[{"external_id":{"pmid":["38740055"]},"language":[{"iso":"eng"}],"quality_controlled":"1","OA_type":"green","citation":{"chicago":"Bravo, Jack Peter Kelly, Delisa A. Ramos, Rodrigo Fregoso Ocampo, Caiden Ingram, and David W. Taylor. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07515-9.","short":"J.P.K. Bravo, D.A. Ramos, R. Fregoso Ocampo, C. Ingram, D.W. Taylor, Nature 630 (2024) 961–967.","mla":"Bravo, Jack Peter Kelly, et al. “Plasmid Targeting and Destruction by the DdmDE Bacterial Defence System.” Nature, vol. 630, no. 8018, Springer Nature, 2024, pp. 961–67, doi:10.1038/s41586-024-07515-9.","ista":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. 2024. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 630(8018), 961–967.","apa":"Bravo, J. P. K., Ramos, D. A., Fregoso Ocampo, R., Ingram, C., & Taylor, D. W. (2024). Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07515-9","ieee":"J. P. K. Bravo, D. A. Ramos, R. Fregoso Ocampo, C. Ingram, and D. W. Taylor, “Plasmid targeting and destruction by the DdmDE bacterial defence system,” Nature, vol. 630, no. 8018. Springer Nature, pp. 961–967, 2024.","ama":"Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW. Plasmid targeting and destruction by the DdmDE bacterial defence system. Nature. 2024;630(8018):961-967. doi:10.1038/s41586-024-07515-9"},"corr_author":"1","year":"2024","date_published":"2024-06-27T00:00:00Z","status":"public","publication_status":"published","author":[{"last_name":"Bravo","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753"},{"full_name":"Ramos, Delisa A.","first_name":"Delisa A.","last_name":"Ramos"},{"first_name":"Rodrigo","full_name":"Fregoso Ocampo, Rodrigo","last_name":"Fregoso Ocampo"},{"first_name":"Caiden","full_name":"Ingram, Caiden","last_name":"Ingram"},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"}],"intvolume":" 630","issue":"8018","abstract":[{"text":"Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation1. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET)2. Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE–guide–target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.\r\n\r\n","lang":"eng"}],"OA_place":"repository","oa":1,"publisher":"Springer Nature","title":"Plasmid targeting and destruction by the DdmDE bacterial defence system","publication":"Nature","date_created":"2024-08-19T09:41:18Z","acknowledgement":"We thank K. Kiernan, G. Hibshman and I. Strohkendl for insightful discussions and comments on the manuscript, and R. Lin for assistance with the ATPase assay. Data were collected at the Sauer Structural Biology Laboratory at the University of Texas at Austin. This work was supported in part by the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) R35GM138348 (to D.W.T.) and Welch Foundation research grant F-1938 (to D.W.T.).","date_updated":"2025-06-24T12:47:21Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11649018/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41586-024-07515-9","day":"27","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"17442","volume":630,"article_type":"original","department":[{"_id":"JaBr"}],"page":"961-967","scopus_import":"1","article_processing_charge":"No","type":"journal_article","month":"06","oa_version":"Submitted Version"},{"corr_author":"1","citation":{"chicago":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” Journal of the London Mathematical Society. Wiley, 2024. https://doi.org/10.1112/jlms.12975.","short":"V. Wang, Journal of the London Mathematical Society 110 (2024).","mla":"Wang, Victor. “Special Cubic Zeros and the Dual Variety.” Journal of the London Mathematical Society, vol. 110, no. 3, e12975, Wiley, 2024, doi:10.1112/jlms.12975.","ama":"Wang V. Special cubic zeros and the dual variety. Journal of the London Mathematical Society. 2024;110(3). doi:10.1112/jlms.12975","ieee":"V. Wang, “Special cubic zeros and the dual variety,” Journal of the London Mathematical Society, vol. 110, no. 3. Wiley, 2024.","apa":"Wang, V. (2024). Special cubic zeros and the dual variety. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12975","ista":"Wang V. 2024. Special cubic zeros and the dual variety. Journal of the London Mathematical Society. 110(3), e12975."},"file_date_updated":"2024-08-21T06:36:40Z","year":"2024","date_published":"2024-08-14T00:00:00Z","status":"public","publication_status":"published","external_id":{"arxiv":["2108.03396"],"isi":["001310529600001"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-0704-7026","full_name":"Wang, Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","first_name":"Victor","last_name":"Wang"}],"intvolume":" 110","license":"https://creativecommons.org/licenses/by/4.0/","issue":"3","has_accepted_license":"1","publisher":"Wiley","ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"90437e19f57520b4d66ca62408f6c81e","creator":"dernst","file_name":"2024_JourLondonMathSoc_Wang.pdf","file_size":438751,"success":1,"file_id":"17454","date_created":"2024-08-21T06:36:40Z","date_updated":"2024-08-21T06:36:40Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Let F be a diagonal cubic form over Z in six variables. From the dual variety in the delta method of Duke–Friedlander–Iwaniec and Heath‐Brown, we unconditionally extract a weighted count of certain special integral zeros of F in regions of diameter X - 8 . Heath‐Brown did the same in four variables, but our analysis differs and captures some novel features. We also put forth an axiomatic framework for more general F."}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T08:58:20Z","arxiv":1,"title":"Special cubic zeros and the dual variety","publication":"Journal of the London Mathematical Society","date_created":"2024-08-20T08:41:40Z","acknowledgement":"This paper is an important component of the thesis work described in [25]; many of my acknowledgements there apply here as well. I also thank my advisor, Peter Sarnak, for many helpful suggestions and questions on the exposition, references, assumptions, and scope of (various drafts of) the present work. I am also grateful to Trevor Wooley for providing some helpful general comments on special subvarieties and the reference [24]. I thank Tim Browning for inspiring part of the current title of the paper. Finally, thanks are due to the referee for providing many helpful suggestions. This work was partially supported by NSF grant DMS-1802211, and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant AgreementNo. 101034413.","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"_id":"17447","volume":110,"doi":"10.1112/jlms.12975","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"14","publication_identifier":{"issn":["0024-6107"],"eissn":["1469-7750"]},"article_number":"e12975","article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"TiBr"}],"scopus_import":"1","isi":1,"ddc":["512"],"type":"journal_article","month":"08","oa_version":"Published Version"},{"quality_controlled":"1","external_id":{"arxiv":["2207.11758"]},"language":[{"iso":"eng"}],"extern":"1","status":"public","publication_status":"published","year":"2024","date_published":"2024-02-06T00:00:00Z","file_date_updated":"2024-08-21T06:46:56Z","citation":{"mla":"Pandey, Mayank, et al. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” Algebra & Number Theory, vol. 18, no. 2, Mathematical Sciences Publishers, 2024, pp. 389–408, doi:10.2140/ant.2024.18.389.","ista":"Pandey M, Wang V, Xu MW. 2024. Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. 18(2), 389–408.","ama":"Pandey M, Wang V, Xu MW. Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. 2024;18(2):389-408. doi:10.2140/ant.2024.18.389","apa":"Pandey, M., Wang, V., & Xu, M. W. (2024). Partial sums of typical multiplicative functions over short moving intervals. Algebra & Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2024.18.389","ieee":"M. Pandey, V. Wang, and M. W. Xu, “Partial sums of typical multiplicative functions over short moving intervals,” Algebra & Number Theory, vol. 18, no. 2. Mathematical Sciences Publishers, pp. 389–408, 2024.","chicago":"Pandey, Mayank, Victor Wang, and Max Wenqiang Xu. “Partial Sums of Typical Multiplicative Functions over Short Moving Intervals.” Algebra & Number Theory. Mathematical Sciences Publishers, 2024. https://doi.org/10.2140/ant.2024.18.389.","short":"M. Pandey, V. Wang, M.W. Xu, Algebra & Number Theory 18 (2024) 389–408."},"has_accepted_license":"1","issue":"2","intvolume":" 18","author":[{"full_name":"Pandey, Mayank","first_name":"Mayank","last_name":"Pandey"},{"id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","orcid":"0000-0002-0704-7026","full_name":"Wang, Victor","first_name":"Victor","last_name":"Wang"},{"last_name":"Xu","full_name":"Xu, Max Wenqiang","first_name":"Max Wenqiang"}],"oa":1,"file":[{"date_updated":"2024-08-21T06:46:56Z","access_level":"open_access","success":1,"date_created":"2024-08-21T06:46:56Z","file_id":"17455","creator":"dernst","file_size":1401725,"file_name":"2024_AlgebraNumberTheory_Pandey.pdf","relation":"main_file","content_type":"application/pdf","checksum":"1e3467a14de754bf8d3bff03a015e1ce"}],"abstract":[{"lang":"eng","text":"We prove that the $k$-th positive integer moment of partial sums of Steinhaus random multiplicative functions over the interval $(x, x+H]$ matches the corresponding Gaussian moment, as long as $H\\ll x/(\\log x)^{2k^2+2+o(1)}$ and $H$ tends to infinity with $x$. We show that properly normalized partial sums of typical multiplicative functions arising from realizations of random multiplicative functions have Gaussian limiting distribution in short moving intervals $(x, x+H]$ with $H\\ll X/(\\log X)^{W(X)}$ tending to infinity with $X$, where $x$ is uniformly chosen from $\\{1,2,\\dots, X\\}$, and $W(X)$ tends to infinity with $X$ arbitrarily slowly. This makes some initial progress on a recent question of Harper."}],"publisher":"Mathematical Sciences Publishers","acknowledgement":"We thank Andrew Granville and the anonymous referee for many detailed comments that led us to significantly improve the results and presentation of our work. We thank and Adam Harper for helpful discussions and useful comments and corrections on earlier versions. We also thank Yuqiu Fu, Larry Guth, Kannan Soundararajan, Katharine Woo, and Liyang Yang for helpful discussions. Finally, we thank Peter Sarnak for introducing us (the authors) to each other during the “50 Years of Number Theory and Random Matrix Theory” Conference at IAS and making the collaboration possible. \r\nOpen Access made possible by participating institutions via Subscribe to Open.","date_created":"2024-08-20T08:48:26Z","publication":"Algebra & Number Theory","title":"Partial sums of typical multiplicative functions over short moving intervals","date_updated":"2024-08-21T06:58:43Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.11758"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1937-0652"],"eissn":["1944-7833"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"06","doi":"10.2140/ant.2024.18.389","volume":18,"_id":"17449","article_type":"original","ddc":["510"],"scopus_import":"1","page":"389-408","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","month":"02","type":"journal_article"},{"publication_identifier":{"eissn":["2332-7812"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1212/NXI.0000000000200284","day":"01","_id":"17457","project":[{"name":"LGI1 antibody-induced pathophysiology in synapses","grant_number":"I04638","_id":"05970B30-7A3F-11EA-A408-12923DDC885E"}],"volume":11,"article_type":"original","scopus_import":"1","isi":1,"ddc":["570"],"department":[{"_id":"RySh"}],"page":"e200284","article_processing_charge":"Yes","oa_version":"Published Version","DOAJ_listed":"1","type":"journal_article","month":"09","quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"external_id":{"isi":["001291908600001"],"pmid":["39141878"]},"language":[{"iso":"eng"}],"date_published":"2024-09-01T00:00:00Z","year":"2024","status":"public","publication_status":"published","OA_type":"gold","citation":{"mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology, Neuroimmunology and Neuroinflammation, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:10.1212/NXI.0000000000200284.","ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. 11(5), e200284.","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. Wolters Kluwer. https://doi.org/10.1212/NXI.0000000000200284","ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology and Neuroinflammation. 2024;11(5):e200284. doi:10.1212/NXI.0000000000200284","ieee":"A. Ritzau-Jost et al., “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” Neurology, Neuroimmunology and Neuroinflammation, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology, Neuroimmunology and Neuroinflammation. Wolters Kluwer, 2024. https://doi.org/10.1212/NXI.0000000000200284.","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology and Neuroinflammation 11 (2024) e200284."},"file_date_updated":"2025-01-09T13:42:42Z","has_accepted_license":"1","intvolume":" 11","issue":"5","author":[{"full_name":"Ritzau-Jost, Andreas","first_name":"Andreas","last_name":"Ritzau-Jost"},{"first_name":"Felix","full_name":"Gsell, Felix","last_name":"Gsell"},{"full_name":"Sell, Josefine","first_name":"Josefine","last_name":"Sell"},{"last_name":"Sachs","full_name":"Sachs, Stefan","first_name":"Stefan"},{"last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"full_name":"Kirmann, Toni","first_name":"Toni","last_name":"Kirmann"},{"last_name":"Maaß","first_name":"Sebastian","full_name":"Maaß, Sebastian"},{"full_name":"Irani, Sarosh R.","first_name":"Sarosh R.","last_name":"Irani"},{"first_name":"Christian","full_name":"Werner, Christian","last_name":"Werner"},{"last_name":"Geis","full_name":"Geis, Christian","first_name":"Christian"},{"first_name":"Markus","full_name":"Sauer, Markus","last_name":"Sauer"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto"},{"first_name":"Stefan","full_name":"Hallermann, Stefan","last_name":"Hallermann"}],"oa":1,"file":[{"file_size":855818,"file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","creator":"dernst","checksum":"1e6d1230e0387f72752e3268f5330c9e","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T13:42:42Z","success":1,"file_id":"18815","date_created":"2025-01-09T13:42:42Z"}],"OA_place":"publisher","abstract":[{"text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening.","lang":"eng"}],"publisher":"Wolters Kluwer","date_created":"2024-08-25T22:01:07Z","acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2023.10.04.560631"}]},"publication":"Neurology, Neuroimmunology and Neuroinflammation","date_updated":"2025-09-08T08:59:37Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"type":"journal_article","month":"08","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"BeVi"}],"scopus_import":"1","isi":1,"ddc":["599"],"article_number":"dev202891","article_type":"original","_id":"17458","volume":151,"day":"14","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1242/dev.202891","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"pmid":1,"date_updated":"2025-09-08T08:58:58Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Compensation of gene dosage on the mammalian X","publication":"Development","date_created":"2024-08-25T22:01:07Z","acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","publisher":"The Company of Biologists","abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"file":[{"success":1,"file_id":"17464","date_created":"2024-08-28T10:32:16Z","access_level":"open_access","date_updated":"2024-08-28T10:32:16Z","relation":"main_file","content_type":"application/pdf","checksum":"5e428bda0440d3f957c694b315a8f2a9","creator":"cchlebak","file_size":2085135,"file_name":"2024_Development_Cecalev.pdf"}],"oa":1,"author":[{"full_name":"Cecalev, Daniela","first_name":"Daniela","last_name":"Cecalev"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"last_name":"Galupa","first_name":"Rafael","full_name":"Galupa, Rafael"}],"intvolume":" 151","issue":"15","has_accepted_license":"1","citation":{"apa":"Cecalev, D., Vicoso, B., & Galupa, R. (2024). Compensation of gene dosage on the mammalian X. Development. The Company of Biologists. https://doi.org/10.1242/dev.202891","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development. 2024;151(15). doi:10.1242/dev.202891","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” Development, vol. 151, no. 15. The Company of Biologists, 2024.","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” Development, vol. 151, no. 15, dev202891, The Company of Biologists, 2024, doi:10.1242/dev.202891.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202891."},"file_date_updated":"2024-08-28T10:32:16Z","year":"2024","date_published":"2024-08-14T00:00:00Z","publication_status":"published","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["001292608800003"],"pmid":["39140247"]},"quality_controlled":"1"},{"volume":20,"_id":"17460","project":[{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/s41567-024-02597-8","day":"01","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"article_type":"original","article_processing_charge":"Yes (in subscription journal)","page":"1670-1678","department":[{"_id":"AnSa"},{"_id":"MaLo"}],"isi":1,"ddc":["570"],"scopus_import":"1","month":"10","type":"journal_article","APC_amount":"12348 EUR","oa_version":"Published Version","corr_author":"1","citation":{"short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02597-8.","ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., & Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02597-8","ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” Nature Physics, vol. 20. Springer Nature, pp. 1670–1678, 2024.","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 2024;20:1670-1678. doi:10.1038/s41567-024-02597-8","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:10.1038/s41567-024-02597-8."},"OA_type":"hybrid","file_date_updated":"2025-04-14T06:06:35Z","publication_status":"published","status":"public","date_published":"2024-10-01T00:00:00Z","year":"2024","external_id":{"pmid":["39416851"],"isi":["001289394500005"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","last_name":"Vanhille-Campos"},{"full_name":"Whitley, Kevin D.","first_name":"Kevin D.","last_name":"Whitley"},{"last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp"},{"first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"last_name":"Holden","full_name":"Holden, Séamus","first_name":"Séamus"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"}],"intvolume":" 20","has_accepted_license":"1","publisher":"Springer Nature","ec_funded":1,"abstract":[{"text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments.","lang":"eng"}],"OA_place":"publisher","file":[{"creator":"dernst","file_name":"2024_NaturePhysics_VanhilleCampos.pdf","file_size":8058249,"content_type":"application/pdf","relation":"main_file","checksum":"c4842152e2b90d67f48ea8c9ed7c473b","date_updated":"2025-04-14T06:06:35Z","access_level":"open_access","date_created":"2025-04-14T06:06:35Z","success":1,"file_id":"19556"}],"oa":1,"date_updated":"2025-09-08T09:02:20Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Nature Physics","title":"Self-organization of mortal filaments and its role in bacterial division ring formation","acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","date_created":"2024-08-25T22:01:08Z"},{"OA_type":"hybrid","citation":{"ista":"Cremer S, Pull C. 2024. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 40(9), 780–787.","apa":"Cremer, S., & Pull, C. (2024). Unconditional versus condition-dependent social immunity. Trends in Parasitology. Elsevier. https://doi.org/10.1016/j.pt.2024.07.014","ama":"Cremer S, Pull C. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 2024;40(9):780-787. doi:10.1016/j.pt.2024.07.014","ieee":"S. Cremer and C. Pull, “Unconditional versus condition-dependent social immunity,” Trends in Parasitology, vol. 40, no. 9. Elsevier, pp. 780–787, 2024.","mla":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” Trends in Parasitology, vol. 40, no. 9, Elsevier, 2024, pp. 780–87, doi:10.1016/j.pt.2024.07.014.","short":"S. Cremer, C. Pull, Trends in Parasitology 40 (2024) 780–787.","chicago":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” Trends in Parasitology. Elsevier, 2024. https://doi.org/10.1016/j.pt.2024.07.014."},"file_date_updated":"2025-01-09T13:46:05Z","corr_author":"1","date_published":"2024-09-01T00:00:00Z","year":"2024","publication_status":"published","status":"public","language":[{"iso":"eng"}],"external_id":{"pmid":["39152078"],"isi":["001307815700001"]},"quality_controlled":"1","author":[{"last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull"}],"intvolume":" 40","issue":"9","has_accepted_license":"1","publisher":"Elsevier","OA_place":"publisher","file":[{"date_updated":"2025-01-09T13:46:05Z","access_level":"open_access","success":1,"file_id":"18816","date_created":"2025-01-09T13:46:05Z","creator":"dernst","file_name":"2024_TrendsParasitology_Cremer.pdf","file_size":1068464,"relation":"main_file","content_type":"application/pdf","checksum":"362fc994e5df66caf3025b7dc437b647"}],"abstract":[{"text":"Socially living animals can counteract disease through cooperative defences, leading to social immunity that collectively exceeds the sum of individual defences. In superorganismal colonies of social insects with permanent caste separation between reproductive queen(s) and nonreproducing workers, workers are obligate altruists and thus engage in unconditional social immunity, including highly specialised and self-sacrificial hygiene behaviours. Contrastingly, cooperation is facultative in cooperatively breeding families, where all members are reproductively totipotent but offspring transiently forgo reproduction to help their parents rear more siblings. Here, helpers should either express condition-dependent social immunity or disperse to pursue independent reproduction. We advocate inclusive fitness theory as a framework to predict when and how indirect fitness gains may outweigh direct fitness costs, thus favouring conditional social immunity.","lang":"eng"}],"oa":1,"pmid":1,"date_updated":"2025-09-08T09:01:42Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Unconditional versus condition-dependent social immunity","publication":"Trends in Parasitology","date_created":"2024-08-25T22:01:08Z","acknowledgement":"We thank Koos Boomsma and two anonymous reviewers for their constructive comments on the manuscript.","_id":"17461","volume":40,"day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1016/j.pt.2024.07.014","publication_identifier":{"eissn":["1471-5007"],"issn":["1471-4922"]},"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SyCr"}],"page":"780-787","scopus_import":"1","isi":1,"ddc":["570"],"type":"journal_article","month":"09","oa_version":"Published Version"},{"article_type":"original","project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"_id":"17462","volume":22,"doi":"10.1137/23M1603819","day":"01","publication_identifier":{"eissn":["1540-3467"],"issn":["1540-3459"]},"type":"journal_article","month":"09","oa_version":"Preprint","article_processing_charge":"No","department":[{"_id":"JuFi"}],"page":"973-1029","scopus_import":"1","isi":1,"author":[{"first_name":"Nicolas","full_name":"Clozeau, Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","last_name":"Clozeau"},{"last_name":"Wang","first_name":"Lihan","full_name":"Wang, Lihan"}],"intvolume":" 22","issue":"3","citation":{"short":"N. Clozeau, L. Wang, Multiscale Modeling and Simulation 22 (2024) 973–1029.","chicago":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” Multiscale Modeling and Simulation. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/23M1603819.","apa":"Clozeau, N., & Wang, L. (2024). Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/23M1603819","ama":"Clozeau N, Wang L. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 2024;22(3):973-1029. doi:10.1137/23M1603819","ieee":"N. Clozeau and L. Wang, “Artificial boundary conditions for random elliptic systems with correlated coefficient field,” Multiscale Modeling and Simulation, vol. 22, no. 3. Society for Industrial and Applied Mathematics, pp. 973–1029, 2024.","ista":"Clozeau N, Wang L. 2024. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 22(3), 973–1029.","mla":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” Multiscale Modeling and Simulation, vol. 22, no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 973–1029, doi:10.1137/23M1603819."},"OA_type":"green","corr_author":"1","year":"2024","date_published":"2024-09-01T00:00:00Z","status":"public","publication_status":"published","external_id":{"arxiv":["2309.06798"],"isi":["001285416500001"]},"language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T09:01:00Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2309.06798"}],"title":"Artificial boundary conditions for random elliptic systems with correlated coefficient field","publication":"Multiscale Modeling and Simulation","date_created":"2024-08-25T22:01:08Z","acknowledgement":"We would like to thank our affiliations, Institute of Science and Technology Austria and Max Planck Institute for Mathematics in the Sciences, for supporting the authors’ visits to each other, which greatly facilitated this work. We would like to thank Marc Josien and Quinn Winters for assistance in numerical implementation.","publisher":"Society for Industrial and Applied Mathematics","ec_funded":1,"OA_place":"repository","abstract":[{"lang":"eng","text":"We are interested in numerical algorithms for computing the electrical field generated by a charge distribution localized on scale l in an infinite heterogeneous correlated random medium, in a situation where the medium is only known in a box of diameter L >>l around the support of the charge. We show that the algorithm in [J. Lu, F. Otto, and L. Wang, Optimal Artificial Boundary Conditions Based on Second-Order Correctors for Three Dimensional Random Ellilptic Media, preprint, arXiv:2109.01616, 2021], suggesting optimal Dirichlet boundary conditions motivated by the multipole expansion [P. Bella, A. Giunti, and F. Otto, Comm. Partial Differential Equations, 45 (2020), pp. 561–640], still performs well in correlated media. With overwhelming probability, we obtain a convergence rate in terms of l, L, and the size of the correlations for which optimality is supported with numerical simulations. These estimates are provided for ensembles which satisfy a multiscale logarithmic Sobolev inequality, where our main tool is an extension of the semigroup estimates in [N. Clozeau, Stoch. Partial Differ. Equ. Anal. Comput., 11 (2023), pp. 1254–1378]. As part of our strategy, we construct sublinear second-order correctors in this correlated setting, which is of independent interest."}],"oa":1},{"article_processing_charge":"Yes (in subscription journal)","isi":1,"ddc":["570"],"scopus_import":"1","page":"911–920 ","department":[{"_id":"FlPr"}],"oa_version":"Published Version","month":"08","type":"journal_article","volume":632,"_id":"17463","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-024-07813-2","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"22","article_type":"original","publisher":"Springer Nature","oa":1,"file":[{"file_size":16572040,"file_name":"2024_Nature_Pillai.pdf","creator":"dernst","checksum":"39127601621a360ec0edc538627eb211","relation":"main_file","content_type":"application/pdf","date_updated":"2024-09-09T12:01:14Z","access_level":"open_access","date_created":"2024-09-09T12:01:14Z","success":1,"file_id":"18005"}],"abstract":[{"text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry.","lang":"eng"}],"date_updated":"2025-09-08T09:00:16Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","date_created":"2024-08-25T22:01:08Z","publication":"Nature","title":"De novo design of allosterically switchable protein assemblies","status":"public","publication_status":"published","date_published":"2024-08-22T00:00:00Z","year":"2024","file_date_updated":"2024-09-09T12:01:14Z","citation":{"mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” Nature, vol. 632, Springer Nature, 2024, pp. 911–920, doi:10.1038/s41586-024-07813-2.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. Nature. 2024;632:911–920. doi:10.1038/s41586-024-07813-2","ieee":"A. Pillai et al., “De novo design of allosterically switchable protein assemblies,” Nature, vol. 632. Springer Nature, pp. 911–920, 2024.","apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. Nature. Springer Nature. https://doi.org/10.1038/s41586-024-07813-2","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” Nature. Springer Nature, 2024. https://doi.org/10.1038/s41586-024-07813-2.","short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920."},"corr_author":"1","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001300534300019"],"pmid":["39143214"]},"intvolume":" 632","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"last_name":"Pillai","full_name":"Pillai, Arvind","first_name":"Arvind"},{"full_name":"Idris, Abbas","first_name":"Abbas","last_name":"Idris"},{"first_name":"Annika","full_name":"Philomin, Annika","last_name":"Philomin"},{"last_name":"Weidle","first_name":"Connor","full_name":"Weidle, Connor"},{"last_name":"Skotheim","full_name":"Skotheim, Rebecca","first_name":"Rebecca"},{"full_name":"Leung, Philip J.Y.","first_name":"Philip J.Y.","last_name":"Leung"},{"last_name":"Broerman","first_name":"Adam","full_name":"Broerman, Adam"},{"full_name":"Demakis, Cullen","first_name":"Cullen","last_name":"Demakis"},{"last_name":"Borst","full_name":"Borst, Andrew J.","first_name":"Andrew J."},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius"},{"first_name":"David","full_name":"Baker, David","last_name":"Baker"}],"has_accepted_license":"1"},{"type":"journal_article","month":"12","oa_version":"Published Version","department":[{"_id":"KrCh"}],"scopus_import":"1","ddc":["000"],"isi":1,"article_processing_charge":"Yes (in subscription journal)","article_type":"original","article_number":"105214","day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1016/j.ic.2024.105214","publication_identifier":{"issn":["0890-5401"],"eissn":["1090-2651"]},"_id":"17474","volume":301,"title":"Entropic risk for turn-based stochastic games","related_material":{"record":[{"id":"14417","relation":"earlier_version","status":"public"}]},"publication":"Information and Computation","date_created":"2024-09-01T22:01:07Z","acknowledgement":"Krishnendu Chatterjee reports financial support was provided by European Research Council.","date_updated":"2025-09-08T09:10:06Z","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. Furthermore, an approximation algorithm for the optimal value of ERisk is provided."}],"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"f68e0c2f46f9b9c86815406bcf2ee2d4","creator":"dernst","file_name":"2024_InformationComputation_Baier.pdf","file_size":724703,"date_created":"2025-01-09T13:49:03Z","file_id":"18817","success":1,"access_level":"open_access","date_updated":"2025-01-09T13:49:03Z"}],"OA_place":"publisher","oa":1,"publisher":"Elsevier","has_accepted_license":"1","author":[{"full_name":"Baier, Christel","first_name":"Christel","last_name":"Baier"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias"},{"first_name":"Jakob","full_name":"Piribauer, Jakob","last_name":"Piribauer"}],"intvolume":" 301","external_id":{"arxiv":["2307.06611"],"isi":["001301143400001"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” Information and Computation, vol. 301, 105214, Elsevier, 2024, doi:10.1016/j.ic.2024.105214.","ista":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2024. Entropic risk for turn-based stochastic games. Information and Computation. 301, 105214.","ama":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. Information and Computation. 2024;301. doi:10.1016/j.ic.2024.105214","ieee":"C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” Information and Computation, vol. 301. Elsevier, 2024.","apa":"Baier, C., Chatterjee, K., Meggendorfer, T., & Piribauer, J. (2024). Entropic risk for turn-based stochastic games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2024.105214","chicago":"Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” Information and Computation. Elsevier, 2024. https://doi.org/10.1016/j.ic.2024.105214.","short":"C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, Information and Computation 301 (2024)."},"OA_type":"hybrid","corr_author":"1","file_date_updated":"2025-01-09T13:49:03Z","date_published":"2024-12-01T00:00:00Z","year":"2024","publication_status":"published","status":"public"},{"publisher":"Oxford University Press","abstract":[{"lang":"eng","text":"As a discrete analogue of Kac’s celebrated question on ‘hearing the shape of a drum’ and towards a practical\r\ngraph isomorphism test, it is of interest to understand which graphs are determined up to isomorphism by\r\ntheir spectrum (of their adjacency matrix). A striking conjecture in this area, due to van Dam and Haemers,\r\nis that ‘almost all graphs are determined by their spectrum’, meaning that the fraction of unlabelled n-vertex\r\ngraphs which are determined by their spectrum converges to 1 as n → ∞.\r\nIn this paper, we make a step towards this conjecture, showing that there are exponentially many n-vertex\r\ngraphs which are determined by their spectrum. This improves on previous bounds (of shape e\r\nc\r\n√\r\nn\r\n). We also\r\npropose a number of further directions of research.\r\n"}],"file":[{"checksum":"abf200d37ad69e6f2c0750a30296ad97","content_type":"application/pdf","relation":"main_file","file_size":946411,"file_name":"2024_QuJofMath_Koval.pdf","creator":"cchlebak","success":1,"file_id":"17851","date_created":"2024-09-06T12:23:57Z","access_level":"open_access","date_updated":"2024-09-06T12:23:57Z"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"date_updated":"2025-09-08T09:09:41Z","publication":"Quarterly Journal of Mathematics","title":"Exponentially many graphs are determined by their spectrum","acknowledgement":"Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777.","date_created":"2024-09-01T22:01:07Z","citation":{"mla":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” Quarterly Journal of Mathematics, vol. 75, no. 3, Oxford University Press, 2024, pp. 869–99, doi:10.1093/qmath/haae030.","ama":"Koval I, Kwan MA. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 2024;75(3):869-899. doi:10.1093/qmath/haae030","apa":"Koval, I., & Kwan, M. A. (2024). Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haae030","ieee":"I. Koval and M. A. Kwan, “Exponentially many graphs are determined by their spectrum,” Quarterly Journal of Mathematics, vol. 75, no. 3. Oxford University Press, pp. 869–899, 2024.","ista":"Koval I, Kwan MA. 2024. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 75(3), 869–899.","chicago":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” Quarterly Journal of Mathematics. Oxford University Press, 2024. https://doi.org/10.1093/qmath/haae030.","short":"I. Koval, M.A. Kwan, Quarterly Journal of Mathematics 75 (2024) 869–899."},"file_date_updated":"2024-09-06T12:23:57Z","corr_author":"1","publication_status":"published","status":"public","year":"2024","date_published":"2024-06-19T00:00:00Z","external_id":{"isi":["001249741500001"],"arxiv":["2309.09788"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"last_name":"Koval","full_name":"Koval, Illya","id":"2eed1f3b-896a-11ed-bdf8-93c7c4bf159e","first_name":"Illya"},{"last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"}],"issue":"3","intvolume":" 75","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","page":"869-899","department":[{"_id":"MaKw"},{"_id":"VaKa"}],"ddc":["500"],"isi":1,"scopus_import":"1","month":"06","type":"journal_article","oa_version":"Published Version","volume":75,"_id":"17475","project":[{"_id":"bd95085b-d553-11ed-ba76-e55d3349be45","grant_number":"101076777","name":"Randomness and structure in combinatorics"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1093/qmath/haae030","day":"19","publication_identifier":{"issn":["0033-5606"],"eissn":["1464-3847"]},"article_type":"original"},{"quality_controlled":"1","external_id":{"isi":["001299497800001"]},"language":[{"iso":"eng"}],"date_published":"2024-08-23T00:00:00Z","year":"2024","publication_status":"published","status":"public","citation":{"chicago":"Lorenc, Dusan, Ayan Zhumekenov, Osman M. Bakr, and Zhanybek Alpichshev. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” Physical Review Materials. American Physical Society, 2024. https://doi.org/10.1103/PhysRevMaterials.8.085403.","short":"D. Lorenc, A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Physical Review Materials 8 (2024).","mla":"Lorenc, Dusan, et al. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” Physical Review Materials, vol. 8, no. 8, 085403, American Physical Society, 2024, doi:10.1103/PhysRevMaterials.8.085403.","ista":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. 2024. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 8(8), 085403.","apa":"Lorenc, D., Zhumekenov, A., Bakr, O. M., & Alpichshev, Z. (2024). No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.8.085403","ama":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 2024;8(8). doi:10.1103/PhysRevMaterials.8.085403","ieee":"D. Lorenc, A. Zhumekenov, O. M. Bakr, and Z. Alpichshev, “No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry,” Physical Review Materials, vol. 8, no. 8. American Physical Society, 2024."},"corr_author":"1","intvolume":" 8","issue":"8","author":[{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc"},{"last_name":"Zhumekenov","first_name":"Ayan","full_name":"Zhumekenov, Ayan"},{"first_name":"Osman M.","full_name":"Bakr, Osman M.","last_name":"Bakr"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","last_name":"Alpichshev"}],"abstract":[{"lang":"eng","text":"Lead halide perovskites have recently been reported to demonstrate an exceptionally high nonlinear (Kerr) refractive index n2 of up to 10−8cm2/W in CH3NH3PbBr3. Other researchers, however, observe different, substantially more conservative numbers. In order to resolve this disagreement, the nonlinear Kerr index of a bulk sample of lead halide perovskite was measured directly by means of an interferometer. This approach has many advantages as compared to the more standard z-scan technique. In particular, this method allows studying the induced changes to the refractive index in a time-resolved manner, thus enabling to separate the different contributions to 𝑛2. The extracted 𝑛2 values for CsPbBr3 and MAPbBr3 at 𝜆≈1µm are 𝑛2=+2.1×10−14cm2/W and 𝑛2=+6×10−15cm2/W, respectively. Hence, these values are substantially lower than what has been indicated in most of the previous reports, implying the latter one should be regarded with great care."}],"publisher":"American Physical Society","date_created":"2024-09-01T22:01:08Z","acknowledgement":"We gratefully acknowledge the assistance of Prof. John\r\nDudley.","title":"No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry","publication":"Physical Review Materials","date_updated":"2025-09-08T09:06:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2475-9953"]},"day":"23","doi":"10.1103/PhysRevMaterials.8.085403","_id":"17476","volume":8,"article_type":"original","article_number":"085403","scopus_import":"1","isi":1,"department":[{"_id":"ZhAl"}],"article_processing_charge":"No","oa_version":"None","type":"journal_article","month":"08"},{"publisher":"American Physical Society","oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"5d39b7dda67fd7b9a960235f6f38e280","creator":"cchlebak","file_size":3909653,"file_name":"2024_PhysRevX_Hawaldar.pdf","file_id":"17757","date_created":"2024-09-06T09:43:53Z","success":1,"date_updated":"2024-09-06T09:43:53Z","access_level":"open_access"}],"abstract":[{"text":"Trapped-ion systems are a leading platform for quantum information processing, but they are currently limited to 1D and 2D arrays, which imposes restrictions on both their scalability and their range of applications. Here, we propose a path to overcome this limitation by demonstrating that Penning traps can be used to realize remarkably clean bilayer crystals, wherein hundreds of ions self-organize into two well-defined layers. These bilayer crystals are made possible by the inclusion of an anharmonic trapping potential, which is readily implementable with current technology. We study the normal modes of this system and discover salient differences compared to the modes of single-plane crystals. The bilayer geometry and the unique properties of the normal modes open new opportunities—in particular, in quantum sensing and quantum simulation—that are not straightforward in single-plane crystals. Furthermore, we illustrate that it may be possible to extend the ideas presented here to realize multilayer crystals with more than two layers. Our work increases the dimensionality of trapped-ion systems by efficiently utilizing all three spatial dimensions, and it lays the foundation for a new generation of quantum information processing experiments with multilayer 3D crystals of trapped ions.","lang":"eng"}],"arxiv":1,"date_updated":"2025-09-08T09:07:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank M. Miskeen Khan, Jennifer Lilieholm, and Wes Johnson for a careful reading and feedback on the manuscript. We acknowledge discussions with Dan Dubin, John Zaris, and Scott Parker. S. H. acknowledges the support of Kishore Vaigyanik Protsahan Yojana, Department of Science and Technology, Government of India. A. S. acknowledges the support of a C. V. Raman post-doctoral fellowship. A. L. C., A. M. R., and J. J. B. acknowledge funding from the U.S. Department of Energy, Office of Science, NQI Science Research Centers, Quantum Systems Accelerator (QSA), a collaboration between the U.S. Department of Energy, Office of Science and other agencies. A. M. R. acknowledges additional support from VBFF, ARO Grant No. W911NF-24-1-0128, by the NSF Grants No. JILA-PFC PHY-2317149 and No. QLCI-OMA-2016244, and by NIST. J. J. B. acknowledges additional support from the DARPA ONISQ program and AFOSR Grant No. FA9550-201-0019.","date_created":"2024-09-01T22:01:08Z","publication":"Physical Review X","title":"Bilayer crystals of trapped ions for quantum information processing","publication_status":"published","status":"public","date_published":"2024-08-16T00:00:00Z","year":"2024","corr_author":"1","citation":{"mla":"Hawaldar, Samarth, et al. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” Physical Review X, vol. 14, no. 3, 031030, American Physical Society, 2024, doi:10.1103/PhysRevX.14.031030.","ieee":"S. Hawaldar, P. Shahi, A. L. Carter, A. M. Rey, J. J. Bollinger, and A. Shankar, “Bilayer crystals of trapped ions for quantum information processing,” Physical Review X, vol. 14, no. 3. American Physical Society, 2024.","apa":"Hawaldar, S., Shahi, P., Carter, A. L., Rey, A. M., Bollinger, J. J., & Shankar, A. (2024). Bilayer crystals of trapped ions for quantum information processing. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.14.031030","ama":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. Bilayer crystals of trapped ions for quantum information processing. Physical Review X. 2024;14(3). doi:10.1103/PhysRevX.14.031030","ista":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. 2024. Bilayer crystals of trapped ions for quantum information processing. Physical Review X. 14(3), 031030.","chicago":"Hawaldar, Samarth, Prakriti Shahi, Allison L. Carter, Ana Maria Rey, John J. Bollinger, and Athreya Shankar. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” Physical Review X. American Physical Society, 2024. https://doi.org/10.1103/PhysRevX.14.031030.","short":"S. Hawaldar, P. Shahi, A.L. Carter, A.M. Rey, J.J. Bollinger, A. Shankar, Physical Review X 14 (2024)."},"file_date_updated":"2024-09-06T09:43:53Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001293977800002"],"arxiv":["2312.10681"]},"issue":"3","intvolume":" 14","author":[{"id":"221708e1-1ff6-11ee-9fa6-85146607433e","full_name":"Hawaldar, Samarth","orcid":"0000-0002-1965-4309","first_name":"Samarth","last_name":"Hawaldar"},{"last_name":"Shahi","full_name":"Shahi, Prakriti","first_name":"Prakriti"},{"last_name":"Carter","full_name":"Carter, Allison L.","first_name":"Allison L."},{"full_name":"Rey, Ana Maria","first_name":"Ana Maria","last_name":"Rey"},{"last_name":"Bollinger","full_name":"Bollinger, John J.","first_name":"John J."},{"first_name":"Athreya","full_name":"Shankar, Athreya","last_name":"Shankar"}],"has_accepted_license":"1","article_processing_charge":"Yes","ddc":["530"],"isi":1,"scopus_import":"1","department":[{"_id":"JoFi"}],"DOAJ_listed":"1","oa_version":"Published Version","month":"08","type":"journal_article","volume":14,"_id":"17477","publication_identifier":{"eissn":["2160-3308"]},"day":"16","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1103/PhysRevX.14.031030","article_number":"031030","article_type":"original"},{"article_processing_charge":"Yes (in subscription journal)","ddc":["510"],"isi":1,"scopus_import":"1","page":"271-309","department":[{"_id":"RoSe"}],"oa_version":"Published Version","month":"12","type":"journal_article","volume":140,"_id":"17478","publication_identifier":{"eissn":["1618-1913"],"issn":["0073-8301"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1007/s10240-024-00150-0","day":"01","article_type":"original","publisher":"Springer Nature","oa":1,"abstract":[{"text":"We study the Fröhlich polaron model in R3, and prove a lower bound on its ground state energy as a function of the total momentum. The bound is asymptotically sharp at large coupling. In combination with a corresponding upper bound proved earlier (Mitrouskas et al. in Forum Math. Sigma 11:1–52, 2023), it shows that the energy is approximately parabolic below the continuum threshold, and that the polaron’s effective mass (defined as the semi-latus rectum of the\r\nparabola) is given by the celebrated Landau–Pekar formula. In particular, it diverges as α4 for large coupling constant α.","lang":"eng"}],"OA_place":"publisher","file":[{"file_size":924342,"file_name":"2024_PublicMathIHES_Brooks.pdf","creator":"dernst","checksum":"af3becc50f7534c9409d3ff8b5c47ed6","relation":"main_file","content_type":"application/pdf","date_updated":"2025-01-13T08:13:42Z","access_level":"open_access","file_id":"18824","success":1,"date_created":"2025-01-13T08:13:42Z"}],"arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T09:08:36Z","date_created":"2024-09-01T22:01:08Z","publication":"Publications Mathematiques de l'Institut des Hautes Etudes Scientifiques","title":"The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass","publication_status":"published","status":"public","date_published":"2024-12-01T00:00:00Z","year":"2024","file_date_updated":"2025-01-13T08:13:42Z","corr_author":"1","citation":{"mla":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques, vol. 140, Springer Nature, 2024, pp. 271–309, doi:10.1007/s10240-024-00150-0.","ista":"Brooks M, Seiringer R. 2024. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques. 140, 271–309.","ieee":"M. Brooks and R. Seiringer, “The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass,” Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques, vol. 140. Springer Nature, pp. 271–309, 2024.","apa":"Brooks, M., & Seiringer, R. (2024). The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques. Springer Nature. https://doi.org/10.1007/s10240-024-00150-0","ama":"Brooks M, Seiringer R. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques. 2024;140:271-309. doi:10.1007/s10240-024-00150-0","chicago":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques. Springer Nature, 2024. https://doi.org/10.1007/s10240-024-00150-0.","short":"M. Brooks, R. Seiringer, Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques 140 (2024) 271–309."},"OA_type":"hybrid","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001297785000001"],"arxiv":["2211.03353"]},"intvolume":" 140","author":[{"first_name":"Morris","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","orcid":"0000-0002-6249-0928","last_name":"Brooks"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert"}],"has_accepted_license":"1"},{"article_type":"original","_id":"17479","volume":11,"doi":"10.1021/acsphotonics.4c00485","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","publication_identifier":{"eissn":["2330-4022"]},"type":"journal_article","month":"09","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"NanoFab"}],"page":"3570-3577","scopus_import":"1","ddc":["530"],"isi":1,"author":[{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"first_name":"Yixi","full_name":"Zhou, Yixi","last_name":"Zhou"},{"first_name":"Ana I.F.","full_name":"Tresguerres-Mata, Ana I.F.","last_name":"Tresguerres-Mata"},{"last_name":"Lanza","first_name":"Christian","full_name":"Lanza, Christian"},{"last_name":"Martínez-Suárez","first_name":"Abel","full_name":"Martínez-Suárez, Abel"},{"last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo"},{"full_name":"Duan, Jiahua","first_name":"Jiahua","last_name":"Duan"},{"first_name":"José Ignacio","full_name":"Martín, José Ignacio","last_name":"Martín"},{"first_name":"María","full_name":"Vélez, María","last_name":"Vélez"},{"last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Bercher","first_name":"Adrien","full_name":"Bercher, Adrien"},{"last_name":"Teyssier","full_name":"Teyssier, Jérémie","first_name":"Jérémie"},{"last_name":"Errea","first_name":"Ion","full_name":"Errea, Ion"},{"last_name":"Nikitin","full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y."},{"last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier","first_name":"Javier"},{"last_name":"Kuzmenko","first_name":"Alexey B.","full_name":"Kuzmenko, Alexey B."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"intvolume":" 11","issue":"9","has_accepted_license":"1","file_date_updated":"2025-01-09T14:01:06Z","OA_type":"hybrid","citation":{"ama":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, et al. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 2024;11(9):3570-3577. doi:10.1021/acsphotonics.4c00485","apa":"Taboada-Gutiérrez, J., Zhou, Y., Tresguerres-Mata, A. I. F., Lanza, C., Martínez-Suárez, A., Álvarez-Pérez, G., … Alonso-González, P. (2024). Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. American Chemical Society. https://doi.org/10.1021/acsphotonics.4c00485","ieee":"J. Taboada-Gutiérrez et al., “Unveiling the mechanism of phonon-polariton damping in α‑MoO3,” ACS Photonics, vol. 11, no. 9. American Chemical Society, pp. 3570–3577, 2024.","ista":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, Lanza C, Martínez-Suárez A, Álvarez-Pérez G, Duan J, Martín JI, Vélez M, Prieto Gonzalez I, Bercher A, Teyssier J, Errea I, Nikitin AY, Martín-Sánchez J, Kuzmenko AB, Alonso-González P. 2024. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 11(9), 3570–3577.","mla":"Taboada-Gutiérrez, Javier, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” ACS Photonics, vol. 11, no. 9, American Chemical Society, 2024, pp. 3570–77, doi:10.1021/acsphotonics.4c00485.","short":"J. Taboada-Gutiérrez, Y. Zhou, A.I.F. Tresguerres-Mata, C. Lanza, A. Martínez-Suárez, G. Álvarez-Pérez, J. Duan, J.I. Martín, M. Vélez, I. Prieto Gonzalez, A. Bercher, J. Teyssier, I. Errea, A.Y. Nikitin, J. Martín-Sánchez, A.B. Kuzmenko, P. Alonso-González, ACS Photonics 11 (2024) 3570–3577.","chicago":"Taboada-Gutiérrez, Javier, Yixi Zhou, Ana I.F. Tresguerres-Mata, Christian Lanza, Abel Martínez-Suárez, Gonzalo Álvarez-Pérez, Jiahua Duan, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” ACS Photonics. American Chemical Society, 2024. https://doi.org/10.1021/acsphotonics.4c00485."},"year":"2024","date_published":"2024-09-01T00:00:00Z","publication_status":"published","status":"public","language":[{"iso":"eng"}],"external_id":{"arxiv":["2408.09811"],"pmid":["39310295"],"isi":["001298164600001"]},"quality_controlled":"1","arxiv":1,"date_updated":"2025-09-08T09:05:01Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Unveiling the mechanism of phonon-polariton damping in α‑MoO3","publication":"ACS Photonics","date_created":"2024-09-01T22:01:09Z","acknowledgement":"Funding Sources ─ A.I.F.T.-M. and G.Á.-P. acknowledge support through the Severo Ochoa program from the Government of the Principality of Asturias (references PA-21-PF-BP20-117 and PA20-PF-BP19-053, respectively). A.B.K. and J.T.-G. acknowledge support from the Swiss National Science Foundation (grant # 200020_201096). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I), the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00/AEI/10.13039/501100011033) and project PCI2022-132953 funded by MCIN/AEI/10.13039/501100011033 and the EU “NextGenerationEU”/PRTR”. P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). A.Y.N. acknowledges the Spanish Ministry of Science and Innovation (grant PID2020-115221GB-C42) and the Basque Department of Education (grant PIBA-2023-1-0007). M.V. and J.I.M. acknowledge support by Spanish MCIN/AEI/10.13039/501100011033/FEDER, UE under grant PID2022-136784NB and by Asturias FICYT under grant AYUD/2021/51185 with the support of FEDER funds. I.E. acknowledges funding from the Spanish Ministry of Science and Innovation (Grant No. PID2022-142861NA-I00) and the Department of Education, Universities, and Research of the Eusko Jaurlaritza and the University of the Basque Country UPV/EHU (Grant No. IT1527-22). J. Duan acknowledges the support from the Beijing Natural Science Foundation (Grant No. Z240005), and National Natural Science Foundation of China.","publisher":"American Chemical Society","file":[{"success":1,"date_created":"2025-01-09T14:01:06Z","file_id":"18819","access_level":"open_access","date_updated":"2025-01-09T14:01:06Z","checksum":"bd7e6a138c406e93eaf0a6268fc42bfe","relation":"main_file","content_type":"application/pdf","file_name":"2024_ACSPhotonics_TaboadaGutierrez_.pdf","file_size":2664512,"creator":"dernst"}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs), light coupled to lattice vibrations, in the highly anisotropic polar layered material molybdenum trioxide (α-MoO3) are currently the focus of intense research efforts due to their extreme subwavelength field confinement, directional propagation, and unprecedented low losses. Nevertheless, prior research has primarily concentrated on exploiting the squeezing and steering capabilities of α-MoO3 PhPs, without inquiring much into the dominant microscopic mechanism that determines their long lifetimes, which is key for their implementation in nanophotonic applications. This study delves into the fundamental processes that govern PhP damping in α-MoO3 by combining ab initio calculations with scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared (FTIR) spectroscopy measurements across a broad temperature range (8–300 K). The remarkable agreement between our theoretical predictions and experimental observations allows us to identify third-order anharmonic phonon–phonon scattering as the main damping mechanism of α-MoO3 PhPs. These findings shed light on the fundamental limits of low-loss PhPs, which is a crucial factor for assessing their implementation into nanophotonic devices."}],"oa":1},{"department":[{"_id":"JuFi"}],"page":"1117-1178","scopus_import":"1","ddc":["510"],"isi":1,"article_processing_charge":"Yes","type":"journal_article","month":"01","oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"24","doi":"10.4171/AIHPC/109","publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"project":[{"call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"_id":"17481","volume":41,"article_type":"original","abstract":[{"text":"Phase-field models such as the Allen–Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow. In the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: as long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε \r\n1/2\r\n ). Our approach is based on the gradient-flow structure of the Allen–Cahn equation and its limiting motion: building on the recent concept of “gradient-flow calibrations” for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen–Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn operator or additional convergence hypotheses for the energy at positive times.","lang":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"b5ad02d9abd5b4701269cd1ad0a1cc8f","creator":"dernst","file_size":1348896,"file_name":"2024_AnnInstHPoincare_Fischer.pdf","date_created":"2024-09-09T07:46:42Z","file_id":"17923","success":1,"date_updated":"2024-09-09T07:46:42Z","access_level":"open_access"}],"oa":1,"publisher":"EMS Press","ec_funded":1,"title":"Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow","publication":"Annales de l'Institut Henri Poincare C","related_material":{"record":[{"relation":"earlier_version","id":"14597","status":"public"}]},"date_created":"2024-09-01T22:01:09Z","acknowledgement":"The authors thank Sebastian Hensel for useful and helpful commentson the first draft of this work.\r\nThis project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement no. 948819.","date_updated":"2025-09-08T09:11:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001293853900003"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"ista":"Fischer JL, Marveggio A. 2024. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. 41(5), 1117–1178.","ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. 2024;41(5):1117-1178. doi:10.4171/AIHPC/109","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow,” Annales de l’Institut Henri Poincare C, vol. 41, no. 5. EMS Press, pp. 1117–1178, 2024.","apa":"Fischer, J. L., & Marveggio, A. (2024). Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. EMS Press. https://doi.org/10.4171/AIHPC/109","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales de l’Institut Henri Poincare C, vol. 41, no. 5, EMS Press, 2024, pp. 1117–78, doi:10.4171/AIHPC/109.","short":"J.L. Fischer, A. Marveggio, Annales de l’Institut Henri Poincare C 41 (2024) 1117–1178.","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales de l’Institut Henri Poincare C. EMS Press, 2024. https://doi.org/10.4171/AIHPC/109."},"file_date_updated":"2024-09-09T07:46:42Z","corr_author":"1","year":"2024","date_published":"2024-01-24T00:00:00Z","status":"public","publication_status":"published","has_accepted_license":"1","author":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"last_name":"Marveggio","first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice"}],"intvolume":" 41","issue":"5"},{"isi":1,"ddc":["530"],"scopus_import":"1","department":[{"_id":"MaSe"}],"article_processing_charge":"Yes","DOAJ_listed":"1","APC_amount":"4863,6 EUR","oa_version":"Published Version","month":"08","type":"journal_article","publication_identifier":{"issn":["2160-3308"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"26","doi":"10.1103/physrevx.14.031035","volume":14,"_id":"17493","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"article_type":"original","article_number":"031035","oa":1,"abstract":[{"text":"Estimating global properties of many-body quantum systems such as entropy or bipartite entanglement is a notoriously difficult task, typically requiring a number of measurements or classical postprocessing resources growing exponentially in the system size. In this work, we address the problem of estimating global entropies and mixed-state entanglement via partial-transposed (PT) moments and show that efficient estimation strategies exist under the assumption that all the spatial correlation lengths are finite. Focusing on one-dimensional systems, we identify a set of approximate factorization conditions (AFCs) on the system density matrix, which allow us to reconstruct entropies and PT moments from information on local subsystems. This identification yields a simple and efficient strategy for entropy and entanglement estimation. Our method could be implemented in different ways, depending on how information on local subsystems is extracted. Focusing on randomized measurements providing a practical and common measurement scheme, we prove that our protocol requires only polynomially many measurements and postprocessing operations, assuming that the state to be measured satisfies the AFCs. We prove that the AFCs hold for finite-depth quantum-circuit states and translation-invariant matrix-product density operators and provide numerical evidence that they are satisfied in more general, physically interesting cases, including thermal states of local Hamiltonians. We argue that our method could be practically useful to detect bipartite mixed-state entanglement for large numbers of qubits available in today’s quantum platforms.","lang":"eng"}],"OA_place":"publisher","file":[{"creator":"cchlebak","file_size":1408836,"file_name":"2024_PhysRevX_Vermersch.pdf","relation":"main_file","content_type":"application/pdf","checksum":"1b114acc89025120727200681e4e9074","date_updated":"2024-09-05T09:39:00Z","access_level":"open_access","date_created":"2024-09-05T09:39:00Z","file_id":"17532","success":1}],"ec_funded":1,"publisher":"American Physical Society","acknowledgement":"B. V. acknowledges funding from the Austrian Science Foundation (Grant No. FWF, P 32597 N), from the French National Research Agency via the JCJC project QRand (Grant No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (Grant No. ANR-22-PETQ-0007), QUBITAF (Grant No. ANR-22-PETQ-0004), and HQI (Grant No. ANR-22-PNCQ-0002). M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M. S. acknowledges the hospitality of KITP supported in part by the National Science Foundation under Grants No. NSF PHY-1748958 and No. NSF PHY-2309135. J. I. C. is supported by the Hightech Agenda Bayern Plus through the Munich Quantum Valley and the German Federal Ministry of Education and Research through EQUAHUMO (Grant No. 13N16066). P. Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 101113690 (PASQuanS2.1).","date_created":"2024-09-04T18:57:11Z","publication":"Physical Review X","title":"Many-body entropies and entanglement from polynomially many local measurements","arxiv":1,"date_updated":"2025-09-08T09:04:14Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","external_id":{"arxiv":["2311.08108"],"isi":["001299667100002"]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2024-08-26T00:00:00Z","year":"2024","OA_type":"gold","citation":{"mla":"Vermersch, Benoît, et al. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” Physical Review X, vol. 14, no. 3, 031035, American Physical Society, 2024, doi:10.1103/physrevx.14.031035.","ista":"Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. 2024. Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. 14(3), 031035.","ama":"Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. 2024;14(3). doi:10.1103/physrevx.14.031035","ieee":"B. Vermersch, M. Ljubotina, J. I. Cirac, P. Zoller, M. Serbyn, and L. Piroli, “Many-body entropies and entanglement from polynomially many local measurements,” Physical Review X, vol. 14, no. 3. American Physical Society, 2024.","apa":"Vermersch, B., Ljubotina, M., Cirac, J. I., Zoller, P., Serbyn, M., & Piroli, L. (2024). Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. American Physical Society. https://doi.org/10.1103/physrevx.14.031035","chicago":"Vermersch, Benoît, Marko Ljubotina, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, and Lorenzo Piroli. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” Physical Review X. American Physical Society, 2024. https://doi.org/10.1103/physrevx.14.031035.","short":"B. Vermersch, M. Ljubotina, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, Physical Review X 14 (2024)."},"file_date_updated":"2024-09-05T09:39:00Z","has_accepted_license":"1","issue":"3","intvolume":" 14","author":[{"last_name":"Vermersch","full_name":"Vermersch, Benoît","first_name":"Benoît"},{"last_name":"Ljubotina","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko"},{"last_name":"Cirac","first_name":"J. Ignacio","full_name":"Cirac, J. Ignacio"},{"first_name":"Peter","full_name":"Zoller, Peter","last_name":"Zoller"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn"},{"last_name":"Piroli","full_name":"Piroli, Lorenzo","first_name":"Lorenzo"}]},{"type":"journal_article","month":"10","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"JaBr"}],"page":"1269-1272","scopus_import":"1","isi":1,"article_type":"letter_note","_id":"17494","volume":19,"doi":"10.1080/17460913.2024.2389720","day":"01","publication_identifier":{"issn":["1746-0913"],"eissn":["1746-0921"]},"date_updated":"2025-09-08T09:03:00Z","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1080/17460913.2024.2389720","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Anti-plasmid immunity: A key to pathogen success?","publication":"Future Microbiology","date_created":"2024-09-05T07:32:00Z","acknowledgement":"I would like to thank K Kiernan for insightful comments and feedback. J P K Bravo is supported by IST Austria.","publisher":"Taylor & Francis","OA_place":"publisher","oa":1,"author":[{"last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"}],"intvolume":" 19","issue":"15","has_accepted_license":"1","OA_type":"free access","corr_author":"1","citation":{"apa":"Bravo, J. P. K. (2024). Anti-plasmid immunity: A key to pathogen success? Future Microbiology. Taylor & Francis. https://doi.org/10.1080/17460913.2024.2389720","ieee":"J. P. K. Bravo, “Anti-plasmid immunity: A key to pathogen success?,” Future Microbiology, vol. 19, no. 15. Taylor & Francis, pp. 1269–1272, 2024.","ama":"Bravo JPK. Anti-plasmid immunity: A key to pathogen success? Future Microbiology. 2024;19(15):1269-1272. doi:10.1080/17460913.2024.2389720","ista":"Bravo JPK. 2024. Anti-plasmid immunity: A key to pathogen success? Future Microbiology. 19(15), 1269–1272.","mla":"Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” Future Microbiology, vol. 19, no. 15, Taylor & Francis, 2024, pp. 1269–72, doi:10.1080/17460913.2024.2389720.","short":"J.P.K. Bravo, Future Microbiology 19 (2024) 1269–1272.","chicago":"Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” Future Microbiology. Taylor & Francis, 2024. https://doi.org/10.1080/17460913.2024.2389720."},"date_published":"2024-10-01T00:00:00Z","year":"2024","publication_status":"published","status":"public","language":[{"iso":"eng"}],"external_id":{"pmid":["39230568"],"isi":["001306115400001"]},"quality_controlled":"1"},{"type":"journal_article","month":"06","oa_version":"Published Version","page":"1115-1139","scopus_import":"1","article_processing_charge":"No","article_type":"original","day":"20","doi":"10.1145/3656422","publication_identifier":{"issn":["2475-1421"]},"_id":"17495","volume":8,"title":"RefinedRust: A type system for high-assurance verification of rust programs","publication":"Proceedings of the ACM on Programming Languages","date_created":"2024-09-05T07:52:27Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3656422"}],"date_updated":"2024-09-10T07:16:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Rust is a modern systems programming language whose ownership-based type system statically guarantees memory safety, making it particularly well-suited to the domain of safety-critical systems. In recent years, a wellspring of automated deductive verification tools have emerged for establishing functional correctness of Rust code. However, none of the previous tools produce foundational proofs (machine-checkable in a general-purpose proof assistant), and all of them are restricted to the safe fragment of Rust. This is a problem because the vast majority of Rust programs make use of unsafe code at critical points, such as in the implementation of widely-used APIs. We propose RefinedRust, a refinement type system—proven sound in the Coq proof assistant—with the goal of establishing foundational semi-automated functional correctness verification of both safe and unsafe Rust code. We have developed a prototype verification tool implementing RefinedRust. Our tool translates Rust code (with user annotations) into a model of Rust embedded in Coq, and then checks its adherence to the RefinedRust type system using separation logic automation in Coq. All proofs generated by RefinedRust are checked by the Coq proof assistant, so the automation and type system do not have to be trusted. We evaluate the effectiveness of RefinedRust by verifying a variant of Rust’s Vec implementation that involves intricate reasoning about unsafe pointer-manipulating code."}],"oa":1,"publisher":"Association for Computing Machinery","author":[{"last_name":"Gäher","full_name":"Gäher, Lennard","first_name":"Lennard"},{"last_name":"Sammler","first_name":"Michael Joachim","full_name":"Sammler, Michael Joachim","id":"510d3901-2a03-11ee-914d-d9ae9011f0a7"},{"last_name":"Jung","first_name":"Ralf","full_name":"Jung, Ralf"},{"first_name":"Robbert","full_name":"Krebbers, Robbert","last_name":"Krebbers"},{"last_name":"Dreyer","first_name":"Derek","full_name":"Dreyer, Derek"}],"intvolume":" 8","issue":"PLDI","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Gäher, Lennard, et al. “RefinedRust: A Type System for High-Assurance Verification of Rust Programs.” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI, Association for Computing Machinery, 2024, pp. 1115–39, doi:10.1145/3656422.","ama":"Gäher L, Sammler MJ, Jung R, Krebbers R, Dreyer D. RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. 2024;8(PLDI):1115-1139. doi:10.1145/3656422","ieee":"L. Gäher, M. J. Sammler, R. Jung, R. Krebbers, and D. Dreyer, “RefinedRust: A type system for high-assurance verification of rust programs,” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI. Association for Computing Machinery, pp. 1115–1139, 2024.","apa":"Gäher, L., Sammler, M. J., Jung, R., Krebbers, R., & Dreyer, D. (2024). RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656422","ista":"Gäher L, Sammler MJ, Jung R, Krebbers R, Dreyer D. 2024. RefinedRust: A type system for high-assurance verification of rust programs. Proceedings of the ACM on Programming Languages. 8(PLDI), 1115–1139.","chicago":"Gäher, Lennard, Michael Joachim Sammler, Ralf Jung, Robbert Krebbers, and Derek Dreyer. “RefinedRust: A Type System for High-Assurance Verification of Rust Programs.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3656422.","short":"L. Gäher, M.J. Sammler, R. Jung, R. Krebbers, D. Dreyer, Proceedings of the ACM on Programming Languages 8 (2024) 1115–1139."},"date_published":"2024-06-20T00:00:00Z","year":"2024","status":"public","publication_status":"published","extern":"1"},{"year":"2024","date_published":"2024-06-20T00:00:00Z","publication_status":"published","status":"public","extern":"1","citation":{"chicago":"Spies, Simon, Lennard Gäher, Michael Joachim Sammler, and Derek Dreyer. “Quiver: Guided Abductive Inference of Separation Logic Specifications in Coq.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3656413.","short":"S. Spies, L. Gäher, M.J. Sammler, D. Dreyer, Proceedings of the ACM on Programming Languages 8 (2024) 889–913.","mla":"Spies, Simon, et al. “Quiver: Guided Abductive Inference of Separation Logic Specifications in Coq.” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI, Association for Computing Machinery, 2024, pp. 889–913, doi:10.1145/3656413.","ista":"Spies S, Gäher L, Sammler MJ, Dreyer D. 2024. Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. 8(PLDI), 889–913.","ieee":"S. Spies, L. Gäher, M. J. Sammler, and D. Dreyer, “Quiver: Guided abductive inference of separation logic specifications in coq,” Proceedings of the ACM on Programming Languages, vol. 8, no. PLDI. Association for Computing Machinery, pp. 889–913, 2024.","apa":"Spies, S., Gäher, L., Sammler, M. J., & Dreyer, D. (2024). Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656413","ama":"Spies S, Gäher L, Sammler MJ, Dreyer D. Quiver: Guided abductive inference of separation logic specifications in coq. Proceedings of the ACM on Programming Languages. 2024;8(PLDI):889-913. doi:10.1145/3656413"},"quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 8","issue":"PLDI","author":[{"last_name":"Spies","first_name":"Simon","full_name":"Spies, Simon"},{"last_name":"Gäher","first_name":"Lennard","full_name":"Gäher, Lennard"},{"last_name":"Sammler","full_name":"Sammler, Michael Joachim","id":"510d3901-2a03-11ee-914d-d9ae9011f0a7","first_name":"Michael Joachim"},{"full_name":"Dreyer, Derek","first_name":"Derek","last_name":"Dreyer"}],"publisher":"Association for Computing Machinery","oa":1,"abstract":[{"text":"Over the past two decades, there has been a great deal of progress on verification of full functional correctness of programs using separation logic, sometimes even producing “foundational” proofs in proof assistants like Coq. Unfortunately, even though existing approaches to this problem provide significant support for automated verification, they still incur a significant specification overhead: the user must supply the specification against which the program is verified, and the specification may be long, complex, or tedious to formulate. In this paper, we introduce Quiver, the first technique for inferring functional correctness specifications in separation logic while simultaneously verifying foundationally that they are correct. To guide Quiver towards the final specification, we take hints from the user in the form of a specification sketch, and then complete the sketch using inference. To do so, Quiver introduces a new abductive deductive verification technique, which integrates ideas from abductive inference (for specification inference) together with deductive separation logic automation (for foundational verification). The result is that users have to provide some guidance, but significantly less than with traditional deductive verification techniques based on separation logic. We have evaluated Quiver on a range of case studies, including code from popular open-source libraries.","lang":"eng"}],"date_updated":"2024-09-10T12:00:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3656413"}],"date_created":"2024-09-05T08:10:41Z","title":"Quiver: Guided abductive inference of separation logic specifications in coq","publication":"Proceedings of the ACM on Programming Languages","_id":"17497","volume":8,"publication_identifier":{"issn":["2475-1421"]},"doi":"10.1145/3656413","day":"20","article_type":"original","article_processing_charge":"No","scopus_import":"1","page":"889-913","oa_version":"Published Version","type":"journal_article","month":"06"}]