[{"day":"01","project":[{"name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445"}],"_id":"14979","author":[{"full_name":"Datler, Julia","orcid":"0000-0002-3616-8580","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Datler"},{"first_name":"Jesse","orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"first_name":"Andreas","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","last_name":"Thader"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"full_name":"Bauer, Lukas W","first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","last_name":"Bauer"},{"full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau"},{"first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001158144600002"],"pmid":["38316877"]},"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"doi":"10.1038/s41594-023-01201-6","ddc":["570"],"month":"07","date_updated":"2026-04-07T12:59:44Z","has_accepted_license":"1","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","OA_type":"hybrid","oa":1,"article_type":"original","oa_version":"Published Version","file_date_updated":"2024-07-22T11:27:22Z","keyword":["Molecular Biology","Structural Biology"],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"18766","relation":"dissertation_contains"}]},"quality_controlled":"1","scopus_import":"1","date_created":"2024-02-12T09:59:45Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":31,"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., &#38; Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>","ieee":"J. Datler <i>et al.</i>, “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31. Springer Nature, pp. 1114–1123, 2024.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41594-023-01201-6\">https://doi.org/10.1038/s41594-023-01201-6</a>.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural &#38; Molecular Biology 31 (2024) 1114–1123.","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural &#38; Molecular Biology. 31, 1114–1123.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. <i>Nature Structural &#38; Molecular Biology</i>. 2024;31:1114-1123. doi:<a href=\"https://doi.org/10.1038/s41594-023-01201-6\">10.1038/s41594-023-01201-6</a>"},"APC_amount":"11700 EUR","pmid":1,"type":"journal_article","year":"2024","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","corr_author":"1","publication":"Nature Structural & Molecular Biology","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_id":"17307","access_level":"open_access","success":1,"date_updated":"2024-07-22T11:27:22Z","date_created":"2024-07-22T11:27:22Z","content_type":"application/pdf","file_size":17485494,"relation":"main_file","checksum":"bda7bf65d81455480efaed8ca293b0db","file_name":"2024_NatureStrucBio_Datler.pdf"}],"intvolume":"        31","date_published":"2024-07-01T00:00:00Z","page":"1114-1123","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"isi":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"license":"https://creativecommons.org/licenses/by/4.0/","OA_place":"publisher"},{"OA_place":"publisher","publication_identifier":{"eissn":["2643-1564"]},"department":[{"_id":"OnHo"}],"arxiv":1,"article_number":"013141","date_published":"2024-02-05T00:00:00Z","DOAJ_listed":"1","intvolume":"         6","file":[{"creator":"dernst","access_level":"open_access","file_id":"14981","success":1,"date_updated":"2024-02-12T11:46:50Z","date_created":"2024-02-12T11:46:50Z","content_type":"application/pdf","relation":"main_file","file_size":1437167,"checksum":"3a39ebffb24c1cc1dd0b547a726dc52d","file_name":"2024_PhysicalRevResearch_Agafonova.pdf"}],"language":[{"iso":"eng"}],"publication":"Physical Review Research","corr_author":"1","title":"Zigzag optical cavity for sensing and controlling torsional motion","type":"journal_article","issue":"1","year":"2024","APC_amount":"2933,65 EUR","citation":{"chicago":"Agafonova, Sofya, Umang Mishra, Fritz R Diorico, and Onur Hosten. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">https://doi.org/10.1103/physrevresearch.6.013141</a>.","apa":"Agafonova, S., Mishra, U., Diorico, F. R., &#38; Hosten, O. (2024). Zigzag optical cavity for sensing and controlling torsional motion. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">https://doi.org/10.1103/physrevresearch.6.013141</a>","ieee":"S. Agafonova, U. Mishra, F. R. Diorico, and O. Hosten, “Zigzag optical cavity for sensing and controlling torsional motion,” <i>Physical Review Research</i>, vol. 6, no. 1. American Physical Society, 2024.","mla":"Agafonova, Sofya, et al. “Zigzag Optical Cavity for Sensing and Controlling Torsional Motion.” <i>Physical Review Research</i>, vol. 6, no. 1, 013141, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">10.1103/physrevresearch.6.013141</a>.","ama":"Agafonova S, Mishra U, Diorico FR, Hosten O. Zigzag optical cavity for sensing and controlling torsional motion. <i>Physical Review Research</i>. 2024;6(1). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.013141\">10.1103/physrevresearch.6.013141</a>","short":"S. Agafonova, U. Mishra, F.R. Diorico, O. Hosten, Physical Review Research 6 (2024).","ista":"Agafonova S, Mishra U, Diorico FR, Hosten O. 2024. Zigzag optical cavity for sensing and controlling torsional motion. Physical Review Research. 6(1), 013141."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":6,"date_created":"2024-02-12T11:42:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","oa_version":"Published Version","file_date_updated":"2024-02-12T11:46:50Z","oa":1,"article_type":"original","OA_type":"gold","acknowledgement":"We thank Pere Rosselló for his contributions to the initial modeling of the presented sensing technique. This work was supported by Institute of Science and Technology Austria, and\r\nthe European Research Council under Grant No. 101087907 (ERC CoG QuHAMP).","has_accepted_license":"1","date_updated":"2025-05-08T09:34:07Z","month":"02","ddc":["530"],"doi":"10.1103/physrevresearch.6.013141","article_processing_charge":"Yes","abstract":[{"text":"Precision sensing and manipulation of milligram-scale mechanical oscillators has attracted growing interest in the fields of table-top explorations of gravity and tests of quantum mechanics at macroscopic scales. Torsional oscillators present an opportunity in this regard due to their remarked isolation from environmental noise. For torsional motion, an effective employment of optical cavities to enhance optomechanical interactions—as already established for linear oscillators—so far faced certain challenges. Here, we propose a concept for sensing and manipulating torsional motion, where exclusively the torsional rotations of a pendulum are mapped onto the path length of a single two-mirror optical cavity. The concept inherently alleviates many limitations of previous approaches. A proof-of-principle experiment is conducted with a rigidly controlled pendulum to explore the sensing aspects of the concept and to identify practical limitations in a potential state-of-the art setup. Based on this study, we anticipate development of precision torque sensors utilizing torsional pendulums that can support sensitivities below 10−19Nm/√Hz, while the motion of the pendulums are dominated by quantum radiation pressure noise at sub-microwatts of incoming laser power. These developments will provide horizons for experiments at the interface of quantum mechanics and gravity.","lang":"eng"}],"author":[{"last_name":"Agafonova","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","first_name":"Sofya","orcid":"0000-0003-0582-2946","full_name":"Agafonova, Sofya"},{"first_name":"Umang","full_name":"Mishra, Umang","last_name":"Mishra","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51"},{"id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico","first_name":"Fritz R","full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"}],"_id":"14980","publication_status":"published","external_id":{"arxiv":["2306.12804"]},"publisher":"American Physical Society","project":[{"grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"day":"05"},{"citation":{"chicago":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae005\">https://doi.org/10.1093/imrn/rnae005</a>.","apa":"Shen, S. (2024). Tamely ramified geometric Langlands correspondence in positive characteristic. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae005\">https://doi.org/10.1093/imrn/rnae005</a>","ieee":"S. Shen, “Tamely ramified geometric Langlands correspondence in positive characteristic,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 7. Oxford University Press, pp. 6176–6208, 2024.","mla":"Shen, Shiyu. “Tamely Ramified Geometric Langlands Correspondence in Positive Characteristic.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 7, Oxford University Press, 2024, pp. 6176–208, doi:<a href=\"https://doi.org/10.1093/imrn/rnae005\">10.1093/imrn/rnae005</a>.","ama":"Shen S. Tamely ramified geometric Langlands correspondence in positive characteristic. <i>International Mathematics Research Notices</i>. 2024;2024(7):6176-6208. doi:<a href=\"https://doi.org/10.1093/imrn/rnae005\">10.1093/imrn/rnae005</a>","short":"S. Shen, International Mathematics Research Notices 2024 (2024) 6176–6208.","ista":"Shen S. 2024. Tamely ramified geometric Langlands correspondence in positive characteristic. International Mathematics Research Notices. 2024(7), 6176–6208."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":2024,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-02-14T12:16:17Z","scopus_import":"1","quality_controlled":"1","file":[{"file_id":"17308","access_level":"open_access","success":1,"creator":"dernst","relation":"main_file","file_size":1488981,"file_name":"2024_IMRN_Shen.pdf","checksum":"e3cd31ebb2e79b5b1f34d1c4ac9f5b0f","date_created":"2024-07-22T11:41:57Z","date_updated":"2024-07-22T11:41:57Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication":"International Mathematics Research Notices","corr_author":"1","title":"Tamely ramified geometric Langlands correspondence in positive characteristic","year":"2024","type":"journal_article","issue":"7","arxiv":1,"page":"6176-6208","PlanS_conform":"1","date_published":"2024-04-01T00:00:00Z","intvolume":"      2024","OA_place":"publisher","isi":1,"publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"department":[{"_id":"TaHa"}],"doi":"10.1093/imrn/rnae005","abstract":[{"text":"We prove a version of the tamely ramified geometric Langlands correspondence in positive characteristic for GLn(k). Let k be an algebraically closed field of characteristic p>n. Let X be a smooth projective curve over k with marked points, and fix a parabolic subgroup of GLn(k) at each marked point. We denote by Bunn,P the moduli stack of (quasi-)parabolic vector bundles on X, and by Locn,P the moduli stack of parabolic flat connections such that the residue is nilpotent with respect to the parabolic reduction at each marked point. We construct an equivalence between the bounded derived category Db(Qcoh(Loc0n,P)) of quasi-coherent sheaves on an open substack Loc0n,P⊂Locn,P, and the bounded derived category Db(D0Bunn,P-mod) of D0Bunn,P-modules, where D0Bunn,P is a localization of DBunn,P the sheaf of crystalline differential operators on Bunn,P. Thus we extend the work of Bezrukavnikov-Braverman to the tamely ramified case. We also prove a correspondence between flat connections on X with regular singularities and meromorphic Higgs bundles on the Frobenius twist X(1) of X with first order poles .","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","_id":"14986","author":[{"first_name":"Shiyu","full_name":"Shen, Shiyu","orcid":"0000-0002-4444-8718","id":"544cccd3-9005-11ec-87bc-94aef1c5b814","last_name":"Shen"}],"publication_status":"published","publisher":"Oxford University Press","external_id":{"arxiv":["1810.12491"],"isi":["001157898100001"]},"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"day":"01","ec_funded":1,"ddc":["510"],"OA_type":"hybrid","acknowledgement":"This work was supported by the NSF [DMS-1502125to S.S.]; and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement [101034413 to S.S.].\r\nI would like to thank my advisor Tom Nevins for many helpful discussions on this subject and for his comments on this paper. I would like to thank Christopher Dodd, Michael Groechenig, and Tamas Hausel for helpful conversations. I would like to thank Tsao-Hsien Chen for useful comments on an earlier version of this paper.","has_accepted_license":"1","date_updated":"2025-09-09T08:30:06Z","month":"04","keyword":["General Mathematics"],"file_date_updated":"2024-07-22T11:41:57Z","oa_version":"Published Version","oa":1,"article_type":"original"},{"article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor."}],"doi":"10.1073/pnas.2220075121","author":[{"id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","last_name":"Curk","first_name":"Samo","full_name":"Curk, Samo","orcid":"0000-0001-6160-9766"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"},{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"_id":"15001","publisher":"National Academy of Sciences","publication_status":"published","external_id":{"pmid":["38335256"],"isi":["001169063600007"]},"day":"13","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"}],"ec_funded":1,"ddc":["570"],"OA_type":"hybrid","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","date_updated":"2025-09-04T12:03:12Z","has_accepted_license":"1","month":"02","oa_version":"Published Version","file_date_updated":"2024-02-26T08:20:00Z","article_type":"original","oa":1,"citation":{"ieee":"S. Curk <i>et al.</i>, “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7. National Academy of Sciences, 2024.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(7). doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7, e2220075121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","APC_amount":"5936,71 EUR","volume":121,"status":"public","date_created":"2024-02-18T23:01:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"related_material":{"record":[{"relation":"research_data","status":"public","id":"15027"}]},"quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"15026","success":1,"creator":"dernst","relation":"main_file","file_size":7699487,"file_name":"2024_PNAS_Curk.pdf","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","date_created":"2024-02-26T08:20:00Z","date_updated":"2024-02-26T08:20:00Z","content_type":"application/pdf"}],"title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","corr_author":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2024","type":"journal_article","issue":"7","pmid":1,"date_published":"2024-02-13T00:00:00Z","article_number":"e2220075121","intvolume":"       121","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"AnSa"}],"publication_identifier":{"eissn":["1091-6490"]},"isi":1},{"day":"30","_id":"15002","external_id":{"arxiv":["2201.10220"],"isi":["001179276700003"],"pmid":["38364163"]},"publication_status":"published","author":[{"full_name":"Petrova, Elena","first_name":"Elena","last_name":"Petrova","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"last_name":"Tiunov","first_name":"Egor S.","full_name":"Tiunov, Egor S."},{"last_name":"Bañuls","full_name":"Bañuls, Mari Carmen","first_name":"Mari Carmen"},{"last_name":"Fedorov","first_name":"Aleksey K.","full_name":"Fedorov, Aleksey K."}],"publisher":"American Physical Society","article_processing_charge":"No","abstract":[{"text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models.","lang":"eng"}],"doi":"10.1103/PhysRevLett.132.050401","month":"01","date_updated":"2025-09-04T12:02:33Z","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.10220"}],"oa":1,"article_type":"original","oa_version":"Preprint","scopus_import":"1","quality_controlled":"1","date_created":"2024-02-18T23:01:00Z","volume":132,"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024).","ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. <i>Physical Review Letters</i>. 2024;132(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.132.050401\">10.1103/PhysRevLett.132.050401</a>","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” <i>Physical Review Letters</i>, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.132.050401\">10.1103/PhysRevLett.132.050401</a>.","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” <i>Physical Review Letters</i>, vol. 132, no. 5. American Physical Society, 2024.","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., &#38; Fedorov, A. K. (2024). Fractal states of the Schwinger model. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.132.050401\">https://doi.org/10.1103/PhysRevLett.132.050401</a>","chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” <i>Physical Review Letters</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevLett.132.050401\">https://doi.org/10.1103/PhysRevLett.132.050401</a>."},"pmid":1,"issue":"5","year":"2024","type":"journal_article","title":"Fractal states of the Schwinger model","publication":"Physical Review Letters","language":[{"iso":"eng"}],"intvolume":"       132","date_published":"2024-01-30T00:00:00Z","article_number":"050401","arxiv":1,"department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"isi":1},{"scopus_import":"1","quality_controlled":"1","date_created":"2024-02-18T23:01:01Z","volume":109,"status":"public","citation":{"short":"D.G. Franco, R. Avalos, D. Hafner, K.A. Modic, Y. Prots, O. Stockert, A. Hoser, P.J.W. Moll, M. Brando, A.A. Aligia, C. Geibel, Physical Review B 109 (2024).","ista":"Franco DG, Avalos R, Hafner D, Modic KA, Prots Y, Stockert O, Hoser A, Moll PJW, Brando M, Aligia AA, Geibel C. 2024. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. 109(5), 054405.","mla":"Franco, D. G., et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” <i>Physical Review B</i>, vol. 109, no. 5, 054405, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevB.109.054405\">10.1103/PhysRevB.109.054405</a>.","ama":"Franco DG, Avalos R, Hafner D, et al. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. <i>Physical Review B</i>. 2024;109(5). doi:<a href=\"https://doi.org/10.1103/PhysRevB.109.054405\">10.1103/PhysRevB.109.054405</a>","apa":"Franco, D. G., Avalos, R., Hafner, D., Modic, K. A., Prots, Y., Stockert, O., … Geibel, C. (2024). Frustrated magnetism in octahedra-based Ce6 Ni6 P17. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.109.054405\">https://doi.org/10.1103/PhysRevB.109.054405</a>","ieee":"D. G. Franco <i>et al.</i>, “Frustrated magnetism in octahedra-based Ce6 Ni6 P17,” <i>Physical Review B</i>, vol. 109, no. 5. American Physical Society, 2024.","chicago":"Franco, D. G., R. Avalos, D. Hafner, Kimberly A Modic, Yu Prots, O. Stockert, A. Hoser, et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevB.109.054405\">https://doi.org/10.1103/PhysRevB.109.054405</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","type":"journal_article","issue":"5","title":"Frustrated magnetism in octahedra-based Ce6 Ni6 P17","publication":"Physical Review B","language":[{"iso":"eng"}],"intvolume":"       109","article_number":"054405","date_published":"2024-02-01T00:00:00Z","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"department":[{"_id":"KiMo"}],"isi":1,"day":"01","_id":"15003","publisher":"American Physical Society","author":[{"last_name":"Franco","full_name":"Franco, D. G.","first_name":"D. G."},{"last_name":"Avalos","full_name":"Avalos, R.","first_name":"R."},{"full_name":"Hafner, D.","first_name":"D.","last_name":"Hafner"},{"id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","first_name":"Kimberly A","full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147"},{"last_name":"Prots","first_name":"Yu","full_name":"Prots, Yu"},{"first_name":"O.","full_name":"Stockert, O.","last_name":"Stockert"},{"first_name":"A.","full_name":"Hoser, A.","last_name":"Hoser"},{"last_name":"Moll","full_name":"Moll, P. J.W.","first_name":"P. J.W."},{"last_name":"Brando","first_name":"M.","full_name":"Brando, M."},{"first_name":"A. A.","full_name":"Aligia, A. A.","last_name":"Aligia"},{"last_name":"Geibel","full_name":"Geibel, C.","first_name":"C."}],"external_id":{"isi":["001198571800008"]},"publication_status":"published","article_processing_charge":"No","abstract":[{"text":"Magnetic frustration allows to access novel and intriguing properties of magnetic systems and has been explored mainly in planar triangular-like arrays of magnetic ions. In this work, we describe the phosphide Ce6Ni6P17, where the Ce+3 ions accommodate in a body-centered cubic lattice of Ce6 regular octahedra. From measurements of magnetization, specific heat, and resistivity, we determine a rich phase diagram as a function of temperature and magnetic field in which different magnetic phases are found. Besides clear evidence of magnetic frustration is obtained from entropy analysis. At zero field, a second-order antiferromagnetic transition occurs at TN1≈1 K followed by a first-order transition at TN2≈0.45 K. With magnetic field new magnetic phases appear, including a weakly first-order transition which ends in a classical critical point and a third magnetic phase. We also study the exact solution of the spin-1/2 Heisenberg model in an octahedron which allows us a qualitative understanding of the phase diagram and compare with the experimental results.","lang":"eng"}],"doi":"10.1103/PhysRevB.109.054405","month":"02","date_updated":"2025-09-04T12:05:01Z","acknowledgement":"The authors thank Bernardo Pentke for the SEM micrographs (Departamento Fisicoquímica de Materiales CABCNEA). We are indebted to Julián Sereni for useful discussions. D. G. F. acknowledges financial support provided by Agencia I+D+i, Argentina, Grant No. PICT-2021-I-INVI00852 and Universidad Nacional de Cuyo (SIIP) Grant No. 06/C018-T1. A. A. A. acknowledges financial support provided by PICT 2018-01546 and PICT 2020A-03661 of the\r\nAgencia I+D+i. ","article_type":"original","oa_version":"None"},{"day":"01","project":[{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"publisher":"American Physical Society","_id":"15004","author":[{"full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001158043800006"],"arxiv":["2307.07256"]},"publication_status":"published","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions."}],"doi":"10.1103/PhysRevA.109.023101","ec_funded":1,"month":"02","date_updated":"2026-04-07T11:48:53Z","acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"article_type":"original","oa":1,"oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","id":"19393","status":"public"}]},"scopus_import":"1","quality_controlled":"1","date_created":"2024-02-18T23:01:01Z","volume":109,"status":"public","citation":{"mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” <i>Physical Review A</i>, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevA.109.023101\">10.1103/PhysRevA.109.023101</a>.","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. <i>Physical Review A</i>. 2024;109(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.109.023101\">10.1103/PhysRevA.109.023101</a>","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101.","chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” <i>Physical Review A</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevA.109.023101\">https://doi.org/10.1103/PhysRevA.109.023101</a>.","apa":"Karle, V., &#38; Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.109.023101\">https://doi.org/10.1103/PhysRevA.109.023101</a>","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” <i>Physical Review A</i>, vol. 109, no. 2. American Physical Society, 2024."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","issue":"2","type":"journal_article","title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","publication":"Physical Review A","corr_author":"1","language":[{"iso":"eng"}],"intvolume":"       109","article_number":"023101","date_published":"2024-02-01T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"department":[{"_id":"MiLe"}],"isi":1},{"arxiv":1,"alternative_title":["LIPIcs"],"date_published":"2024-01-18T00:00:00Z","article_number":"11","intvolume":"       286","isi":1,"publication_identifier":{"isbn":["9783959773089"],"issn":["1868-8969"]},"department":[{"_id":"KrCh"}],"citation":{"mla":"Hirvonen, Juho, et al. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” <i>27th International Conference on Principles of Distributed Systems</i>, vol. 286, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.11\">10.4230/LIPIcs.OPODIS.2023.11</a>.","ama":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. On the convergence time in graphical games: A locality-sensitive approach. In: <i>27th International Conference on Principles of Distributed Systems</i>. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.11\">10.4230/LIPIcs.OPODIS.2023.11</a>","ista":"Hirvonen J, Schmid L, Chatterjee K, Schmid S. 2024. On the convergence time in graphical games: A locality-sensitive approach. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 11.","short":"J. Hirvonen, L. Schmid, K. Chatterjee, S. Schmid, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Hirvonen, Juho, Laura Schmid, Krishnendu Chatterjee, and Stefan Schmid. “On the Convergence Time in Graphical Games: A Locality-Sensitive Approach.” In <i>27th International Conference on Principles of Distributed Systems</i>, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.11\">https://doi.org/10.4230/LIPIcs.OPODIS.2023.11</a>.","apa":"Hirvonen, J., Schmid, L., Chatterjee, K., &#38; Schmid, S. (2024). On the convergence time in graphical games: A locality-sensitive approach. In <i>27th International Conference on Principles of Distributed Systems</i> (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.11\">https://doi.org/10.4230/LIPIcs.OPODIS.2023.11</a>","ieee":"J. Hirvonen, L. Schmid, K. Chatterjee, and S. Schmid, “On the convergence time in graphical games: A locality-sensitive approach,” in <i>27th International Conference on Principles of Distributed Systems</i>, Tokyo, Japan, 2024, vol. 286."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":286,"date_created":"2024-02-18T23:01:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","file":[{"creator":"dernst","file_id":"15028","access_level":"open_access","success":1,"date_updated":"2024-02-26T09:04:58Z","date_created":"2024-02-26T09:04:58Z","content_type":"application/pdf","file_size":867363,"relation":"main_file","checksum":"4fc7eea6e4ba140b904781fc7df868ec","file_name":"2024_LIPICs_Hirvonen.pdf"}],"language":[{"iso":"eng"}],"corr_author":"1","publication":"27th International Conference on Principles of Distributed Systems","title":"On the convergence time in graphical games: A locality-sensitive approach","type":"conference","year":"2024","acknowledgement":"This work was partially funded by the Academy of Finland, grant 314888, the European Research Council CoG 863818 (ForM-SMArt), and the Austrian Science Fund (FWF) project I 4800-N (ADVISE). LS was supported by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324.","has_accepted_license":"1","date_updated":"2025-12-02T13:38:16Z","month":"01","oa_version":"Published Version","file_date_updated":"2024-02-26T09:04:58Z","oa":1,"doi":"10.4230/LIPIcs.OPODIS.2023.11","article_processing_charge":"No","abstract":[{"text":"Graphical games are a useful framework for modeling the interactions of (selfish) agents who are connected via an underlying topology and whose behaviors influence each other. They have wide applications ranging from computer science to economics and biology. Yet, even though an agent’s payoff only depends on the actions of their direct neighbors in graphical games, computing the Nash equilibria and making statements about the convergence time of \"natural\" local dynamics in particular can be highly challenging. In this work, we present a novel approach for classifying complexity of Nash equilibria in graphical games by establishing a connection to local graph algorithms, a subfield of distributed computing. In particular, we make the observation that the equilibria of graphical games are equivalent to locally verifiable labelings (LVL) in graphs; vertex labelings which are verifiable with constant-round local algorithms. This connection allows us to derive novel lower bounds on the convergence time to equilibrium of best-response dynamics in graphical games. Since we establish that distributed convergence can sometimes be provably slow, we also introduce and give bounds on an intuitive notion of \"time-constrained\" inefficiency of best responses. We exemplify how our results can be used in the implementation of mechanisms that ensure convergence of best responses to a Nash equilibrium. Our results thus also give insight into the convergence of strategy-proof algorithms for graphical games, which is still not well understood.","lang":"eng"}],"_id":"15006","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"full_name":"Hirvonen, Juho","first_name":"Juho","last_name":"Hirvonen"},{"last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","first_name":"Laura"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"external_id":{"arxiv":["2102.13457"],"isi":["001585185800011"]},"project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"conference":{"end_date":"2023-12-08","start_date":"2023-12-06","location":"Tokyo, Japan","name":"OPODIS: Conference on Principles of Distributed Systems"},"day":"18","ec_funded":1,"ddc":["000"]},{"date_created":"2024-02-18T23:01:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12.","mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” <i>27th International Conference on Principles of Distributed Systems</i>, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.12\">10.4230/LIPIcs.OPODIS.2023.12</a>.","ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: <i>27th International Conference on Principles of Distributed Systems</i>. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.12\">10.4230/LIPIcs.OPODIS.2023.12</a>","apa":"Alpos, O., Amores-Sesar, I., Cachin, C., &#38; Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In <i>27th International Conference on Principles of Distributed Systems</i> (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.12\">https://doi.org/10.4230/LIPIcs.OPODIS.2023.12</a>","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in <i>27th International Conference on Principles of Distributed Systems</i>, Tokyo, Japan, 2024, vol. 286.","chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In <i>27th International Conference on Principles of Distributed Systems</i>, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2023.12\">https://doi.org/10.4230/LIPIcs.OPODIS.2023.12</a>."},"status":"public","volume":286,"type":"conference","year":"2024","file":[{"file_id":"15031","access_level":"open_access","success":1,"creator":"dernst","file_size":1505994,"relation":"main_file","file_name":"2024_LIPICs_Alpos.pdf","checksum":"2993e810a45e8c8056106834b07aea92","date_created":"2024-02-26T10:16:57Z","date_updated":"2024-02-26T10:16:57Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"corr_author":"1","publication":"27th International Conference on Principles of Distributed Systems","title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","intvolume":"       286","arxiv":1,"alternative_title":["LIPIcs"],"date_published":"2024-01-18T00:00:00Z","article_number":"12","isi":1,"department":[{"_id":"KrPi"}],"publication_identifier":{"isbn":["9783959773089"],"issn":["1868-8969"]},"publication_status":"published","_id":"15007","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Orestis","full_name":"Alpos, Orestis","last_name":"Alpos"},{"last_name":"Amores-Sesar","full_name":"Amores-Sesar, Ignacio","first_name":"Ignacio"},{"last_name":"Cachin","first_name":"Christian","full_name":"Cachin, Christian"},{"full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"}],"external_id":{"isi":["001585185800012"],"arxiv":["2307.02954"]},"day":"18","conference":{"location":"Tokyo, Japan","start_date":"2023-12-06","name":"OPODIS: Conference on Principles of Distributed Systems","end_date":"2023-12-08"},"doi":"10.4230/LIPIcs.OPODIS.2023.12","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead."}],"ddc":["000"],"has_accepted_license":"1","date_updated":"2025-12-02T13:38:53Z","month":"01","acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","oa":1,"file_date_updated":"2024-02-26T10:16:57Z","oa_version":"Published Version"},{"file_date_updated":"2024-02-26T10:10:48Z","oa_version":"Published Version","oa":1,"acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","date_updated":"2025-09-04T12:06:25Z","has_accepted_license":"1","month":"01","ec_funded":1,"ddc":["000"],"article_processing_charge":"No","abstract":[{"text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth.","lang":"eng"}],"doi":"10.4230/LIPIcs.ITCS.2024.55","_id":"15008","external_id":{"arxiv":["2303.02491"],"isi":["001300389400055"]},"author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"first_name":"Harald","full_name":"Räcke, Harald","last_name":"Räcke"},{"full_name":"Sachdeva, Sushant","first_name":"Sushant","last_name":"Sachdeva"},{"last_name":"Sricharan","full_name":"Sricharan, A. R.","first_name":"A. R."}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"24","conference":{"name":"ITCS: Innovations in Theoretical Computer Science","location":"Berkeley, CA, United States","start_date":"2024-01-30","end_date":"2024-02-02"},"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564"},{"name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"department":[{"_id":"MoHe"}],"isi":1,"arxiv":1,"date_published":"2024-01-24T00:00:00Z","article_number":"55","alternative_title":["LIPIcs"],"intvolume":"       287","language":[{"iso":"eng"}],"file":[{"date_created":"2024-02-26T10:10:48Z","date_updated":"2024-02-26T10:10:48Z","content_type":"application/pdf","file_size":1054754,"relation":"main_file","file_name":"2024_LIPICs_Goranci.pdf","checksum":"b89716aae6a5599f187897e39de1e53a","creator":"dernst","access_level":"open_access","file_id":"15030","success":1}],"title":"Electrical flows for polylogarithmic competitive oblivious routing","publication":"15th Innovations in Theoretical Computer Science Conference","corr_author":"1","type":"conference","year":"2024","citation":{"ieee":"G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in <i>15th Innovations in Theoretical Computer Science Conference</i>, Berkeley, CA, United States, 2024, vol. 287.","apa":"Goranci, G., Henzinger, M., Räcke, H., Sachdeva, S., &#38; Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In <i>15th Innovations in Theoretical Computer Science Conference</i> (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">https://doi.org/10.4230/LIPIcs.ITCS.2024.55</a>","chicago":"Goranci, Gramoz, Monika Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In <i>15th Innovations in Theoretical Computer Science Conference</i>, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">https://doi.org/10.4230/LIPIcs.ITCS.2024.55</a>.","short":"G. Goranci, M. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ista":"Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 287, 55.","ama":"Goranci G, Henzinger M, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: <i>15th Innovations in Theoretical Computer Science Conference</i>. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">10.4230/LIPIcs.ITCS.2024.55</a>","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” <i>15th Innovations in Theoretical Computer Science Conference</i>, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITCS.2024.55\">10.4230/LIPIcs.ITCS.2024.55</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":287,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-02-18T23:01:02Z","quality_controlled":"1","scopus_import":"1"},{"publication_status":"published","_id":"15011","author":[{"first_name":"Eldar","full_name":"Kurtic, Eldar","last_name":"Kurtic","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2312.13547"]},"publisher":"ML Research Press","day":"08","conference":{"name":"CPAL: Conference on Parsimony and Learning","start_date":"2024-01-03","location":"Hongkong, China","end_date":"2024-01-06"},"abstract":[{"lang":"eng","text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach."}],"article_processing_charge":"No","oa":1,"oa_version":"Preprint","date_updated":"2024-10-09T21:08:16Z","month":"01","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v234/kurtic24a"}],"year":"2024","type":"conference","language":[{"iso":"eng"}],"corr_author":"1","publication":"Proceedings of Machine Learning Research","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","date_created":"2024-02-18T23:01:03Z","quality_controlled":"1","scopus_import":"1","citation":{"apa":"Kurtic, E., Hoefler, T., &#38; Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In <i>Proceedings of Machine Learning Research</i> (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in <i>Proceedings of Machine Learning Research</i>, Hongkong, China, 2024, vol. 234, pp. 542–553.","chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In <i>Proceedings of Machine Learning Research</i>, 234:542–53. ML Research Press, 2024.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” <i>Proceedings of Machine Learning Research</i>, vol. 234, ML Research Press, 2024, pp. 542–53.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: <i>Proceedings of Machine Learning Research</i>. Vol 234. ML Research Press; 2024:542-553."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":234,"department":[{"_id":"DaAl"}],"publication_identifier":{"eissn":["2640-3498"]},"intvolume":"       234","page":"542-553","arxiv":1,"alternative_title":["PMLR"],"date_published":"2024-01-08T00:00:00Z"},{"date_created":"2024-02-18T23:01:03Z","scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"21253","relation":"later_version"}]},"citation":{"apa":"Pach, J., Saghafian, M., &#38; Schnider, P. (2024). Decomposition of geometric graphs into star-forests. In <i>31st International Symposium on Graph Drawing and Network Visualization</i> (Vol. 14465, pp. 339–346). Isola delle Femmine, Palermo, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>","ieee":"J. Pach, M. Saghafian, and P. Schnider, “Decomposition of geometric graphs into star-forests,” in <i>31st International Symposium on Graph Drawing and Network Visualization</i>, Isola delle Femmine, Palermo, Italy, 2024, vol. 14465, pp. 339–346.","chicago":"Pach, János, Morteza Saghafian, and Patrick Schnider. “Decomposition of Geometric Graphs into Star-Forests.” In <i>31st International Symposium on Graph Drawing and Network Visualization</i>, 14465:339–46. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">https://doi.org/10.1007/978-3-031-49272-3_23</a>.","ista":"Pach J, Saghafian M, Schnider P. 2024. Decomposition of geometric graphs into star-forests. 31st International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 14465, 339–346.","short":"J. Pach, M. Saghafian, P. Schnider, in:, 31st International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2024, pp. 339–346.","mla":"Pach, János, et al. “Decomposition of Geometric Graphs into Star-Forests.” <i>31st International Symposium on Graph Drawing and Network Visualization</i>, vol. 14465, Springer Nature, 2024, pp. 339–46, doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>.","ama":"Pach J, Saghafian M, Schnider P. Decomposition of geometric graphs into star-forests. In: <i>31st International Symposium on Graph Drawing and Network Visualization</i>. Vol 14465. Springer Nature; 2024:339-346. doi:<a href=\"https://doi.org/10.1007/978-3-031-49272-3_23\">10.1007/978-3-031-49272-3_23</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","volume":14465,"type":"conference","year":"2024","language":[{"iso":"eng"}],"publication":"31st International Symposium on Graph Drawing and Network Visualization","title":"Decomposition of geometric graphs into star-forests","intvolume":"     14465","page":"339-346","arxiv":1,"alternative_title":["LNCS"],"date_published":"2024-01-01T00:00:00Z","isi":1,"publication_identifier":{"isbn":["9783031492716"],"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["9783031492723"]},"department":[{"_id":"HeEd"}],"_id":"15012","publisher":"Springer Nature","external_id":{"arxiv":["2306.13201"],"isi":["001207939600023"]},"publication_status":"published","author":[{"first_name":"János","full_name":"Pach, János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"},{"last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza","full_name":"Saghafian, Morteza"},{"last_name":"Schnider","first_name":"Patrick","full_name":"Schnider, Patrick"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}],"day":"01","conference":{"start_date":"2023-09-20","location":"Isola delle Femmine, Palermo, Italy","name":"GD: Graph Drawing and Network Visualization","end_date":"2023-09-22"},"doi":"10.1007/978-3-031-49272-3_23","abstract":[{"text":"We solve a problem of Dujmović and Wood (2007) by showing that a complete convex geometric graph on n vertices cannot be decomposed into fewer than n-1 star-forests, each consisting of noncrossing edges. This bound is clearly tight. We also discuss similar questions for abstract graphs.","lang":"eng"}],"article_processing_charge":"No","ec_funded":1,"date_updated":"2026-04-16T09:12:37Z","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.13201"}],"acknowledgement":"János Pach’s Research partially supported by European Research Council (ERC), grant “GeoScape” No. 882971 and by the Hungarian Science Foundation (NKFIH), grant K-131529. Work by Morteza Saghafian is partially supported by the European Research Council (ERC), grant No. 788183, and by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31.","oa":1,"oa_version":"Preprint"},{"date_created":"2024-02-22T14:10:40Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>.","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">https://doi.org/10.1016/j.mssp.2024.108231</a>","ieee":"Y. Shimura <i>et al.</i>, “Compressively strained epitaxial Ge layers for quantum computing applications,” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5. Elsevier, 2024.","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” <i>Materials Science in Semiconductor Processing</i>, vol. 174, no. 5, 108231, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. <i>Materials Science in Semiconductor Processing</i>. 2024;174(5). doi:<a href=\"https://doi.org/10.1016/j.mssp.2024.108231\">10.1016/j.mssp.2024.108231</a>","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231.","short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":174,"status":"public","issue":"5","year":"2024","type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_id":"17312","access_level":"open_access","success":1,"creator":"dernst","file_size":4220165,"relation":"main_file","file_name":"2024_MaterialsScience_Shimura.pdf","checksum":"62e8e9ae960387a3dca32ec7f5e413ab","date_created":"2024-07-22T11:56:08Z","date_updated":"2024-07-22T11:56:08Z","content_type":"application/pdf"}],"title":"Compressively strained epitaxial Ge layers for quantum computing applications","publication":"Materials Science in Semiconductor Processing","intvolume":"       174","article_number":"108231","date_published":"2024-05-20T00:00:00Z","department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"publication_identifier":{"issn":["1369-8001"]},"isi":1,"OA_place":"publisher","_id":"15018","publication_status":"published","external_id":{"isi":["001188520000001"]},"publisher":"Elsevier","author":[{"last_name":"Shimura","full_name":"Shimura, Yosuke","first_name":"Yosuke"},{"full_name":"Godfrin, Clement","first_name":"Clement","last_name":"Godfrin"},{"last_name":"Hikavyy","full_name":"Hikavyy, Andriy","first_name":"Andriy"},{"last_name":"Li","full_name":"Li, Roy","first_name":"Roy"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros"},{"full_name":"Favia, Paola","first_name":"Paola","last_name":"Favia"},{"last_name":"Han","full_name":"Han, Han","first_name":"Han"},{"last_name":"Wan","full_name":"Wan, Danny","first_name":"Danny"},{"full_name":"de Greve, Kristiaan","first_name":"Kristiaan","last_name":"de Greve"},{"full_name":"Loo, Roger","first_name":"Roger","last_name":"Loo"}],"day":"20","project":[{"grant_number":"101069515","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","name":"Integrated Germanium Quantum Technology"}],"article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"doi":"10.1016/j.mssp.2024.108231","ddc":["530"],"date_updated":"2025-04-14T08:01:27Z","has_accepted_license":"1","month":"05","OA_type":"hybrid","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","article_type":"original","oa":1,"oa_version":"Published Version","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"file_date_updated":"2024-07-22T11:56:08Z"},{"month":"02","date_updated":"2026-04-07T12:59:25Z","has_accepted_license":"1","oa":1,"file_date_updated":"2024-02-23T14:20:16Z","keyword":["Theoretical biology","Optimality","Evolution","Information"],"oa_version":"Published Version","day":"23","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal","first_name":"Michal"}],"_id":"15020","publication_status":"published","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"doi":"10.15479/at:ista:15020","ddc":["576","519"],"ec_funded":1,"date_published":"2024-02-23T00:00:00Z","alternative_title":["ISTA Thesis"],"page":"158","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"supervisor":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"OA_place":"publisher","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"7606","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12081"},{"relation":"part_of_dissertation","status":"public","id":"7553"}]},"date_created":"2024-02-23T14:02:04Z","status":"public","citation":{"ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2024","type":"dissertation","title":"Genetic information and biological optimization","corr_author":"1","language":[{"iso":"eng"}],"file":[{"success":1,"access_level":"open_access","file_id":"15021","creator":"mhledik","file_name":"hledik thesis pdfa 2b.pdf","checksum":"b2d3da47c98d481577a4baf68944fe41","relation":"main_file","file_size":7102089,"content_type":"application/pdf","date_created":"2024-02-23T13:50:53Z","date_updated":"2024-02-23T13:50:53Z"},{"file_id":"15022","access_level":"closed","creator":"mhledik","file_size":14014790,"relation":"source_file","file_name":"hledik thesis source.zip","checksum":"eda9b9430da2610fee7ce1c1419a479a","date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z","content_type":"application/zip"}]},{"acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","month":"02","date_updated":"2025-09-04T12:07:33Z","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2024-02-27T08:12:52Z","article_type":"original","oa":1,"abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"article_processing_charge":"Yes (in subscription journal)","doi":"10.1063/5.0188215","day":"14","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413"}],"_id":"15024","publication_status":"published","publisher":"AIP Publishing","author":[{"last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","first_name":"Paul","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul"}],"external_id":{"arxiv":["2311.11784"],"pmid":["38349632"],"isi":["001161104900003"]},"ec_funded":1,"ddc":["540"],"article_number":"064503","date_published":"2024-02-14T00:00:00Z","arxiv":1,"intvolume":"       160","department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"isi":1,"volume":160,"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. 2024;160(6). doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>.","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>"},"quality_controlled":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-02-25T23:00:55Z","title":"Correlation-induced viscous dissipation in concentrated electrolytes","publication":"Journal of Chemical Physics","corr_author":"1","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"15034","access_level":"open_access","creator":"dernst","checksum":"0a5e0ae70849bce674466fc054390ec0","file_name":"2024_JourChemicalPhysics_Robin.pdf","file_size":5452738,"relation":"main_file","content_type":"application/pdf","date_updated":"2024-02-27T08:12:52Z","date_created":"2024-02-27T08:12:52Z"}],"pmid":1,"issue":"6","year":"2024","type":"journal_article"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.12206"}],"acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","date_updated":"2025-09-04T12:08:11Z","month":"02","oa_version":"Preprint","oa":1,"article_type":"original","doi":"10.1214/23-AAP2000","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble."}],"_id":"15025","external_id":{"isi":["001163006100021"],"arxiv":["2208.12206"]},"publication_status":"published","publisher":"Institute of Mathematical Statistics","author":[{"first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"orcid":"0000-0003-2625-495X","full_name":"McKenna, Benjamin","first_name":"Benjamin","last_name":"McKenna","id":"b0cc634c-d549-11ee-96c8-87338c7ad808"}],"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"day":"01","ec_funded":1,"page":"1623-1662","arxiv":1,"date_published":"2024-02-01T00:00:00Z","intvolume":"        34","isi":1,"department":[{"_id":"LaEr"}],"publication_identifier":{"issn":["1050-5164"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662.","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. 2024;34(1B):1623-1662. doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:<a href=\"https://doi.org/10.1214/23-AAP2000\">10.1214/23-AAP2000</a>.","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” <i>Annals of Applied Probability</i>, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","apa":"Erdös, L., &#38; McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/23-AAP2000\">https://doi.org/10.1214/23-AAP2000</a>."},"status":"public","volume":34,"date_created":"2024-02-25T23:00:56Z","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Annals of Applied Probability","corr_author":"1","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","issue":"1B","type":"journal_article","year":"2024"},{"ddc":["580"],"ec_funded":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"day":"21","external_id":{"isi":["001174278000001"],"pmid":["38381485"]},"_id":"15033","author":[{"first_name":"Maciek","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski"},{"last_name":"Matijevic","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana","first_name":"Ivana"},{"first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"publication_status":"published","publisher":"eLife Sciences Publications","doi":"10.7554/elife.68993","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in <jats:italic>gn</jats:italic> knockouts. The functional GN mutant variant GN<jats:sup>fewerroots</jats:sup>, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"article_processing_charge":"Yes","oa":1,"article_type":"original","file_date_updated":"2024-07-22T11:51:50Z","oa_version":"Published Version","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"month":"02","has_accepted_license":"1","date_updated":"2025-10-15T06:31:47Z","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research Council Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","OA_type":"gold","pmid":1,"year":"2024","type":"journal_article","publication":"eLife","corr_author":"1","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","file":[{"date_updated":"2024-07-22T11:51:50Z","date_created":"2024-07-22T11:51:50Z","content_type":"application/pdf","file_size":15675744,"relation":"main_file","checksum":"b2b2d583b433823af731842f1420113e","file_name":"2024_eLife_Adamowski.pdf","creator":"dernst","file_id":"17310","access_level":"open_access","success":1}],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-02-27T07:10:11Z","status":"public","volume":13,"APC_amount":"2792,52 EUR","citation":{"ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","apa":"Adamowski, M., Matijevic, I., &#38; Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.68993\">https://doi.org/10.7554/elife.68993</a>.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>","mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.68993\">10.7554/elife.68993</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["2050-084X"]},"OA_place":"publisher","intvolume":"        13","DOAJ_listed":"1","date_published":"2024-02-21T00:00:00Z"},{"ddc":["530"],"abstract":[{"lang":"eng","text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport."}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00601-024-01880-x","_id":"15045","publisher":"Springer Nature","external_id":{"arxiv":["2401.08454"],"isi":["001163768200001"]},"publication_status":"published","author":[{"last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"day":"17","file_date_updated":"2024-03-04T07:07:10Z","keyword":["Atomic and Molecular Physics","and Optics"],"oa_version":"Published Version","oa":1,"article_type":"original","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","date_updated":"2025-09-04T12:09:29Z","has_accepted_license":"1","month":"02","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"15049","access_level":"open_access","creator":"dernst","checksum":"c4e08cc7bc756da69b1b36fda7bb92fb","file_name":"2024_FewBodySys_Varshney.pdf","relation":"main_file","file_size":436712,"content_type":"application/pdf","date_updated":"2024-03-04T07:07:10Z","date_created":"2024-03-04T07:07:10Z"}],"title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","publication":"Few-Body Systems","corr_author":"1","year":"2024","type":"journal_article","citation":{"ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. 2024;65. doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>, vol. 65, 12, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00601-024-01880-x\">10.1007/s00601-024-01880-x</a>.","ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024).","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” <i>Few-Body Systems</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>.","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” <i>Few-Body Systems</i>, vol. 65. Springer Nature, 2024.","apa":"Varshney, A., Ghazaryan, A., &#38; Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. <i>Few-Body Systems</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00601-024-01880-x\">https://doi.org/10.1007/s00601-024-01880-x</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":65,"status":"public","date_created":"2024-03-01T11:39:33Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","department":[{"_id":"MiLe"}],"publication_identifier":{"issn":["1432-5411"]},"isi":1,"arxiv":1,"date_published":"2024-02-17T00:00:00Z","article_number":"12","intvolume":"        65"},{"citation":{"mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>.","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. 2024;10(8). doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>.","apa":"Bao, J., Stevens, B., Kluft, L., &#38; Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” <i>Science Advances</i>, vol. 10, no. 8. American Association for the Advancement of Science, 2024."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":10,"status":"public","date_created":"2024-03-03T23:00:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","description":"News on ISTA Website"}]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2024-03-04T07:34:00Z","date_created":"2024-03-04T07:34:00Z","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_name":"2024_ScienceAdv_Bao.pdf","file_size":800926,"relation":"main_file","creator":"dernst","success":1,"file_id":"15051","access_level":"open_access"}],"title":"Intensification of daily tropical precipitation extremes from more organized convection","publication":"Science Advances","issue":"8","type":"journal_article","year":"2024","pmid":1,"article_number":"eadj6801","date_published":"2024-02-23T00:00:00Z","DOAJ_listed":"1","intvolume":"        10","OA_place":"publisher","department":[{"_id":"CaMu"}],"publication_identifier":{"eissn":["2375-2548"]},"isi":1,"abstract":[{"text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.","lang":"eng"}],"article_processing_charge":"Yes","doi":"10.1126/sciadv.adj6801","publication_status":"published","_id":"15047","author":[{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","last_name":"Bao","full_name":"Bao, Jiawei","first_name":"Jiawei"},{"last_name":"Stevens","first_name":"Bjorn","full_name":"Stevens, Bjorn"},{"first_name":"Lukas","full_name":"Kluft, Lukas","last_name":"Kluft"},{"first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"publisher":"American Association for the Advancement of Science","external_id":{"pmid":["38394192"],"isi":["001300045100007"]},"day":"23","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041"}],"ec_funded":1,"ddc":["550"],"OA_type":"gold","acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","date_updated":"2025-09-04T12:11:18Z","has_accepted_license":"1","month":"02","oa_version":"Published Version","file_date_updated":"2024-03-04T07:34:00Z","article_type":"original","oa":1},{"date_published":"2024-02-01T00:00:00Z","page":"1-18","intvolume":"       151","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":151,"status":"public","citation":{"ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"14926","status":"public","relation":"research_data"}]},"quality_controlled":"1","scopus_import":"1","date_created":"2024-03-03T23:00:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","corr_author":"1","publication":"Development","language":[{"iso":"eng"}],"file":[{"file_size":14839986,"relation":"main_file","checksum":"6961ea10012bf0d266681f9628bb8f13","file_name":"2024_Development_Schauer.pdf","date_updated":"2024-03-04T07:24:43Z","date_created":"2024-03-04T07:24:43Z","content_type":"application/pdf","file_id":"15050","access_level":"open_access","success":1,"creator":"dernst"}],"pmid":1,"year":"2024","type":"journal_article","issue":"4","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","month":"02","date_updated":"2025-09-04T12:10:40Z","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2024-03-04T07:24:43Z","article_type":"original","oa":1,"abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1242/dev.202316","day":"01","project":[{"call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"_id":"15048","publisher":"The Company of Biologists","external_id":{"pmid":["38372390"],"isi":["001170580200001"]},"publication_status":"published","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","first_name":"Alexandra","full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142"},{"first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"ec_funded":1,"ddc":["570"]}]