[{"day":"01","oa":1,"_id":"12707","scopus_import":"1","date_updated":"2025-04-14T07:57:19Z","author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","orcid":"0000-0003-1559-1205","full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","last_name":"Xu"}],"date_created":"2023-03-05T23:01:05Z","year":"2023","publication_status":"published","language":[{"iso":"eng"}],"status":"public","external_id":{"isi":["000947270100008"],"arxiv":["2112.12093 "]},"date_published":"2023-05-01T00:00:00Z","publication_identifier":{"issn":["1350-7265"]},"volume":29,"ec_funded":1,"article_type":"original","isi":1,"intvolume":"        29","article_processing_charge":"No","month":"05","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2112.12093"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"publisher":"Bernoulli Society for Mathematical Statistics and Probability","citation":{"ama":"Erdös L, Xu Y. Small deviation estimates for the largest eigenvalue of Wigner matrices. <i>Bernoulli</i>. 2023;29(2):1063-1079. doi:<a href=\"https://doi.org/10.3150/22-BEJ1490\">10.3150/22-BEJ1490</a>","ieee":"L. Erdös and Y. Xu, “Small deviation estimates for the largest eigenvalue of Wigner matrices,” <i>Bernoulli</i>, vol. 29, no. 2. Bernoulli Society for Mathematical Statistics and Probability, pp. 1063–1079, 2023.","mla":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” <i>Bernoulli</i>, vol. 29, no. 2, Bernoulli Society for Mathematical Statistics and Probability, 2023, pp. 1063–79, doi:<a href=\"https://doi.org/10.3150/22-BEJ1490\">10.3150/22-BEJ1490</a>.","apa":"Erdös, L., &#38; Xu, Y. (2023). Small deviation estimates for the largest eigenvalue of Wigner matrices. <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability. <a href=\"https://doi.org/10.3150/22-BEJ1490\">https://doi.org/10.3150/22-BEJ1490</a>","ista":"Erdös L, Xu Y. 2023. Small deviation estimates for the largest eigenvalue of Wigner matrices. Bernoulli. 29(2), 1063–1079.","chicago":"Erdös, László, and Yuanyuan Xu. “Small Deviation Estimates for the Largest Eigenvalue of Wigner Matrices.” <i>Bernoulli</i>. Bernoulli Society for Mathematical Statistics and Probability, 2023. <a href=\"https://doi.org/10.3150/22-BEJ1490\">https://doi.org/10.3150/22-BEJ1490</a>.","short":"L. Erdös, Y. Xu, Bernoulli 29 (2023) 1063–1079."},"page":"1063-1079","oa_version":"Preprint","title":"Small deviation estimates for the largest eigenvalue of Wigner matrices","type":"journal_article","abstract":[{"text":"We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.","lang":"eng"}],"arxiv":1,"issue":"2","department":[{"_id":"LaEr"}],"publication":"Bernoulli","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.3150/22-BEJ1490"},{"department":[{"_id":"AnSa"}],"has_accepted_license":"1","publication":"Soft Matter","arxiv":1,"doi":"10.1039/d2sm01562e","quality_controlled":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"publisher":"Royal Society of Chemistry","article_processing_charge":"No","month":"02","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"type":"journal_article","title":"Steering self-organisation through confinement","oa_version":"Published Version","page":"1695-1704","citation":{"ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704."},"ec_funded":1,"volume":19,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"file":[{"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_size":3581939,"file_name":"2023_SoftMatter_Araujo.pdf","file_id":"12711","date_updated":"2023-03-07T09:19:41Z","creator":"cchlebak","date_created":"2023-03-07T09:19:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1}],"intvolume":"        19","isi":1,"article_type":"original","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","file_date_updated":"2023-03-07T09:19:41Z","scopus_import":"1","ddc":["540"],"_id":"12708","oa":1,"day":"06","external_id":{"isi":["000940388100001"],"pmid":["36779972"],"arxiv":["2204.10059"]},"date_published":"2023-02-06T00:00:00Z","language":[{"iso":"eng"}],"status":"public","publication_status":"published","year":"2023","date_updated":"2025-04-23T08:48:51Z","date_created":"2023-03-05T23:01:06Z","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"full_name":"Barois, Thomas","first_name":"Thomas","last_name":"Barois"},{"first_name":"Guido","last_name":"Boffetta","full_name":"Boffetta, Guido"},{"first_name":"Itai","last_name":"Cohen","full_name":"Cohen, Itai"},{"last_name":"Corbetta","first_name":"Alessandro","full_name":"Corbetta, Alessandro"},{"last_name":"Dauchot","first_name":"Olivier","full_name":"Dauchot, Olivier"},{"full_name":"Dijkstra, Marjolein","first_name":"Marjolein","last_name":"Dijkstra"},{"full_name":"Durham, William M.","last_name":"Durham","first_name":"William M."},{"first_name":"Audrey","last_name":"Dussutour","full_name":"Dussutour, Audrey"},{"full_name":"Garnier, Simon","first_name":"Simon","last_name":"Garnier"},{"first_name":"Hanneke","last_name":"Gelderblom","full_name":"Gelderblom, Hanneke"},{"full_name":"Golestanian, Ramin","last_name":"Golestanian","first_name":"Ramin"},{"first_name":"Lucio","last_name":"Isa","full_name":"Isa, Lucio"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"first_name":"Hartmut","last_name":"Löwen","full_name":"Löwen, Hartmut"},{"last_name":"Metzler","first_name":"Ralf","full_name":"Metzler, Ralf"},{"full_name":"Polin, Marco","first_name":"Marco","last_name":"Polin"},{"first_name":"C. Patrick","last_name":"Royall","full_name":"Royall, C. Patrick"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"first_name":"Cécile","last_name":"Sykes","full_name":"Sykes, Cécile"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"first_name":"Idan","last_name":"Tuval","full_name":"Tuval, Idan"},{"full_name":"Vogel, Nicolas","first_name":"Nicolas","last_name":"Vogel"},{"last_name":"Yeomans","first_name":"Julia M.","full_name":"Yeomans, Julia M."},{"full_name":"Zuriguel, Iker","last_name":"Zuriguel","first_name":"Iker"},{"last_name":"Marin","first_name":"Alvaro","full_name":"Marin, Alvaro"},{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"}]},{"external_id":{"pmid":["37581017"],"arxiv":["2103.07823"],"isi":["000936496800001"]},"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"9605"}]},"date_published":"2023-09-01T00:00:00Z","status":"public","language":[{"iso":"eng"}],"publication_status":"published","year":"2023","date_created":"2023-03-05T23:01:06Z","author":[{"first_name":"René","last_name":"Corbet","full_name":"Corbet, René"},{"last_name":"Kerber","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"last_name":"Lesnick","first_name":"Michael","full_name":"Lesnick, Michael"},{"first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"}],"date_updated":"2025-07-10T12:01:57Z","acknowledgement":"We thank the anonymous reviewers for many helpful comments and suggestions, which led to substantial improvements of the paper. The first two authors were supported by the Austrian Science Fund (FWF) grant number P 29984-N35 and W1230. The first author was partly supported by an Austrian Marshall Plan Scholarship, and by the Brummer & Partners MathDataLab. A conference version of this paper was presented at the 37th International Symposium on Computational Geometry (SoCG 2021). Open access funding provided by the Royal Institute of Technology.","scopus_import":"1","file_date_updated":"2023-03-07T14:40:14Z","oa":1,"_id":"12709","ddc":["000"],"day":"01","isi":1,"intvolume":"        70","article_type":"original","volume":70,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"file":[{"creator":"cchlebak","date_created":"2023-03-07T14:40:14Z","date_updated":"2023-03-07T14:40:14Z","file_id":"12715","file_name":"2023_DisCompGeo_Corbet.pdf","file_size":1359323,"checksum":"71ce7e59f7ee4620acc704fecca620c2","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness."}],"type":"journal_article","title":"Computing the multicover bifiltration","oa_version":"Published Version","page":"376-405","citation":{"chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-022-00476-8\">https://doi.org/10.1007/s00454-022-00476-8</a>.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, Discrete and Computational Geometry 70 (2023) 376–405.","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” <i>Discrete and Computational Geometry</i>, vol. 70. Springer Nature, pp. 376–405, 2023.","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. <i>Discrete and Computational Geometry</i>. 2023;70:376-405. doi:<a href=\"https://doi.org/10.1007/s00454-022-00476-8\">10.1007/s00454-022-00476-8</a>","apa":"Corbet, R., Kerber, M., Lesnick, M., &#38; Osang, G. F. (2023). Computing the multicover bifiltration. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00476-8\">https://doi.org/10.1007/s00454-022-00476-8</a>","mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” <i>Discrete and Computational Geometry</i>, vol. 70, Springer Nature, 2023, pp. 376–405, doi:<a href=\"https://doi.org/10.1007/s00454-022-00476-8\">10.1007/s00454-022-00476-8</a>.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2023. Computing the multicover bifiltration. Discrete and Computational Geometry. 70, 376–405."},"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"Yes (via OA deal)","month":"09","doi":"10.1007/s00454-022-00476-8","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"HeEd"}],"publication":"Discrete and Computational Geometry","has_accepted_license":"1","arxiv":1},{"doi":"10.1002/adma.202206110","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"EdHa"}],"has_accepted_license":"1","publication":"Advanced Materials","issue":"13","type":"journal_article","abstract":[{"text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.","lang":"eng"}],"title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","oa_version":"Published Version","article_number":"2206110","citation":{"chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” <i>Advanced Materials</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/adma.202206110\">https://doi.org/10.1002/adma.202206110</a>.","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. <i>Advanced Materials</i>. 2023;35(13). doi:<a href=\"https://doi.org/10.1002/adma.202206110\">10.1002/adma.202206110</a>","ieee":"B. Schamberger <i>et al.</i>, “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” <i>Advanced Materials</i>, vol. 35, no. 13. Wiley, 2023.","mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” <i>Advanced Materials</i>, vol. 35, no. 13, 2206110, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/adma.202206110\">10.1002/adma.202206110</a>.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.202206110\">https://doi.org/10.1002/adma.202206110</a>","ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110."},"publisher":"Wiley","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","month":"03","intvolume":"        35","isi":1,"article_type":"review","volume":35,"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"file":[{"file_size":2898063,"checksum":"5c04d68130e97a0ecd1ca27fbc15a246","file_name":"2023_AdvancedMaterials_Schamberger.pdf","creator":"dernst","date_created":"2023-09-26T10:51:56Z","date_updated":"2023-09-26T10:51:56Z","file_id":"14373","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1}],"external_id":{"pmid":["36461812"],"isi":["000941068900001"]},"date_published":"2023-03-29T00:00:00Z","status":"public","language":[{"iso":"eng"}],"publication_status":"published","year":"2023","author":[{"last_name":"Schamberger","first_name":"Barbara","full_name":"Schamberger, Barbara"},{"full_name":"Ziege, Ricardo","last_name":"Ziege","first_name":"Ricardo"},{"full_name":"Anselme, Karine","last_name":"Anselme","first_name":"Karine"},{"full_name":"Ben Amar, Martine","first_name":"Martine","last_name":"Ben Amar"},{"last_name":"Bykowski","first_name":"Michał","full_name":"Bykowski, Michał"},{"last_name":"Castro","first_name":"André P.G.","full_name":"Castro, André P.G."},{"full_name":"Cipitria, Amaia","first_name":"Amaia","last_name":"Cipitria"},{"full_name":"Coles, Rhoslyn A.","first_name":"Rhoslyn A.","last_name":"Coles"},{"full_name":"Dimova, Rumiana","last_name":"Dimova","first_name":"Rumiana"},{"first_name":"Michaela","last_name":"Eder","full_name":"Eder, Michaela"},{"full_name":"Ehrig, Sebastian","last_name":"Ehrig","first_name":"Sebastian"},{"full_name":"Escudero, Luis M.","last_name":"Escudero","first_name":"Luis M."},{"full_name":"Evans, Myfanwy E.","first_name":"Myfanwy E.","last_name":"Evans"},{"first_name":"Paulo R.","last_name":"Fernandes","full_name":"Fernandes, Paulo R."},{"full_name":"Fratzl, Peter","last_name":"Fratzl","first_name":"Peter"},{"first_name":"Liesbet","last_name":"Geris","full_name":"Geris, Liesbet"},{"full_name":"Gierlinger, Notburga","first_name":"Notburga","last_name":"Gierlinger"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Iglič, Aleš","last_name":"Iglič","first_name":"Aleš"},{"full_name":"Kirkensgaard, Jacob J.K.","last_name":"Kirkensgaard","first_name":"Jacob J.K."},{"full_name":"Kollmannsberger, Philip","first_name":"Philip","last_name":"Kollmannsberger"},{"full_name":"Kowalewska, Łucja","first_name":"Łucja","last_name":"Kowalewska"},{"full_name":"Kurniawan, Nicholas A.","first_name":"Nicholas A.","last_name":"Kurniawan"},{"first_name":"Ioannis","last_name":"Papantoniou","full_name":"Papantoniou, Ioannis"},{"full_name":"Pieuchot, Laurent","last_name":"Pieuchot","first_name":"Laurent"},{"first_name":"Tiago H.V.","last_name":"Pires","full_name":"Pires, Tiago H.V."},{"full_name":"Renner, Lars D.","first_name":"Lars D.","last_name":"Renner"},{"first_name":"Andrew O.","last_name":"Sageman-Furnas","full_name":"Sageman-Furnas, Andrew O."},{"last_name":"Schröder-Turk","first_name":"Gerd E.","full_name":"Schröder-Turk, Gerd E."},{"full_name":"Sengupta, Anupam","first_name":"Anupam","last_name":"Sengupta"},{"full_name":"Sharma, Vikas R.","first_name":"Vikas R.","last_name":"Sharma"},{"full_name":"Tagua, Antonio","first_name":"Antonio","last_name":"Tagua"},{"first_name":"Caterina","last_name":"Tomba","full_name":"Tomba, Caterina"},{"last_name":"Trepat","first_name":"Xavier","full_name":"Trepat, Xavier"},{"last_name":"Waters","first_name":"Sarah L.","full_name":"Waters, Sarah L."},{"full_name":"Yeo, Edwina F.","first_name":"Edwina F.","last_name":"Yeo"},{"full_name":"Roschger, Andreas","last_name":"Roschger","first_name":"Andreas"},{"first_name":"Cécile M.","last_name":"Bidan","full_name":"Bidan, Cécile M."},{"last_name":"Dunlop","first_name":"John W.C.","full_name":"Dunlop, John W.C."}],"date_created":"2023-03-05T23:01:06Z","date_updated":"2023-09-26T10:56:46Z","acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","scopus_import":"1","file_date_updated":"2023-09-26T10:51:56Z","oa":1,"_id":"12710","ddc":["570"],"day":"29"},{"date_updated":"2025-04-23T08:49:38Z","date_created":"2023-03-12T23:01:02Z","author":[{"full_name":"Bernabeu, Elena","first_name":"Elena","last_name":"Bernabeu"},{"full_name":"Mccartney, Daniel L.","first_name":"Daniel L.","last_name":"Mccartney"},{"first_name":"Danni A.","last_name":"Gadd","full_name":"Gadd, Danni A."},{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"full_name":"Lu, Ake T.","first_name":"Ake T.","last_name":"Lu"},{"full_name":"Murphy, Lee","last_name":"Murphy","first_name":"Lee"},{"full_name":"Wrobel, Nicola","last_name":"Wrobel","first_name":"Nicola"},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"full_name":"Liewald, David","first_name":"David","last_name":"Liewald"},{"first_name":"Caroline","last_name":"Hayward","full_name":"Hayward, Caroline"},{"full_name":"Sudlow, Cathie","first_name":"Cathie","last_name":"Sudlow"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"first_name":"Steve","last_name":"Horvath","full_name":"Horvath, Steve"},{"full_name":"Mcintosh, Andrew M.","first_name":"Andrew M.","last_name":"Mcintosh"},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"first_name":"Catalina A.","last_name":"Vallejos","full_name":"Vallejos, Catalina A."},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"publication_status":"published","year":"2023","language":[{"iso":"eng"}],"status":"public","external_id":{"isi":["000940286600001"],"pmid":["36855161"]},"date_published":"2023-02-28T00:00:00Z","day":"28","oa":1,"_id":"12719","ddc":["570"],"file_date_updated":"2023-03-14T10:29:47Z","scopus_import":"1","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","article_type":"original","intvolume":"        15","isi":1,"file":[{"checksum":"833b837910c4db42fb5f0f34125f77a7","file_size":4275987,"file_name":"2023_GenomeMed_Bernabeu.pdf","file_id":"12722","date_updated":"2023-03-14T10:29:47Z","creator":"cchlebak","date_created":"2023-03-14T10:29:47Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1}],"publication_identifier":{"eissn":["1756-994X"]},"volume":15,"article_number":"12","citation":{"ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01161-y\">10.1186/s13073-023-01161-y</a>","ieee":"E. Bernabeu <i>et al.</i>, “Refining epigenetic prediction of chronological and biological age,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01161-y\">https://doi.org/10.1186/s13073-023-01161-y</a>","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” <i>Genome Medicine</i>, vol. 15, 12, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01161-y\">10.1186/s13073-023-01161-y</a>.","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01161-y\">https://doi.org/10.1186/s13073-023-01161-y</a>.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023)."},"oa_version":"Published Version","title":"Refining epigenetic prediction of chronological and biological age","type":"journal_article","abstract":[{"lang":"eng","text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age."}],"article_processing_charge":"No","month":"02","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Springer Nature","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1186/s13073-023-01161-y","has_accepted_license":"1","department":[{"_id":"MaRo"}],"publication":"Genome Medicine"},{"intvolume":"      2633","OA_type":"green","volume":2633,"OA_place":"repository","alternative_title":["Methods in Molecular Biology"],"publication_identifier":{"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"],"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"]},"language":[{"iso":"eng"}],"status":"public","external_id":{"pmid":["36853454"]},"date_published":"2023-03-01T00:00:00Z","date_updated":"2025-06-25T05:56:45Z","date_created":"2023-03-12T23:01:02Z","author":[{"last_name":"Arroyo-Urea","first_name":"Sandra","full_name":"Arroyo-Urea, Sandra"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake"},{"full_name":"García-Nafría, Javier","last_name":"García-Nafría","first_name":"Javier"}],"publication_status":"published","year":"2023","scopus_import":"1","editor":[{"full_name":"Scarlett, Garry","last_name":"Scarlett","first_name":"Garry"}],"series_title":"MIMB","day":"01","oa":1,"_id":"12720","doi":"10.1007/978-1-0716-3004-4_3","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"New York, NY, United States","quality_controlled":"1","publication":"DNA Manipulation and Analysis","department":[{"_id":"PeJo"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"type":"book_chapter","citation":{"ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>.","apa":"Arroyo-Urea, S., Watson, J., &#38; García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), <i>DNA Manipulation and Analysis</i> (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. <i>DNA Manipulation and Analysis</i>. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">10.1007/978-1-0716-3004-4_3</a>","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in <i>DNA Manipulation and Analysis</i>, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In <i>DNA Manipulation and Analysis</i>, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3004-4_3\">https://doi.org/10.1007/978-1-0716-3004-4_3</a>."},"oa_version":"Submitted Version","page":"33-44","publisher":"Springer Nature","article_processing_charge":"No","month":"03","main_file_link":[{"url":"https://zaguan.unizar.es/record/125930/files/texto_completo.pdf","open_access":"1"}]},{"day":"10","_id":"12723","oa":1,"scopus_import":"1","date_created":"2023-03-14T13:11:59Z","author":[{"last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abhishek","last_name":"Shiva Kumar","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","full_name":"Shiva Kumar, Abhishek"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","first_name":"Dusan"},{"last_name":"Ashourishokri","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes"},{"last_name":"Zhumekenov","first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A."},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"}],"date_updated":"2025-04-23T08:53:33Z","year":"2023","publication_status":"published","keyword":["General Physics and Astronomy"],"status":"public","language":[{"iso":"eng"}],"date_published":"2023-03-10T00:00:00Z","external_id":{"isi":["000982435900002"],"pmid":["36962044"],"arxiv":["2203.09443"]},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"volume":130,"article_type":"original","isi":1,"intvolume":"       130","month":"03","article_processing_charge":"No","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"publisher":"American Physical Society","article_number":"106901","citation":{"short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>.","ieee":"A. Volosniev <i>et al.</i>, “Spin-electric coupling in lead halide perovskites,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901."},"oa_version":"Preprint","title":"Spin-electric coupling in lead halide perovskites","type":"journal_article","abstract":[{"lang":"eng","text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order."}],"arxiv":1,"publication":"Physical Review Letters","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","doi":"10.1103/physrevlett.130.106901"},{"scopus_import":"1","oa":1,"_id":"12724","day":"15","date_published":"2023-03-15T00:00:00Z","external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"language":[{"iso":"eng"}],"status":"public","publication_status":"published","year":"2023","date_updated":"2024-10-09T21:04:46Z","author":[{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev"},{"last_name":"Shiva Kumar","first_name":"Abhishek","full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"last_name":"Lorenc","first_name":"Dusan","full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Younes","last_name":"Ashourishokri","id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes"},{"full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov","first_name":"Ayan"},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek"}],"date_created":"2023-03-14T13:13:05Z","volume":107,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"intvolume":"       107","isi":1,"article_type":"original","publisher":"American Physical Society","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"article_processing_charge":"No","month":"03","type":"journal_article","abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"title":"Effective model for studying optical properties of lead halide perovskites","oa_version":"Preprint","article_number":"125201","citation":{"ieee":"A. Volosniev <i>et al.</i>, “Effective model for studying optical properties of lead halide perovskites,” <i>Physical Review B</i>, vol. 107, no. 12. American Physical Society, 2023.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. 2023;107(12). doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023)."},"issue":"12","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication":"Physical Review B","arxiv":1,"doi":"10.1103/physrevb.107.125201","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_identifier":{"isbn":["9798400700156"]},"scopus_import":"1","conference":{"start_date":"2023-02-25","location":"Montreal, QC, Canada","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"day":"25","_id":"12735","oa":1,"language":[{"iso":"eng"}],"status":"public","date_published":"2023-02-25T00:00:00Z","external_id":{"arxiv":["2211.04986"]},"date_updated":"2023-03-20T07:29:28Z","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"date_created":"2023-03-19T23:00:58Z","publication_status":"published","year":"2023","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","department":[{"_id":"DaAl"}],"arxiv":1,"doi":"10.1145/3572848.3577481","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Association for Computing Machinery","article_processing_charge":"No","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"title":"Fast and scalable channels in Kotlin Coroutines","abstract":[{"text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.","lang":"eng"}],"type":"conference","citation":{"ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2023:107-118. doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Montreal, QC, Canada, 2023, pp. 107–118.","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 107–18, doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>.","ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 107–18. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118."},"page":"107-118","oa_version":"Preprint"},{"status":"public","language":[{"iso":"eng"}],"title":"Unexpected scaling in path copying trees","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"type":"conference_poster","date_published":"2023-02-25T00:00:00Z","citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. <i>Unexpected Scaling in Path Copying Trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. <i>Unexpected Scaling in Path Copying Trees</i>. Association for Computing Machinery; 2023:438-440. doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, <i>Unexpected scaling in path copying trees</i>. Association for Computing Machinery, 2023, pp. 438–440.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 438–40, doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., &#38; Kokorin, I. (2023). <i>Unexpected scaling in path copying trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p."},"author":[{"full_name":"Aksenov, Vitaly","last_name":"Aksenov","first_name":"Vitaly"},{"last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"last_name":"Kokorin","first_name":"Ilya","full_name":"Kokorin, Ilya"}],"date_created":"2023-03-19T23:00:58Z","date_updated":"2024-10-21T06:01:21Z","oa_version":"Published Version","page":"438-440","year":"2023","publication_status":"published","publisher":"Association for Computing Machinery","scopus_import":"1","conference":{"start_date":"2023-02-25","location":"Montreal, QB, Canada","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","article_processing_charge":"No","day":"25","month":"02","main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"_id":"12736","oa":1,"doi":"10.1145/3572848.3577512","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_identifier":{"isbn":["9798400700156"]}},{"doi":"10.1021/acs.inorgchem.3c00057","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","publication":"Inorganic Chemistry","department":[{"_id":"StFr"}],"issue":"11","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","type":"journal_article","abstract":[{"text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed.","lang":"eng"}],"citation":{"ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","ieee":"Á. García-Romero <i>et al.</i>, “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” <i>Inorganic Chemistry</i>, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. 2023;62(11):4625-4636. doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” <i>Inorganic Chemistry</i>, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., &#38; Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>","chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” <i>Inorganic Chemistry</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636."},"page":"4625-4636","oa_version":"Submitted Version","publisher":"American Chemical Society","month":"03","article_processing_charge":"No","main_file_link":[{"url":"https://uvadoc.uva.es/handle/10324/59798","open_access":"1"}],"isi":1,"intvolume":"        62","OA_type":"green","article_type":"original","volume":62,"OA_place":"repository","publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"status":"public","language":[{"iso":"eng"}],"date_published":"2023-03-08T00:00:00Z","external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"date_created":"2023-03-19T23:00:59Z","author":[{"full_name":"García-Romero, Álvaro","last_name":"García-Romero","first_name":"Álvaro"},{"last_name":"Waters","first_name":"Jessica E.","full_name":"Waters, Jessica E."},{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","last_name":"Jethwa"},{"full_name":"Bond, Andrew D.","last_name":"Bond","first_name":"Andrew D."},{"first_name":"Annie L.","last_name":"Colebatch","full_name":"Colebatch, Annie L."},{"full_name":"García-Rodríguez, Raúl","first_name":"Raúl","last_name":"García-Rodríguez"},{"first_name":"Dominic S.","last_name":"Wright","full_name":"Wright, Dominic S."}],"date_updated":"2025-04-24T11:32:09Z","publication_status":"published","year":"2023","scopus_import":"1","acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","day":"08","oa":1,"_id":"12737"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","doi":"10.1038/s42255-023-00766-2","department":[{"_id":"Bio"}],"publication":"Nature Metabolism","citation":{"ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023.","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515."},"page":"495-515","oa_version":"Preprint","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","type":"journal_article","abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}],"month":"03","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"publisher":"Springer Nature","article_type":"original","isi":1,"intvolume":"         5","publication_identifier":{"issn":["2522-5812"]},"volume":5,"date_created":"2023-03-23T12:58:43Z","author":[{"full_name":"Cikes, Domagoj","first_name":"Domagoj","last_name":"Cikes"},{"last_name":"Elsayad","first_name":"Kareem","full_name":"Elsayad, Kareem"},{"first_name":"Erdinc","last_name":"Sezgin","full_name":"Sezgin, Erdinc"},{"first_name":"Erika","last_name":"Koitai","full_name":"Koitai, Erika"},{"full_name":"Ferenc, Torma","first_name":"Torma","last_name":"Ferenc"},{"first_name":"Michael","last_name":"Orthofer","full_name":"Orthofer, Michael"},{"full_name":"Yarwood, Rebecca","first_name":"Rebecca","last_name":"Yarwood"},{"full_name":"Heinz, Leonhard X.","last_name":"Heinz","first_name":"Leonhard X."},{"full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov","first_name":"Vitaly"},{"last_name":"Darwish-Miranda","first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","full_name":"Darwish-Miranda, Nasser"},{"full_name":"Taylor, Adrian","last_name":"Taylor","first_name":"Adrian"},{"full_name":"Grapentine, Sophie","first_name":"Sophie","last_name":"Grapentine"},{"first_name":"Fathiya","last_name":"al-Murshedi","full_name":"al-Murshedi, Fathiya"},{"full_name":"Abot, Anne","first_name":"Anne","last_name":"Abot"},{"full_name":"Weidinger, Adelheid","last_name":"Weidinger","first_name":"Adelheid"},{"last_name":"Kutchukian","first_name":"Candice","full_name":"Kutchukian, Candice"},{"first_name":"Colline","last_name":"Sanchez","full_name":"Sanchez, Colline"},{"full_name":"Cronin, Shane J. F.","first_name":"Shane J. F.","last_name":"Cronin"},{"full_name":"Novatchkova, Maria","last_name":"Novatchkova","first_name":"Maria"},{"last_name":"Kavirayani","first_name":"Anoop","full_name":"Kavirayani, Anoop"},{"full_name":"Schuetz, Thomas","first_name":"Thomas","last_name":"Schuetz"},{"full_name":"Haubner, Bernhard","first_name":"Bernhard","last_name":"Haubner"},{"full_name":"Haas, Lisa","first_name":"Lisa","last_name":"Haas"},{"last_name":"Hagelkruys","first_name":"Astrid","full_name":"Hagelkruys, Astrid"},{"last_name":"Jackowski","first_name":"Suzanne","full_name":"Jackowski, Suzanne"},{"first_name":"Andrey","last_name":"Kozlov","full_name":"Kozlov, Andrey"},{"full_name":"Jacquemond, Vincent","last_name":"Jacquemond","first_name":"Vincent"},{"full_name":"Knauf, Claude","first_name":"Claude","last_name":"Knauf"},{"full_name":"Superti-Furga, Giulio","last_name":"Superti-Furga","first_name":"Giulio"},{"full_name":"Rullman, Eric","last_name":"Rullman","first_name":"Eric"},{"first_name":"Thomas","last_name":"Gustafsson","full_name":"Gustafsson, Thomas"},{"first_name":"John","last_name":"McDermot","full_name":"McDermot, John"},{"full_name":"Lowe, Martin","first_name":"Martin","last_name":"Lowe"},{"full_name":"Radak, Zsolt","first_name":"Zsolt","last_name":"Radak"},{"first_name":"Jeffrey S.","last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S."},{"full_name":"Bakovic, Marica","first_name":"Marica","last_name":"Bakovic"},{"full_name":"Banka, Siddharth","first_name":"Siddharth","last_name":"Banka"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."}],"date_updated":"2023-11-28T07:31:33Z","year":"2023","publication_status":"published","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"status":"public","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"date_published":"2023-03-20T00:00:00Z","day":"20","oa":1,"_id":"12747","scopus_import":"1","acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation."},{"has_accepted_license":"1","department":[{"_id":"AnSa"}],"publication":"Science Advances","issue":"11","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"doi":"10.1126/sciadv.ade5224","corr_author":"1","month":"03","article_processing_charge":"No","publisher":"American Association for the Advancement of Science","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","article_number":"eade5224","citation":{"ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>.","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023)."},"abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"type":"journal_article","title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","publication_identifier":{"eissn":["2375-2548"]},"file":[{"file_size":1826471,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","date_created":"2023-03-27T06:24:49Z","creator":"dernst","date_updated":"2023-03-27T06:24:49Z","file_id":"12768","file_name":"2023_ScienceAdvances_Hurtig.pdf","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access"}],"ec_funded":1,"volume":9,"article_type":"original","isi":1,"intvolume":"         9","ddc":["570"],"_id":"12756","oa":1,"day":"17","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","scopus_import":"1","file_date_updated":"2023-03-27T06:24:49Z","year":"2023","publication_status":"published","date_created":"2023-03-26T22:01:06Z","author":[{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Burgers, Thomas C.Q.","last_name":"Burgers","first_name":"Thomas C.Q."},{"last_name":"Cezanne","first_name":"Alice","full_name":"Cezanne, Alice"},{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"full_name":"Mol, Frank N.","last_name":"Mol","first_name":"Frank N."},{"last_name":"Traparić","first_name":"Jovan","full_name":"Traparić, Jovan"},{"full_name":"Pulschen, Andre Arashiro","first_name":"Andre Arashiro","last_name":"Pulschen"},{"first_name":"Tim","last_name":"Nierhaus","full_name":"Nierhaus, Tim"},{"full_name":"Tarrason-Risa, Gabriel","first_name":"Gabriel","last_name":"Tarrason-Risa"},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"full_name":"Löwe, Jan","first_name":"Jan","last_name":"Löwe"},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"last_name":"Vlijm","first_name":"Rifka","full_name":"Vlijm, Rifka"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"}],"date_updated":"2025-04-23T08:50:02Z","date_published":"2023-03-17T00:00:00Z","external_id":{"isi":["000968083500010"],"pmid":["36921039"]},"status":"public","language":[{"iso":"eng"}]},{"article_type":"review","isi":1,"intvolume":"       480","publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"volume":480,"year":"2023","publication_status":"published","author":[{"first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-03-26T22:01:06Z","date_updated":"2024-10-09T21:04:50Z","date_published":"2023-03-15T00:00:00Z","external_id":{"isi":["000957065700001"],"pmid":["36920092"]},"status":"public","language":[{"iso":"eng"}],"_id":"12757","ddc":["570"],"oa":1,"day":"15","scopus_import":"1","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"doi":"10.1042/BCJ20210285","department":[{"_id":"LeSa"}],"has_accepted_license":"1","publication":"The Biochemical Journal","issue":"5","page":"319-333","oa_version":"Published Version","citation":{"chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. 2023;480(5):319-333. doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” <i>The Biochemical Journal</i>, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. Portland Press. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>"},"abstract":[{"lang":"eng","text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues."}],"type":"journal_article","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"month":"03","article_processing_charge":"No","publisher":"Portland Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"last_name":"Markhieva","first_name":"Karina A.","full_name":"Markhieva, Karina A."},{"first_name":"Mariia S.","last_name":"Novikova","full_name":"Novikova, Mariia S."},{"first_name":"Dmitry S.","last_name":"Petrov","full_name":"Petrov, Dmitry S."},{"last_name":"Vorobyev","first_name":"Ilya S.","full_name":"Vorobyev, Ilya S."},{"full_name":"Maksimova, Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Maksimova"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Ivankov, Dmitry N.","first_name":"Dmitry N.","last_name":"Ivankov"}],"date_created":"2023-03-26T22:01:07Z","date_updated":"2025-04-23T08:50:30Z","publication_status":"published","year":"2023","status":"public","language":[{"iso":"eng"}],"external_id":{"pmid":["36928239"],"isi":["000985134400106"]},"date_published":"2023-03-16T00:00:00Z","day":"16","oa":1,"_id":"12758","ddc":["570"],"scopus_import":"1","file_date_updated":"2023-03-27T07:09:08Z","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.","article_type":"original","isi":1,"intvolume":"        18","file":[{"date_updated":"2023-03-27T07:09:08Z","file_id":"12771","date_created":"2023-03-27T07:09:08Z","creator":"dernst","file_name":"2023_PLoSOne_Pak.pdf","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","file_size":856625,"success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"eissn":["1932-6203"]},"volume":18,"article_number":"e0282689","citation":{"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>","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>.","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>","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.","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).","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>."},"oa_version":"Published Version","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","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"}],"type":"journal_article","month":"03","article_processing_charge":"No","publisher":"Public Library of Science","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0282689","publication":"PLoS ONE","has_accepted_license":"1","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"issue":"3"},{"quality_controlled":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1371/journal.pone.0277148","issue":"3 March","has_accepted_license":"1","publication":"PLoS ONE","department":[{"_id":"PeJo"}],"oa_version":"Published Version","article_number":"e0277148","citation":{"chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","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.","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>","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>.","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."},"acknowledged_ssus":[{"_id":"EM-Fac"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","month":"03","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses","grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425"}],"publisher":"Public Library of Science","article_type":"original","isi":1,"intvolume":"        18","publication_identifier":{"eissn":["1932-6203"]},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_size":7290413,"checksum":"2380331ec27cc87808826fc64419ac1c","file_name":"2023_PLoSOne_Rothman.pdf","creator":"dernst","date_created":"2023-03-27T06:51:09Z","date_updated":"2023-03-27T06:51:09Z","file_id":"12770"}],"ec_funded":1,"volume":18,"publication_status":"published","year":"2023","date_updated":"2025-04-23T08:50:50Z","date_created":"2023-03-26T22:01:07Z","author":[{"first_name":"Jason Seth","last_name":"Rothman","full_name":"Rothman, Jason Seth"},{"id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","last_name":"Borges Merjane","first_name":"Carolina"},{"full_name":"Holderith, Noemi","first_name":"Noemi","last_name":"Holderith"},{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Angus Silver","first_name":"R.","full_name":"Angus Silver, R."}],"date_published":"2023-03-17T00:00:00Z","external_id":{"isi":["001024737400001"],"pmid":["36930689"]},"language":[{"iso":"eng"}],"status":"public","ddc":["570"],"_id":"12759","oa":1,"day":"17","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).","file_date_updated":"2023-03-27T06:51:09Z","scopus_import":"1"},{"article_processing_charge":"No","month":"03","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_number":"36","citation":{"chicago":"Henzinger, Monika, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>.","short":"M. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Hamburg, Germany, 2023, vol. 254.","ama":"Henzinger M, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: <i>40th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>","mla":"Henzinger, Monika, et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>.","apa":"Henzinger, M., Neumann, S., Räcke, H., &#38; Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In <i>40th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>","ista":"Henzinger M, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36."},"oa_version":"Published Version","title":"Dynamic maintenance of monotone dynamic programs and applications","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."}],"type":"conference","arxiv":1,"publication":"40th International Symposium on Theoretical Aspects of Computer Science","department":[{"_id":"MoHe"}],"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","doi":"10.4230/LIPIcs.STACS.2023.36","day":"01","ddc":["000"],"_id":"12760","oa":1,"scopus_import":"1","file_date_updated":"2023-03-27T06:37:22Z","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.","conference":{"start_date":"2023-03-07","location":"Hamburg, Germany","end_date":"2023-03-09","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"date_updated":"2025-09-09T12:22:44Z","date_created":"2023-03-26T22:01:07Z","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger"},{"last_name":"Neumann","first_name":"Stefan","full_name":"Neumann, Stefan"},{"full_name":"Räcke, Harald","first_name":"Harald","last_name":"Räcke"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"year":"2023","publication_status":"published","language":[{"iso":"eng"}],"status":"public","external_id":{"arxiv":["2301.01744"],"isi":["001532693100036"]},"date_published":"2023-03-01T00:00:00Z","alternative_title":["LIPIcs"],"file":[{"success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"dernst","date_created":"2023-03-27T06:37:22Z","file_id":"12769","date_updated":"2023-03-27T06:37:22Z","file_name":"2023_LIPICS_HenzingerM.pdf","file_size":872706,"checksum":"22141ab8bc55188e2dfff665e5daecbd"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772662"]},"volume":254,"ec_funded":1,"intvolume":"       254","isi":1},{"status":"public","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","external_id":{"arxiv":["2012.13218"],"isi":["000946432400015"]},"author":[{"full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992","first_name":"Giorgio","last_name":"Cipolloni"},{"last_name":"Erdös","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"date_created":"2023-03-26T22:01:08Z","date_updated":"2025-04-14T07:57:19Z","year":"2023","publication_status":"published","scopus_import":"1","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.","day":"01","_id":"12761","oa":1,"intvolume":"        33","isi":1,"article_type":"original","volume":33,"ec_funded":1,"publication_identifier":{"issn":["1050-5164"]},"title":"Functional central limit theorems for Wigner matrices","type":"journal_article","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"}],"citation":{"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>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489.","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.","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>","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>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489."},"page":"447-489","oa_version":"Preprint","publisher":"Institute of Mathematical Statistics","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"article_processing_charge":"No","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.13218"}],"corr_author":"1","doi":"10.1214/22-AAP1820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Annals of Applied Probability","department":[{"_id":"LaEr"}],"issue":"1","arxiv":1},{"volume":3,"ec_funded":1,"file":[{"checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_size":4474284,"file_name":"2023_NatureCompScience_Lombardi.pdf","date_updated":"2023-08-16T12:39:57Z","file_id":"14073","creator":"dernst","date_created":"2023-08-16T12:39:57Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1}],"publication_identifier":{"eissn":["2662-8457"]},"intvolume":"         3","isi":1,"article_type":"original","scopus_import":"1","file_date_updated":"2023-08-16T12:39:57Z","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.).","day":"20","_id":"12762","ddc":["570"],"oa":1,"status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["000968161800002"],"arxiv":["2108.06686"],"pmid":["38177880"]},"date_published":"2023-03-20T00:00:00Z","author":[{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"last_name":"Pepic","first_name":"Selver","full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"}],"date_created":"2023-03-26T22:01:08Z","date_updated":"2025-09-09T12:23:42Z","publication_status":"published","year":"2023","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"publication":"Nature Computational Science","has_accepted_license":"1","arxiv":1,"doi":"10.1038/s43588-023-00410-9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"quality_controlled":"1","publisher":"Springer Nature","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","month":"03","corr_author":"1","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","type":"journal_article","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."}],"citation":{"ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023.","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>","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>","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.","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."},"page":"254-263","oa_version":"Published Version"},{"title":"The reach of subsets of manifolds","abstract":[{"text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.","lang":"eng"}],"type":"journal_article","citation":{"short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>.","apa":"Boissonnat, J. D., &#38; Wintraecken, M. (2023). The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>","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>.","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>","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."},"oa_version":"Submitted Version","page":"619-641","publisher":"Springer Nature","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"month":"09","article_processing_charge":"No","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1"}],"doi":"10.1007/s41468-023-00116-x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication":"Journal of Applied and Computational Topology","department":[{"_id":"HeEd"}],"status":"public","language":[{"iso":"eng"}],"date_published":"2023-09-01T00:00:00Z","author":[{"first_name":"Jean Daniel","last_name":"Boissonnat","full_name":"Boissonnat, Jean Daniel"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken"}],"date_created":"2023-03-26T22:01:08Z","date_updated":"2025-04-14T07:44:01Z","publication_status":"published","year":"2023","scopus_import":"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.","day":"01","oa":1,"_id":"12763","intvolume":"         7","article_type":"original","volume":7,"ec_funded":1,"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]}}]