[{"issue":"21","abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"doi":"10.1016/j.molcel.2022.10.010","author":[{"first_name":"David","full_name":"Zapletal, David","last_name":"Zapletal"},{"first_name":"Eliska","full_name":"Taborska, Eliska","last_name":"Taborska"},{"last_name":"Pasulka","full_name":"Pasulka, Josef","first_name":"Josef"},{"first_name":"Radek","full_name":"Malik, Radek","last_name":"Malik"},{"first_name":"Karel","last_name":"Kubicek","full_name":"Kubicek, Karel"},{"first_name":"Martina","last_name":"Zanova","full_name":"Zanova, Martina"},{"full_name":"Much, Christian","last_name":"Much","first_name":"Christian"},{"full_name":"Sebesta, Marek","last_name":"Sebesta","first_name":"Marek"},{"full_name":"Buccheri, Valeria","last_name":"Buccheri","first_name":"Valeria"},{"first_name":"Filip","full_name":"Horvat, Filip","last_name":"Horvat"},{"first_name":"Irena","full_name":"Jenickova, Irena","last_name":"Jenickova"},{"last_name":"Prochazkova","full_name":"Prochazkova, Michaela","first_name":"Michaela"},{"last_name":"Prochazka","full_name":"Prochazka, Jan","first_name":"Jan"},{"first_name":"Matyas","last_name":"Pinkas","full_name":"Pinkas, Matyas"},{"last_name":"Novacek","full_name":"Novacek, Jiri","first_name":"Jiri"},{"full_name":"Joseph, Diego F.","last_name":"Joseph","first_name":"Diego F."},{"last_name":"Sedlacek","full_name":"Sedlacek, Radislav","first_name":"Radislav"},{"orcid":"0000-0003-0893-7036","last_name":"Bernecky","full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O’Carroll","full_name":"O’Carroll, Dónal","first_name":"Dónal"},{"first_name":"Richard","full_name":"Stefl, Richard","last_name":"Stefl"},{"first_name":"Petr","full_name":"Svoboda, Petr","last_name":"Svoboda"}],"title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","_id":"12143","status":"public","publication_status":"published","acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","publication_identifier":{"issn":["1097-2765"]},"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","day":"03","citation":{"chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>.","mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” <i>Molecular Cell</i>, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>.","ieee":"D. Zapletal <i>et al.</i>, “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” <i>Molecular Cell</i>, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022.","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">https://doi.org/10.1016/j.molcel.2022.10.010</a>","ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. <i>Molecular Cell</i>. 2022;82(21):4064-4079.e13. doi:<a href=\"https://doi.org/10.1016/j.molcel.2022.10.010\">10.1016/j.molcel.2022.10.010</a>"},"month":"11","ddc":["570"],"pmid":1,"file_date_updated":"2023-01-24T09:29:02Z","has_accepted_license":"1","volume":82,"article_processing_charge":"No","file":[{"date_created":"2023-01-24T09:29:02Z","file_id":"12354","checksum":"999e443b54e4fdaa2542ca5a97619731","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-24T09:29:02Z","success":1,"file_size":7368534,"relation":"main_file","creator":"dernst","file_name":"2022_MolecularCell_Zapletal.pdf"}],"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"},"year":"2022","keyword":["Cell Biology","Molecular Biology"],"oa":1,"article_type":"original","page":"4064-4079.e13","publication":"Molecular Cell","date_updated":"2023-08-04T08:57:17Z","date_published":"2022-11-03T00:00:00Z","external_id":{"pmid":["36332606"],"isi":["000898565300011"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"scopus_import":"1","date_created":"2023-01-12T12:05:36Z","department":[{"_id":"CaBe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        82","publisher":"Elsevier"},{"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer Nature","main_file_link":[{"url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf","open_access":"1"}],"intvolume":"       611","date_created":"2023-01-12T12:06:05Z","scopus_import":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"date_published":"2022-11-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"page":"133-138","article_type":"original","date_updated":"2023-10-03T11:04:53Z","publication":"Nature","year":"2022","oa":1,"volume":611,"article_processing_charge":"No","oa_version":"Submitted Version","month":"11","pmid":1,"citation":{"chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>.","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>.","ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. 2022;611(7934):133-138. doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>","short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>","ieee":"L. Qi <i>et al.</i>, “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” <i>Nature</i>, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022."},"day":"03","ec_funded":1,"status":"public","acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","publication_status":"published","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"doi":"10.1038/s41586-022-05369-7","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants."}],"issue":"7934","_id":"12144","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","author":[{"first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401"},{"last_name":"Kwiatkowski","full_name":"Kwiatkowski, Mateusz","first_name":"Mateusz"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","full_name":"Chen, Huihuang","last_name":"Chen"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926"},{"orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","last_name":"Sinclair","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","full_name":"Zou, Minxia","last_name":"Zou"},{"first_name":"Charo I.","full_name":"del Genio, Charo I.","last_name":"del Genio"},{"first_name":"Martin F.","full_name":"Kubeš, Martin F.","last_name":"Kubeš"},{"first_name":"Richard","full_name":"Napier, Richard","last_name":"Napier"},{"first_name":"Krzysztof","full_name":"Jaworski, Krzysztof","last_name":"Jaworski"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}]},{"external_id":{"isi":["000865267300002"],"arxiv":["2105.14640"]},"date_published":"2022-10-03T00:00:00Z","scopus_import":"1","date_created":"2023-01-12T12:06:49Z","department":[{"_id":"VaKa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.14640"}],"intvolume":"        27","publisher":"Springer Nature","year":"2022","keyword":["Mechanical Engineering","Applied Mathematics","Mathematical Physics","Modeling and Simulation","Statistical and Nonlinear Physics","Mathematics (miscellaneous)"],"oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1134/s1560354722060107"}]},"article_type":"original","page":"525-537","publication":"Regular and Chaotic Dynamics","date_updated":"2023-08-04T08:59:14Z","oa_version":"Preprint","day":"03","citation":{"chicago":"Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards under Conjugacy.” <i>Regular and Chaotic Dynamics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1134/S1560354722050021\">https://doi.org/10.1134/S1560354722050021</a>.","mla":"Koudjinan, Edmond, and Vadim Kaloshin. “On Some Invariants of Birkhoff Billiards under Conjugacy.” <i>Regular and Chaotic Dynamics</i>, vol. 27, no. 6, Springer Nature, 2022, pp. 525–37, doi:<a href=\"https://doi.org/10.1134/S1560354722050021\">10.1134/S1560354722050021</a>.","ieee":"E. Koudjinan and V. Kaloshin, “On some invariants of Birkhoff billiards under conjugacy,” <i>Regular and Chaotic Dynamics</i>, vol. 27, no. 6. Springer Nature, pp. 525–537, 2022.","apa":"Koudjinan, E., &#38; Kaloshin, V. (2022). On some invariants of Birkhoff billiards under conjugacy. <i>Regular and Chaotic Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S1560354722050021\">https://doi.org/10.1134/S1560354722050021</a>","ama":"Koudjinan E, Kaloshin V. On some invariants of Birkhoff billiards under conjugacy. <i>Regular and Chaotic Dynamics</i>. 2022;27(6):525-537. doi:<a href=\"https://doi.org/10.1134/S1560354722050021\">10.1134/S1560354722050021</a>","short":"E. Koudjinan, V. Kaloshin, Regular and Chaotic Dynamics 27 (2022) 525–537.","ista":"Koudjinan E, Kaloshin V. 2022. On some invariants of Birkhoff billiards under conjugacy. Regular and Chaotic Dynamics. 27(6), 525–537."},"month":"10","volume":27,"article_processing_charge":"No","arxiv":1,"issue":"6","abstract":[{"text":"In the class of strictly convex smooth boundaries each of which has no strip around its boundary foliated by invariant curves, we prove that the Taylor coefficients of the “normalized” Mather’s β-function are invariant under C∞-conjugacies. In contrast, we prove that any two elliptic billiard maps are C0-conjugate near their respective boundaries, and C∞-conjugate, near the boundary and away from a line passing through the center of the underlying ellipse. We also prove that, if the billiard maps corresponding to two ellipses are topologically conjugate, then the two ellipses are similar.","lang":"eng"}],"doi":"10.1134/S1560354722050021","author":[{"orcid":"0000-0003-2640-4049","first_name":"Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","last_name":"Koudjinan","full_name":"Koudjinan, Edmond"},{"orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"}],"title":"On some invariants of Birkhoff billiards under conjugacy","_id":"12145","publication_status":"published","acknowledgement":"We are grateful to the anonymous referees for their careful reading and valuable remarks and\r\ncomments which helped to improve the paper significantly. We gratefully acknowledge support from the European Research Council (ERC) through the Advanced Grant “SPERIG” (#885707).","status":"public","ec_funded":1,"publication_identifier":{"eissn":["1468-4845"],"issn":["1560-3547"]},"project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows"}]},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"AIP Publishing","main_file_link":[{"open_access":"1","url":"https://upcommons.upc.edu/handle/2117/385635"}],"intvolume":"        34","date_created":"2023-01-12T12:06:58Z","scopus_import":"1","external_id":{"isi":["000880665300024"]},"date_published":"2022-11-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"article_number":"114111","article_type":"original","date_updated":"2023-10-03T11:07:58Z","publication":"Physics of Fluids","keyword":["Condensed Matter Physics","Fluid Flow and Transfer Processes","Mechanics of Materials","Computational Mechanics","Mechanical Engineering"],"year":"2022","oa":1,"article_processing_charge":"No","volume":34,"oa_version":"Submitted Version","month":"11","citation":{"mla":"Wang, B., et al. “Phase-Locking Flows between Orthogonally Stretching Parallel Plates.” <i>Physics of Fluids</i>, vol. 34, no. 11, 114111, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0124152\">10.1063/5.0124152</a>.","chicago":"Wang, B., Roger Ayats López, A. Meseguer, and F. Marques. “Phase-Locking Flows between Orthogonally Stretching Parallel Plates.” <i>Physics of Fluids</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0124152\">https://doi.org/10.1063/5.0124152</a>.","ista":"Wang B, Ayats López R, Meseguer A, Marques F. 2022. Phase-locking flows between orthogonally stretching parallel plates. Physics of Fluids. 34(11), 114111.","short":"B. Wang, R. Ayats López, A. Meseguer, F. Marques, Physics of Fluids 34 (2022).","ama":"Wang B, Ayats López R, Meseguer A, Marques F. Phase-locking flows between orthogonally stretching parallel plates. <i>Physics of Fluids</i>. 2022;34(11). doi:<a href=\"https://doi.org/10.1063/5.0124152\">10.1063/5.0124152</a>","ieee":"B. Wang, R. Ayats López, A. Meseguer, and F. Marques, “Phase-locking flows between orthogonally stretching parallel plates,” <i>Physics of Fluids</i>, vol. 34, no. 11. AIP Publishing, 2022.","apa":"Wang, B., Ayats López, R., Meseguer, A., &#38; Marques, F. (2022). Phase-locking flows between orthogonally stretching parallel plates. <i>Physics of Fluids</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0124152\">https://doi.org/10.1063/5.0124152</a>"},"day":"04","publication_status":"published","acknowledgement":"This work was supported by the Spanish MINECO under Grant Nos. FIS2017-85794-P and PRX18/00179, the Spanish MICINN through Grant No. PID2020-114043GB-I00, and the\r\nGeneralitat de Catalunya under Grant No. 2017-SGR-785. B.W.’s research was also supported by the Chinese Scholarship Council through Grant CSC No. 201806440152.","status":"public","publication_identifier":{"eissn":["1089-7666"],"issn":["1070-6631"]},"doi":"10.1063/5.0124152","abstract":[{"lang":"eng","text":"In this paper, we explore the stability and dynamical relevance of a wide variety of steady, time-periodic, quasiperiodic, and chaotic flows arising between orthogonally stretching parallel plates. We first explore the stability of all the steady flow solution families formerly identified by Ayats et al. [“Flows between orthogonally stretching parallel plates,” Phys. Fluids 33, 024103 (2021)], concluding that only the one that originates from the Stokesian approximation is actually stable. When both plates are shrinking at identical or nearly the same deceleration rates, this Stokesian flow exhibits a Hopf bifurcation that leads to stable time-periodic regimes. The resulting time-periodic orbits or flows are tracked for different Reynolds numbers and stretching rates while monitoring their Floquet exponents to identify secondary instabilities. It is found that these time-periodic flows also exhibit Neimark–Sacker bifurcations, generating stable quasiperiodic flows (tori) that may sometimes give rise to chaotic dynamics through a Ruelle–Takens–Newhouse scenario. However, chaotic dynamics is unusually observed, as the quasiperiodic flows generally become phase-locked through a resonance mechanism before a strange attractor may arise, thus restoring the time-periodicity of the flow. In this work, we have identified and tracked four different resonance regions, also known as Arnold tongues or horns. In particular, the 1 : 4 strong resonance region is explored in great detail, where the identified scenarios are in very good agreement with normal form theory. "}],"issue":"11","_id":"12146","title":"Phase-locking flows between orthogonally stretching parallel plates","author":[{"first_name":"B.","full_name":"Wang, B.","last_name":"Wang"},{"full_name":"Ayats López, Roger","last_name":"Ayats López","id":"ab77522d-073b-11ed-8aff-e71b39258362","first_name":"Roger","orcid":"0000-0001-6572-0621"},{"last_name":"Meseguer","full_name":"Meseguer, A.","first_name":"A."},{"last_name":"Marques","full_name":"Marques, F.","first_name":"F."}]},{"publisher":"Springer Nature","intvolume":"         4","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000884215600003"],"arxiv":["2106.13898"]},"date_published":"2022-11-15T00:00:00Z","date_created":"2023-01-12T12:07:21Z","scopus_import":"1","publication":"Nature Machine Intelligence","date_updated":"2023-08-04T09:00:10Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s42256-022-00597-y","relation":"erratum"}]},"page":"992-1003","article_type":"original","oa":1,"year":"2022","keyword":["Artificial Intelligence","Computer Networks and Communications","Computer Vision and Pattern Recognition","Human-Computer Interaction","Software"],"arxiv":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"},"file":[{"date_updated":"2023-01-24T09:49:44Z","success":1,"checksum":"b4789122ce04bfb4ac042390f59aaa8b","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":3259553,"file_name":"2022_NatureMachineIntelligence_Hasani.pdf","date_created":"2023-01-24T09:49:44Z","file_id":"12355"}],"has_accepted_license":"1","volume":4,"article_processing_charge":"No","citation":{"ieee":"R. Hasani <i>et al.</i>, “Closed-form continuous-time neural networks,” <i>Nature Machine Intelligence</i>, vol. 4, no. 11. Springer Nature, pp. 992–1003, 2022.","apa":"Hasani, R., Lechner, M., Amini, A., Liebenwein, L., Ray, A., Tschaikowski, M., … Rus, D. (2022). Closed-form continuous-time neural networks. <i>Nature Machine Intelligence</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42256-022-00556-7\">https://doi.org/10.1038/s42256-022-00556-7</a>","ista":"Hasani R, Lechner M, Amini A, Liebenwein L, Ray A, Tschaikowski M, Teschl G, Rus D. 2022. Closed-form continuous-time neural networks. Nature Machine Intelligence. 4(11), 992–1003.","short":"R. Hasani, M. Lechner, A. Amini, L. Liebenwein, A. Ray, M. Tschaikowski, G. Teschl, D. Rus, Nature Machine Intelligence 4 (2022) 992–1003.","ama":"Hasani R, Lechner M, Amini A, et al. Closed-form continuous-time neural networks. <i>Nature Machine Intelligence</i>. 2022;4(11):992-1003. doi:<a href=\"https://doi.org/10.1038/s42256-022-00556-7\">10.1038/s42256-022-00556-7</a>","mla":"Hasani, Ramin, et al. “Closed-Form Continuous-Time Neural Networks.” <i>Nature Machine Intelligence</i>, vol. 4, no. 11, Springer Nature, 2022, pp. 992–1003, doi:<a href=\"https://doi.org/10.1038/s42256-022-00556-7\">10.1038/s42256-022-00556-7</a>.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Lucas Liebenwein, Aaron Ray, Max Tschaikowski, Gerald Teschl, and Daniela Rus. “Closed-Form Continuous-Time Neural Networks.” <i>Nature Machine Intelligence</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42256-022-00556-7\">https://doi.org/10.1038/s42256-022-00556-7</a>."},"day":"15","month":"11","ddc":["000"],"file_date_updated":"2023-01-24T09:49:44Z","oa_version":"Published Version","publication_identifier":{"issn":["2522-5839"]},"project":[{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"status":"public","publication_status":"published","acknowledgement":"This research was supported in part by the AI2050 program at Schmidt Futures (grant G-22-63172), the Boeing Company, and the United States Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under cooperative agreement number FA8750-19-2-1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes, notwithstanding any copyright notation herein. This work was further supported by The Boeing Company and Office of Naval Research grant N00014-18-1-2830. M.T. is supported by the Poul Due Jensen Foundation, grant 883901. M.L. was supported in part by the Austrian Science Fund under grant Z211-N23 (Wittgenstein Award). A.A. was supported by the National Science Foundation Graduate Research Fellowship Program. We thank T.-H. Wang, P. Kao, M. Chahine, W. Xiao, X. Li, L. Yin and Y. Ben for useful suggestions and for testing of CfC models to confirm the results across other domains.","title":"Closed-form continuous-time neural networks","author":[{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"last_name":"Liebenwein","full_name":"Liebenwein, Lucas","first_name":"Lucas"},{"first_name":"Aaron","full_name":"Ray, Aaron","last_name":"Ray"},{"first_name":"Max","last_name":"Tschaikowski","full_name":"Tschaikowski, Max"},{"last_name":"Teschl","full_name":"Teschl, Gerald","first_name":"Gerald"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"}],"_id":"12147","abstract":[{"text":"Continuous-time neural networks are a class of machine learning systems that can tackle representation learning on spatiotemporal decision-making tasks. These models are typically represented by continuous differential equations. However, their expressive power when they are deployed on computers is bottlenecked by numerical differential equation solvers. This limitation has notably slowed down the scaling and understanding of numerous natural physical phenomena such as the dynamics of nervous systems. Ideally, we would circumvent this bottleneck by solving the given dynamical system in closed form. This is known to be intractable in general. Here, we show that it is possible to closely approximate the interaction between neurons and synapses—the building blocks of natural and artificial neural networks—constructed by liquid time-constant networks efficiently in closed form. To this end, we compute a tightly bounded approximation of the solution of an integral appearing in liquid time-constant dynamics that has had no known closed-form solution so far. This closed-form solution impacts the design of continuous-time and continuous-depth neural models. For instance, since time appears explicitly in closed form, the formulation relaxes the need for complex numerical solvers. Consequently, we obtain models that are between one and five orders of magnitude faster in training and inference compared with differential equation-based counterparts. More importantly, in contrast to ordinary differential equation-based continuous networks, closed-form networks can scale remarkably well compared with other deep learning instances. Lastly, as these models are derived from liquid networks, they show good performance in time-series modelling compared with advanced recurrent neural network models.","lang":"eng"}],"issue":"11","doi":"10.1038/s42256-022-00556-7"},{"doi":"10.1017/fms.2022.86","abstract":[{"text":"We prove a general local law for Wigner matrices that optimally handles observables of arbitrary rank and thus unifies the well-known averaged and isotropic local laws. As an application, we prove a central limit theorem in quantum unique ergodicity (QUE): that is, we show that the quadratic forms of a general deterministic matrix A on the bulk eigenvectors of a Wigner matrix have approximately Gaussian fluctuation. For the bulk spectrum, we thus generalise our previous result [17] as valid for test matrices A of large rank as well as the result of Benigni and Lopatto [7] as valid for specific small-rank observables.","lang":"eng"}],"_id":"12148","title":"Rank-uniform local law for Wigner matrices","author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"}],"ec_funded":1,"acknowledgement":"L.E. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331. D.S. acknowledges the support of Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","status":"public","publication_status":"published","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"publication_identifier":{"issn":["2050-5094"]},"oa_version":"Published Version","month":"10","file_date_updated":"2023-01-24T10:02:40Z","ddc":["510"],"citation":{"apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Rank-uniform local law for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2022.86\">https://doi.org/10.1017/fms.2022.86</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Rank-uniform local law for Wigner matrices,” <i>Forum of Mathematics, Sigma</i>, vol. 10. Cambridge University Press, 2022.","ama":"Cipolloni G, Erdös L, Schröder DJ. Rank-uniform local law for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. 2022;10. doi:<a href=\"https://doi.org/10.1017/fms.2022.86\">10.1017/fms.2022.86</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Rank-uniform local law for Wigner matrices. Forum of Mathematics, Sigma. 10, e96.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Forum of Mathematics, Sigma 10 (2022).","mla":"Cipolloni, Giorgio, et al. “Rank-Uniform Local Law for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>, vol. 10, e96, Cambridge University Press, 2022, doi:<a href=\"https://doi.org/10.1017/fms.2022.86\">10.1017/fms.2022.86</a>.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Rank-Uniform Local Law for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2022. <a href=\"https://doi.org/10.1017/fms.2022.86\">https://doi.org/10.1017/fms.2022.86</a>."},"day":"27","volume":10,"article_processing_charge":"No","has_accepted_license":"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"},"file":[{"creator":"dernst","relation":"main_file","file_size":817089,"file_name":"2022_ForumMath_Cipolloni.pdf","date_updated":"2023-01-24T10:02:40Z","success":1,"checksum":"94a049aeb1eea5497aa097712a73c400","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-24T10:02:40Z","file_id":"12356"}],"keyword":["Computational Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Mathematical Physics","Statistics and Probability","Algebra and Number Theory","Theoretical Computer Science","Analysis"],"year":"2022","oa":1,"article_number":"e96","article_type":"original","date_updated":"2023-08-04T09:00:35Z","publication":"Forum of Mathematics, Sigma","date_created":"2023-01-12T12:07:30Z","scopus_import":"1","external_id":{"isi":["000873719200001"]},"date_published":"2022-10-27T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LaEr"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Cambridge University Press","intvolume":"        10"},{"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Frontiers Media","intvolume":"        16","external_id":{"isi":["000886671400001"]},"date_published":"2022-10-26T00:00:00Z","date_created":"2023-01-12T12:07:39Z","scopus_import":"1","department":[{"_id":"JoCs"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1028154","article_type":"letter_note","publication":"Frontiers in Neural Circuits","date_updated":"2023-08-04T09:01:06Z","year":"2022","keyword":["Cellular and Molecular Neuroscience","Cognitive Neuroscience","Sensory Systems","Neuroscience (miscellaneous)"],"oa":1,"has_accepted_license":"1","volume":16,"article_processing_charge":"No","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"},"file":[{"date_created":"2023-01-24T10:10:43Z","file_id":"12357","file_size":110031,"creator":"dernst","relation":"main_file","file_name":"2022_FrontiersNeuralCircuits_Gambino.pdf","checksum":"457aa00e1800847abb340853058531de","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-24T10:10:43Z","success":1}],"oa_version":"Published Version","citation":{"chicago":"Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig, Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>.","mla":"Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>, vol. 16, 1028154, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>.","apa":"Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J. F., &#38; Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>","ieee":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas, and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels,” <i>Frontiers in Neural Circuits</i>, vol. 16. Frontiers Media, 2022.","ista":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154.","short":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas, D. Zaldivar, Frontiers in Neural Circuits 16 (2022).","ama":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>"},"day":"26","ddc":["570"],"month":"10","file_date_updated":"2023-01-24T10:10:43Z","acknowledgement":"This work was supported by a DFG grant ZA990/1 to DZ. This work was supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020 - Research and Innovation Framework Programme to JFRV.","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["1662-5110"]},"project":[{"name":"The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory Consolidation","call_identifier":"H2020","grant_number":"841301","_id":"26BAE2E4-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Editorial on the Research Topic"}],"doi":"10.3389/fncir.2022.1028154","title":"Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels","author":[{"full_name":"Gambino, Giuditta","last_name":"Gambino","first_name":"Giuditta"},{"first_name":"Rebecca","full_name":"Bhik-Ghanie, Rebecca","last_name":"Bhik-Ghanie"},{"last_name":"Giglia","full_name":"Giglia, Giuseppe","first_name":"Giuseppe"},{"full_name":"Puig, M. Victoria","last_name":"Puig","first_name":"M. Victoria"},{"id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F","full_name":"Ramirez Villegas, Juan F","last_name":"Ramirez Villegas"},{"full_name":"Zaldivar, Daniel","last_name":"Zaldivar","first_name":"Daniel"}],"_id":"12149"},{"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"American Physical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.15193","open_access":"1"}],"intvolume":"       106","date_created":"2023-01-12T12:07:49Z","scopus_import":"1","external_id":{"isi":["000875189100005"],"arxiv":["2105.15193"]},"date_published":"2022-10-15T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"article_number":"155127","article_type":"original","date_updated":"2023-08-04T09:01:48Z","publication":"Physical Review B","year":"2022","oa":1,"volume":106,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"10","citation":{"mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Nonadditive Systems.” <i>Physical Review B</i>, vol. 106, no. 15, 155127, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.106.155127\">10.1103/physrevb.106.155127</a>.","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Nonadditive Systems.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.106.155127\">https://doi.org/10.1103/physrevb.106.155127</a>.","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for nonadditive systems,” <i>Physical Review B</i>, vol. 106, no. 15. American Physical Society, 2022.","apa":"Rzadkowski, W., Lemeshko, M., &#38; Mentink, J. H. (2022). Artificial neural network states for nonadditive systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.106.155127\">https://doi.org/10.1103/physrevb.106.155127</a>","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, Physical Review B 106 (2022).","ista":"Rzadkowski W, Lemeshko M, Mentink JH. 2022. Artificial neural network states for nonadditive systems. Physical Review B. 106(15), 155127.","ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for nonadditive systems. <i>Physical Review B</i>. 2022;106(15). doi:<a href=\"https://doi.org/10.1103/physrevb.106.155127\">10.1103/physrevb.106.155127</a>"},"day":"15","ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"We acknowledge fruitful discussions with G. Bighin, G. Fabiani, A. Ghazaryan, C. Lampert, and A. Volosniev at various stages of this work. W.R. acknowledges support through a DOC Fellowship of the Austrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M.L. and J.H.M. acknowledge support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON) and Synergy Grant No. 856538 (3D-MAGiC), respectively. This work is part of the Shell-NWO/FOMinitiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW. ","project":[{"name":"Analytic and machine learning approaches to composite quantum impurities","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","grant_number":"25681"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"doi":"10.1103/physrevb.106.155127","abstract":[{"lang":"eng","text":"Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of nonadditive systems very well. In particular, we recover exact diagonalization in all regimes tested and observe substantial improvement over the standard coherent state estimates in the most challenging intermediate-coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications."}],"issue":"15","_id":"12150","title":"Artificial neural network states for nonadditive systems","author":[{"full_name":"Rzadkowski, Wojciech","last_name":"Rzadkowski","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","orcid":"0000-0002-1106-4419"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"full_name":"Mentink, Johan H.","last_name":"Mentink","first_name":"Johan H."}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaKw"}],"date_created":"2023-01-12T12:07:59Z","scopus_import":"1","date_published":"2022-11-23T00:00:00Z","external_id":{"arxiv":["2103.09114"],"isi":["000886839900006"]},"publisher":"Springer Nature","intvolume":"       168","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2103.09114"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"keyword":["graphon","k-sample","graphon forcing","graph container"],"year":"2022","date_updated":"2023-08-04T09:02:37Z","publication":"Acta Mathematica Hungarica","page":"1-26","article_type":"original","month":"11","citation":{"apa":"Cooley, O., Kang, M., &#38; Pikhurko, O. (2022). On a question of Vera T. Sós about size forcing of graphons. <i>Acta Mathematica Hungarica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10474-022-01265-8\">https://doi.org/10.1007/s10474-022-01265-8</a>","ieee":"O. Cooley, M. Kang, and O. Pikhurko, “On a question of Vera T. Sós about size forcing of graphons,” <i>Acta Mathematica Hungarica</i>, vol. 168. Springer Nature, pp. 1–26, 2022.","ama":"Cooley O, Kang M, Pikhurko O. On a question of Vera T. Sós about size forcing of graphons. <i>Acta Mathematica Hungarica</i>. 2022;168:1-26. doi:<a href=\"https://doi.org/10.1007/s10474-022-01265-8\">10.1007/s10474-022-01265-8</a>","short":"O. Cooley, M. Kang, O. Pikhurko, Acta Mathematica Hungarica 168 (2022) 1–26.","ista":"Cooley O, Kang M, Pikhurko O. 2022. On a question of Vera T. Sós about size forcing of graphons. Acta Mathematica Hungarica. 168, 1–26.","chicago":"Cooley, Oliver, M. Kang, and O. Pikhurko. “On a Question of Vera T. Sós about Size Forcing of Graphons.” <i>Acta Mathematica Hungarica</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s10474-022-01265-8\">https://doi.org/10.1007/s10474-022-01265-8</a>.","mla":"Cooley, Oliver, et al. “On a Question of Vera T. Sós about Size Forcing of Graphons.” <i>Acta Mathematica Hungarica</i>, vol. 168, Springer Nature, 2022, pp. 1–26, doi:<a href=\"https://doi.org/10.1007/s10474-022-01265-8\">10.1007/s10474-022-01265-8</a>."},"day":"23","oa_version":"Preprint","arxiv":1,"volume":168,"article_processing_charge":"No","_id":"12151","title":"On a question of Vera T. Sós about size forcing of graphons","author":[{"last_name":"Cooley","full_name":"Cooley, Oliver","first_name":"Oliver","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d"},{"first_name":"M.","full_name":"Kang, M.","last_name":"Kang"},{"full_name":"Pikhurko, O.","last_name":"Pikhurko","first_name":"O."}],"doi":"10.1007/s10474-022-01265-8","abstract":[{"lang":"eng","text":"The k-sample G(k,W) from a graphon W:[0,1]2→[0,1] is the random graph on {1,…,k}, where we sample x1,…,xk∈[0,1] uniformly at random and make each pair {i,j}⊆{1,…,k} an edge with probability W(xi,xj), with all these choices being mutually independent. Let the random variable Xk(W) be the number of edges in  G(k,W). Vera T. Sós asked in 2012 whether two graphons U, W are necessarily weakly isomorphic if the random variables Xk(U) and Xk(W) have the same distribution for every integer k≥2. This question when one of the graphons W is a constant function was answered positively by Endre Csóka and independently by Jacob Fox, Tomasz Łuczak and Vera T. Sós. Here we investigate the question when W is a 2-step graphon and prove that the answer is positive for a 3-dimensional family of such graphons. We also present some related results."}],"publication_identifier":{"issn":["0236-5294"],"eissn":["1588-2632"]},"publication_status":"published","status":"public","acknowledgement":"Supported by Austrian Science Fund (FWF) Grant I3747. Supported by ERC Advanced Grant 101020255 and Leverhulme Research Project Grant RPG-2018-424.\r\nAn extended abstract of this paper appeared in the Proceedings of the European Conference\r\non Combinatorics, Graph Theory and Applications (EuroComb 2021), CRM Research Perspectives, Springer."},{"volume":18,"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2023-01-24T10:45:01Z","file_id":"12359","file_size":2641067,"creator":"dernst","relation":"main_file","file_name":"2022_PLoSCompBio_Jiang.pdf","checksum":"bada6a7865e470cf42bbdfa67dd471d2","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-24T10:45:01Z","success":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"},"oa_version":"Published Version","ddc":["570"],"month":"10","file_date_updated":"2023-01-24T10:45:01Z","day":"17","citation":{"chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>.","ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960"},{"name":"The evolution of trafficking: from archaea to eukaryotes","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752"}],"publication_identifier":{"issn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1010586","issue":"10","abstract":[{"text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.","lang":"eng"}],"_id":"12152","author":[{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"first_name":"Lena","full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos"},{"first_name":"Anna-Katharina","last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina"},{"full_name":"Lominadze, Elene","last_name":"Lominadze","first_name":"Elene"},{"first_name":"Aurélien","last_name":"Roux","full_name":"Roux, Aurélien"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"        18","publisher":"Public Library of Science","scopus_import":"1","date_created":"2023-01-12T12:08:10Z","external_id":{"isi":["000924885500005"]},"date_published":"2022-10-17T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"AnSa"}],"article_type":"original","article_number":"e1010586","related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"date_updated":"2023-08-04T09:03:21Z","publication":"PLOS Computational Biology","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"year":"2022","oa":1},{"keyword":["Physics and Astronomy (miscellaneous)","General Mathematics","Chemistry (miscellaneous)","Computer Science (miscellaneous)"],"year":"2022","oa":1,"article_number":"2182","article_type":"original","date_updated":"2023-08-09T10:13:17Z","publication":"Symmetry","date_created":"2023-01-12T12:08:31Z","scopus_import":"1","date_published":"2022-10-17T00:00:00Z","external_id":{"isi":["000875039200001"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"publisher":"MDPI","intvolume":"        14","doi":"10.3390/sym14102182","abstract":[{"lang":"eng","text":"We review our theoretical results of the sound propagation in two-dimensional (2D) systems of ultracold fermionic and bosonic atoms. In the superfluid phase, characterized by the spontaneous symmetry breaking of the U(1) symmetry, there is the coexistence of first and second sound. In the case of weakly-interacting repulsive bosons, we model the recent measurements of the sound velocities of 39K atoms in 2D obtained in the weakly-interacting regime and around the Berezinskii–Kosterlitz–Thouless (BKT) superfluid-to-normal transition temperature. In particular, we perform a quite accurate computation of the superfluid density and show that it is reasonably consistent with the experimental results. For superfluid attractive fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover. In the low-temperature regime, we reproduce the recent measurements of first-sound speed with 6Li atoms. We also predict that there is mixing between sound modes only in the finite-temperature BEC regime."}],"issue":"10","_id":"12154","title":"First and second sound in two-dimensional bosonic and fermionic superfluids","author":[{"first_name":"Luca","full_name":"Salasnich, Luca","last_name":"Salasnich"},{"orcid":"0000-0001-6110-2359","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro","full_name":"Cappellaro, Alberto"},{"full_name":"Furutani, Koichiro","last_name":"Furutani","first_name":"Koichiro"},{"first_name":"Andrea","full_name":"Tononi, Andrea","last_name":"Tononi"},{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"}],"status":"public","publication_status":"published","acknowledgement":"This research is partially supported by University of Padova, BIRD grant “Ultracold atoms\r\nin curved geometries”. KF is supported by Fondazione CARIPARO with a PhD fellowship. AT is\r\npartially supported by French National Research Agency ANR Grant Droplets N. ANR-19-CE30-0003-02. LS thanks Herwig Ott and Sandro Wimberger for their kind invitation to the\r\nInternational Workshop “Quantum Transport with ultracold atoms” (2022).","publication_identifier":{"issn":["2073-8994"]},"oa_version":"Published Version","month":"10","ddc":["530"],"file_date_updated":"2023-01-24T10:56:12Z","citation":{"apa":"Salasnich, L., Cappellaro, A., Furutani, K., Tononi, A., &#38; Bighin, G. (2022). First and second sound in two-dimensional bosonic and fermionic superfluids. <i>Symmetry</i>. MDPI. <a href=\"https://doi.org/10.3390/sym14102182\">https://doi.org/10.3390/sym14102182</a>","ieee":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, and G. Bighin, “First and second sound in two-dimensional bosonic and fermionic superfluids,” <i>Symmetry</i>, vol. 14, no. 10. MDPI, 2022.","ama":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. First and second sound in two-dimensional bosonic and fermionic superfluids. <i>Symmetry</i>. 2022;14(10). doi:<a href=\"https://doi.org/10.3390/sym14102182\">10.3390/sym14102182</a>","ista":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. 2022. First and second sound in two-dimensional bosonic and fermionic superfluids. Symmetry. 14(10), 2182.","short":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, G. Bighin, Symmetry 14 (2022).","chicago":"Salasnich, Luca, Alberto Cappellaro, Koichiro Furutani, Andrea Tononi, and Giacomo Bighin. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” <i>Symmetry</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/sym14102182\">https://doi.org/10.3390/sym14102182</a>.","mla":"Salasnich, Luca, et al. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” <i>Symmetry</i>, vol. 14, no. 10, 2182, MDPI, 2022, doi:<a href=\"https://doi.org/10.3390/sym14102182\">10.3390/sym14102182</a>."},"day":"17","volume":14,"article_processing_charge":"Yes","has_accepted_license":"1","file":[{"date_created":"2023-01-24T10:56:12Z","file_id":"12361","checksum":"9b6bd0e484834dd76d7b26e3c5fba8bd","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-24T10:56:12Z","success":1,"creator":"dernst","file_size":843723,"relation":"main_file","file_name":"2022_Symmetry_Salsnich.pdf"}],"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"}},{"keyword":["Pollution","Nuclear Energy and Engineering","Renewable Energy","Sustainability and the Environment","Environmental Chemistry"],"year":"2022","page":"4527-4541","article_type":"original","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1039/d3ee90067c"}]},"date_updated":"2024-01-22T08:13:43Z","publication":"Energy & Environmental Science","date_created":"2023-01-12T12:08:41Z","scopus_import":"1","date_published":"2022-11-01T00:00:00Z","external_id":{"isi":["000863642400001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Royal Society of Chemistry","intvolume":"        15","doi":"10.1039/d2ee02408j","abstract":[{"lang":"eng","text":"The growing demand of thermal management in various fields such as miniaturized 5G chips has motivated researchers to develop new and high-performance solid-state refrigeration technologies, typically including multicaloric and thermoelectric (TE) cooling. Among them, TE cooling has attracted huge attention owing to its advantages of rapid response, large cooling temperature difference, high stability, and tunable device size. Bi2Te3-based alloys have long been the only commercialized TE cooling materials, while novel systems SnSe and Mg3(Bi,Sb)2 have recently been discovered as potential candidates. However, challenges and problems still require to be summarized and further resolved for realizing better cooling performance. In this review, we systematically investigate TE cooling from its internal mechanism, crucial parameters, to device design and applications. Furthermore, we summarize the current optimization strategies for existing TE cooling materials, and finally provide some personal prospects especially the material-planification concept on future research on establishing better TE cooling."}],"issue":"11","_id":"12155","title":"Solid-state cooling: Thermoelectrics","author":[{"first_name":"Yongxin","last_name":"Qin","full_name":"Qin, Yongxin"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"last_name":"Wang","full_name":"Wang, Dongyang","first_name":"Dongyang"},{"orcid":"0000-0002-9515-4277","last_name":"Chang","full_name":"Chang, Cheng","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Zhao, Li-Dong","last_name":"Zhao","first_name":"Li-Dong"}],"status":"public","acknowledgement":"We acknowledge support from the National Key Research and Development Program of China (2018YFA0702100), the National Natural Science Foundation of China (51571007, 51772012, 52002011 and 52002042), the Basic Science Center Project of National Natural Science Foundation of China (51788104), Beijing Natural Science Foundation (JQ18004), 111 Project (B17002), and the National Science Fund for Distinguished Young Scholars (51925101).","publication_status":"published","publication_identifier":{"issn":["1754-5692"],"eissn":["1754-5706"]},"oa_version":"None","month":"11","citation":{"chicago":"Qin, Yongxin, Bingchao Qin, Dongyang Wang, Cheng Chang, and Li-Dong Zhao. “Solid-State Cooling: Thermoelectrics.” <i>Energy &#38; Environmental Science</i>. Royal Society of Chemistry, 2022. <a href=\"https://doi.org/10.1039/d2ee02408j\">https://doi.org/10.1039/d2ee02408j</a>.","mla":"Qin, Yongxin, et al. “Solid-State Cooling: Thermoelectrics.” <i>Energy &#38; Environmental Science</i>, vol. 15, no. 11, Royal Society of Chemistry, 2022, pp. 4527–41, doi:<a href=\"https://doi.org/10.1039/d2ee02408j\">10.1039/d2ee02408j</a>.","apa":"Qin, Y., Qin, B., Wang, D., Chang, C., &#38; Zhao, L.-D. (2022). Solid-state cooling: Thermoelectrics. <i>Energy &#38; Environmental Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2ee02408j\">https://doi.org/10.1039/d2ee02408j</a>","ieee":"Y. Qin, B. Qin, D. Wang, C. Chang, and L.-D. Zhao, “Solid-state cooling: Thermoelectrics,” <i>Energy &#38; Environmental Science</i>, vol. 15, no. 11. Royal Society of Chemistry, pp. 4527–4541, 2022.","ama":"Qin Y, Qin B, Wang D, Chang C, Zhao L-D. Solid-state cooling: Thermoelectrics. <i>Energy &#38; Environmental Science</i>. 2022;15(11):4527-4541. doi:<a href=\"https://doi.org/10.1039/d2ee02408j\">10.1039/d2ee02408j</a>","short":"Y. Qin, B. Qin, D. Wang, C. Chang, L.-D. Zhao, Energy &#38; Environmental Science 15 (2022) 4527–4541.","ista":"Qin Y, Qin B, Wang D, Chang C, Zhao L-D. 2022. Solid-state cooling: Thermoelectrics. Energy &#38; Environmental Science. 15(11), 4527–4541."},"day":"01","volume":15,"article_processing_charge":"No"},{"oa":1,"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"year":"2022","date_updated":"2023-02-13T09:20:34Z","publication":"Current Opinion in Systems Biology","article_number":"100435","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"date_created":"2023-01-12T12:08:51Z","scopus_import":"1","date_published":"2022-09-01T00:00:00Z","publisher":"Elsevier","intvolume":"        31","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","_id":"12156","title":"Eukaryotic gene regulation at equilibrium, or non?","author":[{"first_name":"Benjamin","full_name":"Zoller, Benjamin","last_name":"Zoller"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"doi":"10.1016/j.coisb.2022.100435","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"issue":"9","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"publication_identifier":{"issn":["2452-3100"]},"acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","publication_status":"published","status":"public","month":"09","ddc":["570"],"file_date_updated":"2023-01-24T12:14:10Z","citation":{"ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>."},"day":"01","oa_version":"Published Version","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"},"file":[{"date_created":"2023-01-24T12:14:10Z","file_id":"12362","date_updated":"2023-01-24T12:14:10Z","success":1,"content_type":"application/pdf","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","access_level":"open_access","relation":"main_file","file_size":2214944,"creator":"dernst","file_name":"2022_CurrentBiology_Zoller.pdf"}],"volume":31,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"volume":11,"article_processing_charge":"No","has_accepted_license":"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"},"file":[{"date_created":"2023-01-24T12:21:32Z","file_id":"12363","file_size":18935612,"creator":"dernst","relation":"main_file","file_name":"2022_eLife_Hayward.pdf","date_updated":"2023-01-24T12:21:32Z","success":1,"checksum":"28de155b231ac1c8d4501c98b2fb359a","content_type":"application/pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"09","file_date_updated":"2023-01-24T12:21:32Z","ddc":["570"],"day":"26","citation":{"mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","short":"L. Hayward, G. Sella, ELife 11 (2022).","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","status":"public","publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/elife.66697","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"_id":"12157","author":[{"full_name":"Hayward, Laura","last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura"},{"last_name":"Sella","full_name":"Sella, Guy","first_name":"Guy"}],"title":"Polygenic adaptation after a sudden change in environment","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"        11","publisher":"eLife Sciences Publications","scopus_import":"1","date_created":"2023-01-12T12:09:00Z","date_published":"2022-09-26T00:00:00Z","external_id":{"isi":["000890735600001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"article_type":"original","article_number":"66697","date_updated":"2023-08-04T09:04:58Z","publication":"eLife","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"year":"2022","oa":1},{"scopus_import":"1","date_created":"2023-01-12T12:09:28Z","date_published":"2022-11-29T00:00:00Z","external_id":{"isi":["000895984800009"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ElKo"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"isi":1,"intvolume":"      2022","publisher":"Institute of Electrical and Electronics Engineers","year":"2022","page":"45-52","date_updated":"2023-08-04T09:06:02Z","publication":"42nd International Conference on Distributed Computing Systems Workshops","conference":{"name":"ICDCSW: International Conference on Distributed Computing Systems Workshop","end_date":"2022-07-10","location":"Bologna, Italy","start_date":"2022-07-10"},"oa_version":"None","month":"11","day":"29","citation":{"chicago":"De la Rocha, Alfonso, Eleftherios Kokoris Kogias, Jorge M. Soares, and Marko Vukolic. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” In <i>42nd International Conference on Distributed Computing Systems Workshops</i>, 2022:45–52. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">https://doi.org/10.1109/icdcsw56584.2022.00018</a>.","mla":"De la Rocha, Alfonso, et al. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” <i>42nd International Conference on Distributed Computing Systems Workshops</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52, doi:<a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">10.1109/icdcsw56584.2022.00018</a>.","ama":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. Hierarchical consensus: A horizontal scaling framework for blockchains. In: <i>42nd International Conference on Distributed Computing Systems Workshops</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:45-52. doi:<a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">10.1109/icdcsw56584.2022.00018</a>","ista":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. 2022. Hierarchical consensus: A horizontal scaling framework for blockchains. 42nd International Conference on Distributed Computing Systems Workshops. ICDCSW: International Conference on Distributed Computing Systems Workshop vol. 2022, 45–52.","short":"A. De la Rocha, E. Kokoris Kogias, J.M. Soares, M. Vukolic, in:, 42nd International Conference on Distributed Computing Systems Workshops, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52.","ieee":"A. De la Rocha, E. Kokoris Kogias, J. M. Soares, and M. Vukolic, “Hierarchical consensus: A horizontal scaling framework for blockchains,” in <i>42nd International Conference on Distributed Computing Systems Workshops</i>, Bologna, Italy, 2022, vol. 2022, pp. 45–52.","apa":"De la Rocha, A., Kokoris Kogias, E., Soares, J. M., &#38; Vukolic, M. (2022). Hierarchical consensus: A horizontal scaling framework for blockchains. In <i>42nd International Conference on Distributed Computing Systems Workshops</i> (Vol. 2022, pp. 45–52). Bologna, Italy: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icdcsw56584.2022.00018\">https://doi.org/10.1109/icdcsw56584.2022.00018</a>"},"article_processing_charge":"No","volume":2022,"doi":"10.1109/icdcsw56584.2022.00018","abstract":[{"text":"We present the Filecoin Hierarchical Consensus framework, which aims to overcome the throughput challenges of blockchain consensus by horizontally scaling the network. Unlike traditional sharding designs, based on partitioning the state of the network, our solution centers on the concept of subnets -which are organized hierarchically- and can be spawned on-demand to manage new state. Child sub nets are firewalled from parent subnets, have their own specific policies, and run a different consensus algorithm, increasing the network capacity and enabling new applications. Moreover, they benefit from the security of parent subnets by periodically checkpointing state. In this paper, we introduce the overall system architecture, our detailed designs for cross-net transaction handling, and the open questions that we are still exploring.","lang":"eng"}],"_id":"12160","author":[{"first_name":"Alfonso","full_name":"De la Rocha, Alfonso","last_name":"De la Rocha"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Soares, Jorge M.","last_name":"Soares","first_name":"Jorge M."},{"last_name":"Vukolic","full_name":"Vukolic, Marko","first_name":"Marko"}],"title":"Hierarchical consensus: A horizontal scaling framework for blockchains","publication_status":"published","status":"public","publication_identifier":{"eissn":["2332-5666"],"eisbn":["9781665488792"]}},{"date_updated":"2023-08-04T09:06:34Z","publication":"26th International Conference on Pattern Recognition","page":"2128-2134","oa":1,"year":"2022","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.05181","open_access":"1"}],"intvolume":"      2022","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ChLa"}],"scopus_import":"1","date_created":"2023-01-12T12:09:38Z","date_published":"2022-11-29T00:00:00Z","external_id":{"arxiv":["2206.05181"],"isi":["000897707602018"]},"publication_identifier":{"eissn":["2831-7475"],"eisbn":["9781665490627"]},"publication_status":"published","status":"public","_id":"12161","author":[{"first_name":"Paulina","last_name":"Tomaszewska","full_name":"Tomaszewska, Paulina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"title":"Lightweight conditional model extrapolation for streaming data under class-prior shift","doi":"10.1109/icpr56361.2022.9956195","abstract":[{"text":"We introduce LIMES, a new method for learning with non-stationary streaming data, inspired by the recent success of meta-learning. The main idea is not to attempt to learn a single classifier that would have to work well across all occurring data distributions, nor many separate classifiers, but to exploit a hybrid strategy: we learn a single set of model parameters from which a specific classifier for any specific data distribution is derived via classifier adaptation. Assuming a multiclass classification setting with class-prior shift, the adaptation step can be performed analytically with only the classifier’s bias terms being affected. Another contribution of our work is an extrapolation step that predicts suitable adaptation parameters for future time steps based on the previous data. In combination, we obtain a lightweight procedure for learning from streaming data with varying class distribution that adds no trainable parameters and almost no memory or computational overhead compared to training a single model. Experiments on a set of exemplary tasks using Twitter data show that LIMES achieves higher accuracy than alternative approaches, especially with respect to the relevant real-world metric of lowest within-day accuracy.","lang":"eng"}],"arxiv":1,"volume":2022,"article_processing_charge":"No","month":"11","day":"29","citation":{"ieee":"P. Tomaszewska and C. Lampert, “Lightweight conditional model extrapolation for streaming data under class-prior shift,” in <i>26th International Conference on Pattern Recognition</i>, Montreal, Canada, 2022, vol. 2022, pp. 2128–2134.","apa":"Tomaszewska, P., &#38; Lampert, C. (2022). Lightweight conditional model extrapolation for streaming data under class-prior shift. In <i>26th International Conference on Pattern Recognition</i> (Vol. 2022, pp. 2128–2134). Montreal, Canada: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">https://doi.org/10.1109/icpr56361.2022.9956195</a>","short":"P. Tomaszewska, C. Lampert, in:, 26th International Conference on Pattern Recognition, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–2134.","ista":"Tomaszewska P, Lampert C. 2022. Lightweight conditional model extrapolation for streaming data under class-prior shift. 26th International Conference on Pattern Recognition. ICPR: International Conference on Pattern Recognition vol. 2022, 2128–2134.","ama":"Tomaszewska P, Lampert C. Lightweight conditional model extrapolation for streaming data under class-prior shift. In: <i>26th International Conference on Pattern Recognition</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2128-2134. doi:<a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">10.1109/icpr56361.2022.9956195</a>","mla":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” <i>26th International Conference on Pattern Recognition</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–34, doi:<a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">10.1109/icpr56361.2022.9956195</a>.","chicago":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” In <i>26th International Conference on Pattern Recognition</i>, 2022:2128–34. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/icpr56361.2022.9956195\">https://doi.org/10.1109/icpr56361.2022.9956195</a>."},"conference":{"name":"ICPR: International Conference on Pattern Recognition","end_date":"2022-08-25","location":"Montreal, Canada","start_date":"2022-08-21"},"oa_version":"Preprint"},{"article_processing_charge":"No","volume":32,"oa_version":"Published Version","day":"28","citation":{"mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>.","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” <i>Molecular Ecology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>.","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” <i>Molecular Ecology</i>, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","apa":"Westram, A. M., &#38; Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16779\">https://doi.org/10.1111/mec.16779</a>","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. <i>Molecular Ecology</i>. 2022;32(1):26-29. doi:<a href=\"https://doi.org/10.1111/mec.16779\">10.1111/mec.16779</a>"},"month":"11","publication_status":"published","status":"public","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"issue":"1","abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"doi":"10.1111/mec.16779","author":[{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","_id":"12166","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"intvolume":"        32","publisher":"Wiley","date_published":"2022-11-28T00:00:00Z","external_id":{"isi":["000892168800001"]},"scopus_import":"1","date_created":"2023-01-12T12:10:28Z","department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"letter_note","page":"26-29","publication":"Molecular Ecology","date_updated":"2023-08-04T09:09:15Z","year":"2022","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"oa":1},{"conference":{"location":"Grenada","start_date":"2022-05-02","end_date":"2022-05-06","name":"FC: Financial Cryptography and Data Security"},"oa_version":"Preprint","month":"10","day":"22","citation":{"ista":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. 2022. Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13411, 358–373.","ama":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. In: <i>Financial Cryptography and Data Security</i>. Vol 13411. Springer Nature; 2022:358-373. doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">10.1007/978-3-031-18283-9_17</a>","short":"G. Avarikioti, K.Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, M.X. Yeo, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 358–373.","ieee":"G. Avarikioti, K. Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, and M. X. Yeo, “Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks,” in <i>Financial Cryptography and Data Security</i>, Grenada, 2022, vol. 13411, pp. 358–373.","apa":"Avarikioti, G., Pietrzak, K. Z., Salem, I., Schmid, S., Tiwari, S., &#38; Yeo, M. X. (2022). Hide &#38; Seek: Privacy-preserving rebalancing on payment channel networks. In <i>Financial Cryptography and Data Security</i> (Vol. 13411, pp. 358–373). Grenada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">https://doi.org/10.1007/978-3-031-18283-9_17</a>","mla":"Avarikioti, Georgia, et al. “Hide &#38; Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” <i>Financial Cryptography and Data Security</i>, vol. 13411, Springer Nature, 2022, pp. 358–73, doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">10.1007/978-3-031-18283-9_17</a>.","chicago":"Avarikioti, Georgia, Krzysztof Z Pietrzak, Iosif Salem, Stefan Schmid, Samarth Tiwari, and Michelle X Yeo. “Hide &#38; Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” In <i>Financial Cryptography and Data Security</i>, 13411:358–73. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_17\">https://doi.org/10.1007/978-3-031-18283-9_17</a>."},"volume":13411,"article_processing_charge":"No","arxiv":1,"doi":"10.1007/978-3-031-18283-9_17","abstract":[{"text":"Payment channels effectively move the transaction load off-chain thereby successfully addressing the inherent scalability problem most cryptocurrencies face. A major drawback of payment channels is the need to “top up” funds on-chain when a channel is depleted. Rebalancing was proposed to alleviate this issue, where parties with depleting channels move their funds along a cycle to replenish their channels off-chain. Protocols for rebalancing so far either introduce local solutions or compromise privacy.\r\nIn this work, we present an opt-in rebalancing protocol that is both private and globally optimal, meaning our protocol maximizes the total amount of rebalanced funds. We study rebalancing from the framework of linear programming. To obtain full privacy guarantees, we leverage multi-party computation in solving the linear program, which is executed by selected participants to maintain efficiency. Finally, we efficiently decompose the rebalancing solution into incentive-compatible cycles which conserve user balances when executed atomically.","lang":"eng"}],"_id":"12167","author":[{"full_name":"Avarikioti, Georgia","last_name":"Avarikioti","id":"c20482a0-3b89-11eb-9862-88cf6404b88c","first_name":"Georgia"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Iosif","last_name":"Salem","full_name":"Salem, Iosif"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"},{"last_name":"Tiwari","full_name":"Tiwari, Samarth","first_name":"Samarth"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"title":"Hide & Seek: Privacy-preserving rebalancing on payment channel networks","status":"public","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031182839"],"issn":["0302-9743"],"isbn":["9783031182822"]},"scopus_import":"1","date_created":"2023-01-12T12:10:38Z","external_id":{"arxiv":["2110.08848"]},"date_published":"2022-10-22T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrPi"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"intvolume":"     13411","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2110.08848","open_access":"1"}],"publisher":"Springer Nature","year":"2022","alternative_title":["LNCS"],"oa":1,"page":"358-373","date_updated":"2023-09-05T15:10:57Z","publication":"Financial Cryptography and Data Security"},{"month":"10","day":"22","citation":{"ista":"Cohen S, Gelashvili R, Kokoris Kogias E, Li Z, Malkhi D, Sonnino A, Spiegelman A. 2022. Be aware of your leaders. International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13411, 279–295.","short":"S. Cohen, R. Gelashvili, E. Kokoris Kogias, Z. Li, D. Malkhi, A. Sonnino, A. Spiegelman, in:, International Conference on Financial Cryptography and Data Security, Springer Nature, 2022, pp. 279–295.","ama":"Cohen S, Gelashvili R, Kokoris Kogias E, et al. Be aware of your leaders. In: <i>International Conference on Financial Cryptography and Data Security</i>. Vol 13411. Springer Nature; 2022:279-295. doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_13\">10.1007/978-3-031-18283-9_13</a>","apa":"Cohen, S., Gelashvili, R., Kokoris Kogias, E., Li, Z., Malkhi, D., Sonnino, A., &#38; Spiegelman, A. (2022). Be aware of your leaders. In <i>International Conference on Financial Cryptography and Data Security</i> (Vol. 13411, pp. 279–295). Grenada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_13\">https://doi.org/10.1007/978-3-031-18283-9_13</a>","ieee":"S. Cohen <i>et al.</i>, “Be aware of your leaders,” in <i>International Conference on Financial Cryptography and Data Security</i>, Grenada, 2022, vol. 13411, pp. 279–295.","chicago":"Cohen, Shir, Rati Gelashvili, Eleftherios Kokoris Kogias, Zekun Li, Dahlia Malkhi, Alberto Sonnino, and Alexander Spiegelman. “Be Aware of Your Leaders.” In <i>International Conference on Financial Cryptography and Data Security</i>, 13411:279–95. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-18283-9_13\">https://doi.org/10.1007/978-3-031-18283-9_13</a>.","mla":"Cohen, Shir, et al. “Be Aware of Your Leaders.” <i>International Conference on Financial Cryptography and Data Security</i>, vol. 13411, Springer Nature, 2022, pp. 279–95, doi:<a href=\"https://doi.org/10.1007/978-3-031-18283-9_13\">10.1007/978-3-031-18283-9_13</a>."},"conference":{"end_date":"2022-05-06","start_date":"2022-05-02","location":"Grenada","name":"FC: Financial Cryptography and Data Security"},"oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":13411,"_id":"12168","author":[{"full_name":"Cohen, Shir","last_name":"Cohen","first_name":"Shir"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Zekun","last_name":"Li","full_name":"Li, Zekun"},{"last_name":"Malkhi","full_name":"Malkhi, Dahlia","first_name":"Dahlia"},{"first_name":"Alberto","last_name":"Sonnino","full_name":"Sonnino, Alberto"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"title":"Be aware of your leaders","doi":"10.1007/978-3-031-18283-9_13","abstract":[{"lang":"eng","text":"Advances in blockchains have influenced the State-Machine-Replication (SMR) world and many state-of-the-art blockchain-SMR solutions are based on two pillars: Chaining and Leader-rotation. A predetermined round-robin mechanism used for Leader-rotation, however, has an undesirable behavior: crashed parties become designated leaders infinitely often, slowing down overall system performance. In this paper, we provide a new Leader-Aware SMR framework that, among other desirable properties, formalizes a Leader-utilization requirement that bounds the number of rounds whose leaders are faulty in crash-only executions.\r\nWe introduce Carousel, a novel, reputation-based Leader-rotation solution to achieve Leader-Aware SMR. The challenge in adaptive Leader-rotation is that it cannot rely on consensus to determine a leader, since consensus itself needs a leader. Carousel uses the available on-chain information to determine a leader locally and achieves Liveness despite this difficulty. A HotStuff implementation fitted with Carousel demonstrates drastic performance improvements: it increases throughput over 2x in faultless settings and provided a 20x throughput increase and 5x latency reduction in the presence of faults."}],"publication_identifier":{"eisbn":["9783031182839"],"issn":["0302-9743"],"isbn":["9783031182822"],"eissn":["1611-3349"]},"publication_status":"published","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ElKo"}],"scopus_import":"1","date_created":"2023-01-12T12:10:49Z","external_id":{"arxiv":["2110.00960"]},"date_published":"2022-10-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2110.00960"}],"intvolume":"     13411","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","oa":1,"year":"2022","alternative_title":["LNCS"],"date_updated":"2023-09-05T15:11:35Z","publication":"International Conference on Financial Cryptography and Data Security","page":"279-295"},{"month":"10","day":"21","citation":{"mla":"Meggendorfer, Tobias. “PET – A Partial Exploration Tool for Probabilistic Verification.” <i>20th International Symposium on Automated Technology for Verification and Analysis</i>, vol. 13505, Springer Nature, 2022, pp. 320–26, doi:<a href=\"https://doi.org/10.1007/978-3-031-19992-9_20\">10.1007/978-3-031-19992-9_20</a>.","chicago":"Meggendorfer, Tobias. “PET – A Partial Exploration Tool for Probabilistic Verification.” In <i>20th International Symposium on Automated Technology for Verification and Analysis</i>, 13505:320–26. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-19992-9_20\">https://doi.org/10.1007/978-3-031-19992-9_20</a>.","ama":"Meggendorfer T. PET – A partial exploration tool for probabilistic verification. In: <i>20th International Symposium on Automated Technology for Verification and Analysis</i>. Vol 13505. Springer Nature; 2022:320-326. doi:<a href=\"https://doi.org/10.1007/978-3-031-19992-9_20\">10.1007/978-3-031-19992-9_20</a>","ista":"Meggendorfer T. 2022. PET – A partial exploration tool for probabilistic verification. 20th International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 13505, 320–326.","short":"T. Meggendorfer, in:, 20th International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2022, pp. 320–326.","ieee":"T. Meggendorfer, “PET – A partial exploration tool for probabilistic verification,” in <i>20th International Symposium on Automated Technology for Verification and Analysis</i>, Virtual, 2022, vol. 13505, pp. 320–326.","apa":"Meggendorfer, T. (2022). PET – A partial exploration tool for probabilistic verification. In <i>20th International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 13505, pp. 320–326). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-19992-9_20\">https://doi.org/10.1007/978-3-031-19992-9_20</a>"},"conference":{"end_date":"2022-10-28","location":"Virtual","start_date":"2022-10-25","name":"ATVA: Automated Technology for Verification and Analysis"},"oa_version":"None","article_processing_charge":"No","volume":13505,"_id":"12170","author":[{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","orcid":"0000-0002-1712-2165"}],"title":"PET – A partial exploration tool for probabilistic verification","doi":"10.1007/978-3-031-19992-9_20","abstract":[{"lang":"eng","text":"We present PET, a specialized and highly optimized framework for partial exploration on probabilistic systems. Over the last decade, several significant advances in the analysis of Markov decision processes employed partial exploration. In a nutshell, this idea allows to focus computation on specific parts of the system, guided by heuristics, while maintaining correctness. In particular, only relevant parts of the system are constructed on demand, which in turn potentially allows to omit constructing large parts of the system. Depending on the model, this leads to dramatic speed-ups, in extreme cases even up to an arbitrary factor. PET unifies several previous implementations and provides a flexible framework to easily implement partial exploration for many further problems. Our experimental evaluation shows significant improvements compared to the previous implementations while vastly reducing the overhead required to add support for additional properties."}],"publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031199929"],"issn":["0302-9743"],"isbn":["9783031199912"]},"publication_status":"published","acknowledgement":"We thank Pranav Ashok and Maximilian Weininger for their contributions to spiritual predecessors of PET as well as motivating the initial development of this tool.","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"scopus_import":"1","date_created":"2023-01-12T12:11:07Z","date_published":"2022-10-21T00:00:00Z","intvolume":"     13505","publisher":"Springer Nature","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"year":"2022","date_updated":"2023-09-05T15:11:51Z","publication":"20th International Symposium on Automated Technology for Verification and Analysis","page":"320-326"}]