[{"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","file_date_updated":"2023-03-27T07:09:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","ieee":"M. A. Pak <i>et al.</i>, “Using AlphaFold to predict the impact of single mutations on protein stability and function,” <i>PLoS ONE</i>, vol. 18, no. 3. Public Library of Science, 2023.","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. 2023;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689."},"year":"2023","date_created":"2023-03-26T22:01:07Z","article_type":"original","quality_controlled":"1","type":"journal_article","day":"16","volume":18,"publisher":"Public Library of Science","publication":"PLoS ONE","issue":"3","article_processing_charge":"No","status":"public","_id":"12758","abstract":[{"text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.","lang":"eng"}],"intvolume":"        18","pmid":1,"file":[{"file_size":856625,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","file_id":"12771","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-03-27T07:09:08Z","file_name":"2023_PLoSOne_Pak.pdf","success":1,"creator":"dernst","date_updated":"2023-03-27T07:09:08Z"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"FyKo"},{"_id":"MaRo"}],"article_number":"e0282689","publication_identifier":{"eissn":["1932-6203"]},"acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","doi":"10.1371/journal.pone.0282689","month":"03","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["36928239"],"isi":["000985134400106"]},"date_updated":"2025-04-23T08:50:30Z","ddc":["570"],"date_published":"2023-03-16T00:00:00Z","author":[{"first_name":"Marina A.","full_name":"Pak, Marina A.","last_name":"Pak"},{"full_name":"Markhieva, Karina A.","last_name":"Markhieva","first_name":"Karina A."},{"last_name":"Novikova","full_name":"Novikova, Mariia S.","first_name":"Mariia S."},{"last_name":"Petrov","full_name":"Petrov, Dmitry S.","first_name":"Dmitry S."},{"full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev","first_name":"Ilya S."},{"first_name":"Ekaterina","full_name":"Maksimova, Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","file_date_updated":"2023-03-27T06:51:09Z","article_type":"original","quality_controlled":"1","year":"2023","date_created":"2023-03-26T22:01:07Z","citation":{"ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. 2023;18(3 March). doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., &#38; Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” <i>PLoS ONE</i>, vol. 18, no. 3 March. Public Library of Science, 2023.","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>."},"oa":1,"article_processing_charge":"No","publisher":"Public Library of Science","issue":"3 March","publication":"PLoS ONE","day":"17","volume":18,"type":"journal_article","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2023_PLoSOne_Rothman.pdf","date_created":"2023-03-27T06:51:09Z","creator":"dernst","success":1,"date_updated":"2023-03-27T06:51:09Z","checksum":"2380331ec27cc87808826fc64419ac1c","file_size":7290413,"file_id":"12770","access_level":"open_access"}],"publication_status":"published","status":"public","intvolume":"        18","_id":"12759","abstract":[{"text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.","lang":"eng"}],"pmid":1,"article_number":"e0277148","department":[{"_id":"PeJo"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"doi":"10.1371/journal.pone.0277148","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","publication_identifier":{"eissn":["1932-6203"]},"external_id":{"pmid":["36930689"],"isi":["001024737400001"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"03","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","first_name":"Carolina"},{"first_name":"Noemi","last_name":"Holderith","full_name":"Holderith, Noemi"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"full_name":"Angus Silver, R.","last_name":"Angus Silver","first_name":"R."}],"ddc":["570"],"date_published":"2023-03-17T00:00:00Z","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-04-23T08:50:50Z"},{"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"03","external_id":{"arxiv":["2301.01744"],"isi":["001532693100036"]},"conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","location":"Hamburg, Germany","start_date":"2023-03-07","end_date":"2023-03-09"},"language":[{"iso":"eng"}],"project":[{"grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"date_updated":"2025-09-09T12:22:44Z","author":[{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Neumann","full_name":"Neumann, Stefan","first_name":"Stefan"},{"last_name":"Räcke","full_name":"Räcke, Harald","first_name":"Harald"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"alternative_title":["LIPIcs"],"ddc":["000"],"date_published":"2023-03-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"MoHe"}],"article_number":"36","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"doi":"10.4230/LIPIcs.STACS.2023.36","day":"01","volume":254,"type":"conference","article_processing_charge":"No","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"40th International Symposium on Theoretical Aspects of Computer Science","status":"public","_id":"12760","intvolume":"       254","abstract":[{"lang":"eng","text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack."}],"file":[{"checksum":"22141ab8bc55188e2dfff665e5daecbd","file_size":872706,"file_id":"12769","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-03-27T06:37:22Z","file_name":"2023_LIPICS_HenzingerM.pdf","creator":"dernst","success":1,"date_updated":"2023-03-27T06:37:22Z"}],"publication_status":"published","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"title":"Dynamic maintenance of monotone dynamic programs and applications","file_date_updated":"2023-03-27T06:37:22Z","citation":{"ama":"Henzinger M, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: <i>40th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>","ista":"Henzinger M, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","apa":"Henzinger, M., Neumann, S., Räcke, H., &#38; Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In <i>40th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>","chicago":"Henzinger, Monika, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>.","ieee":"M. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Hamburg, Germany, 2023, vol. 254.","mla":"Henzinger, Monika, et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>.","short":"M. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"oa":1,"quality_controlled":"1","corr_author":"1","year":"2023","date_created":"2023-03-26T22:01:07Z"},{"doi":"10.1214/22-AAP1820","publication_identifier":{"issn":["1050-5164"]},"acknowledgement":"The second author is partially funded by the ERC Advanced Grant “RMTBEYOND” No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","isi":1,"department":[{"_id":"LaEr"}],"date_published":"2023-02-01T00:00:00Z","author":[{"full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","orcid":"0000-0002-4901-7992"},{"first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"date_updated":"2025-04-14T07:57:19Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2012.13218"],"isi":["000946432400015"]},"month":"02","scopus_import":"1","oa_version":"Preprint","year":"2023","date_created":"2023-03-26T22:01:08Z","article_type":"original","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner matrices. <i>Annals of Applied Probability</i>. 2023;33(1):447-489. doi:<a href=\"https://doi.org/10.1214/22-AAP1820\">10.1214/22-AAP1820</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Functional central limit theorems for Wigner matrices. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-AAP1820\">https://doi.org/10.1214/22-AAP1820</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central Limit Theorems for Wigner Matrices.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/22-AAP1820\">https://doi.org/10.1214/22-AAP1820</a>.","mla":"Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.” <i>Annals of Applied Probability</i>, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 447–89, doi:<a href=\"https://doi.org/10.1214/22-AAP1820\">10.1214/22-AAP1820</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems for Wigner matrices,” <i>Annals of Applied Probability</i>, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 447–489, 2023.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489."},"ec_funded":1,"title":"Functional central limit theorems for Wigner matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication_status":"published","status":"public","_id":"12761","abstract":[{"text":"We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent\r\nmultiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"intvolume":"        33","main_file_link":[{"url":"https://arxiv.org/abs/2012.13218","open_access":"1"}],"publisher":"Institute of Mathematical Statistics","issue":"1","publication":"Annals of Applied Probability","article_processing_charge":"No","type":"journal_article","page":"447-489","day":"01","volume":33},{"doi":"10.1038/s43588-023-00410-9","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","publication_identifier":{"eissn":["2662-8457"]},"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"author":[{"first_name":"Fabrizio","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Pepic, Selver","last_name":"Pepic","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"first_name":"Daniele","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino"}],"date_published":"2023-03-20T00:00:00Z","ddc":["570"],"date_updated":"2025-09-09T12:23:42Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"external_id":{"pmid":["38177880"],"isi":["000968161800002"],"arxiv":["2108.06686"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"03","quality_controlled":"1","corr_author":"1","article_type":"original","date_created":"2023-03-26T22:01:08Z","year":"2023","citation":{"ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>, vol. 3, Springer Nature, 2023, pp. 254–63, doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. 2023;3:254-263. doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>"},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2023-08-16T12:39:57Z","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","ec_funded":1,"publication_status":"published","file":[{"access_level":"open_access","file_id":"14073","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_size":4474284,"date_updated":"2023-08-16T12:39:57Z","creator":"dernst","success":1,"file_name":"2023_NatureCompScience_Lombardi.pdf","date_created":"2023-08-16T12:39:57Z","content_type":"application/pdf","relation":"main_file"}],"arxiv":1,"_id":"12762","abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"pmid":1,"intvolume":"         3","status":"public","article_processing_charge":"No","publication":"Nature Computational Science","publisher":"Springer Nature","volume":3,"day":"20","page":"254-263","type":"journal_article"},{"page":"619-641","day":"01","volume":7,"type":"journal_article","article_processing_charge":"No","publisher":"Springer Nature","publication":"Journal of Applied and Computational Topology","main_file_link":[{"url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1","open_access":"1"}],"status":"public","_id":"12763","intvolume":"         7","abstract":[{"text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"The reach of subsets of manifolds","citation":{"ista":"Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 7, 619–641.","ama":"Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. 2023;7:619-641. doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>.","apa":"Boissonnat, J. D., &#38; Wintraecken, M. (2023). The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","mla":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>, vol. 7, Springer Nature, 2023, pp. 619–41, doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>.","ieee":"J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,” <i>Journal of Applied and Computational Topology</i>, vol. 7. Springer Nature, pp. 619–641, 2023."},"oa":1,"article_type":"original","corr_author":"1","quality_controlled":"1","year":"2023","date_created":"2023-03-26T22:01:08Z","oa_version":"Submitted Version","scopus_import":"1","month":"09","language":[{"iso":"eng"}],"date_updated":"2025-04-14T07:44:01Z","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"author":[{"full_name":"Boissonnat, Jean Daniel","last_name":"Boissonnat","first_name":"Jean Daniel"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"date_published":"2023-09-01T00:00:00Z","department":[{"_id":"HeEd"}],"acknowledgement":"We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu for encouragement. We further acknowledge the anonymous reviewers whose comments helped improve the exposition.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). The first author is further supported by the French government, through the 3IA Côte d’Azur Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-19-P3IA-0002. The second author is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073.","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"doi":"10.1007/s41468-023-00116-x"},{"external_id":{"pmid":["37292248"],"isi":["000948148000001"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"07","author":[{"last_name":"Kourimska","full_name":"Kourimska, Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091","first_name":"Hana"}],"ddc":["510"],"date_published":"2023-07-01T00:00:00Z","project":[{"call_identifier":"FWF","_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology","grant_number":"I04245"}],"date_updated":"2025-04-23T08:59:15Z","department":[{"_id":"HeEd"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"doi":"10.1007/s00454-023-00484-2","acknowledgement":"Open access funding provided by the Austrian Science Fund (FWF). This research was supported by the FWF grant, Project number I4245-N35, and by the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) - Project-ID 195170736 - TRR109.","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","publication":"Discrete and Computational Geometry","day":"01","page":"123-153","volume":70,"type":"journal_article","file":[{"date_updated":"2023-10-04T11:46:24Z","creator":"dernst","success":1,"date_created":"2023-10-04T11:46:24Z","file_name":"2023_DiscreteGeometry_Kourimska.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"14396","checksum":"cdbf90ba4a7ddcb190d37b9e9d4cb9d3","file_size":1026683}],"publication_status":"published","status":"public","intvolume":"        70","_id":"12764","pmid":1,"abstract":[{"lang":"eng","text":"We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Discrete yamabe problem for polyhedral surfaces","file_date_updated":"2023-10-04T11:46:24Z","article_type":"original","quality_controlled":"1","corr_author":"1","year":"2023","date_created":"2023-03-26T22:01:09Z","citation":{"ista":"Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 70, 123–153.","ama":"Kourimska H. Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. 2023;70:123-153. doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>","chicago":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>.","apa":"Kourimska, H. (2023). Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>","ieee":"H. Kourimska, “Discrete yamabe problem for polyhedral surfaces,” <i>Discrete and Computational Geometry</i>, vol. 70. Springer Nature, pp. 123–153, 2023.","short":"H. Kourimska, Discrete and Computational Geometry 70 (2023) 123–153.","mla":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>, vol. 70, Springer Nature, 2023, pp. 123–53, doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>."},"oa":1},{"isi":1,"department":[{"_id":"SyCr"}],"doi":"10.1111/1365-2435.14310","publication_identifier":{"eissn":["1365-2435"],"issn":["0269-8463"]},"language":[{"iso":"eng"}],"external_id":{"isi":["000948940500001"]},"month":"04","oa_version":"Submitted Version","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","author":[{"first_name":"Sebastian","last_name":"Stockmaier","full_name":"Stockmaier, Sebastian"},{"first_name":"Yuko","full_name":"Ulrich, Yuko","last_name":"Ulrich"},{"first_name":"Gregory F.","last_name":"Albery","full_name":"Albery, Gregory F."},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Patricia C.","full_name":"Lopes, Patricia C.","last_name":"Lopes"}],"date_updated":"2025-07-10T11:50:31Z","OA_place":"repository","title":"Behavioural defences against parasites across host social structures","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","date_created":"2023-03-26T22:01:09Z","article_type":"review","quality_controlled":"1","oa":1,"citation":{"ista":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. 2023. Behavioural defences against parasites across host social structures. Functional Ecology. 37(4), 809–820.","ama":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. 2023;37(4):809-820. doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>","chicago":"Stockmaier, Sebastian, Yuko Ulrich, Gregory F. Albery, Sylvia Cremer, and Patricia C. Lopes. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>. British Ecological Society, 2023. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>.","apa":"Stockmaier, S., Ulrich, Y., Albery, G. F., Cremer, S., &#38; Lopes, P. C. (2023). Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. British Ecological Society. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>","mla":"Stockmaier, Sebastian, et al. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>, vol. 37, no. 4, British Ecological Society, 2023, pp. 809–20, doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>.","ieee":"S. Stockmaier, Y. Ulrich, G. F. Albery, S. Cremer, and P. C. Lopes, “Behavioural defences against parasites across host social structures,” <i>Functional Ecology</i>, vol. 37, no. 4. British Ecological Society, pp. 809–820, 2023.","short":"S. Stockmaier, Y. Ulrich, G.F. Albery, S. Cremer, P.C. Lopes, Functional Ecology 37 (2023) 809–820."},"publisher":"British Ecological Society","publication":"Functional Ecology","issue":"4","article_processing_charge":"No","OA_type":"green","type":"journal_article","page":"809-820","day":"01","volume":37,"publication_status":"published","status":"public","_id":"12765","intvolume":"        37","abstract":[{"text":"Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection.\r\nBecause they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group.\r\nHere, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals.\r\nWe discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies.\r\nFinally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.","lang":"eng"}],"main_file_link":[{"url":"https://digitalcommons.chapman.edu/cgi/viewcontent.cgi?article=1585&context=sees_articles","open_access":"1"}]},{"date_updated":"2023-12-13T11:15:58Z","date_published":"2023-03-25T00:00:00Z","ddc":["570"],"author":[{"first_name":"Danyang","last_name":"Zhang","full_name":"Zhang, Danyang"},{"last_name":"Lape","full_name":"Lape, Remigijus","first_name":"Remigijus"},{"first_name":"Saher A.","full_name":"Shaikh, Saher A.","last_name":"Shaikh"},{"first_name":"Bianka K.","full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","orcid":"0000-0002-8698-3823","first_name":"Jake"},{"full_name":"Cais, Ondrej","last_name":"Cais","first_name":"Ondrej"},{"last_name":"Nakagawa","full_name":"Nakagawa, Terunaga","first_name":"Terunaga"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"month":"03","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001066658700003"]},"publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","doi":"10.1038/s41467-023-37259-5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"PeJo"}],"isi":1,"article_number":"1659","intvolume":"        14","_id":"12786","abstract":[{"lang":"eng","text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators."}],"status":"public","publication_status":"published","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2023_NatureComm_Zhang.pdf","date_created":"2023-04-03T06:38:56Z","success":1,"creator":"dernst","date_updated":"2023-04-03T06:38:56Z","file_size":2613996,"checksum":"0a97b31191432dae5853bbb5ccb7698d","file_id":"12797","access_level":"open_access"}],"type":"journal_article","volume":14,"day":"25","publication":"Nature Communications","publisher":"Springer Nature","article_processing_charge":"No","oa":1,"citation":{"short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>, vol. 14, 1659, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>.","ieee":"D. Zhang <i>et al.</i>, “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>.","apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>"},"date_created":"2023-04-02T22:01:09Z","year":"2023","quality_controlled":"1","article_type":"original","file_date_updated":"2023-04-03T06:38:56Z","title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"ScWa"}],"isi":1,"article_number":"034901","acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. 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. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"doi":"10.1103/PhysRevE.107.034901","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"03","external_id":{"pmid":["37072968"],"isi":["000992142700001"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","grant_number":"949120"}],"date_updated":"2025-04-14T07:54:10Z","author":[{"first_name":"Nicolás","last_name":"Mujica","full_name":"Mujica, Nicolás"},{"last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176"}],"ddc":["530"],"date_published":"2023-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Accurate determination of the shapes of granular charge distributions","ec_funded":1,"file_date_updated":"2023-11-27T09:51:48Z","citation":{"mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>.","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” <i>Physical Review E</i>, vol. 107, no. 3. American Physical Society, 2023.","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>.","apa":"Mujica, N., &#38; Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>"},"oa":1,"article_type":"original","quality_controlled":"1","corr_author":"1","year":"2023","date_created":"2023-04-02T22:01:10Z","day":"01","volume":107,"type":"journal_article","article_processing_charge":"No","publisher":"American Physical Society","issue":"3","publication":"Physical Review E","status":"public","_id":"12789","pmid":1,"intvolume":"       107","abstract":[{"lang":"eng","text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior."}],"file":[{"file_size":1428631,"checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","file_id":"14612","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"PhysRevE.107.034901 (1).pdf","date_created":"2023-11-27T09:51:48Z","success":1,"creator":"swaituka","date_updated":"2023-11-27T09:51:48Z"}],"publication_status":"published"},{"year":"2023","date_created":"2023-04-02T22:01:10Z","article_type":"original","quality_controlled":"1","oa":1,"citation":{"mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” <i>Physical Review B</i>, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">10.1103/PhysRevB.107.104502</a>.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” <i>Physical Review B</i>, vol. 107, no. 10. American Physical Society, 2023.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. <i>Physical Review B</i>. 2023;107(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">10.1103/PhysRevB.107.104502</a>","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502.","apa":"Ghazaryan, A., Holder, T., Berg, E., &#38; Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">https://doi.org/10.1103/PhysRevB.107.104502</a>","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.107.104502\">https://doi.org/10.1103/PhysRevB.107.104502</a>."},"title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"description":"News on the ISTA website","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/","relation":"press_release"}]},"arxiv":1,"publication_status":"published","status":"public","_id":"12790","intvolume":"       107","abstract":[{"lang":"eng","text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02492"}],"publisher":"American Physical Society","publication":"Physical Review B","issue":"10","article_processing_charge":"No","type":"journal_article","day":"01","volume":107,"doi":"10.1103/PhysRevB.107.104502","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","article_number":"104502","isi":1,"department":[{"_id":"MaSe"},{"_id":"MiLe"}],"date_published":"2023-03-01T00:00:00Z","author":[{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"first_name":"Tobias","full_name":"Holder, Tobias","last_name":"Holder"},{"first_name":"Erez","full_name":"Berg, Erez","last_name":"Berg"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"date_updated":"2023-08-01T13:59:29Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"month":"03","scopus_import":"1","oa_version":"Preprint"},{"publication_status":"published","arxiv":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2301.07769"}],"intvolume":"        46","_id":"12791","abstract":[{"text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra.","lang":"eng"}],"pmid":1,"status":"public","article_processing_charge":"No","publication":"The European Physical Journal E","issue":"3","publisher":"Springer Nature","volume":46,"day":"20","type":"journal_article","quality_controlled":"1","article_type":"original","date_created":"2023-04-02T22:01:11Z","year":"2023","citation":{"ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” <i>The European Physical Journal E</i>, vol. 46, no. 3. Springer Nature, 2023.","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” <i>The European Physical Journal E</i>, vol. 46, no. 3, 16, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">10.1140/epje/s10189-023-00276-9</a>.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., &#38; Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. <i>The European Physical Journal E</i>. Springer Nature. <a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">https://doi.org/10.1140/epje/s10189-023-00276-9</a>","chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” <i>The European Physical Journal E</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">https://doi.org/10.1140/epje/s10189-023-00276-9</a>.","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. <i>The European Physical Journal E</i>. 2023;46(3). doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00276-9\">10.1140/epje/s10189-023-00276-9</a>","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","author":[{"first_name":"Patricio","last_name":"Clark Di Leoni","full_name":"Clark Di Leoni, Patricio"},{"id":"cd100965-0804-11ed-9c55-f4878ff4e877","full_name":"Agasthya, Lokahith N","last_name":"Agasthya","first_name":"Lokahith N"},{"first_name":"Michele","full_name":"Buzzicotti, Michele","last_name":"Buzzicotti"},{"full_name":"Biferale, Luca","last_name":"Biferale","first_name":"Luca"}],"date_published":"2023-03-20T00:00:00Z","date_updated":"2025-04-23T08:52:35Z","external_id":{"arxiv":["2301.07769"],"isi":["000956387200001"],"pmid":["36939938"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","scopus_import":"1","month":"03","doi":"10.1140/epje/s10189-023-00276-9","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"article_number":"16","department":[{"_id":"CaMu"}],"isi":1},{"year":"2023","date_created":"2023-04-02T22:01:11Z","article_type":"original","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “On the spectral form factor for random matrices,” <i>Communications in Mathematical Physics</i>, vol. 401. Springer Nature, pp. 1665–1700, 2023.","mla":"Cipolloni, Giorgio, et al. “On the Spectral Form Factor for Random Matrices.” <i>Communications in Mathematical Physics</i>, vol. 401, Springer Nature, 2023, pp. 1665–700, doi:<a href=\"https://doi.org/10.1007/s00220-023-04692-y\">10.1007/s00220-023-04692-y</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 401 (2023) 1665–1700.","ama":"Cipolloni G, Erdös L, Schröder DJ. On the spectral form factor for random matrices. <i>Communications in Mathematical Physics</i>. 2023;401:1665-1700. doi:<a href=\"https://doi.org/10.1007/s00220-023-04692-y\">10.1007/s00220-023-04692-y</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random matrices. Communications in Mathematical Physics. 401, 1665–1700.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). On the spectral form factor for random matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-023-04692-y\">https://doi.org/10.1007/s00220-023-04692-y</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Spectral Form Factor for Random Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00220-023-04692-y\">https://doi.org/10.1007/s00220-023-04692-y</a>."},"ec_funded":1,"title":"On the spectral form factor for random matrices","file_date_updated":"2023-10-04T12:09:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","success":1,"date_updated":"2023-10-04T12:09:18Z","relation":"main_file","content_type":"application/pdf","file_name":"2023_CommMathPhysics_Cipolloni.pdf","date_created":"2023-10-04T12:09:18Z","file_id":"14397","access_level":"open_access","checksum":"72057940f76654050ca84a221f21786c","file_size":859967}],"publication_status":"published","status":"public","_id":"12792","abstract":[{"text":"In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.","lang":"eng"}],"intvolume":"       401","publisher":"Springer Nature","publication":"Communications in Mathematical Physics","article_processing_charge":"Yes (via OA deal)","type":"journal_article","day":"01","page":"1665-1700","volume":401,"doi":"10.1007/s00220-023-04692-y","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"acknowledgement":"We are grateful to the authors of [25] for sharing with us their insights and preliminary numerical results. We are especially thankful to Stephen Shenker for very valuable advice over several email communications. Helpful comments on the manuscript from Peter Forrester and from the anonymous referees are also acknowledged.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nLászló Erdős: Partially supported by ERC Advanced Grant \"RMTBeyond\" No. 101020331. Dominik Schröder: Supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","department":[{"_id":"LaEr"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"ddc":["510"],"date_published":"2023-07-01T00:00:00Z","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","orcid":"0000-0002-4901-7992"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László"},{"full_name":"Schröder, Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J"}],"project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"date_updated":"2025-04-14T07:57:19Z","language":[{"iso":"eng"}],"external_id":{"isi":["000957343500001"]},"month":"07","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-04-11T06:27:00Z","title":"Curvature induces active velocity waves in rotating spherical tissues","citation":{"ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>, vol. 14, 1643, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., &#38; Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>."},"oa":1,"quality_controlled":"1","article_type":"original","date_created":"2023-04-09T22:01:00Z","year":"2023","volume":14,"day":"24","type":"journal_article","article_processing_charge":"No","publication":"Nature Communications","publisher":"Springer Nature","_id":"12818","intvolume":"        14","pmid":1,"abstract":[{"text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues.","lang":"eng"}],"status":"public","publication_status":"published","file":[{"file_size":4146777,"checksum":"54f06f9eee11d43bab253f3492c983ba","access_level":"open_access","file_id":"12821","date_created":"2023-04-11T06:27:00Z","file_name":"2023_NatureComm_Brandstaetter.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2023-04-11T06:27:00Z","creator":"dernst","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"EdHa"}],"isi":1,"article_number":"1643","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-37054-2","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","month":"03","external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"language":[{"iso":"eng"}],"date_updated":"2023-08-01T14:05:30Z","author":[{"full_name":"Brandstätter, Tom","last_name":"Brandstätter","first_name":"Tom"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David","first_name":"David","orcid":"0000-0001-7205-2975"},{"first_name":"Yu Long","last_name":"Han","full_name":"Han, Yu Long"},{"last_name":"Alert","full_name":"Alert, Ricard","first_name":"Ricard"},{"first_name":"Ming","last_name":"Guo","full_name":"Guo, Ming"},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."}],"date_published":"2023-03-24T00:00:00Z","ddc":["570"]},{"publication_status":"published","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2209.05165"}],"abstract":[{"lang":"eng","text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds."}],"_id":"12819","intvolume":"       107","status":"public","article_processing_charge":"No","issue":"3","publication":"Physical Review A","publisher":"American Physical Society","volume":107,"day":"22","type":"journal_article","quality_controlled":"1","article_type":"letter_note","date_created":"2023-04-09T22:01:00Z","year":"2023","citation":{"ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701.","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. <i>Physical Review A</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">10.1103/PhysRevA.107.L031701</a>","chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">https://doi.org/10.1103/PhysRevA.107.L031701</a>.","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., &#38; Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">https://doi.org/10.1103/PhysRevA.107.L031701</a>","ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” <i>Physical Review A</i>, vol. 107, no. 3. American Physical Society, 2023.","short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” <i>Physical Review A</i>, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.L031701\">10.1103/PhysRevA.107.L031701</a>."},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","author":[{"last_name":"Sokolova","full_name":"Sokolova, Alesya","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","first_name":"Alesya","orcid":"0000-0002-8308-4144"},{"first_name":"D. A.","full_name":"Kalacheva, D. A.","last_name":"Kalacheva"},{"first_name":"G. P.","last_name":"Fedorov","full_name":"Fedorov, G. P."},{"last_name":"Astafiev","full_name":"Astafiev, O. V.","first_name":"O. V."}],"date_published":"2023-03-22T00:00:00Z","date_updated":"2023-08-01T14:06:05Z","external_id":{"isi":["000957799000006"],"arxiv":["2209.05165"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","scopus_import":"1","month":"03","doi":"10.1103/PhysRevA.107.L031701","acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"article_number":"L031701","department":[{"_id":"JoFi"}],"isi":1},{"citation":{"chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">https://doi.org/10.15479/AT:ISTA:12820</a>.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">https://doi.org/10.15479/AT:ISTA:12820</a>","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>","mla":"Schanda, Paul. <i>Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12820\">10.15479/AT:ISTA:12820</a>.","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","short":"P. Schanda, (2023)."},"oa":1,"corr_author":"1","doi":"10.15479/AT:ISTA:12820","date_created":"2023-04-10T05:55:56Z","year":"2023","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"department":[{"_id":"PaSc"}],"related_material":{"record":[{"status":"public","id":"13095","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-04-14T09:39:58Z","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","abstract":[{"lang":"eng","text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript"}],"_id":"12820","date_updated":"2024-10-09T21:05:30Z","status":"public","file":[{"checksum":"54a619605e44c871214fb0e07b05c6bf","file_size":54184807,"file_id":"12823","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-04-14T09:39:33Z","file_name":"data_deposition.zip","creator":"pschanda","success":1,"date_updated":"2023-04-14T09:39:33Z"},{"file_size":4978,"checksum":"8dede9fc78399d13144eb05c62bf5750","access_level":"open_access","file_id":"12824","file_name":"README","date_created":"2023-04-14T09:39:58Z","relation":"main_file","content_type":"application/octet-stream","date_updated":"2023-04-14T09:39:58Z","creator":"pschanda","success":1}],"author":[{"orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"date_published":"2023-04-18T00:00:00Z","ddc":["570"],"oa_version":"Published Version","has_accepted_license":"1","day":"18","month":"04","type":"research_data","contributor":[{"contributor_type":"researcher","first_name":"Laura","last_name":"Troussicot"},{"contributor_type":"researcher","first_name":"Björn M.","last_name":"Burmann"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Rotation control, interlocking, and self‐positioning of active cogwheels","file_date_updated":"2023-04-17T06:44:17Z","article_type":"original","quality_controlled":"1","corr_author":"1","year":"2023","date_created":"2023-04-12T08:30:03Z","citation":{"short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).","ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” <i>Advanced Intelligent Systems</i>, vol. 5, no. 1. Wiley, 2023.","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” <i>Advanced Intelligent Systems</i>, vol. 5, no. 1, 2200129, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/aisy.202200129\">10.1002/aisy.202200129</a>.","ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. <i>Advanced Intelligent Systems</i>. 2023;5(1). doi:<a href=\"https://doi.org/10.1002/aisy.202200129\">10.1002/aisy.202200129</a>","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","apa":"Martinet, Q., Aubret, A., &#38; Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. <i>Advanced Intelligent Systems</i>. Wiley. <a href=\"https://doi.org/10.1002/aisy.202200129\">https://doi.org/10.1002/aisy.202200129</a>","chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” <i>Advanced Intelligent Systems</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/aisy.202200129\">https://doi.org/10.1002/aisy.202200129</a>."},"oa":1,"article_processing_charge":"No","publisher":"Wiley","publication":"Advanced Intelligent Systems","issue":"1","day":"01","volume":5,"type":"journal_article","file":[{"file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","date_created":"2023-04-17T06:44:17Z","content_type":"application/pdf","relation":"main_file","date_updated":"2023-04-17T06:44:17Z","creator":"dernst","success":1,"checksum":"d48fc41d39892e7fa0d44cb352dd46aa","file_size":2414125,"access_level":"open_access","file_id":"12840"}],"publication_status":"published","arxiv":1,"status":"public","abstract":[{"lang":"eng","text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter."}],"_id":"12822","intvolume":"         5","article_number":"2200129","department":[{"_id":"JePa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"doi":"10.1002/aisy.202200129","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","publication_identifier":{"issn":["2640-4567"]},"external_id":{"arxiv":["2201.03333"],"isi":["000852291200001"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"01","author":[{"orcid":"0000-0002-2916-6632","first_name":"Quentin","last_name":"Martinet","full_name":"Martinet, Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"ddc":["530"],"date_published":"2023-01-01T00:00:00Z","date_updated":"2024-10-09T21:04:56Z"},{"citation":{"chicago":"Montaña-Mora, Guillem, Xueqiang Qi, Xiang Wang, Jesus Chacón-Borrero, Paulina R. Martinez-Alanis, Xiaoting Yu, Junshan Li, et al. “Phosphorous Incorporation into Palladium Tin Nanoparticles for the Electrocatalytic Formate Oxidation Reaction.” <i>Journal of Electroanalytical Chemistry</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jelechem.2023.117369\">https://doi.org/10.1016/j.jelechem.2023.117369</a>.","apa":"Montaña-Mora, G., Qi, X., Wang, X., Chacón-Borrero, J., Martinez-Alanis, P. R., Yu, X., … Cabot, A. (2023). Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction. <i>Journal of Electroanalytical Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jelechem.2023.117369\">https://doi.org/10.1016/j.jelechem.2023.117369</a>","ista":"Montaña-Mora G, Qi X, Wang X, Chacón-Borrero J, Martinez-Alanis PR, Yu X, Li J, Xue Q, Arbiol J, Ibáñez M, Cabot A. 2023. Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction. Journal of Electroanalytical Chemistry. 936, 117369.","ama":"Montaña-Mora G, Qi X, Wang X, et al. Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction. <i>Journal of Electroanalytical Chemistry</i>. 2023;936. doi:<a href=\"https://doi.org/10.1016/j.jelechem.2023.117369\">10.1016/j.jelechem.2023.117369</a>","short":"G. Montaña-Mora, X. Qi, X. Wang, J. Chacón-Borrero, P.R. Martinez-Alanis, X. Yu, J. Li, Q. Xue, J. Arbiol, M. Ibáñez, A. Cabot, Journal of Electroanalytical Chemistry 936 (2023).","ieee":"G. Montaña-Mora <i>et al.</i>, “Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction,” <i>Journal of Electroanalytical Chemistry</i>, vol. 936. Elsevier, 2023.","mla":"Montaña-Mora, Guillem, et al. “Phosphorous Incorporation into Palladium Tin Nanoparticles for the Electrocatalytic Formate Oxidation Reaction.” <i>Journal of Electroanalytical Chemistry</i>, vol. 936, 117369, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jelechem.2023.117369\">10.1016/j.jelechem.2023.117369</a>."},"corr_author":"1","quality_controlled":"1","article_type":"original","date_created":"2023-04-16T22:01:06Z","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction","_id":"12829","intvolume":"       936","abstract":[{"text":"The deployment of direct formate fuel cells (DFFCs) relies on the development of active and stable catalysts for the formate oxidation reaction (FOR). Palladium, providing effective full oxidation of formate to CO2, has been widely used as FOR catalyst, but it suffers from low stability, moderate activity, and high cost. Herein, we detail a colloidal synthesis route for the incorporation of P on Pd2Sn nanoparticles. These nanoparticles are dispersed on carbon black and the obtained composite is used as electrocatalytic material for the FOR. The Pd2Sn0.8P-based electrodes present outstanding catalytic activities with record mass current densities up to 10.0 A mgPd-1, well above those of Pd1.6Sn/C reference electrode. These high current densities are further enhanced by increasing the temperature from 25 °C to 40 °C. The Pd2Sn0.8P electrode also allows for slowing down the rapid current decay that generally happens during operation and can be rapidly re-activated through potential cycling. The excellent catalytic performance obtained is rationalized using density functional theory (DFT) calculations.","lang":"eng"}],"status":"public","publication_status":"published","volume":936,"day":"01","type":"journal_article","article_processing_charge":"No","publication":"Journal of Electroanalytical Chemistry","publisher":"Elsevier","acknowledgement":"This work was carried out within the framework of the project Combenergy, PID2019-105490RB-C32, financed by the Spanish MCIN/AEI/10.13039/501100011033. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. Part of the present work has been performed in the frameworks of the Universitat de Barcelona Nanoscience PhD program. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the European Union. The project on which these results are based has received funding from the European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No. 801342 (Tecniospring INDUSTRY) and the Government of Catalonia's Agency for Business Competitiveness (ACCIÓ). J. Li is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I.  acknowledges funding by ISTA and the Werner Siemens Foundation.","publication_identifier":{"issn":["1572-6657"]},"doi":"10.1016/j.jelechem.2023.117369","department":[{"_id":"MaIb"}],"isi":1,"article_number":"117369","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"date_updated":"2025-04-15T06:36:40Z","author":[{"last_name":"Montaña-Mora","full_name":"Montaña-Mora, Guillem","first_name":"Guillem"},{"first_name":"Xueqiang","last_name":"Qi","full_name":"Qi, Xueqiang"},{"first_name":"Xiang","last_name":"Wang","full_name":"Wang, Xiang"},{"last_name":"Chacón-Borrero","full_name":"Chacón-Borrero, Jesus","first_name":"Jesus"},{"first_name":"Paulina R.","full_name":"Martinez-Alanis, Paulina R.","last_name":"Martinez-Alanis"},{"first_name":"Xiaoting","full_name":"Yu, Xiaoting","last_name":"Yu"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"first_name":"Qian","full_name":"Xue, Qian","last_name":"Xue"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"date_published":"2023-05-01T00:00:00Z","scopus_import":"1","oa_version":"None","month":"05","external_id":{"isi":["000967060900001"]},"language":[{"iso":"eng"}]},{"quality_controlled":"1","corr_author":"1","article_type":"original","date_created":"2023-04-16T22:01:07Z","year":"2023","citation":{"ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. 2023;58(7):582-596.e7. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">https://doi.org/10.1016/j.devcel.2023.02.016</a>.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” <i>Developmental Cell</i>, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.02.016\">10.1016/j.devcel.2023.02.016</a>.","ieee":"K. Huljev <i>et al.</i>, “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” <i>Developmental Cell</i>, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-04-17T07:41:25Z","ec_funded":1,"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","publication_status":"published","file":[{"date_updated":"2023-04-17T07:41:25Z","creator":"dernst","success":1,"date_created":"2023-04-17T07:41:25Z","file_name":"2023_DevelopmentalCell_Huljev.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"12842","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","file_size":7925886}],"_id":"12830","pmid":1,"intvolume":"        58","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"status":"public","article_processing_charge":"Yes (via OA deal)","issue":"7","publication":"Developmental Cell","publisher":"Elsevier","volume":58,"page":"582-596.e7","day":"10","type":"journal_article","doi":"10.1016/j.devcel.2023.02.016","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"CaHe"},{"_id":"Bio"}],"author":[{"first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"last_name":"Nunes Pinheiro","full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","orcid":"0000-0003-4333-7503"},{"last_name":"Preusser","full_name":"Preusser, Friedrich","first_name":"Friedrich"},{"first_name":"Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"full_name":"Naik, Suyash","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","first_name":"Suyash"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"date_published":"2023-04-10T00:00:00Z","ddc":["570"],"date_updated":"2025-04-23T08:51:34Z","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"grant_number":"ALTF 850-2017","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["36931269"],"isi":["000982111800001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"04"},{"arxiv":1,"publication_status":"published","file":[{"file_size":7388057,"checksum":"8d801babea4df48e08895c76571bb19e","file_id":"12841","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2023_JourChemicalPhysics_Zeng.pdf","date_created":"2023-04-17T07:28:38Z","creator":"dernst","success":1,"date_updated":"2023-04-17T07:28:38Z"}],"_id":"12831","intvolume":"       158","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"pmid":1,"status":"public","publication":"The Journal of Chemical Physics","issue":"13","publisher":"American Institute of Physics","article_processing_charge":"No","type":"journal_article","volume":158,"day":"07","date_created":"2023-04-16T22:01:07Z","year":"2023","quality_controlled":"1","article_type":"original","oa":1,"citation":{"ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. <i>The Journal of Chemical Physics</i>. 2023;158(13). doi:<a href=\"https://doi.org/10.1063/5.0135893\">10.1063/5.0135893</a>","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2023. <a href=\"https://doi.org/10.1063/5.0135893\">https://doi.org/10.1063/5.0135893</a>.","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., &#38; Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0135893\">https://doi.org/10.1063/5.0135893</a>","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” <i>The Journal of Chemical Physics</i>, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:<a href=\"https://doi.org/10.1063/5.0135893\">10.1063/5.0135893</a>.","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” <i>The Journal of Chemical Physics</i>, vol. 158, no. 13. American Institute of Physics, 2023.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023)."},"file_date_updated":"2023-04-17T07:28:38Z","title":"Variational theory of angulons and their rotational spectroscopy","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-04-07T00:00:00Z","ddc":["530"],"author":[{"last_name":"Zeng","full_name":"Zeng, Zhongda","first_name":"Zhongda"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"full_name":"Shi, Tao","last_name":"Shi","first_name":"Tao"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"}],"project":[{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"date_updated":"2025-04-23T08:55:25Z","language":[{"iso":"eng"}],"external_id":{"isi":["000970038800001"],"pmid":["37031113"],"arxiv":["2211.08070"]},"month":"04","oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","doi":"10.1063/5.0135893","publication_identifier":{"eissn":["1089-7690"]},"acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","article_number":"134301","department":[{"_id":"MiLe"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1}]