[{"publication_status":"published","publication_identifier":{"eissn":["1932-6203"]},"citation":{"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>.","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.","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.","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>","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>"},"file_date_updated":"2023-03-27T07:09:08Z","type":"journal_article","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"}],"scopus_import":"1","_id":"12758","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Public Library of Science","file":[{"file_id":"12771","content_type":"application/pdf","creator":"dernst","file_size":856625,"relation":"main_file","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","access_level":"open_access","success":1,"file_name":"2023_PLoSOne_Pak.pdf","date_created":"2023-03-27T07:09:08Z","date_updated":"2023-03-27T07:09:08Z"}],"title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","author":[{"last_name":"Pak","first_name":"Marina A.","full_name":"Pak, Marina A."},{"full_name":"Markhieva, Karina A.","last_name":"Markhieva","first_name":"Karina A."},{"last_name":"Novikova","first_name":"Mariia S.","full_name":"Novikova, Mariia S."},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev","first_name":"Ilya S."},{"last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","full_name":"Maksimova, Ekaterina"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1371/journal.pone.0282689","publication":"PLoS ONE","isi":1,"oa_version":"Published Version","volume":18,"date_created":"2023-03-26T22:01:07Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"day":"16","status":"public","external_id":{"isi":["000985134400106"]},"year":"2023","intvolume":"        18","month":"03","date_published":"2023-03-16T00:00:00Z","article_number":"e0282689","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.","date_updated":"2023-08-01T13:47:14Z","issue":"3","oa":1},{"external_id":{"isi":["001024737400001"]},"year":"2023","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).","article_number":"e0277148","date_published":"2023-03-17T00:00:00Z","month":"03","intvolume":"        18","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa":1,"issue":"3 March","date_updated":"2023-08-01T13:46:39Z","publication":"PLoS ONE","doi":"10.1371/journal.pone.0277148","ec_funded":1,"oa_version":"Published Version","isi":1,"volume":18,"status":"public","day":"17","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-03-26T22:01:07Z","department":[{"_id":"PeJo"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Public Library of Science","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"full_name":"Borges Merjane, Carolina","first_name":"Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X"},{"full_name":"Holderith, Noemi","first_name":"Noemi","last_name":"Holderith"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"first_name":"R.","last_name":"Angus Silver","full_name":"Angus Silver, R."}],"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","file":[{"content_type":"application/pdf","file_id":"12770","creator":"dernst","file_size":7290413,"checksum":"2380331ec27cc87808826fc64419ac1c","access_level":"open_access","relation":"main_file","success":1,"file_name":"2023_PLoSOne_Rothman.pdf","date_updated":"2023-03-27T06:51:09Z","date_created":"2023-03-27T06:51:09Z"}],"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"call_identifier":"FWF","grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"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"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2023-03-27T06:51:09Z","publication_identifier":{"eissn":["1932-6203"]},"citation":{"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>.","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>.","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>","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.","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.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023)."},"quality_controlled":"1","_id":"12759"},{"publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"citation":{"apa":"Henzinger, M. H., 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>","mla":"Henzinger, Monika H., 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.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ista":"Henzinger MH, 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.","ieee":"M. H. 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.","ama":"Henzinger MH, 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>","chicago":"Henzinger, Monika H, 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>."},"file_date_updated":"2023-03-27T06:37:22Z","type":"conference","scopus_import":"1","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."}],"arxiv":1,"_id":"12760","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"file_id":"12769","content_type":"application/pdf","file_size":872706,"creator":"dernst","checksum":"22141ab8bc55188e2dfff665e5daecbd","access_level":"open_access","relation":"main_file","success":1,"file_name":"2023_LIPICS_HenzingerM.pdf","date_created":"2023-03-27T06:37:22Z","date_updated":"2023-03-27T06:37:22Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dynamic maintenance of monotone dynamic programs and applications","author":[{"full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"article_processing_charge":"No","department":[{"_id":"MoHe"}],"language":[{"iso":"eng"}],"volume":254,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-03-26T22:01:07Z","ddc":["000"],"day":"01","status":"public","doi":"10.4230/LIPIcs.STACS.2023.36","publication":"40th International Symposium on Theoretical Aspects of Computer Science","oa_version":"Published Version","intvolume":"       254","month":"03","date_published":"2023-03-01T00:00:00Z","alternative_title":["LIPIcs"],"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.","article_number":"36","date_updated":"2023-03-27T06:46:27Z","oa":1,"external_id":{"arxiv":["2301.01744"]},"conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2023-03-09","start_date":"2023-03-07","location":"Hamburg, Germany"},"year":"2023"},{"oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"Annals of Applied Probability","main_file_link":[{"url":"https://arxiv.org/abs/2012.13218","open_access":"1"}],"doi":"10.1214/22-AAP1820","date_created":"2023-03-26T22:01:08Z","day":"01","status":"public","volume":33,"year":"2023","external_id":{"arxiv":["2012.13218"],"isi":["000946432400015"]},"page":"447-489","date_updated":"2023-10-17T12:48:52Z","oa":1,"issue":"1","date_published":"2023-02-01T00:00:00Z","month":"02","intvolume":"        33","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.","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","grant_number":"101020331"}],"publication_status":"published","_id":"12761","quality_controlled":"1","publication_identifier":{"issn":["1050-5164"]},"citation":{"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.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489.","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>","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>.","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>","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>."},"scopus_import":"1","arxiv":1,"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"}],"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"LaEr"}],"author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Functional central limit theorems for Wigner matrices","publisher":"Institute of Mathematical Statistics"},{"date_published":"2023-03-20T00:00:00Z","intvolume":"         3","month":"03","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.).","date_updated":"2023-08-16T12:41:53Z","oa":1,"external_id":{"arxiv":["2108.06686"]},"page":"254-263","year":"2023","volume":3,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-03-26T22:01:08Z","ddc":["570"],"status":"public","day":"20","publication":"Nature Computational Science","doi":"10.1038/s43588-023-00410-9","ec_funded":1,"oa_version":"Published Version","has_accepted_license":"1","publisher":"Springer Nature","author":[{"last_name":"Lombardi","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio"},{"last_name":"Pepic","first_name":"Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","full_name":"Pepic, Selver"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"}],"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2023-08-16T12:39:57Z","date_updated":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf","success":1,"relation":"main_file","access_level":"open_access","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_size":4474284,"creator":"dernst","file_id":"14073","content_type":"application/pdf"}],"article_processing_charge":"No","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"article_type":"original","citation":{"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>.","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>","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>.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","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.","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>"},"publication_identifier":{"eissn":["2662-8457"]},"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."}],"arxiv":1,"scopus_import":"1","type":"journal_article","file_date_updated":"2023-08-16T12:39:57Z","_id":"12762","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"publication_status":"published"},{"scopus_import":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","citation":{"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>.","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>","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>.","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","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.","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>"},"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"quality_controlled":"1","_id":"12763","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Boissonnat","first_name":"Jean Daniel","full_name":"Boissonnat, Jean Daniel"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220"}],"title":"The reach of subsets of manifolds","department":[{"_id":"HeEd"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"volume":7,"status":"public","day":"01","date_created":"2023-03-26T22:01:08Z","publication":"Journal of Applied and Computational Topology","doi":"10.1007/s41468-023-00116-x","main_file_link":[{"url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1","open_access":"1"}],"oa_version":"Submitted Version","ec_funded":1,"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.","date_published":"2023-09-01T00:00:00Z","month":"09","intvolume":"         7","oa":1,"date_updated":"2023-10-04T12:07:18Z","page":"619-641","year":"2023"},{"volume":70,"date_created":"2023-03-26T22:01:09Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"day":"01","status":"public","publication":"Discrete and Computational Geometry","doi":"10.1007/s00454-023-00484-2","oa_version":"Published Version","isi":1,"date_published":"2023-07-01T00:00:00Z","month":"07","intvolume":"        70","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.","date_updated":"2023-10-04T11:46:48Z","oa":1,"external_id":{"isi":["000948148000001"]},"page":"123-153","year":"2023","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"citation":{"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>.","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>","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.","ista":"Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 70, 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>.","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>"},"scopus_import":"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."}],"type":"journal_article","file_date_updated":"2023-10-04T11:46:24Z","_id":"12764","quality_controlled":"1","project":[{"grant_number":"I04245","call_identifier":"FWF","_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology"}],"publication_status":"published","has_accepted_license":"1","publisher":"Springer Nature","title":"Discrete yamabe problem for polyhedral surfaces","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kourimska, Hana","last_name":"Kourimska","orcid":"0000-0001-7841-0091","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","first_name":"Hana"}],"file":[{"creator":"dernst","file_size":1026683,"file_id":"14396","content_type":"application/pdf","access_level":"open_access","checksum":"cdbf90ba4a7ddcb190d37b9e9d4cb9d3","relation":"main_file","file_name":"2023_DiscreteGeometry_Kourimska.pdf","success":1,"date_updated":"2023-10-04T11:46:24Z","date_created":"2023-10-04T11:46:24Z"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"article_type":"original"},{"type":"journal_article","scopus_import":"1","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"}],"citation":{"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>.","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>","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.","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.","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>."},"publication_identifier":{"issn":["0269-8463"],"eissn":["1365-2435"]},"quality_controlled":"1","_id":"12765","publication_status":"published","publisher":"British Ecological Society","author":[{"first_name":"Sebastian","last_name":"Stockmaier","full_name":"Stockmaier, Sebastian"},{"first_name":"Yuko","last_name":"Ulrich","full_name":"Ulrich, Yuko"},{"full_name":"Albery, Gregory F.","last_name":"Albery","first_name":"Gregory F."},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"full_name":"Lopes, Patricia C.","first_name":"Patricia C.","last_name":"Lopes"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Behavioural defences against parasites across host social structures","department":[{"_id":"SyCr"}],"article_processing_charge":"No","article_type":"review","language":[{"iso":"eng"}],"volume":37,"status":"public","day":"01","date_created":"2023-03-26T22:01:09Z","doi":"10.1111/1365-2435.14310","publication":"Functional Ecology","isi":1,"oa_version":"None","intvolume":"        37","month":"04","date_published":"2023-04-01T00:00:00Z","issue":"4","date_updated":"2023-10-04T11:50:15Z","page":"809-820","external_id":{"isi":["000948940500001"]},"year":"2023"},{"related_material":{"record":[{"id":"12138","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","degree_awarded":"PhD","doi":"10.15479/at:ista:12781","ddc":["570","572"],"date_created":"2023-03-31T12:24:42Z","supervisor":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"status":"public","day":"23","year":"2023","page":"127","date_updated":"2023-08-04T08:54:51Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"03","alternative_title":["ISTA Thesis"],"date_published":"2023-03-23T00:00:00Z","project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","grant_number":"101020697"}],"publication_status":"published","_id":"12781","citation":{"chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>"},"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]},"file_date_updated":"2023-04-20T07:02:59Z","type":"dissertation","abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"file":[{"embargo":"2024-04-20","relation":"main_file","access_level":"closed","checksum":"5ebb6345cb4119f93460c81310265a6d","content_type":"application/pdf","file_id":"12852","embargo_to":"local","file_size":6071553,"creator":"vkravchu","date_updated":"2023-04-19T14:33:41Z","date_created":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf"},{"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","date_updated":"2023-04-20T07:02:59Z","date_created":"2023-04-19T14:33:52Z","file_id":"12853","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"local","file_size":19468766,"creator":"vkravchu","embargo":"2024-04-20","access_level":"closed","relation":"source_file","checksum":"c12055c48411d030d2afa51de2166221"}],"author":[{"last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","full_name":"Kravchuk, Vladyslav"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"publication_status":"published","citation":{"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>.","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>","short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","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.","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>.","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>"},"publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","file_date_updated":"2023-04-03T06:38:56Z","scopus_import":"1","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."}],"_id":"12786","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Springer Nature","file":[{"relation":"main_file","access_level":"open_access","checksum":"0a97b31191432dae5853bbb5ccb7698d","creator":"dernst","file_size":2613996,"file_id":"12797","content_type":"application/pdf","date_created":"2023-04-03T06:38:56Z","date_updated":"2023-04-03T06:38:56Z","file_name":"2023_NatureComm_Zhang.pdf","success":1}],"title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Zhang, Danyang","last_name":"Zhang","first_name":"Danyang"},{"first_name":"Remigijus","last_name":"Lape","full_name":"Lape, Remigijus"},{"last_name":"Shaikh","first_name":"Saher A.","full_name":"Shaikh, Saher A."},{"full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi","first_name":"Bianka K."},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"full_name":"Cais, Ondrej","last_name":"Cais","first_name":"Ondrej"},{"first_name":"Terunaga","last_name":"Nakagawa","full_name":"Nakagawa, Terunaga"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"doi":"10.1038/s41467-023-37259-5","publication":"Nature Communications","isi":1,"oa_version":"Published Version","volume":14,"date_created":"2023-04-02T22:01:09Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"status":"public","day":"25","external_id":{"isi":["001066658700003"]},"year":"2023","month":"03","intvolume":"        14","date_published":"2023-03-25T00:00:00Z","article_number":"1659","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.","date_updated":"2023-12-13T11:15:58Z","oa":1},{"volume":479,"day":"29","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-04-02T22:01:09Z","ddc":["000"],"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","doi":"10.1098/rspa.2022.0685","oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"link":[{"relation":"research_data","url":"https://doi.org/10.6084/m9.figshare.21261771.v1"}]},"acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","article_number":"20220685","date_published":"2023-03-29T00:00:00Z","month":"03","intvolume":"       479","oa":1,"issue":"2271","date_updated":"2025-07-14T09:09:51Z","external_id":{"isi":["000957125500002"]},"year":"2023","scopus_import":"1","abstract":[{"lang":"eng","text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results."}],"type":"journal_article","file_date_updated":"2023-04-03T06:25:29Z","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"citation":{"ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2023;479(2271). doi:<a href=\"https://doi.org/10.1098/rspa.2022.0685\">10.1098/rspa.2022.0685</a>","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 479, no. 2271. The Royal Society, 2023.","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society, 2023. <a href=\"https://doi.org/10.1098/rspa.2022.0685\">https://doi.org/10.1098/rspa.2022.0685</a>.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., &#38; Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspa.2022.0685\">https://doi.org/10.1098/rspa.2022.0685</a>","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rspa.2022.0685\">10.1098/rspa.2022.0685</a>."},"quality_controlled":"1","_id":"12787","publication_status":"published","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"publisher":"The Royal Society","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Coexistence times in the Moran process with environmental heterogeneity","author":[{"full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda"},{"full_name":"Tkadlec, Josef","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684"},{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"file":[{"creator":"dernst","file_size":827784,"content_type":"application/pdf","file_id":"12796","access_level":"open_access","checksum":"13953d349fbefcb5d21ccc6b303297eb","relation":"main_file","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","success":1,"date_updated":"2023-04-03T06:25:29Z","date_created":"2023-04-03T06:25:29Z"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"year":"2023","external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"oa":1,"issue":"10","date_updated":"2023-08-01T14:02:06Z","article_number":"103202","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_published":"2023-03-10T00:00:00Z","month":"03","intvolume":"       130","ec_funded":1,"oa_version":"Preprint","isi":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/","description":"News on the ISTA website","relation":"press_release"}]},"publication":"Physical Review Letters","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.07067"}],"doi":"10.1103/PhysRevLett.130.103202","day":"10","status":"public","date_created":"2023-04-02T22:01:10Z","volume":130,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"article_processing_charge":"No","title":"Topological charges of periodically kicked molecules","author":[{"full_name":"Karle, Volker","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","publication_status":"published","project":[{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"}],"quality_controlled":"1","_id":"12788","arxiv":1,"abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"citation":{"mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>.","apa":"Karle, V., Ghazaryan, A., &#38; Lemeshko, M. (2023). Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>.","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023)."}},{"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"ScWa"}],"article_processing_charge":"No","title":"Accurate determination of the shapes of granular charge distributions","author":[{"full_name":"Mujica, Nicolás","last_name":"Mujica","first_name":"Nicolás"},{"orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-11-27T09:51:48Z","date_created":"2023-11-27T09:51:48Z","file_name":"PhysRevE.107.034901 (1).pdf","success":1,"relation":"main_file","checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","access_level":"open_access","file_size":1428631,"creator":"swaituka","content_type":"application/pdf","file_id":"14612"}],"publisher":"American Physical Society","has_accepted_license":"1","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"quality_controlled":"1","_id":"12789","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2023-11-27T09:51:48Z","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"citation":{"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>","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>."},"year":"2023","external_id":{"isi":["000992142700001"]},"oa":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"issue":"3","date_updated":"2023-11-28T09:22:25Z","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.","article_number":"034901","date_published":"2023-03-01T00:00:00Z","month":"03","intvolume":"       107","ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"Physical Review E","doi":"10.1103/PhysRevE.107.034901","day":"01","status":"public","date_created":"2023-04-02T22:01:10Z","ddc":["530"],"volume":107},{"publication_status":"published","citation":{"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.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","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.","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>","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>.","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>","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>."},"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"scopus_import":"1","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."}],"arxiv":1,"type":"journal_article","_id":"12790","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"full_name":"Holder, Tobias","first_name":"Tobias","last_name":"Holder"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","publication":"Physical Review B","doi":"10.1103/PhysRevB.107.104502","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.02492"}],"related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/"}]},"oa_version":"Preprint","isi":1,"volume":107,"date_created":"2023-04-02T22:01:10Z","status":"public","day":"01","external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"year":"2023","date_published":"2023-03-01T00:00:00Z","intvolume":"       107","month":"03","article_number":"104502","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.","date_updated":"2023-08-01T13:59:29Z","oa":1,"issue":"10"},{"publication":"The European Physical Journal E","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2301.07769","open_access":"1"}],"doi":"10.1140/epje/s10189-023-00276-9","oa_version":"Preprint","isi":1,"volume":46,"date_created":"2023-04-02T22:01:11Z","status":"public","day":"20","external_id":{"arxiv":["2301.07769"],"isi":["000956387200001"]},"year":"2023","date_published":"2023-03-20T00:00:00Z","intvolume":"        46","month":"03","article_number":"16","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))","date_updated":"2023-08-01T14:03:47Z","oa":1,"issue":"3","publication_status":"published","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"citation":{"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>","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","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.","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.","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>.","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>","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>."},"scopus_import":"1","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"}],"arxiv":1,"type":"journal_article","_id":"12791","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"CaMu"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer Nature","author":[{"first_name":"Patricio","last_name":"Clark Di Leoni","full_name":"Clark Di Leoni, Patricio"},{"full_name":"Agasthya, Lokahith N","first_name":"Lokahith N","id":"cd100965-0804-11ed-9c55-f4878ff4e877","last_name":"Agasthya"},{"full_name":"Buzzicotti, Michele","first_name":"Michele","last_name":"Buzzicotti"},{"full_name":"Biferale, Luca","first_name":"Luca","last_name":"Biferale"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks"},{"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"publication_status":"published","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"citation":{"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>.","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>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. On the spectral form factor for random matrices. Communications in Mathematical Physics. 401, 1665–1700.","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.","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>"},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"file_date_updated":"2023-10-04T12:09:18Z","type":"journal_article","_id":"12792","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Springer Nature","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","orcid":"0000-0002-4901-7992"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"title":"On the spectral form factor for random matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2023_CommMathPhysics_Cipolloni.pdf","success":1,"date_created":"2023-10-04T12:09:18Z","date_updated":"2023-10-04T12:09:18Z","creator":"dernst","file_size":859967,"file_id":"14397","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"72057940f76654050ca84a221f21786c"}],"publication":"Communications in Mathematical Physics","doi":"10.1007/s00220-023-04692-y","ec_funded":1,"oa_version":"Published Version","isi":1,"volume":401,"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-04-02T22:01:11Z","day":"01","status":"public","external_id":{"isi":["000957343500001"]},"page":"1665-1700","year":"2023","date_published":"2023-07-01T00:00:00Z","intvolume":"       401","month":"07","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.","date_updated":"2023-10-04T12:10:31Z","oa":1},{"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"full_name":"Julseth, Mara","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","file":[{"access_level":"closed","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","relation":"supplementary_material","embargo_to":"open_access","file_size":52795,"creator":"mjulseth","file_id":"12805","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T06:09:40Z","file_name":"Dispersaldata.xlsx"},{"file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_created":"2023-04-06T06:11:27Z","date_updated":"2023-06-02T22:30:04Z","creator":"mjulseth","file_size":787239,"file_id":"12806","content_type":"application/vnd.wolfram.nb","relation":"supplementary_material","embargo":"2023-06-01","access_level":"open_access","checksum":"5a13b6d204371572e249f03795bc0d04"},{"date_created":"2023-04-06T08:26:12Z","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.docx","relation":"source_file","access_level":"closed","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_size":1061763,"creator":"mjulseth","embargo_to":"open_access","file_id":"12812","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","embargo":"2023-06-01","access_level":"open_access","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_id":"12813","content_type":"application/pdf","file_size":1741364,"creator":"mjulseth","date_created":"2023-04-06T08:26:37Z","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","_id":"12800","citation":{"chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>"},"publication_identifier":{"issn":["2791-4585"]},"abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"file_date_updated":"2023-06-02T22:30:04Z","type":"dissertation","year":"2023","page":"21","date_updated":"2023-06-02T22:30:05Z","oa":1,"alternative_title":["ISTA Master's Thesis"],"date_published":"2023-04-05T00:00:00Z","month":"04","oa_version":"Published Version","degree_awarded":"MS","doi":"10.15479/at:ista:12800","date_created":"2023-04-04T18:57:11Z","ddc":["576"],"status":"public","day":"05","supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}]},{"related_material":{"link":[{"url":"https://ista.ac.at/en/news/feed-them-or-lose-them/","description":"News on ISTA Website","relation":"press_release"}],"record":[{"id":"13107","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"Cell","doi":"10.1016/j.cell.2023.02.037","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2023-04-05T08:15:40Z","ddc":["570"],"status":"public","day":"27","volume":186,"year":"2023","external_id":{"isi":["000991468700001"]},"page":"1950-1967.e25","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_updated":"2024-02-07T08:03:32Z","oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"issue":"9","date_published":"2023-04-27T00:00:00Z","month":"04","intvolume":"       186","acknowledgement":"We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N.","project":[{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"}],"publication_status":"published","_id":"12802","quality_controlled":"1","publication_identifier":{"issn":["0092-8674"]},"citation":{"chicago":"Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>.","ama":"Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. 2023;186(9):1950-1967.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>","ieee":"L. Knaus <i>et al.</i>, “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” <i>Cell</i>, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023.","ista":"Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25.","short":"L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25.","mla":"Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” <i>Cell</i>, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">10.1016/j.cell.2023.02.037</a>.","apa":"Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2023.02.037\">https://doi.org/10.1016/j.cell.2023.02.037</a>"},"abstract":[{"lang":"eng","text":"Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction."}],"scopus_import":"1","file_date_updated":"2023-05-02T09:26:21Z","type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SiHi"},{"_id":"GaNo"}],"title":"Large neutral amino acid levels tune perinatal neuronal excitability and survival","author":[{"last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","full_name":"Knaus, Lisa"},{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","orcid":"0000-0003-1843-3173"},{"first_name":"Daniel","last_name":"Malzl","full_name":"Malzl, Daniel"},{"full_name":"Gerykova Bujalkova, Maria","first_name":"Maria","last_name":"Gerykova Bujalkova"},{"first_name":"Mateja","last_name":"Smogavec","full_name":"Smogavec, Mateja"},{"first_name":"Lena A.","last_name":"Schwarz","full_name":"Schwarz, Lena A."},{"last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f","first_name":"Sarah","full_name":"Gorkiewicz, Sarah"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","last_name":"Amberg","orcid":"0000-0002-3183-8207"},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"full_name":"Knittl-Frank, Christian","last_name":"Knittl-Frank","first_name":"Christian"},{"first_name":"Marianna","id":"7af593f1-d44a-11ed-bf94-a3646a6bb35e","last_name":"Tassinari","full_name":"Tassinari, Marianna"},{"full_name":"Maulide, Nuno","last_name":"Maulide","first_name":"Nuno"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"first_name":"Jörg","last_name":"Menche","full_name":"Menche, Jörg"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":15712841,"content_type":"application/pdf","file_id":"12889","relation":"main_file","access_level":"open_access","checksum":"47e94fbe19e86505b429cb7a5b503ce6","file_name":"2023_Cell_Knaus.pdf","success":1,"date_updated":"2023-05-02T09:26:21Z","date_created":"2023-05-02T09:26:21Z"}],"has_accepted_license":"1","publisher":"Elsevier"},{"year":"2023","page":"115","date_updated":"2023-04-26T12:16:56Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"month":"04","alternative_title":["ISTA Thesis"],"date_published":"2023-04-06T00:00:00Z","oa_version":"Published 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Technology Austria","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"12809","citation":{"ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>."},"publication_identifier":{"issn":["2663 - 337X"]},"file_date_updated":"2023-04-07T06:18:05Z","type":"dissertation","abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}]},{"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)"},"_id":"12817","date_created":"2023-04-07T11:37:40Z","day":"19","status":"public","citation":{"ama":"Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>","ieee":"J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023.","ista":"Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>.","short":"J.G. Danzl, (2023).","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12817\">https://doi.org/10.15479/AT:ISTA:12817</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12817\">10.15479/AT:ISTA:12817</a>."},"file_date_updated":"2023-05-18T19:51:52Z","type":"research_data","abstract":[{"text":"3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.","lang":"eng"}],"related_material":{"record":[{"id":"13267","status":"public","relation":"used_in_publication"}]},"contributor":[{"last_name":"Velicky","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"last_name":"Wei","first_name":"Donglai"},{"first_name":"Zudi","last_name":"Lin"},{"last_name":"Watson","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"first_name":"Jakob","last_name":"Troidl"},{"last_name":"Beyer","first_name":"Johanna"},{"last_name":"Ben Simon","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr"},{"last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Broichhagen","first_name":"Johannes"},{"first_name":"Seth G. 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