],"alternative_title":["ISTA Thesis"],"doi_confirm":"1","project":[{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"},{"_id":"23813290-32DE-11EA-91FC-C7463DDC885E","name":"Control of gene expression at the endoplasmic reticulum","grant_number":"ALTF 302-2019"}],"date_updated":"2026-08-13T13:05:37Z","ddc":["570"],"OA_place":"publisher","citation":{"ama":"Schön H. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>","ista":"Schön H. 2025. The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs. Institute of Science and Technology Austria.","ieee":"H. Schön, “The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs,” Institute of Science and Technology Austria, 2025.","apa":"Schön, H. (2025). <i>The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>","short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","mla":"Schön, Hanna. <i>The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20167\">10.15479/AT-ISTA-20167</a>.","chicago":"Schön, Hanna. “The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20167\">https://doi.org/10.15479/AT-ISTA-20167</a>."},"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","oa_version":"Published Version","date_created":"2025-08-13T11:13:13Z","type":"dissertation","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"day":"13","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-061-9"],"issn":["2663-337X"]},"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)"},"article_processing_charge":"No","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT-ISTA-20167","acknowledgement":"This work was supported by EMBO (ALTF 302-2019 to Niko Amin-Wetzel), the FWF\r\n(ESPRIT PR1054E140 to Niko Amin-Wetzel), the European Research Council\r\n(Advanced Grant 269058 to Mario de Bono) and Wellcome (209504/A/17/Z\r\nInvestigator Award to Mario de Bono). ","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2025-09-08T14:33:50Z","relation":"source_file","creator":"hschoen","access_level":"closed","checksum":"b40c74404b8d9593802dabf57bfdf10f","date_updated":"2025-09-09T08:57:04Z","file_id":"20311","file_name":"2025_Schoen_Hanna_Thesis.docx","file_size":78812587},{"file_size":9667057,"embargo_to":"open_access","checksum":"16abc3ff66396ce2457fe07ffa8bed90","file_id":"20347","file_name":"2025_Schoen_Hanna_Thesis.pdf","embargo":"2027-03-15","date_updated":"2026-08-13T13:05:36Z","creator":"hschoen","relation":"main_file","access_level":"closed","content_type":"application/pdf","date_created":"2025-09-11T14:20:59Z"}],"_id":"20167","date_published":"2025-08-13T00:00:00Z","supervisor":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443"}]},{"article_number":"169465","_id":"20538","quality_controlled":"1","date_published":"2025-12-01T00:00:00Z","publisher":"Elsevier","doi":"10.1016/j.jmb.2025.169465","acknowledgement":"A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70.","file":[{"content_type":"application/pdf","date_created":"2025-12-30T10:29:08Z","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"checksum":"feb92f9c79032c261165f4ca573f444a","file_id":"20915","file_name":"2025_JourMolecularBiology_Knoedlstorfer.pdf","date_updated":"2025-12-30T10:29:08Z","file_size":3076611}],"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)"},"PlanS_conform":"1","publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"PaSc"},{"_id":"GradSch"}],"day":"01","title":"A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"citation":{"ama":"Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>","ieee":"S. Knödlstorfer <i>et al.</i>, “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.","ista":"Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465.","apa":"Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>","short":"S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025).","mla":"Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169465, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>.","chicago":"Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>."},"article_type":"original","external_id":{"pmid":["41016549"]},"has_accepted_license":"1","status":"public","abstract":[{"text":"In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins.","lang":"eng"}],"type":"journal_article","date_created":"2025-10-26T23:01:35Z","scopus_import":"1","oa_version":"Published Version","publication":"Journal of Molecular Biology","project":[{"name":"Structure and mechanism of the mitochondrial MIM insertase","_id":"bdb9578d-d553-11ed-ba76-ed5d39fce6f0","grant_number":"I06223"},{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"}],"OA_type":"hybrid","ddc":["540"],"date_updated":"2026-08-13T14:19:02Z","OA_place":"publisher","intvolume":"       437","pmid":1,"author":[{"full_name":"Knödlstorfer, Sonja","last_name":"Knödlstorfer","first_name":"Sonja"},{"first_name":"Giorgia","last_name":"Toscano","full_name":"Toscano, Giorgia","id":"334a5e40-8747-11f0-b671-ba1f5154b4b4"},{"full_name":"Ptaszek, Aleksandra L.","last_name":"Ptaszek","first_name":"Aleksandra L."},{"last_name":"Kontaxis","first_name":"Georg","full_name":"Kontaxis, Georg"},{"last_name":"Napoli","orcid":"0000-0002-9043-136X","first_name":"Federico","full_name":"Napoli, Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b"},{"id":"64368429-eb97-11eb-a6c2-c980b1f44415","full_name":"Schneider, Jakob","last_name":"Schneider","first_name":"Jakob"},{"full_name":"Maier, Katharina","last_name":"Maier","first_name":"Katharina"},{"first_name":"Anna","last_name":"Kapitonova","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","full_name":"Kapitonova, Anna"},{"last_name":"Lichtenecker","first_name":"Roman J.","full_name":"Lichtenecker, Roman J."},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"}],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"month":"12","volume":437,"issue":"23","file_date_updated":"2025-12-30T10:29:08Z","publication_status":"published","year":"2025"},{"date_published":"2025-12-01T00:00:00Z","_id":"20258","quality_controlled":"1","article_number":"169379","file":[{"content_type":"application/pdf","date_created":"2025-12-29T14:51:40Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2025_JourMolecularBiology_Rohden.pdf","file_id":"20876","date_updated":"2025-12-29T14:51:40Z","checksum":"90d50594d8ea9860ac5da41297992847","success":1,"file_size":2270555}],"doi":"10.1016/j.jmb.2025.169379","acknowledgement":"This work was supported financially by the Austrian Science Fund (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent support of the NMR facility.","isi":1,"publisher":"Elsevier","article_processing_charge":"Yes (via OA deal)","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)"},"publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"PlanS_conform":"1","day":"01","department":[{"_id":"PaSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme","oa":1,"language":[{"iso":"eng"}],"citation":{"short":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda, Journal of Molecular Biology 437 (2025).","mla":"Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169379, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>.","ista":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 437(23), 169379.","ama":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>","ieee":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P. Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.","apa":"Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., &#38; Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>","chicago":"Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>."},"article_type":"original","corr_author":"1","type":"journal_article","oa_version":"Published Version","publication":"Journal of Molecular Biology","scopus_import":"1","date_created":"2025-08-31T22:01:33Z","external_id":{"isi":["001618289100020"]},"has_accepted_license":"1","status":"public","abstract":[{"text":"The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR.","lang":"eng"}],"OA_type":"hybrid","project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812"}],"intvolume":"       437","OA_place":"publisher","ddc":["540"],"date_updated":"2026-08-13T14:19:01Z","author":[{"last_name":"Rohden","first_name":"Darja","id":"81dc668a-19fa-11f0-bf31-d56534059ef3","full_name":"Rohden, Darja"},{"full_name":"Napoli, Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","orcid":"0000-0002-9043-136X","first_name":"Federico","last_name":"Napoli"},{"full_name":"Kapitonova, Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","first_name":"Anna","last_name":"Kapitonova"},{"last_name":"Tatman","first_name":"Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f","full_name":"Tatman, Benjamin"},{"full_name":"Lichtenecker, Roman J.","last_name":"Lichtenecker","first_name":"Roman J."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"volume":437,"issue":"23","related_material":{"record":[{"relation":"research_data","id":"19956","status":"public"}]},"month":"12","year":"2025","file_date_updated":"2025-12-29T14:51:40Z","publication_status":"published"},{"doi":"10.15479/AT-ISTA-19956","file":[{"content_type":"application/octet-stream","date_created":"2025-07-03T10:30:14Z","creator":"pschanda","relation":"main_file","access_level":"open_access","success":1,"checksum":"a2ef61aa9fb5313c7d426913eb0482c0","file_id":"19960","file_name":"README","date_updated":"2025-07-03T10:30:14Z","file_size":1160},{"access_level":"open_access","creator":"pschanda","relation":"main_file","date_created":"2025-07-03T10:30:55Z","content_type":"application/zip","file_size":128597184,"file_id":"19961","file_name":"data_Arg_MASNMR_Rohden.zip","date_updated":"2025-07-03T10:30:55Z","checksum":"8fb77b96d0fcc95c9903005652207a8c","success":1},{"relation":"main_file","creator":"pschanda","access_level":"open_access","date_created":"2025-08-14T07:06:58Z","content_type":"application/x-xz","file_size":4766564,"checksum":"a60cc16d20b089c4bef94040a99cfba5","success":1,"date_updated":"2025-08-14T07:06:58Z","file_id":"20172","file_name":"20240903_ubi_DN_Argd1C13_2D_spectra.tar.xz"}],"publisher":"Institute of Science and Technology Austria","_id":"19956","date_published":"2025-07-03T00:00:00Z","day":"03","department":[{"_id":"PaSc"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","license":"https://creativecommons.org/licenses/by-nc/4.0/","title":"Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812"}],"ddc":["572"],"date_updated":"2026-08-13T14:19:01Z","citation":{"ista":"Schanda P. 2025. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>.","ama":"Schanda P. Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>","ieee":"P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025.","apa":"Schanda, P. (2025). Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">https://doi.org/10.15479/AT-ISTA-19956</a>","short":"P. Schanda, (2025).","mla":"Schanda, Paul. <i>Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19956\">10.15479/AT-ISTA-19956</a>.","chicago":"Schanda, Paul. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19956\">https://doi.org/10.15479/AT-ISTA-19956</a>."},"type":"research_data","corr_author":"1","oa_version":"Published Version","date_created":"2025-07-03T04:21:37Z","has_accepted_license":"1","status":"public","abstract":[{"text":"The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"20258","relation":"used_in_publication"}]},"month":"07","year":"2025","contributor":[{"contributor_type":"researcher","last_name":"Rohden","first_name":"Darja"},{"first_name":"Federico","last_name":"Napoli","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Ben","last_name":"Tatman"},{"contributor_type":"researcher","last_name":"Schanda","first_name":"Paul"}],"file_date_updated":"2025-08-14T07:06:58Z","author":[{"first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}]},{"_id":"19395","date_published":"2025-03-13T00:00:00Z","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","file":[{"date_created":"2025-03-12T14:14:49Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"amonzer","date_updated":"2025-03-12T14:14:49Z","file_id":"19396","file_name":"Final Thesis Aline Monzer.pdf","success":1,"checksum":"9a3dd03bb4ec6b9907a325c3c4e8a1d7","file_size":13119670},{"access_level":"closed","relation":"source_file","creator":"amonzer","date_created":"2025-03-12T14:15:19Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":13774837,"date_updated":"2025-04-01T07:55:27Z","file_id":"19397","file_name":"Thesis Aline.docx","checksum":"a353ce1ee2eabce37bca35499e76dbf1"}],"doi":"10.15479/AT-ISTA-19395","acknowledgement":"I would like to acknowledge the facilities at ISTA, particularly LSF, IOF, and, of course, the plant facility, for providing the necessary resources for my research.","publication_identifier":{"eissn":["2663-337X"],"eisbn":["978-3-99078-054-1"]},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"day":"13","title":"Cell-surface auxin signaling: Linking molecular pathways to plant development","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"citation":{"ista":"Monzer A. 2025. Cell-surface auxin signaling: Linking molecular pathways to plant development. Institute of Science and Technology Austria.","ieee":"A. Monzer, “Cell-surface auxin signaling: Linking molecular pathways to plant development,” Institute of Science and Technology Austria, 2025.","ama":"Monzer A. Cell-surface auxin signaling: Linking molecular pathways to plant development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>","apa":"Monzer, A. (2025). <i>Cell-surface auxin signaling: Linking molecular pathways to plant development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>","short":"A. Monzer, Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development, Institute of Science and Technology Austria, 2025.","mla":"Monzer, Aline. <i>Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19395\">10.15479/AT-ISTA-19395</a>.","chicago":"Monzer, Aline. “Cell-Surface Auxin Signaling: Linking Molecular Pathways to Plant Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19395\">https://doi.org/10.15479/AT-ISTA-19395</a>."},"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Plant growth and development rely significantly on phytohormones, with auxin serving as a master regulator, orchestrating processes from embryogenesis to organogenesis, vascular patterning, and environmental adaptation. Since its conceptual proposition by Charles Darwin in 1880 as an endogenous chemical signal influencing phototropism in grass, auxin has captivated scientists seeking to understand how such a small molecule exerts a profound influence on plant development.\r\nOne particularly fascinating aspect of auxin function is its ability to self-organize its transport. Through a feedback mechanism between auxin perception and directional transport—primarily mediated by PIN auxin transporters—auxin establishes narrow transport channels. This phenomenon, known as auxin canalization, is fundamental to vascular formation, regeneration, and other key developmental processes. Despite advances in our understanding, driven by experimental studies and computational models, auxin canalization remains an enigma, with many unanswered questions.\r\nLike other hormones, auxin functions through intricate signaling pathways. It operates through at least two distinct signaling mechanisms: the well-characterized canonical pathway and the less understood non-canonical pathway. While significant progress has been made in elucidating the canonical pathway, the non-canonical mechanisms remain less defined and require further investigation.\r\nIn this study, we revisit the non-canonical auxin signaling pathway mediated by the cell-surface complex Auxin Binding Protein 1-Transmembrane Kinase 1 (ABP1-TMK1), with a particular focus on its downstream phosphorylation events. We reveal that this auxin-mediated phosphorylation is conserved across the green lineage, underscoring its fundamental role in plant development. We explore key phosphorylation targets, particularly PIN2, which is essential for root gravitropism. To further understand TMK1’s role in diverse developmental processes, we identified and investigated its interactors as potential co-receptors or regulatory components within its signaling network.\r\nGiven the previously established role of ABP1-TMK1 in auxin canalization, we sought to further investigate this process and identified several TMK1 interactors also involved in this intricate mechanism.\r\nThese findings provide new insights into the complex regulation of auxin canalization, highlighting a broader and more interconnected signaling framework than previously understood."}],"type":"dissertation","corr_author":"1","oa_version":"Published Version","date_created":"2025-03-12T14:25:42Z","doi_confirm":"1","ddc":["580"],"date_updated":"2026-08-14T09:33:46Z","OA_place":"publisher","page":"160","author":[{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"alternative_title":["ISTA Thesis"],"month":"03","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12291"},{"relation":"part_of_dissertation","status":"public","id":"14826"},{"status":"public","id":"19399","relation":"part_of_dissertation"},{"id":"19398","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2025-04-01T07:55:27Z","publication_status":"published","year":"2025"},{"das_tickbox":"1","_id":"19399","date_published":"2025-02-20T00:00:00Z","doi":"10.1101/2022.11.30.518503","acknowledgement":"We thank W. Gray for providing material; N. Gnyliukh and E. Cervenova for help with manuscript preparation; J. Schmid for help with cloning. We thank Dolf Weijers, Mark Roosjen, and Andre Kuhn for discussions and support with phospho-proteomic analyses. We thank the Bioimaging and Life Science facilities at ISTA for their excellent service and assistance. The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F; National Natural Science Foundation of China (Grant 32130010, 31422008), start-up funds from FAFU to T.X., Y.J. was funded by ERC no. 3363360-APPL under FP/2007-2013. L.R. was supported by FP7-PEOPLE-2011-COFUND ISTFELLOW program (IC1023FELL01) and the European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 985- 2016). S.T. was supported by the National Natural Science Foundation of China (32321001).","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism","day":"20","department":[{"_id":"JiFr"},{"_id":"XiFe"}],"date_created":"2025-03-13T08:36:48Z","publication":"bioRxiv","oa_version":"Published Version","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.11.30.518503"}],"corr_author":"1","abstract":[{"text":"Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.","lang":"eng"}],"status":"public","ec_funded":1,"citation":{"mla":"Rodriguez Solovey, Lesia, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","short":"L. Rodriguez Solovey, L. Fiedler, M. Zou, C. Giannini, A. Monzer, D. Vladimirtsev, M. Randuch, Y. Yu, Z. Gelová, I. Verstraeten, J. Hajny, M. Chen, S. Tan, L. Hörmayer, L. Li, M.M. Marques-Bueno, Z. Quddoos, G. Molnar, T. Xu, I. Kulich, Y. Jaillais, J. Friml, BioRxiv (n.d.).","apa":"Rodriguez Solovey, L., Fiedler, L., Zou, M., Giannini, C., Monzer, A., Vladimirtsev, D., … Friml, J. (n.d.). ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>","ista":"Rodriguez Solovey L, Fiedler L, Zou M, Giannini C, Monzer A, Vladimirtsev D, Randuch M, Yu Y, Gelová Z, Verstraeten I, Hajny J, Chen M, Tan S, Hörmayer L, Li L, Marques-Bueno MM, Quddoos Z, Molnar G, Xu T, Kulich I, Jaillais Y, Friml J. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. bioRxiv, <a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>.","ama":"Rodriguez Solovey L, Fiedler L, Zou M, et al. ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.11.30.518503\">10.1101/2022.11.30.518503</a>","ieee":"L. Rodriguez Solovey <i>et al.</i>, “ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism,” <i>bioRxiv</i>. .","chicago":"Rodriguez Solovey, Lesia, Lukas Fiedler, Minxia Zou, Caterina Giannini, Aline Monzer, Dmitrii Vladimirtsev, Marek Randuch, et al. “ABP1/ABL3-TMK1 Cell-Surface Auxin Signaling Directly Targets PIN2-Mediated Auxin Fluxes for Root Gravitropism.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.11.30.518503\">https://doi.org/10.1101/2022.11.30.518503</a>."},"language":[{"iso":"eng"}],"OA_place":"repository","date_updated":"2026-08-14T09:33:45Z","ddc":["580"],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"ALTF 985-2016","_id":"26060676-B435-11E9-9278-68D0E5697425","name":"Cell surface receptor complexes for auxin signaling in plants"}],"OA_type":"green","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237"},{"first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Minxia","last_name":"Zou","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"first_name":"Dmitrii","last_name":"Vladimirtsev","id":"60466724-5355-11ee-ae5a-fa55e8f99c3d","full_name":"Vladimirtsev, Dmitrii"},{"last_name":"Randuch","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek"},{"full_name":"Yu, Yongfan","first_name":"Yongfan","last_name":"Yu"},{"full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"full_name":"Chen, Meng","last_name":"Chen","first_name":"Meng"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","first_name":"Shutang","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X"},{"full_name":"Marques-Bueno, Maria Mar","first_name":"Maria Mar","last_name":"Marques-Bueno"},{"id":"32ff3c64-04a0-11f0-a50f-d0c45bfac466","full_name":"Quddoos, Zainab","last_name":"Quddoos","first_name":"Zainab"},{"first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"first_name":"Ivan","last_name":"Kulich","full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54"},{"first_name":"Yvon","last_name":"Jaillais","full_name":"Jaillais, Yvon"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2025","publication_status":"draft","related_material":{"record":[{"relation":"later_version","id":"20656","status":"public"},{"id":"20364","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"19395","status":"public"}]},"month":"02"},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No","title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"day":"02","das_tickbox":"1","date_published":"2025-03-02T00:00:00Z","_id":"19398","doi":"10.1101/2025.02.28.640727","acknowledgement":"We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance.","author":[{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"first_name":"Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"last_name":"Smejkal","first_name":"Michael","full_name":"Smejkal, Michael","id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9"},{"first_name":"Ema","last_name":"Cervenova","full_name":"Cervenova, Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_status":"draft","year":"2025","month":"03","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"}]},"has_accepted_license":"1","status":"public","abstract":[{"text":"Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.","lang":"eng"}],"corr_author":"1","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.02.28.640727"}],"date_created":"2025-03-12T14:28:53Z","oa_version":"Published Version","publication":"bioRxiv","language":[{"iso":"eng"}],"citation":{"chicago":"Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>.","apa":"Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>","ieee":"A. Monzer <i>et al.</i>, “TMK interacting network of receptor like kinases for auxin canalization and beyond,” <i>bioRxiv</i>. .","ista":"Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","ama":"Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>","mla":"Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","short":"A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.)."},"ddc":["580"],"date_updated":"2026-08-14T09:33:45Z","OA_place":"repository","OA_type":"green"},{"article_processing_charge":"No","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)"},"publication_identifier":{"isbn":["9783959773720"]},"day":"30","department":[{"_id":"MoHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Incremental approximate maximum flow via residual graph sparsification","oa":1,"quality_controlled":"1","_id":"21280","date_published":"2025-06-30T00:00:00Z","file":[{"date_created":"2026-02-18T09:02:33Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"21315","file_name":"2025_ICALP_Goranci.pdf","date_updated":"2026-02-18T09:02:33Z","success":1,"checksum":"c178cf554e44204b9f64ebd9b54cf7ba","file_size":944824}],"acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI\r\n10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Harald Räcke: This project has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 498605858 and 470029389.","doi":"10.4230/lipics.icalp.2025.91","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Aarhus, Denmark","start_date":"2025-07-08","end_date":"2025-07-11"},"page":"91:1-91:20","alternative_title":["LIPIcs"],"author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Räcke, Harald","first_name":"Harald","last_name":"Räcke"},{"last_name":"Sricharan","first_name":"A.","full_name":"Sricharan, A."}],"volume":334,"related_material":{"record":[{"status":"public","id":"22716","relation":"later_version"}]},"month":"06","year":"2025","publication_status":"published","file_date_updated":"2026-02-18T09:02:33Z","language":[{"iso":"eng"}],"citation":{"chicago":"Goranci, Gramoz, Monika Henzinger, Harald Räcke, and A. Sricharan. “Incremental Approximate Maximum Flow via Residual Graph Sparsification.” In <i>52nd International Colloquium on Automata, Languages, and Programming</i>, 334:91:1-91:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025. <a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">https://doi.org/10.4230/lipics.icalp.2025.91</a>.","ama":"Goranci G, Henzinger M, Räcke H, Sricharan A. Incremental approximate maximum flow via residual graph sparsification. In: <i>52nd International Colloquium on Automata, Languages, and Programming</i>. Vol 334. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2025:91:1-91:20. doi:<a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">10.4230/lipics.icalp.2025.91</a>","ieee":"G. Goranci, M. Henzinger, H. Räcke, and A. Sricharan, “Incremental approximate maximum flow via residual graph sparsification,” in <i>52nd International Colloquium on Automata, Languages, and Programming</i>, Aarhus, Denmark, 2025, vol. 334, p. 91:1-91:20.","ista":"Goranci G, Henzinger M, Räcke H, Sricharan A. 2025. Incremental approximate maximum flow via residual graph sparsification. 52nd International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 334, 91:1-91:20.","apa":"Goranci, G., Henzinger, M., Räcke, H., &#38; Sricharan, A. (2025). Incremental approximate maximum flow via residual graph sparsification. In <i>52nd International Colloquium on Automata, Languages, and Programming</i> (Vol. 334, p. 91:1-91:20). Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">https://doi.org/10.4230/lipics.icalp.2025.91</a>","short":"G. Goranci, M. Henzinger, H. Räcke, A. Sricharan, in:, 52nd International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 91:1-91:20.","mla":"Goranci, Gramoz, et al. “Incremental Approximate Maximum Flow via Residual Graph Sparsification.” <i>52nd International Colloquium on Automata, Languages, and Programming</i>, vol. 334, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2025, p. 91:1-91:20, doi:<a href=\"https://doi.org/10.4230/lipics.icalp.2025.91\">10.4230/lipics.icalp.2025.91</a>."},"ec_funded":1,"corr_author":"1","type":"conference","date_created":"2026-02-17T08:26:06Z","oa_version":"Published Version","scopus_import":"1","publication":"52nd International Colloquium on Automata, Languages, and Programming","external_id":{"arxiv":["2502.09105"]},"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"We give an algorithm that, with high probability, maintains a (1-ε)-approximate s-t maximum flow in undirected, uncapacitated n-vertex graphs undergoing m edge insertions in Õ(m+ n F^*/ε) total update time, where F^{*} is the maximum flow on the final graph. This is the first algorithm to achieve polylogarithmic amortized update time for dense graphs (m = Ω(n²)), and more generally, for graphs where F^* = Õ(m/n). At the heart of our incremental algorithm is the residual graph sparsification technique of Karger and Levine [SICOMP '15], originally designed for computing exact maximum flows in the static setting. Our main contributions are (i) showing how to maintain such sparsifiers for approximate maximum flows in the incremental setting and (ii) generalizing the cut sparsification framework of Fung et al. [SICOMP '19] from undirected graphs to balanced directed graphs."}],"OA_type":"gold","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"intvolume":"       334","OA_place":"publisher","arxiv":1,"ddc":["000"],"date_updated":"2026-08-20T06:28:00Z"},{"page":"141-172","alternative_title":["LNCS"],"author":[{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","full_name":"Auerbach, Benedikt","last_name":"Auerbach","first_name":"Benedikt","orcid":"0000-0002-7553-6606"},{"orcid":"0000-0002-2505-4246","first_name":"Miguel","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc"},{"last_name":"Erol","first_name":"Boran","full_name":"Erol, Boran"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"22664","status":"public"}]},"volume":16007,"month":"08","year":"2025","publication_status":"published","citation":{"apa":"Auerbach, B., Cueto Noval, M., Erol, B., &#38; Pietrzak, K. Z. (2025). Continuous group-key agreement: Concurrent updates without pruning. In <i>45th Annual International Cryptology Conference</i> (Vol. 16007, pp. 141–172). Santa Barbara, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">https://doi.org/10.1007/978-3-032-01913-4_5</a>","ieee":"B. Auerbach, M. Cueto Noval, B. Erol, and K. Z. Pietrzak, “Continuous group-key agreement: Concurrent updates without pruning,” in <i>45th Annual International Cryptology Conference</i>, Santa Barbara, CA, United States, 2025, vol. 16007, pp. 141–172.","ama":"Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. Continuous group-key agreement: Concurrent updates without pruning. In: <i>45th Annual International Cryptology Conference</i>. Vol 16007. Springer Nature; 2025:141-172. doi:<a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">10.1007/978-3-032-01913-4_5</a>","ista":"Auerbach B, Cueto Noval M, Erol B, Pietrzak KZ. 2025. Continuous group-key agreement: Concurrent updates without pruning. 45th Annual International Cryptology Conference. CRYPTO: International Cryptology Conference, LNCS, vol. 16007, 141–172.","mla":"Auerbach, Benedikt, et al. “Continuous Group-Key Agreement: Concurrent Updates without Pruning.” <i>45th Annual International Cryptology Conference</i>, vol. 16007, Springer Nature, 2025, pp. 141–72, doi:<a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">10.1007/978-3-032-01913-4_5</a>.","short":"B. Auerbach, M. Cueto Noval, B. Erol, K.Z. Pietrzak, in:, 45th Annual International Cryptology Conference, Springer Nature, 2025, pp. 141–172.","chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Boran Erol, and Krzysztof Z Pietrzak. “Continuous Group-Key Agreement: Concurrent Updates without Pruning.” In <i>45th Annual International Cryptology Conference</i>, 16007:141–72. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-3-032-01913-4_5\">https://doi.org/10.1007/978-3-032-01913-4_5</a>."},"language":[{"iso":"eng"}],"date_created":"2026-02-17T07:41:04Z","oa_version":"Preprint","publication":"45th Annual International Cryptology Conference","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/1035"}],"type":"conference","abstract":[{"text":"Continuous Group Key Agreement (CGKA) is the primitive underlying secure group messaging. It allows a large group of N users to maintain a shared secret key that is frequently rotated by the\r\ngroup members in order to achieve forward secrecy and post compromise security. The group messaging scheme Messaging Layer Security (MLS) standardized by the IETF makes use of a CGKA called TreeKEM which arranges the N group members in a binary tree. Here, each node is associated with a public-key, each user is assigned one of the leaves, and a user knows the corresponding secret keys from their leaf to the root. To update the key material known to them, a user must just replace keys at log(N) nodes, which requires them to create and upload log(N) ciphertexts. Such updates must be processed sequentially by all users, which for large groups is impractical. To allow for concurrent updates, TreeKEM uses the “propose and commit” paradigm, where multiple users can concurrently propose to update (by just sampling a fresh leaf key), and a single user can then commit to all proposals at once. Unfortunately, this process destroys the binary tree structure as the tree gets pruned and some nodes must be “blanked” at the cost of increasing the in-degree of others, which makes the commit operation, as well as, future commits more costly. In the worst case, the update cost (in terms of uploaded ciphertexts) per user can grow from log(N) to Ω(N). In this work we provide two main contributions. First, we show that MLS’ communication complexity is bad not only in the worst case but also if the proposers and committers are chosen at random: even if there’s just one update proposal for every commit the expected cost is already over √N, and it approaches N as this ratio changes towards more proposals. Our second contribution is a new variant of propose and commit for\r\nTreeKEM which for moderate amounts of update proposals per commit provably achieves an update cost of Θ(log(N)) assuming the proposers and committers are chosen at random.","lang":"eng"}],"status":"public","OA_type":"green","intvolume":"     16007","OA_place":"repository","date_updated":"2026-08-21T10:53:16Z","article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783032019134"],"eissn":["1611-3349"],"isbn":["9783032019127"]},"day":"17","department":[{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Continuous group-key agreement: Concurrent updates without pruning","quality_controlled":"1","_id":"21262","date_published":"2025-08-17T00:00:00Z","doi":"10.1007/978-3-032-01913-4_5","acknowledgement":"B. Auerbach and B. Erol—Conducted part of this work at ISTA.","publisher":"Springer Nature","conference":{"name":"CRYPTO: International Cryptology Conference","start_date":"2025-08-17","location":"Santa Barbara, CA, United States","end_date":"2025-08-21"}},{"corr_author":"1","type":"journal_article","oa_version":"Published Version","publication":"Nature","scopus_import":"1","date_created":"2025-03-02T23:01:52Z","status":"public","external_id":{"isi":["001428076100015"],"pmid":["39972227"]},"has_accepted_license":"1","abstract":[{"text":"When two insulating, neutral materials are contacted and separated, they exchange electrical charge1. Experiments have long suggested that this ‘contact electrification’ is transitive, with different materials ordering into ‘triboelectric series’ based on the sign of charge acquired2. At the same time, the effect is plagued by unpredictability, preventing consensus on the mechanism and casting doubt on the rhyme and reason that series imply3. Here we expose an unanticipated connection between the unpredictability and order in contact electrification: nominally identical materials initially exchange charge randomly and intransitively, but—over repeated experiments—order into triboelectric series. We find that this evolution is driven by the act of contact itself—samples with more contacts in their history charge negatively to ones with fewer contacts. Capturing this ‘contact bias’ in a minimal model, we recreate both the initial randomness and ultimate order in numerical simulations and use it experimentally to force the appearance of a triboelectric series of our choosing. With a set of surface-sensitive techniques to search for the underlying alterations contact creates, we only find evidence of nanoscale morphological changes, pointing to a mechanism strongly coupled with mechanics. Our results highlight the centrality of contact history in contact electrification and suggest that focusing on the unpredictability that has long plagued the effect may hold the key to understanding it.","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"apa":"Sobarzo Ponce, J. C. A., Pertl, F., Balazs, D., Costanzo, T., Sauer, M., Foelske, A., … Waitukaitis, S. R. (2025). Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>","ieee":"J. C. A. Sobarzo Ponce <i>et al.</i>, “Spontaneous ordering of identical materials into a triboelectric series,” <i>Nature</i>, vol. 638, no. 8051. Springer Nature, 2025.","ama":"Sobarzo Ponce JCA, Pertl F, Balazs D, et al. Spontaneous ordering of identical materials into a triboelectric series. <i>Nature</i>. 2025;638(8051). doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>","ista":"Sobarzo Ponce JCA, Pertl F, Balazs D, Costanzo T, Sauer M, Foelske A, Ostermann M, Pichler CM, Wang Y, Nagata Y, Bonn M, Waitukaitis SR. 2025. Spontaneous ordering of identical materials into a triboelectric series. Nature. 638(8051), 664–669.","mla":"Sobarzo Ponce, Juan Carlos A., et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>, vol. 638, no. 8051, 664–669, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41586-024-08530-6\">10.1038/s41586-024-08530-6</a>.","short":"J.C.A. Sobarzo Ponce, F. Pertl, D. Balazs, T. Costanzo, M. Sauer, A. Foelske, M. Ostermann, C.M. Pichler, Y. Wang, Y. Nagata, M. Bonn, S.R. Waitukaitis, Nature 638 (2025).","chicago":"Sobarzo Ponce, Juan Carlos A, Felix Pertl, Daniel Balazs, Tommaso Costanzo, Markus Sauer, Annette Foelske, Markus Ostermann, et al. “Spontaneous Ordering of Identical Materials into a Triboelectric Series.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08530-6\">https://doi.org/10.1038/s41586-024-08530-6</a>."},"article_type":"original","ec_funded":1,"OA_place":"publisher","intvolume":"       638","ddc":["530"],"date_updated":"2026-08-27T11:42:43Z","OA_type":"hybrid","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"}],"author":[{"last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"first_name":"Felix","orcid":"0000-0003-0463-5794","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix"},{"last_name":"Balazs","first_name":"Daniel","orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel"},{"last_name":"Costanzo","orcid":"0000-0001-9732-3815","first_name":"Tommaso","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"last_name":"Sauer","first_name":"Markus","full_name":"Sauer, Markus"},{"full_name":"Foelske, Annette","first_name":"Annette","last_name":"Foelske"},{"full_name":"Ostermann, Markus","last_name":"Ostermann","first_name":"Markus"},{"first_name":"Christian M.","last_name":"Pichler","full_name":"Pichler, Christian M."},{"first_name":"Yongkang","last_name":"Wang","full_name":"Wang, Yongkang"},{"full_name":"Nagata, Yuki","first_name":"Yuki","last_name":"Nagata"},{"full_name":"Bonn, Mischa","first_name":"Mischa","last_name":"Bonn"},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"year":"2025","publication_status":"published","file_date_updated":"2025-03-04T10:05:18Z","volume":638,"issue":"8051","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"20203"},{"status":"public","id":"22684","relation":"dissertation_contains"}]},"month":"02","_id":"19278","quality_controlled":"1","date_published":"2025-02-20T00:00:00Z","article_number":"664-669","isi":1,"doi":"10.1038/s41586-024-08530-6","file":[{"checksum":"fecf302274dd3218d3e7dd22f39a6c0c","success":1,"date_updated":"2025-03-04T10:05:18Z","file_name":"2025_Nature_Sobarzo.pdf","file_id":"19289","file_size":3807415,"date_created":"2025-03-04T10:05:18Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access"}],"acknowledgement":"This project has received financing from the European Research Council grant agreement no. 949120 under the European Union’s Horizon 2020 research and innovation programme. The Analytical Instrumentation Center of the TU Wien acknowledges support by the FFG project ‘ELSA’ under grant no. 884672. C.M.P. and M.O. acknowledge the state of Lower Austria and the European Regional Development Fund under grant no. WST3-F-542638/004-2021. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Miba Machine Shop, Nanofabrication Facility, Scientific Computing facility, Electron Microscopy Facility and Lab Support Facility. We thank J. Garcia-Suarez and G. Anciaux for the suggestion to look into the roughness power spectral density. We thank I.-M. Strugaru for help with testing the device for Young’s modulus measurements. Open access funding provided by Institute of Science and Technology (IST Austria).","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","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)"},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Spontaneous ordering of identical materials into a triboelectric series","oa":1,"day":"20","department":[{"_id":"ScWa"},{"_id":"LifeSc"},{"_id":"EM-Fac"}]},{"_id":"20481","date_published":"2025-09-30T00:00:00Z","quality_controlled":"1","article_number":"146202","isi":1,"doi":"10.1103/lcsm-xxty","file":[{"file_size":1692251,"file_id":"20522","file_name":"2025_PhysReviewLetters_Pertl.pdf","date_updated":"2025-10-23T09:32:31Z","success":1,"checksum":"7e45e89b8db0b7f01e63185c68e4b0f9","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2025-10-23T09:32:31Z"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop, the Nanofabrication Facility and Lab Support Facility.","publisher":"American Physical Society","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"PlanS_conform":"1","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)"},"day":"30","department":[{"_id":"ScWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces","citation":{"chicago":"Pertl, Felix, Isaac C Lenton, Tobias Cramer, and Scott R Waitukaitis. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>.","mla":"Pertl, Felix, et al. “No Time for Surface Charge: How Bulk Conductivity Hides Charge Patterns from Kelvin Probe Force Microscopy in Contact-Electrified Surfaces.” <i>Physical Review Letters</i>, vol. 135, no. 14, 146202, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>.","short":"F. Pertl, I.C. Lenton, T. Cramer, S.R. Waitukaitis, Physical Review Letters 135 (2025).","apa":"Pertl, F., Lenton, I. C., Cramer, T., &#38; Waitukaitis, S. R. (2025). No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/lcsm-xxty\">https://doi.org/10.1103/lcsm-xxty</a>","ama":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. <i>Physical Review Letters</i>. 2025;135(14). doi:<a href=\"https://doi.org/10.1103/lcsm-xxty\">10.1103/lcsm-xxty</a>","ieee":"F. Pertl, I. C. Lenton, T. Cramer, and S. R. Waitukaitis, “No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces,” <i>Physical Review Letters</i>, vol. 135, no. 14. American Physical Society, 2025.","ista":"Pertl F, Lenton IC, Cramer T, Waitukaitis SR. 2025. No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces. Physical Review Letters. 135(14), 146202."},"ec_funded":1,"article_type":"original","language":[{"iso":"eng"}],"publication":"Physical Review Letters","oa_version":"Published Version","date_created":"2025-10-16T13:13:29Z","scopus_import":"1","corr_author":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Kelvin probe force microscopy (KPFM) is widely used in stationary and dynamic studies of contact electrification. An obvious question that connects these two has been overlooked: when are charge dynamics too fast for stationary studies to be meaningful? Using a rapid transfer system to quickly perform KPFM after contact, we find the dynamics are too fast in all but the best insulators. Our data further suggest that dynamics are caused by bulk as opposed to surface conductivity, and that charge-transfer heterogeneity is less prevalent than previously suggested."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001587263900003"],"arxiv":["2502.12718"]},"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","grant_number":"949120"}],"OA_type":"hybrid","OA_place":"publisher","intvolume":"       135","date_updated":"2026-08-27T11:42:43Z","arxiv":1,"ddc":["530"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"}],"author":[{"first_name":"Felix","orcid":"0000-0003-0463-5794","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","full_name":"Pertl, Felix"},{"full_name":"Lenton, Isaac C","id":"a550210f-223c-11ec-8182-e2d45e817efb","last_name":"Lenton","orcid":"0000-0002-5010-6984","first_name":"Isaac C"},{"last_name":"Cramer","first_name":"Tobias","full_name":"Cramer, Tobias"},{"orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87"}],"issue":"14","related_material":{"record":[{"id":"20523","status":"public","relation":"research_data"},{"id":"22684","status":"public","relation":"dissertation_contains"}]},"volume":135,"month":"09","year":"2025","file_date_updated":"2025-10-23T09:32:31Z","publication_status":"published"},{"volume":16,"related_material":{"record":[{"id":"22770","status":"public","relation":"research_data"}]},"month":"10","year":"2025","file_date_updated":"2025-10-13T07:54:51Z","publication_status":"published","pmid":1,"dataavailabilitystatement":"The training sets, training scripts, MD input files, and trained CACE potentials are available at https://github.com/BingqingCheng/cace-lr-fit; see https://doi.org/10.5281/zenodo.16415061. Source data for all figures are provided with this paper. Source data are provided with this paper.","author":[{"first_name":"Daniel S.","last_name":"King","full_name":"King, Daniel S."},{"full_name":"Kim, Dongjin","first_name":"Dongjin","last_name":"Kim"},{"full_name":"Zhong, Peichen","first_name":"Peichen","last_name":"Zhong"},{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"}],"OA_type":"gold","OA_place":"publisher","intvolume":"        16","ddc":["000"],"date_updated":"2026-08-27T12:16:47Z","supplementarymaterial":"no","language":[{"iso":"eng"}],"DOAJ_listed":"1","citation":{"short":"D.S. King, D. Kim, P. Zhong, B. Cheng, Nature Communications 16 (2025).","mla":"King, Daniel S., et al. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>, vol. 16, 8763, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>.","ista":"King DS, Kim D, Zhong P, Cheng B. 2025. Machine learning of charges and long-range interactions from energies and forces. Nature Communications. 16, 8763.","ama":"King DS, Kim D, Zhong P, Cheng B. Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-63852-x\">10.1038/s41467-025-63852-x</a>","ieee":"D. S. King, D. Kim, P. Zhong, and B. Cheng, “Machine learning of charges and long-range interactions from energies and forces,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","apa":"King, D. S., Kim, D., Zhong, P., &#38; Cheng, B. (2025). Machine learning of charges and long-range interactions from energies and forces. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>","chicago":"King, Daniel S., Dongjin Kim, Peichen Zhong, and Bingqing Cheng. “Machine Learning of Charges and Long-Range Interactions from Energies and Forces.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-63852-x\">https://doi.org/10.1038/s41467-025-63852-x</a>."},"article_type":"original","type":"journal_article","corr_author":"1","date_created":"2025-10-12T22:01:25Z","publication":"Nature Communications","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","status":"public","external_id":{"pmid":["41034200"],"isi":["001586620700015"]},"abstract":[{"lang":"eng","text":"Accurate modeling of long-range forces is critical in atomistic simulations, as they play a central role in determining the properties of material and chemical systems. However, standard machine learning interatomic potentials (MLIPs) often rely on short-range approximations, limiting their applicability to systems with significant electrostatics and dispersion forces. We recently introduced the Latent Ewald Summation (LES) method, which captures long-range electrostatics without explicitly learning atomic charges or charge equilibration. We benchmark LES on diverse and challenging systems, including charged molecules, ionic liquids, electrolyte solutions, polar dipeptides, surface adsorption, electrolyte/solid interfaces, and solid-solid interfaces. Here we show that LES can reproduce the exact atomic charges for classical systems with fixed charges and can infer dipole and quadrupole moments, as well as the dipole derivative with respect to atomic positions, for quantum mechanical systems. Moreover, LES can achieve better accuracy in energy and force predictions compared to methods that explicitly learn from charges."}],"day":"01","researchdata_availability":"no","department":[{"_id":"BiCh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Machine learning of charges and long-range interactions from energies and forces","oa":1,"article_processing_charge":"Yes","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)"},"PlanS_conform":"1","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We thank Chunyi Zhang for providing the TiO2(101)/NaCl+NaOH+HCl(aq) dataset and for useful discussions. We thank Jia-Xin Zhu for providing the Pt(111)/KF(aq) dataset. We thank Tsz Wai Ko and Jonas Finkler for useful discussions and for the DFT-optimized Au2-MgO(001) structures. We thank Junmin Chen for discussions. D.K and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship.","file":[{"date_created":"2025-10-13T07:54:51Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"34b6005d349bbff85839c4e51d6c8725","success":1,"file_id":"20460","file_name":"2025_NatureComm_King.pdf","date_updated":"2025-10-13T07:54:51Z","file_size":4907055}],"isi":1,"doi":"10.1038/s41467-025-63852-x","publisher":"Springer Nature","quality_controlled":"1","_id":"20452","date_published":"2025-10-01T00:00:00Z","article_number":"8763","das_tickbox":"1"},{"ddc":["000"],"date_updated":"2026-08-27T12:16:48Z","OA_place":"repository","publisher":"Repository","OA_type":"green","doi":"10.5281/zenodo.16415060","status":"public","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.16415061"}],"date_created":"2026-08-27T12:13:55Z","oa_version":"None","citation":{"ieee":"B. Cheng, D. King, D. Kim, and P. Zhong, “BingqingCheng/cace-lr-fit: V0.” Repository, 2025.","ista":"Cheng B, King D, Kim D, Zhong P. 2025. BingqingCheng/cace-lr-fit: V0, Repository, <a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","ama":"Cheng B, King D, Kim D, Zhong P. BingqingCheng/cace-lr-fit: V0. 2025. doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>","apa":"Cheng, B., King, D., Kim, D., &#38; Zhong, P. (2025). BingqingCheng/cace-lr-fit: V0. Repository. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>","short":"B. Cheng, D. King, D. Kim, P. Zhong, (2025).","mla":"Cheng, Bingqing, et al. <i>BingqingCheng/Cace-Lr-Fit: V0</i>. Repository, 2025, doi:<a href=\"https://doi.org/10.5281/zenodo.16415060\">10.5281/zenodo.16415060</a>.","chicago":"Cheng, Bingqing, Daniel King, Dongjin Kim, and Peichen Zhong. “BingqingCheng/Cace-Lr-Fit: V0.” Repository, 2025. <a href=\"https://doi.org/10.5281/zenodo.16415060\">https://doi.org/10.5281/zenodo.16415060</a>."},"_id":"22770","date_published":"2025-07-24T00:00:00Z","title":"BingqingCheng/cace-lr-fit: V0","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2025","department":[{"_id":"BiCh"}],"month":"07","related_material":{"record":[{"id":"20452","status":"public","relation":"used_in_publication"}]},"day":"24","author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"King, Daniel","last_name":"King","first_name":"Daniel"},{"full_name":"Kim, Dongjin","first_name":"Dongjin","last_name":"Kim"},{"full_name":"Zhong, Peichen","first_name":"Peichen","last_name":"Zhong"}],"article_processing_charge":"No"},{"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. \r\n\r\nInitially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits.\r\n\r\nIn more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution.\r\n\r\nIn larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process.\r\n\r\nFinally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate."}],"type":"dissertation","corr_author":"1","oa_version":"Published Version","date_created":"2025-05-12T15:12:28Z","language":[{"iso":"eng"}],"citation":{"chicago":"Yalniz, Gökhan. “Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>.","ista":"Yalniz G. 2025. Transition to turbulence: Data-, solution-, and pattern-driven approaches. Institute of Science and Technology Austria.","ieee":"G. Yalniz, “Transition to turbulence: Data-, solution-, and pattern-driven approaches,” Institute of Science and Technology Austria, 2025.","ama":"Yalniz G. Transition to turbulence: Data-, solution-, and pattern-driven approaches. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>","apa":"Yalniz, G. (2025). <i>Transition to turbulence: Data-, solution-, and pattern-driven approaches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19684\">https://doi.org/10.15479/AT-ISTA-19684</a>","short":"G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.","mla":"Yalniz, Gökhan. <i>Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19684\">10.15479/AT-ISTA-19684</a>."},"ddc":["514","519","532","004"],"date_updated":"2026-09-02T08:16:32Z","OA_place":"publisher","doi_confirm":"1","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960"}],"author":[{"full_name":"Yalniz, Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","last_name":"Yalniz","orcid":"0000-0002-8490-9312","first_name":"Gökhan"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"page":"155","file_date_updated":"2025-05-12T15:43:28Z","publication_status":"published","year":"2025","month":"05","related_material":{"record":[{"id":"9558","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12105","status":"public"},{"id":"13274","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14466"},{"id":"7563","status":"public","relation":"part_of_dissertation"}]},"supervisor":[{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2025-05-13T00:00:00Z","_id":"19684","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","file":[{"file_size":20058169,"success":1,"checksum":"0e452642b79f13633f1595bde71a67e3","date_updated":"2025-05-12T15:13:28Z","file_name":"Gökhan Yalnız - PhD thesis.pdf","file_id":"19685","relation":"main_file","creator":"gyalniz","access_level":"open_access","date_created":"2025-05-12T15:13:28Z","content_type":"application/pdf"},{"content_type":"video/mp4","date_created":"2025-05-12T15:15:59Z","access_level":"open_access","relation":"supplementary_material","creator":"gyalniz","date_updated":"2025-05-12T15:43:28Z","file_id":"19686","file_name":"Movie 2A.1.mp4","title":"Chapter 2 - Movie 2A.1","checksum":"921099d76adab2df784ce12ce41cfb22","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. 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Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_size":5893993},{"access_level":"open_access","creator":"gyalniz","relation":"supplementary_material","date_created":"2025-05-12T15:17:49Z","content_type":"video/mp4","description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P =660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","file_size":3990352,"file_name":"Movie 5A.2.mp4","file_id":"19693","title":"Chapter 5 - Movie 5A.2","date_updated":"2025-05-12T15:43:28Z","checksum":"fd17eabb70129ceaa414e40924d1d2fe"},{"relation":"supplementary_material","creator":"gyalniz","access_level":"open_access","content_type":"video/mp4","date_created":"2025-05-12T15:17:58Z","file_size":5171009,"description":"Streamwise velocity fluctuations (from laminar) of plane-Poiseuille flow (Re^P=660) at the y = 0.5 wall-normal plane in coordinates stationary with respect to the average velocity of the downstream tip of the stripe. Here, x is the streamwise direction (the mean negative pressure gradient is to the right) and z is the spanwise direction. Time is in advectime time units. 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