[{"has_accepted_license":"1","file_date_updated":"2025-05-19T07:55:51Z","date_published":"2025-05-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","fulldoi":"https://doi.org/10.1146/annurev-biophys-060524-102720","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","pmid":1,"year":"2025","quality_controlled":"1","intvolume":"        54","isi":1,"volume":54,"doi":"10.1146/annurev-biophys-060524-102720","file":[{"file_id":"19710","file_size":317925,"content_type":"application/pdf","date_updated":"2025-05-19T07:55:51Z","file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f","date_created":"2025-05-19T07:55:51Z","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access"}],"day":"01","corr_author":"1","oa":1,"external_id":{"pmid":["39929539"],"isi":["001488641500013"]},"publisher":"Annual Reviews","month":"05","department":[{"_id":"GaTk"}],"license":"https://creativecommons.org/licenses/by/4.0/","page":"249-274","citation":{"ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual Review of Biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>","chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>."},"project":[{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"},{"grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"date_updated":"2026-08-12T09:25:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Information processing in biochemical networks","_id":"19701","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"full_name":"Wolde, Pieter Rein Ten","last_name":"Wolde","first_name":"Pieter Rein Ten"}],"status":"public","date_created":"2025-05-18T22:02:50Z","type":"journal_article","oa_version":"Published Version","article_type":"original","abstract":[{"lang":"eng","text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components."}],"OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"publication":"Annual Review of Biophysics","scopus_import":"1","publication_identifier":{"eissn":["1936-1238"]},"acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065)."},{"intvolume":"       152","publication_status":"published","quality_controlled":"1","pmid":1,"year":"2025","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1242/dev.204261","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","date_published":"2025-06-27T00:00:00Z","file_date_updated":"2025-07-23T08:43:01Z","publisher":"Company of Biologists","month":"06","department":[{"_id":"CaHe"}],"external_id":{"isi":["001525252300001"],"pmid":["40576478"]},"corr_author":"1","oa":1,"day":"27","doi":"10.1242/dev.204261","file":[{"file_id":"20070","file_name":"2025_Development_Moriyama.pdf","date_updated":"2025-07-23T08:43:01Z","content_type":"application/pdf","file_size":25935563,"success":1,"checksum":"808d8aa28df79d23fb661838d1fdc1be","date_created":"2025-07-23T08:43:01Z","access_level":"open_access","relation":"main_file","creator":"dernst"}],"volume":152,"isi":1,"article_number":"dev204261","abstract":[{"text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","article_type":"original","status":"public","date_created":"2025-07-21T08:10:32Z","author":[{"full_name":"Moriyama, Yuuta","orcid":"0000-0002-2853-8051","last_name":"Moriyama","first_name":"Yuuta","id":"addc9b8c-67a0-11f0-b374-a2e094825470"},{"full_name":"Mitsui, Toshiyuki","last_name":"Mitsui","first_name":"Toshiyuki"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","_id":"20048","PlanS_conform":"1","date_updated":"2026-08-12T10:01:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. Company of Biologists, 2025.","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>."},"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","scopus_import":"1","issue":"12","publication":"Development","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid"},{"volume":12,"file":[{"checksum":"828577ea48ac6109d3e9dd1aeddd45c4","date_created":"2026-02-24T07:56:34Z","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"21356","file_size":1003689,"file_name":"2025_JEP_Browning.pdf","content_type":"application/pdf","date_updated":"2026-02-24T07:56:34Z"}],"doi":"10.5802/jep.320","researchdata_availability":"no","day":"21","oa":1,"corr_author":"1","external_id":{"arxiv":["2411.09264"]},"department":[{"_id":"TiBr"}],"month":"10","publisher":"Ecole Polytechnique","date_published":"2025-10-21T00:00:00Z","file_date_updated":"2026-02-24T07:56:34Z","has_accepted_license":"1","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.5802/jep.320","das_tickbox":"0","arxiv":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"quality_controlled":"1","year":"2025","publication_status":"published","intvolume":"        12","OA_type":"gold","OA_place":"publisher","language":[{"iso":"eng"}],"publication":"Journal de l'Ecole Polytechnique - Mathematiques","scopus_import":"1","acknowledgement":"While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278).","publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"project":[{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"citation":{"ama":"Browning TD, Chan S. Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2025;12:1677-1691. doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>","mla":"Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>.","ieee":"T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025.","short":"T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691.","ista":"Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.","chicago":"Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2025. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>.","apa":"Browning, T. D., &#38; Chan, S. (2025). Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>"},"page":"1677-1691","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T11:17:50Z","supplementarymaterial":"no","PlanS_conform":"1","_id":"21343","title":"Solubility of a resultant equation and applications","date_created":"2026-02-22T23:01:36Z","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chan","first_name":"Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","full_name":"Chan, Yik Tung","orcid":"0000-0001-8467-4106"}],"status":"public","article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given"},{"text":" Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques.","lang":"fre"}]},{"dataavailabilitystatement":"The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page.","day":"01","oa":1,"corr_author":"1","external_id":{"isi":["001552779800001"],"arxiv":["2407.16315"]},"department":[{"_id":"TiBr"}],"month":"09","publisher":"Springer Nature","article_number":"81","isi":1,"volume":31,"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"89352f1f7e8d2b367ae5f4e9bf9eb1f5","date_created":"2025-09-03T06:44:44Z","date_updated":"2025-09-03T06:44:44Z","content_type":"application/pdf","file_name":"2025_SelectaMathematica_Browning.pdf","file_size":2484757,"file_id":"20281"}],"researchdata_availability":"yes","doi":"10.1007/s00029-025-01074-1","ddc":["500"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","year":"2025","publication_status":"published","intvolume":"        31","date_published":"2025-09-01T00:00:00Z","file_date_updated":"2025-09-03T06:44:44Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.1007/s00029-025-01074-1","das_tickbox":"1","arxiv":1,"publication":"Selecta Mathematica New Series","issue":"4","scopus_import":"1","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"acknowledgement":"The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","OA_type":"hybrid","OA_place":"publisher","language":[{"iso":"eng"}],"_id":"20249","title":"Integral points on cubic surfaces: heuristics and numerics","author":[{"last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"orcid":"0000-0001-7302-8256","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425"}],"status":"public","date_created":"2025-08-31T22:01:31Z","article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces."}],"related_material":{"record":[{"id":"22234","relation":"research_data","status":"public"}],"link":[{"relation":"software","url":"https://github.com/fwilsch/cubicpts"}]},"project":[{"call_identifier":"FWF","name":"New frontiers of the Manin conjecture","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","grant_number":"P32428"},{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"citation":{"mla":"Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4, 81, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>.","ama":"Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. 2025;31(4). doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>","short":"T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).","ieee":"T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4. Springer Nature, 2025.","ista":"Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.","chicago":"Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>.","apa":"Browning, T. D., &#38; Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supplementarymaterial":"yes","date_updated":"2026-08-12T12:15:32Z","PlanS_conform":"1"},{"article_type":"original","type":"journal_article","oa_version":"Published Version","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."}],"_id":"20218","title":"Roadmap for animate matter","status":"public","date_created":"2025-08-24T22:01:30Z","author":[{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"last_name":"Guix","first_name":"Maria","full_name":"Guix, Maria"},{"full_name":"Miodownik, Mark","last_name":"Miodownik","first_name":"Mark"},{"full_name":"Martin, Nicolas","last_name":"Martin","first_name":"Nicolas"},{"last_name":"Alvarez","first_name":"Laura","full_name":"Alvarez, Laura"},{"last_name":"Simmchen","first_name":"Juliane","full_name":"Simmchen, Juliane"},{"full_name":"Leonardo, Roberto Di","last_name":"Leonardo","first_name":"Roberto Di"},{"full_name":"Pellicciotta, Nicola","last_name":"Pellicciotta","first_name":"Nicola"},{"orcid":"0000-0002-2916-6632","full_name":"Martinet, Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","last_name":"Martinet","first_name":"Quentin"},{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci"},{"full_name":"Ng, Wai Kit","last_name":"Ng","first_name":"Wai Kit"},{"full_name":"Saxena, Dhruv","last_name":"Saxena","first_name":"Dhruv"},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"},{"first_name":"Sara","last_name":"Nadine","full_name":"Nadine, Sara"},{"full_name":"Mano, João F.","first_name":"João F.","last_name":"Mano"},{"full_name":"Mahdavi, Reza","last_name":"Mahdavi","first_name":"Reza"},{"last_name":"Beck Adiels","first_name":"Caroline","full_name":"Beck Adiels, Caroline"},{"last_name":"Forth","first_name":"Joe","full_name":"Forth, Joe"},{"first_name":"Christian","last_name":"Santangelo","full_name":"Santangelo, Christian"},{"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.","first_name":"Victoria A.","last_name":"Webster-Wood"},{"full_name":"Wang, Shuhong","last_name":"Wang","first_name":"Shuhong"},{"full_name":"Yao, Lining","first_name":"Lining","last_name":"Yao"},{"first_name":"Amirreza","last_name":"Aghakhani","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"},{"last_name":"Van Hecke","first_name":"Martin","full_name":"Van Hecke, Martin"},{"first_name":"Christopher J.","last_name":"Pierce","full_name":"Pierce, Christopher J."},{"last_name":"Wang","first_name":"Tianyu","full_name":"Wang, Tianyu"},{"first_name":"Baxi","last_name":"Chong","full_name":"Chong, Baxi"},{"full_name":"Goldman, Daniel I.","last_name":"Goldman","first_name":"Daniel I."},{"first_name":"Andreagiovanni","last_name":"Reina","full_name":"Reina, Andreagiovanni"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"first_name":"Giovanni","last_name":"Volpe","full_name":"Volpe, Giovanni"},{"last_name":"Beckett","first_name":"Richard","full_name":"Beckett, Richard"},{"full_name":"Nair, Sean P.","first_name":"Sean P.","last_name":"Nair"},{"first_name":"Rachel","last_name":"Armstrong","full_name":"Armstrong, Rachel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T14:00:12Z","PlanS_conform":"1","citation":{"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.","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).","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>","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>.","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>","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>."},"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).","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"publication":"Journal of Physics: Condensed Matter","issue":"33","scopus_import":"1","language":[{"iso":"eng"}],"OA_type":"hybrid","OA_place":"publisher","year":"2025","quality_controlled":"1","publication_status":"published","intvolume":"        37","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"fulldoi":"https://doi.org/10.1088/1361-648X/adebd3","arxiv":1,"date_published":"2025-08-18T00:00:00Z","file_date_updated":"2025-09-02T07:22:48Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001550090200001"],"arxiv":["2407.10623"]},"department":[{"_id":"JePa"}],"month":"08","publisher":"IOP Publishing","day":"18","oa":1,"volume":37,"file":[{"date_created":"2025-09-02T07:22:48Z","checksum":"7309274f78bed785b158bd290337f456","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"20271","file_size":8997829,"content_type":"application/pdf","date_updated":"2025-09-02T07:22:48Z","file_name":"2025_CondensedMatter_Volpe.pdf"}],"doi":"10.1088/1361-648X/adebd3","article_number":"333501","isi":1},{"external_id":{"isi":["001585824100001"],"pmid":["40967257"]},"month":"10","department":[{"_id":"KiMo"}],"publisher":"IOP Publishing","day":"06","oa":1,"corr_author":"1","volume":37,"file":[{"date_created":"2025-10-13T06:34:15Z","checksum":"b182856a5a655496e149afa49ec464f3","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"20458","file_size":1709516,"file_name":"2025_JourPhysicsCondMatter_Farooq.pdf","date_updated":"2025-10-13T06:34:15Z","content_type":"application/pdf"}],"doi":"10.1088/1361-648X/ae0913","article_number":"405801","isi":1,"year":"2025","pmid":1,"quality_controlled":"1","publication_status":"published","intvolume":"        37","ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1088/1361-648X/ae0913","file_date_updated":"2025-10-13T06:34:15Z","date_published":"2025-10-06T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"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.","publication":"Journal of Physics: Condensed Matter","issue":"40","scopus_import":"1","language":[{"iso":"eng"}],"OA_type":"hybrid","OA_place":"publisher","article_type":"original","type":"journal_article","oa_version":"Published Version","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."}],"_id":"20453","title":"Non-linear magnetotropic susceptibility in FePS3","author":[{"first_name":"Hamza","last_name":"Farooq","full_name":"Farooq, Hamza"},{"orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","last_name":"Nauman","first_name":"Muhammad"}],"status":"public","date_created":"2025-10-12T22:01:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T14:00:34Z","PlanS_conform":"1","citation":{"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>.","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>","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.","short":"H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).","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>.","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>"}},{"fulldoi":"https://doi.org/10.1098/rsif.2025.0202","date_published":"2025-08-13T00:00:00Z","article_processing_charge":"No","year":"2025","quality_controlled":"1","pmid":1,"publication_status":"published","intvolume":"        22","volume":22,"doi":"10.1098/rsif.2025.0202","article_number":"20250202","isi":1,"external_id":{"pmid":["40799050"],"isi":["001548084900001"]},"month":"08","department":[{"_id":"SyCr"}],"publisher":"Royal Society","day":"13","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T14:09:20Z","citation":{"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>","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>.","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.","ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202.","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>"},"article_type":"original","type":"journal_article","oa_version":"None","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."}],"_id":"20219","title":"Interplay of asexual and sexual reproduction in bifunctional insects","date_created":"2025-08-24T22:01:30Z","status":"public","author":[{"full_name":"Ayalon, Oran","last_name":"Ayalon","first_name":"Oran"},{"full_name":"Rajendran, Harikrishnan","last_name":"Rajendran","first_name":"Harikrishnan","id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416"}],"language":[{"iso":"eng"}],"OA_type":"closed access","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.","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"publication":"Journal of the Royal Society Interface","issue":"229","scopus_import":"1"},{"oa":1,"day":"23","department":[{"_id":"SiHi"}],"biorxivid":1,"month":"05","external_id":{"biorxivid":["10.1101/2025.05.22.655488"]},"doi":"10.1101/2025.05.22.655488","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publication_status":"submitted","year":"2025","article_processing_charge":"No","date_published":"2025-05-23T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.22.655488","open_access":"1"}],"fulldoi":"https://doi.org/10.1101/2025.05.22.655488","publication":"bioRxiv","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).","OA_place":"repository","OA_type":"green","language":[{"iso":"eng"}],"author":[{"first_name":"Adrián","last_name":"Cárdenas","full_name":"Cárdenas, Adrián"},{"last_name":"Çelik","first_name":"Irem","full_name":"Çelik, Irem"},{"full_name":"Espinós, Alexandre","last_name":"Espinós","first_name":"Alexandre"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"last_name":"López-González","first_name":"Lara","full_name":"López-González, Lara"},{"full_name":"del-Valle-Anton, Lucia","last_name":"del-Valle-Anton","first_name":"Lucia"},{"full_name":"Fernández, Virginia","first_name":"Virginia","last_name":"Fernández"},{"full_name":"Amin, Salma","last_name":"Amin","first_name":"Salma"},{"full_name":"Negri, Enrico","last_name":"Negri","first_name":"Enrico"},{"first_name":"Eduardo Fernández","last_name":"Ortuño","full_name":"Ortuño, Eduardo Fernández"},{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"last_name":"Borrell","first_name":"Víctor","full_name":"Borrell, Víctor"}],"status":"public","date_created":"2025-05-29T10:45:55Z","title":"Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development","_id":"19762","abstract":[{"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.","lang":"eng"}],"type":"preprint","oa_version":"Preprint","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>.","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>. .","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.).","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>.","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>.","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>"},"project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2026-08-13T07:18:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"19717","title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","status":"public","date_created":"2025-05-20T10:19:29Z","author":[{"full_name":"Varela-Martínez, I","last_name":"Varela-Martínez","first_name":"I"},{"last_name":"Villalba Requena","first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana"},{"full_name":"Garcia-Marqués, J.","last_name":"Garcia-Marqués","first_name":"J."},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"},{"full_name":"Nieto, M.","first_name":"M.","last_name":"Nieto"}],"year":"2025","publication_status":"submitted","type":"preprint","oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"date_published":"2025-05-07T00:00:00Z","article_processing_charge":"No","citation":{"short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.).","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>. .","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>.","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>","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>.","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>","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>."},"fulldoi":"https://doi.org/10.1101/2025.05.07.652665","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-13T07:16:48Z","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.07.652665","open_access":"1"}],"publication":"bioRxiv","day":"07","oa":1,"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","month":"05","department":[{"_id":"SiHi"}],"OA_place":"repository","OA_type":"green","language":[{"iso":"eng"}],"doi":"10.1101/2025.05.07.652665"},{"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","publication":"arXiv","language":[{"iso":"eng"}],"OA_place":"repository","OA_type":"green","oa_version":"Preprint","type":"preprint","abstract":[{"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).","lang":"eng"}],"_id":"19674","title":"ResiDual transformer alignment with spectral decomposition","date_created":"2025-05-11T22:02:41Z","status":"public","author":[{"full_name":"Basile, Lorenzo","last_name":"Basile","first_name":"Lorenzo"},{"last_name":"Maiorca","first_name":"Valentino","full_name":"Maiorca, Valentino"},{"full_name":"Bortolussi, Luca","first_name":"Luca","last_name":"Bortolussi"},{"full_name":"Rodolà, Emanuele","last_name":"Rodolà","first_name":"Emanuele"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-13T07:33:41Z","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>","chicago":"Basile, Lorenzo, Valentino Maiorca, Luca Bortolussi, Emanuele Rodolà, and Francesco Locatello. “ResiDual Transformer Alignment with Spectral Decomposition.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2411.00246\">https://doi.org/10.48550/arXiv.2411.00246</a>.","ista":"Basile L, Maiorca V, Bortolussi L, Rodolà E, Locatello F. ResiDual transformer alignment with spectral decomposition. arXiv, 2411.00246.","short":"L. Basile, V. Maiorca, L. Bortolussi, E. Rodolà, F. Locatello, ArXiv (n.d.).","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>","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>."},"external_id":{"arxiv":["2411.00246"]},"month":"04","department":[{"_id":"FrLo"}],"day":"14","oa":1,"doi":"10.48550/arXiv.2411.00246","article_number":"2411.00246","year":"2025","publication_status":"submitted","ddc":["000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.48550/arXiv.2411.00246","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2411.00246","open_access":"1"}],"date_published":"2025-04-14T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No"},{"publication_status":"published","year":"2025","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-20167","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","file_date_updated":"2026-08-13T13:05:36Z","date_published":"2025-08-13T00:00:00Z","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","month":"08","department":[{"_id":"GradSch"},{"_id":"MaDe"}],"day":"13","corr_author":"1","doi":"10.15479/AT-ISTA-20167","file":[{"access_level":"closed","relation":"source_file","creator":"hschoen","checksum":"b40c74404b8d9593802dabf57bfdf10f","date_created":"2025-09-08T14:33:50Z","date_updated":"2025-09-09T08:57:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2025_Schoen_Hanna_Thesis.docx","file_size":78812587,"file_id":"20311"},{"file_size":9667057,"file_name":"2025_Schoen_Hanna_Thesis.pdf","content_type":"application/pdf","date_updated":"2026-08-13T13:05:36Z","embargo":"2027-03-15","file_id":"20347","embargo_to":"open_access","creator":"hschoen","relation":"main_file","access_level":"closed","date_created":"2025-09-11T14:20:59Z","checksum":"16abc3ff66396ce2457fe07ffa8bed90"}],"supervisor":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"de Bono","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443"}],"oa_version":"Published Version","type":"dissertation","title":"The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs","_id":"20167","date_created":"2025-08-13T11:13:13Z","author":[{"id":"C8E17EDC-D7AA-11E9-B7B7-45ECE5697425","first_name":"Hanna","last_name":"Schön","full_name":"Schön, Hanna"}],"status":"public","date_updated":"2026-08-13T13:05:37Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"171","citation":{"short":"H. Schön, The ER Complex SUTU-7/MACO-1 Regulates the Fate of MRNAs Encoding GPCRs, Institute of Science and Technology Austria, 2025.","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.","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>.","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>","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>","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>."},"project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"},{"_id":"23813290-32DE-11EA-91FC-C7463DDC885E","name":"Control of gene expression at the endoplasmic reticulum","grant_number":"ALTF 302-2019"}],"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). ","publication_identifier":{"isbn":["978-3-99078-061-9"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"OA_place":"publisher"},{"language":[{"iso":"eng"}],"OA_type":"hybrid","OA_place":"publisher","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.","publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"publication":"Journal of Molecular Biology","issue":"23","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-13T14:19:02Z","PlanS_conform":"1","project":[{"name":"Structure and mechanism of the mitochondrial MIM insertase","_id":"bdb9578d-d553-11ed-ba76-ed5d39fce6f0","grant_number":"I06223"},{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"}],"citation":{"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>.","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>","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>","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>.","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).","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."},"article_type":"original","type":"journal_article","oa_version":"Published Version","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"}],"_id":"20538","title":"A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0","status":"public","author":[{"last_name":"Knödlstorfer","first_name":"Sonja","full_name":"Knödlstorfer, Sonja"},{"last_name":"Toscano","first_name":"Giorgia","id":"334a5e40-8747-11f0-b671-ba1f5154b4b4","full_name":"Toscano, Giorgia"},{"first_name":"Aleksandra L.","last_name":"Ptaszek","full_name":"Ptaszek, Aleksandra L."},{"full_name":"Kontaxis, Georg","last_name":"Kontaxis","first_name":"Georg"},{"full_name":"Napoli, Federico","orcid":"0000-0002-9043-136X","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","last_name":"Napoli","first_name":"Federico"},{"full_name":"Schneider, Jakob","last_name":"Schneider","first_name":"Jakob","id":"64368429-eb97-11eb-a6c2-c980b1f44415"},{"last_name":"Maier","first_name":"Katharina","full_name":"Maier, 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."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"first_name":"Robert","last_name":"Konrat","full_name":"Konrat, Robert"}],"date_created":"2025-10-26T23:01:35Z","volume":437,"file":[{"date_created":"2025-12-30T10:29:08Z","checksum":"feb92f9c79032c261165f4ca573f444a","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"20915","file_size":3076611,"content_type":"application/pdf","date_updated":"2025-12-30T10:29:08Z","file_name":"2025_JourMolecularBiology_Knoedlstorfer.pdf"}],"doi":"10.1016/j.jmb.2025.169465","article_number":"169465","external_id":{"pmid":["41016549"]},"department":[{"_id":"PaSc"},{"_id":"GradSch"}],"month":"12","publisher":"Elsevier","day":"01","oa":1,"fulldoi":"https://doi.org/10.1016/j.jmb.2025.169465","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"date_published":"2025-12-01T00:00:00Z","file_date_updated":"2025-12-30T10:29:08Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","pmid":1,"year":"2025","quality_controlled":"1","publication_status":"published","intvolume":"       437","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["540"]},{"publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"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.","issue":"23","scopus_import":"1","publication":"Journal of Molecular Biology","language":[{"iso":"eng"}],"OA_place":"publisher","OA_type":"hybrid","abstract":[{"lang":"eng","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."}],"article_type":"original","oa_version":"Published Version","type":"journal_article","date_created":"2025-08-31T22:01:33Z","author":[{"id":"81dc668a-19fa-11f0-bf31-d56534059ef3","first_name":"Darja","last_name":"Rohden","full_name":"Rohden, Darja"},{"last_name":"Napoli","first_name":"Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","orcid":"0000-0002-9043-136X","full_name":"Napoli, Federico"},{"full_name":"Kapitonova, Anna","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","first_name":"Anna","last_name":"Kapitonova"},{"full_name":"Tatman, Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f","last_name":"Tatman","first_name":"Benjamin"},{"last_name":"Lichtenecker","first_name":"Roman J.","full_name":"Lichtenecker, Roman J."},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"}],"status":"public","_id":"20258","title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme","PlanS_conform":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-13T14:19:01Z","project":[{"name":"AlloSpace. 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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"}],"type":"research_data","oa_version":"Published Version","author":[{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"date_created":"2025-07-03T04:21:37Z","status":"public","_id":"19956","title":"Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_updated":"2026-08-13T14:19:01Z","project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812"}],"citation":{"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>","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>.","short":"P. Schanda, (2025).","ieee":"P. Schanda, “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” Institute of Science and Technology Austria, 2025.","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>","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>."},"related_material":{"record":[{"status":"public","id":"20258","relation":"used_in_publication"}]},"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"publication":"bioRxiv","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.","OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}],"_id":"19398","title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","date_created":"2025-03-12T14:28:53Z","author":[{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"first_name":"Michael","last_name":"Smejkal","id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9","full_name":"Smejkal, Michael"},{"last_name":"Cervenova","first_name":"Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f","full_name":"Cervenova, Ema"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"status":"public","type":"preprint","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19395"}]},"citation":{"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>.","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>","ista":"Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. 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(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>","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>.","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.","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.","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.","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>","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>."},"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"date_updated":"2026-08-20T06:28:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Incremental approximate maximum flow via residual graph sparsification","_id":"21280","author":[{"full_name":"Goranci, Gramoz","first_name":"Gramoz","last_name":"Goranci"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger"},{"last_name":"Räcke","first_name":"Harald","full_name":"Räcke, Harald"},{"full_name":"Sricharan, A.","first_name":"A.","last_name":"Sricharan"}],"date_created":"2026-02-17T08:26:06Z","status":"public","type":"conference","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"OA_type":"gold","OA_place":"publisher","language":[{"iso":"eng"}],"publication":"52nd International Colloquium on Automata, Languages, and Programming","scopus_import":"1","publication_identifier":{"isbn":["9783959773720"]},"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.","ec_funded":1},{"doi":"10.1007/978-3-032-01913-4_5","volume":16007,"oa":1,"day":"17","publisher":"Springer Nature","month":"08","department":[{"_id":"KrPi"}],"article_processing_charge":"No","conference":{"location":"Santa Barbara, CA, United States","name":"CRYPTO: International Cryptology Conference","end_date":"2025-08-21","start_date":"2025-08-17"},"alternative_title":["LNCS"],"date_published":"2025-08-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/1035"}],"fulldoi":"https://doi.org/10.1007/978-3-032-01913-4_5","intvolume":"     16007","publication_status":"published","year":"2025","quality_controlled":"1","OA_type":"green","OA_place":"repository","language":[{"iso":"eng"}],"publication":"45th Annual International Cryptology Conference","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783032019134"],"isbn":["9783032019127"],"issn":["0302-9743"]},"acknowledgement":"B. Auerbach and B. Erol—Conducted part of this work at ISTA.","citation":{"short":"B. Auerbach, M. Cueto Noval, B. Erol, K.Z. Pietrzak, in:, 45th Annual International Cryptology Conference, Springer Nature, 2025, pp. 141–172.","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.","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.","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>.","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>","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>","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>."},"page":"141-172","related_material":{"record":[{"relation":"dissertation_contains","id":"22664","status":"public"}]},"date_updated":"2026-08-21T10:53:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-02-17T07:41:04Z","status":"public","author":[{"id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","first_name":"Benedikt","full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606"},{"last_name":"Cueto Noval","first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246"},{"last_name":"Erol","first_name":"Boran","full_name":"Erol, Boran"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"title":"Continuous group-key agreement: Concurrent updates without pruning","_id":"21262","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","type":"conference"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-08-27T11:42:43Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20203"},{"relation":"dissertation_contains","id":"22684","status":"public"}],"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/an-electrifying-turn-in-an-age-old-quest/"}]},"project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"citation":{"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>.","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>","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>","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>.","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.","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.","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)."},"article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"19278","title":"Spontaneous ordering of identical materials into a triboelectric series","author":[{"id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A"},{"first_name":"Felix","last_name":"Pertl","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo"},{"full_name":"Sauer, Markus","first_name":"Markus","last_name":"Sauer"},{"last_name":"Foelske","first_name":"Annette","full_name":"Foelske, Annette"},{"last_name":"Ostermann","first_name":"Markus","full_name":"Ostermann, Markus"},{"full_name":"Pichler, Christian M.","last_name":"Pichler","first_name":"Christian M."},{"first_name":"Yongkang","last_name":"Wang","full_name":"Wang, Yongkang"},{"last_name":"Nagata","first_name":"Yuki","full_name":"Nagata, Yuki"},{"first_name":"Mischa","last_name":"Bonn","full_name":"Bonn, Mischa"},{"full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","last_name":"Waitukaitis"}],"status":"public","date_created":"2025-03-02T23:01:52Z","language":[{"iso":"eng"}],"OA_type":"hybrid","OA_place":"publisher","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"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).","ec_funded":1,"publication":"Nature","issue":"8051","scopus_import":"1","fulldoi":"https://doi.org/10.1038/s41586-024-08530-6","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"file_date_updated":"2025-03-04T10:05:18Z","date_published":"2025-02-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","pmid":1,"quality_controlled":"1","year":"2025","publication_status":"published","intvolume":"       638","ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":638,"file":[{"file_size":3807415,"file_name":"2025_Nature_Sobarzo.pdf","date_updated":"2025-03-04T10:05:18Z","content_type":"application/pdf","file_id":"19289","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2025-03-04T10:05:18Z","checksum":"fecf302274dd3218d3e7dd22f39a6c0c","success":1}],"doi":"10.1038/s41586-024-08530-6","article_number":"664-669","isi":1,"external_id":{"pmid":["39972227"],"isi":["001428076100015"]},"department":[{"_id":"ScWa"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"month":"02","publisher":"Springer Nature","day":"20","oa":1,"corr_author":"1"},{"publication":"Physical Review Letters","issue":"14","scopus_import":"1","ec_funded":1,"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.","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"OA_type":"hybrid","OA_place":"publisher","language":[{"iso":"eng"}],"_id":"20481","title":"No time for surface charge: How bulk conductivity hides charge patterns from Kelvin probe force microscopy in contact-electrified surfaces","author":[{"last_name":"Pertl","first_name":"Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","orcid":"0000-0003-0463-5794","full_name":"Pertl, Felix"},{"full_name":"Lenton, Isaac C","orcid":"0000-0002-5010-6984","id":"a550210f-223c-11ec-8182-e2d45e817efb","first_name":"Isaac C","last_name":"Lenton"},{"full_name":"Cramer, Tobias","first_name":"Tobias","last_name":"Cramer"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"date_created":"2025-10-16T13:13:29Z","status":"public","article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"20523","relation":"research_data"},{"id":"22684","relation":"dissertation_contains","status":"public"}]},"project":[{"grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"citation":{"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>","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).","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.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-27T11:42:43Z","PlanS_conform":"1","day":"30","corr_author":"1","oa":1,"external_id":{"arxiv":["2502.12718"],"isi":["001587263900003"]},"month":"09","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","article_number":"146202","isi":1,"volume":135,"file":[{"file_id":"20522","file_size":1692251,"date_updated":"2025-10-23T09:32:31Z","content_type":"application/pdf","file_name":"2025_PhysReviewLetters_Pertl.pdf","date_created":"2025-10-23T09:32:31Z","checksum":"7e45e89b8db0b7f01e63185c68e4b0f9","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access"}],"doi":"10.1103/lcsm-xxty","ddc":["530"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","year":"2025","publication_status":"published","intvolume":"       135","file_date_updated":"2025-10-23T09:32:31Z","date_published":"2025-09-30T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.1103/lcsm-xxty","arxiv":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"}]},{"language":[{"iso":"eng"}],"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"The work in this thesis was supported by a grant from the Simons Foundation (662960, BH).\r\n","date_updated":"2026-09-02T08:16:32Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"155","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>.","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>","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>","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>.","short":"G. Yalniz, Transition to Turbulence: Data-, Solution-, and Pattern-Driven Approaches, Institute of Science and Technology Austria, 2025.","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."},"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics","grant_number":"662960"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9558"},{"status":"public","id":"12105","relation":"part_of_dissertation"},{"id":"13274","relation":"part_of_dissertation","status":"public"},{"id":"14466","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7563"}]},"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","oa_version":"Published Version","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"}],"author":[{"first_name":"Gökhan","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312"}],"date_created":"2025-05-12T15:12:28Z","status":"public","title":"Transition to turbulence: Data-, solution-, and pattern-driven approaches","_id":"19684","doi":"10.15479/AT-ISTA-19684","file":[{"file_size":20058169,"date_updated":"2025-05-12T15:13:28Z","content_type":"application/pdf","file_name":"Gökhan Yalnız - PhD thesis.pdf","file_id":"19685","relation":"main_file","creator":"gyalniz","access_level":"open_access","checksum":"0e452642b79f13633f1595bde71a67e3","date_created":"2025-05-12T15:13:28Z","success":1},{"file_name":"Movie 2A.1.mp4","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_size":37763743,"file_id":"19686","access_level":"open_access","relation":"supplementary_material","creator":"gyalniz","description":"3D visualizations of the turbulent flow (left) and the periodic orbits (middle) that are being shadowed along with the local state space projections (right) onto the principal components of the respective periodic orbit. Shown here are the isosurfaces of velocity (red/blue: ±95% of the instantaneous maximum) and vorticity (purple/green: ±65% of the instantaneous maximum) in the x-direction. Markers along the projections are in sync with the 3D visualizations. The movie corresponds to the initial time interval (up to t = 100) of figure 2.2 (a,b); periodic orbits and the state space projections are shown only through the shadowing events indicated in figure 2.2 (b).","title":"Chapter 2 - Movie 2A.1","checksum":"921099d76adab2df784ce12ce41cfb22","date_created":"2025-05-12T15:15:59Z"},{"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_name":"Movie 3A.1.mp4","file_size":3902655,"file_id":"19687","access_level":"open_access","description":"Turbulent flow (left) in HKW domain and its symmetry reduction (right). 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Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","creator":"gyalniz","relation":"supplementary_material","title":"Chapter 3 - Movie 3A.2","checksum":"ef8d270e066c1a9c3cb5ae46acf945e6","date_created":"2025-05-12T15:16:21Z","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_name":"Movie 3A.2.mp4","file_size":7043169,"file_id":"19688"},{"file_id":"19689","file_size":7748659,"file_name":"Movie 3A.3.mp4","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","date_created":"2025-05-12T15:16:36Z","checksum":"7ed871f428100d6827ac9b0e8ca8e985","title":"Chapter 3 - Movie 3A.3","relation":"supplementary_material","creator":"gyalniz","description":"Relative periodic orbit RPO_79.4 (left) of the plane-Couette flow (HKW domain) and its symmetry reduction (right). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","access_level":"open_access"},{"file_size":5873052,"file_name":"Movie 3A.4.mp4","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_id":"19690","creator":"gyalniz","relation":"supplementary_material","description":"Symmetry-reduced flow (left), its SRDMD approximation (middle), and state space projection (right) showing the spiral-out episode in P2K domain (figure 3.6 (b) and figure 3.8 (b)). Shown here are the isosurfaces of streamwise velocity (red/blue: u = 0.5 max/min u) and streamwise vorticity (green/purple: ω_x = 0.5 max/min ω_x).","access_level":"open_access","checksum":"dd5a252e1da00c8f303588e22e2baeef","date_created":"2025-05-12T15:16:50Z","title":"Chapter 3 - Movie 3A.4"},{"access_level":"open_access","creator":"gyalniz","relation":"supplementary_material","description":"Movie demonstrating the quasi-steady Reynolds number descent from turbulence to a periodic orbit.","title":"Chapter 4 - Movie 4A.1","date_created":"2025-05-12T15:17:11Z","checksum":"5ac58b86810698db28cbfc28f351ff70","file_name":"Movie 4A.1.mp4","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_size":9209327,"file_id":"19691"},{"file_size":5893993,"date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_name":"Movie 5A.1.mp4","file_id":"19692","description":"Streamwise velocity fluctuations (from laminar) of plane-Couette flow (Re^C =335) at the y = 0 wall-normal plane in coordinates stationary with respect to the bulk velocity. Here, x is the streamwise direction (the wall at y = 1 moves to the right) and z is the spanwise direction. Time is in advectime time units. Shown is the full (L_x = L_z = 400) domain.","relation":"supplementary_material","creator":"gyalniz","access_level":"open_access","checksum":"ac877f1e1ef39439911bf37cb1793b8e","date_created":"2025-05-12T15:17:43Z","title":"Chapter 5 - Movie 5A.1"},{"title":"Chapter 5 - Movie 5A.2","date_created":"2025-05-12T15:17:49Z","checksum":"fd17eabb70129ceaa414e40924d1d2fe","access_level":"open_access","creator":"gyalniz","relation":"supplementary_material","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_id":"19693","file_name":"Movie 5A.2.mp4","date_updated":"2025-05-12T15:43:28Z","content_type":"video/mp4","file_size":3990352},{"file_name":"Movie 5A.3.mp4","content_type":"video/mp4","date_updated":"2025-05-12T15:43:28Z","file_size":5171009,"file_id":"19694","access_level":"open_access","creator":"gyalniz","relation":"supplementary_material","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. Shown is a zoom-in of the full (L_x = L_z) domain.","title":"Chapter 5 - Movie 5A.3","checksum":"32f904497ab0bbee38f0788d96b91454","date_created":"2025-05-12T15:17:58Z"},{"file_size":18991996,"file_name":"Gökhan Yalnız - PhD thesis.zip","content_type":"application/x-zip-compressed","date_updated":"2025-05-12T15:43:28Z","file_id":"19695","relation":"source_file","creator":"gyalniz","access_level":"closed","checksum":"f313261b9bb12dfb943fead8318954c6","date_created":"2025-05-12T15:27:10Z"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"month":"05","doi_confirm":"1","corr_author":"1","oa":1,"day":"13","acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT-ISTA-19684","article_processing_charge":"No","has_accepted_license":"1","date_published":"2025-05-13T00:00:00Z","file_date_updated":"2025-05-12T15:43:28Z","alternative_title":["ISTA Thesis"],"publication_status":"published","year":"2025","ddc":["514","519","532","004"]}]