[{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"content_type":"application/pdf","file_id":"14620","success":1,"file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","checksum":"f668ee0d07096eef81159d05bc27aabc","creator":"dernst","file_size":6276059,"relation":"main_file","date_updated":"2023-11-28T08:39:06Z","access_level":"open_access","date_created":"2023-11-28T08:39:06Z"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.","lang":"eng"}],"language":[{"iso":"eng"}],"corr_author":"1","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","day":"14","year":"2023","article_type":"original","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-11-14T00:00:00Z","month":"11","ddc":["530","540"],"publication":"Journal of Chemical Physics","date_updated":"2025-09-09T13:32:46Z","date_created":"2023-11-26T23:00:54Z","citation":{"mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>.","ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” <i>Journal of Chemical Physics</i>, vol. 159, no. 18. AIP Publishing, 2023.","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. 2023;159(18). doi:<a href=\"https://doi.org/10.1063/5.0173341\">10.1063/5.0173341</a>","apa":"Reinhardt, A., Chew, P. Y., &#38; Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0173341\">https://doi.org/10.1063/5.0173341</a>"},"department":[{"_id":"BiCh"}],"volume":159,"file_date_updated":"2023-11-28T08:39:06Z","oa_version":"Published Version","_id":"14603","oa":1,"external_id":{"pmid":["37962445"],"isi":["001137066700001"],"arxiv":["2308.10886"]},"publisher":"AIP Publishing","arxiv":1,"issue":"18","acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","has_accepted_license":"1","status":"public","isi":1,"doi":"10.1063/5.0173341","intvolume":"       159","publication_status":"published","author":[{"first_name":"Aleks","full_name":"Reinhardt, Aleks","last_name":"Reinhardt"},{"last_name":"Chew","first_name":"Pin Yu","full_name":"Chew, Pin Yu"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"type":"journal_article","article_number":"184110","related_material":{"record":[{"status":"public","id":"14619","relation":"research_data"}]},"pmid":1,"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1"},{"citation":{"ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” <i>Evolution</i>, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. 2023;77(11):2504-2511. doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>"},"department":[{"_id":"BeVi"}],"_id":"14604","oa_version":"Published Version","oa":1,"volume":77,"file_date_updated":"2023-11-28T08:12:15Z","publisher":"Oxford University Press","external_id":{"pmid":["37738212"],"isi":["001170341900014"]},"status":"public","has_accepted_license":"1","acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","issue":"11","intvolume":"        77","doi":"10.1093/evolut/qpad169","isi":1,"type":"journal_article","publication_status":"published","author":[{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","pmid":1,"related_material":{"record":[{"id":"14616","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"14617"}],"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"publication_identifier":{"eissn":["1558-5646"]},"file":[{"content_type":"application/pdf","success":1,"file_id":"14618","checksum":"b66dc10edae92d38918d534e64dda77c","creator":"dernst","file_name":"2023_Evolution_Toups.pdf","relation":"main_file","file_size":1399102,"date_updated":"2023-11-28T08:12:15Z","date_created":"2023-11-28T08:12:15Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"day":"02","title":"The X chromosome of insects likely predates the origin of class Insecta","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","scopus_import":"1","year":"2023","month":"11","date_published":"2023-11-02T00:00:00Z","date_created":"2023-11-26T23:00:54Z","date_updated":"2025-09-09T13:32:06Z","publication":"Evolution","ddc":["570"],"page":"2504-2511"},{"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"abstract":[{"lang":"eng","text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments."}],"language":[{"iso":"eng"}],"corr_author":"1","date_published":"2023-11-01T00:00:00Z","ec_funded":1,"month":"11","date_created":"2023-11-26T23:00:54Z","date_updated":"2025-09-09T13:31:19Z","publication":"Physical Review B","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","day":"01","article_type":"original","year":"2023","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Physical Society","external_id":{"isi":["001101152500001"]},"citation":{"ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” <i>Physical Review B</i>, vol. 108, no. 17. American Physical Society, 2023.","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. 2023;108(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">10.1103/PhysRevB.108.174302</a>","apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., &#38; Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>","chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.174302\">https://doi.org/10.1103/PhysRevB.108.174302</a>."},"department":[{"_id":"BiCh"}],"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"volume":108,"oa_version":"None","_id":"14605","publication_status":"published","author":[{"first_name":"Niuchang","full_name":"Ouyang, Niuchang","last_name":"Ouyang"},{"full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng"},{"full_name":"Wang, Chen","first_name":"Chen","last_name":"Wang"},{"first_name":"Qi","full_name":"Wang, Qi","last_name":"Wang"},{"last_name":"Chen","full_name":"Chen, Yue","first_name":"Yue"}],"type":"journal_article","article_number":"174302","quality_controlled":"1","article_processing_charge":"No","issue":"17","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","status":"public","isi":1,"intvolume":"       108","doi":"10.1103/PhysRevB.108.174302"},{"date_created":"2023-11-26T23:00:55Z","date_updated":"2025-04-15T08:16:55Z","publication":"32nd USENIX Security Symposium","ddc":["000"],"page":"5359-5376","month":"08","date_published":"2023-08-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","scopus_import":"1","day":"15","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","corr_author":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713879497"]},"abstract":[{"lang":"eng","text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art."}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1389"}],"file":[{"relation":"main_file","file_size":704331,"date_updated":"2023-11-28T09:14:34Z","access_level":"open_access","date_created":"2023-11-28T09:14:34Z","content_type":"application/pdf","success":1,"file_id":"14621","checksum":"1a730765930138e23c6efd2575872641","creator":"dernst","file_name":"2023_USENIX_Das.pdf"}],"article_processing_charge":"No","quality_controlled":"1","type":"conference","publication_status":"published","author":[{"last_name":"Das","full_name":"Das, Sourav","first_name":"Sourav"},{"first_name":"Zhuolun","full_name":"Xiang, Zhuolun","last_name":"Xiang"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"last_name":"Ren","full_name":"Ren, Ling","first_name":"Ling"}],"intvolume":"         8","status":"public","has_accepted_license":"1","acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","publisher":"Usenix","conference":{"end_date":"2023-08-11","start_date":"2023-08-09","name":"USENIX Security Symposium","location":"Anaheim, CA, United States"},"_id":"14609","oa":1,"oa_version":"Published Version","file_date_updated":"2023-11-28T09:14:34Z","volume":8,"citation":{"mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” <i>32nd USENIX Security Symposium</i>, vol. 8, Usenix, 2023, pp. 5359–76.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in <i>32nd USENIX Security Symposium</i>, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In <i>32nd USENIX Security Symposium</i>, 8:5359–76. Usenix, 2023.","short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: <i>32nd USENIX Security Symposium</i>. Vol 8. Usenix; 2023:5359-5376.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., &#38; Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In <i>32nd USENIX Security Symposium</i> (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix."},"department":[{"_id":"ElKo"}],"project":[{"grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Security and Privacy by Design for Complex Systems"}]},{"file":[{"content_type":"application/pdf","file_id":"17248","success":1,"checksum":"b939a19e4c228fbf3beca298ac2ac014","creator":"dernst","file_name":"2023_Nature_Bussi.pdf","date_updated":"2024-07-16T07:41:39Z","file_size":17047711,"relation":"main_file","date_created":"2024-07-16T07:41:39Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host."}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-11-30T00:00:00Z","month":"11","ddc":["570"],"page":"1062-1069","date_created":"2023-11-27T07:56:37Z","date_updated":"2025-09-09T13:30:34Z","publication":"Nature","title":"Stress granules plug and stabilize damaged endolysosomal membranes","day":"30","scopus_import":"1","year":"2023","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","external_id":{"pmid":["37968398"],"isi":["001105882300018"]},"department":[{"_id":"AnSa"}],"citation":{"short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature 623 (2023) 1062–1069.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023;623:1062-1069. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>, vol. 623. Springer Nature, pp. 1062–1069, 2023.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 623, 1062–1069.","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>."},"volume":623,"file_date_updated":"2024-07-16T07:41:39Z","_id":"14610","oa_version":"Published Version","oa":1,"author":[{"last_name":"Bussi","full_name":"Bussi, Claudio","first_name":"Claudio"},{"full_name":"Mangiarotti, Agustín","first_name":"Agustín","last_name":"Mangiarotti"},{"first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos"},{"full_name":"Aylan, Beren","first_name":"Beren","last_name":"Aylan"},{"first_name":"Enrica","full_name":"Pellegrino, Enrica","last_name":"Pellegrino"},{"last_name":"Athanasiadi","full_name":"Athanasiadi, Natalia","first_name":"Natalia"},{"last_name":"Fearns","first_name":"Antony","full_name":"Fearns, Antony"},{"full_name":"Rodgers, Angela","first_name":"Angela","last_name":"Rodgers"},{"full_name":"Franzmann, Titus M.","first_name":"Titus M.","last_name":"Franzmann"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Dimova","full_name":"Dimova, Rumiana","first_name":"Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","first_name":"Maximiliano G.","last_name":"Gutierrez"}],"publication_status":"published","type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"relation":"research_data","status":"public","id":"14472"}]},"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","pmid":1,"status":"public","has_accepted_license":"1","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","isi":1,"intvolume":"       623","doi":"10.1038/s41586-023-06726-w"},{"oa_version":"Published Version","_id":"14614","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Panorpa","scorpionfly","genome","transcriptome"],"file_date_updated":"2023-11-30T14:16:59Z","department":[{"_id":"BeVi"}],"citation":{"ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","apa":"Lasne, C., &#38; Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>","short":"C. Lasne, M.N. Elkrewi, (2023).","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>","chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>."},"corr_author":"1","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"file":[{"checksum":"cd0f13322b5156819ecaebd2bc8e7d12","creator":"clasne","file_name":"panorpaX.zip","content_type":"application/zip","success":1,"file_id":"14625","date_updated":"2023-11-28T13:15:26Z","relation":"main_file","file_size":404968272,"date_created":"2023-11-28T13:15:26Z","access_level":"open_access"},{"access_level":"open_access","date_created":"2023-11-30T14:16:59Z","file_size":2625,"date_updated":"2023-11-30T14:16:59Z","relation":"main_file","success":1,"file_id":"14634","content_type":"text/plain","creator":"clasne","checksum":"9ff600416577687a737cb3c96dfcb26c","file_name":"panorpa_readme.txt"}],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:14614","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","contributor_type":"researcher","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"year":"2023","day":"01","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","status":"public","has_accepted_license":"1","date_updated":"2025-09-09T13:33:22Z","date_created":"2023-11-27T16:39:19Z","article_processing_charge":"No","ddc":["576"],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14613"}]},"type":"research_data","month":"12","author":[{"full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","last_name":"Lasne"},{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"}],"date_published":"2023-12-01T00:00:00Z"},{"related_material":{"record":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"ddc":["570"],"date_updated":"2025-09-09T13:32:05Z","date_created":"2023-11-28T08:01:53Z","article_processing_charge":"No","date_published":"2023-09-15T00:00:00Z","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"month":"09","type":"research_data_reference","year":"2023","doi":"10.5061/DRYAD.HX3FFBGKT","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","status":"public","title":"The X chromosome of insects likely predates the origin of Class Insecta","day":"15","main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}],"publisher":"Dryad","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","oa":1,"_id":"14616","oa_version":"Published Version","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"department":[{"_id":"BeVi"}],"citation":{"ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>","short":"M.A. Toups, B. Vicoso, (2023).","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Dryad, 2023, doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>."}},{"citation":{"apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>","short":"M.A. Toups, B. Vicoso, (2023).","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>."},"department":[{"_id":"BeVi"}],"oa_version":"Published Version","_id":"14617","oa":1,"abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}],"publisher":"Zenodo","day":"15","title":"The X chromosome of insects likely predates the origin of Class Insecta","has_accepted_license":"1","status":"public","doi":"10.5281/ZENODO.8138705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","month":"09","type":"research_data_reference","other_data_license":"MIT License","date_published":"2023-09-15T00:00:00Z","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"date_updated":"2025-09-09T13:32:05Z","date_created":"2023-11-28T08:04:03Z","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","id":"14604","status":"public"}]},"ddc":["570"]},{"author":[{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"date_published":"2023-10-02T00:00:00Z","month":"10","type":"research_data_reference","ddc":["530"],"related_material":{"record":[{"status":"public","id":"14603","relation":"used_in_publication"}]},"date_updated":"2025-09-09T13:32:46Z","date_created":"2023-11-28T08:32:18Z","article_processing_charge":"No","title":"BingqingCheng/solubility: V1.0","has_accepted_license":"1","status":"public","day":"02","year":"2023","doi":"10.5281/ZENODO.8398094","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8398094","open_access":"1"}],"publisher":"Zenodo","abstract":[{"text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341).","lang":"eng"}],"corr_author":"1","citation":{"chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>.","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8398094\">https://doi.org/10.5281/ZENODO.8398094</a>","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>","short":"B. Cheng, (2023).","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","mla":"Cheng, Bingqing. <i>BingqingCheng/Solubility: V1.0</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8398094\">10.5281/ZENODO.8398094</a>.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023."},"department":[{"_id":"BiCh"}],"oa":1,"_id":"14619","oa_version":"Published Version"},{"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"citation":{"ieee":"L. Makatura <i>et al.</i>, “Procedural metamaterials: A unified procedural graph for metamaterial design,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>.","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., &#38; Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3605389\">10.1145/3605389</a>","chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3605389\">https://doi.org/10.1145/3605389</a>."},"department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"_id":"14628","oa_version":"Published Version","oa":1,"volume":42,"file_date_updated":"2023-12-04T08:04:14Z","external_id":{"isi":["001086833300007"]},"publisher":"Association for Computing Machinery","has_accepted_license":"1","status":"public","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program.","issue":"5","doi":"10.1145/3605389","intvolume":"        42","isi":1,"type":"journal_article","author":[{"last_name":"Makatura","first_name":"Liane","full_name":"Makatura, Liane"},{"last_name":"Wang","first_name":"Bohan","full_name":"Wang, Bohan"},{"last_name":"Chen","full_name":"Chen, Yi-Lu","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"}],"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_number":"168","keyword":["Computer Graphics and Computer-Aided Design"],"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"abstract":[{"text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.","lang":"eng"}],"file":[{"success":1,"file_id":"14630","content_type":"application/zip","file_name":"tog-22-0089-File004.zip","creator":"yichen","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","access_level":"open_access","date_created":"2023-11-29T15:16:01Z","file_size":95467870,"relation":"main_file","date_updated":"2023-11-29T15:16:01Z"},{"relation":"main_file","file_size":103731880,"date_updated":"2023-11-29T15:16:01Z","date_created":"2023-11-29T15:16:01Z","access_level":"open_access","content_type":"application/zip","file_id":"14631","success":1,"checksum":"7fb024963be81933494f38de191e4710","creator":"yichen","file_name":"tog-22-0089-File005.zip"},{"content_type":"application/pdf","file_id":"14638","success":1,"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","creator":"dernst","file_name":"2023_ACMToG_Makatura.pdf","date_updated":"2023-12-04T08:04:14Z","file_size":57067476,"relation":"main_file","date_created":"2023-12-04T08:04:14Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"day":"01","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2023","scopus_import":"1","article_type":"original","month":"10","date_published":"2023-10-01T00:00:00Z","date_updated":"2025-09-09T13:33:58Z","publication":"ACM Transactions on Graphics","date_created":"2023-11-29T15:02:03Z","ddc":["531","006"]},{"file":[{"access_level":"open_access","date_created":"2023-12-04T08:15:43Z","file_size":14791081,"date_updated":"2023-12-04T08:15:43Z","relation":"main_file","success":1,"file_id":"14640","content_type":"application/pdf","creator":"dernst","checksum":"279efd212005549aba817a487d56d363","file_name":"2023_GenomeMed_Lin.pdf"}],"abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"publication_identifier":{"issn":["1756-994X"]},"language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-11-23T00:00:00Z","month":"11","ddc":["570"],"date_created":"2023-12-04T08:10:55Z","publication":"Genome Medicine","date_updated":"2023-12-04T08:17:22Z","title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","day":"23","year":"2023","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","citation":{"ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>, vol. 15, 102, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” <i>Genome Medicine</i>, vol. 15. Springer Nature, 2023.","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” <i>Genome Medicine</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>.","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-023-01258-4\">https://doi.org/10.1186/s13073-023-01258-4</a>","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. <i>Genome Medicine</i>. 2023;15. doi:<a href=\"https://doi.org/10.1186/s13073-023-01258-4\">10.1186/s13073-023-01258-4</a>"},"volume":15,"file_date_updated":"2023-12-04T08:15:43Z","oa_version":"Published Version","_id":"14639","oa":1,"publication_status":"published","author":[{"full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia","last_name":"Lin"},{"last_name":"Vona","full_name":"Vona, Barbara","first_name":"Barbara"},{"last_name":"Lau","full_name":"Lau, Tracy","first_name":"Tracy"},{"last_name":"Huang","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin","orcid":"0000-0002-2512-7812"},{"first_name":"Maha S.","full_name":"Zaki, Maha S.","last_name":"Zaki"},{"last_name":"Aldeen","full_name":"Aldeen, Huda Shujaa","first_name":"Huda Shujaa"},{"full_name":"Karimiani, Ehsan Ghayoor","first_name":"Ehsan Ghayoor","last_name":"Karimiani"},{"first_name":"Clarissa","full_name":"Rocca, Clarissa","last_name":"Rocca"},{"last_name":"Noureldeen","first_name":"Mahmoud M.","full_name":"Noureldeen, Mahmoud M."},{"last_name":"Saad","full_name":"Saad, Ahmed K.","first_name":"Ahmed K."},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"last_name":"Bartolomaeus","first_name":"Tobias","full_name":"Bartolomaeus, Tobias"},{"last_name":"Abou Jamra","first_name":"Rami","full_name":"Abou Jamra, Rami"},{"full_name":"Zifarelli, Giovanni","first_name":"Giovanni","last_name":"Zifarelli"},{"last_name":"Gotkhindikar","full_name":"Gotkhindikar, Aditi","first_name":"Aditi"},{"full_name":"Wentzensen, Ingrid M.","first_name":"Ingrid M.","last_name":"Wentzensen"},{"first_name":"Mingjuan","full_name":"Liao, Mingjuan","last_name":"Liao"},{"last_name":"Cork","first_name":"Emalyn Elise","full_name":"Cork, Emalyn Elise"},{"last_name":"Varshney","first_name":"Pratishtha","full_name":"Varshney, Pratishtha"},{"last_name":"Hashemi","first_name":"Narges","full_name":"Hashemi, Narges"},{"last_name":"Mohammadi","first_name":"Mohammad Hasan","full_name":"Mohammadi, Mohammad Hasan"},{"last_name":"Rad","full_name":"Rad, Aboulfazl","first_name":"Aboulfazl"},{"full_name":"Neira, Juanita","first_name":"Juanita","last_name":"Neira"},{"last_name":"Toosi","full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi"},{"full_name":"Knopp, Cordula","first_name":"Cordula","last_name":"Knopp"},{"full_name":"Kurth, Ingo","first_name":"Ingo","last_name":"Kurth"},{"full_name":"Challman, Thomas D.","first_name":"Thomas D.","last_name":"Challman"},{"first_name":"Rebecca","full_name":"Smith, Rebecca","last_name":"Smith"},{"first_name":"Asmahan","full_name":"Abdalla, Asmahan","last_name":"Abdalla"},{"last_name":"Haaf","full_name":"Haaf, Thomas","first_name":"Thomas"},{"last_name":"Suri","first_name":"Mohnish","full_name":"Suri, Mohnish"},{"last_name":"Joshi","full_name":"Joshi, Manali","first_name":"Manali"},{"first_name":"Wendy K.","full_name":"Chung, Wendy K.","last_name":"Chung"},{"full_name":"Moreno-De-Luca, Andres","first_name":"Andres","last_name":"Moreno-De-Luca"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"},{"last_name":"Varshney","first_name":"Gaurav K.","full_name":"Varshney, Gaurav K."}],"extern":"1","type":"journal_article","article_number":"102","quality_controlled":"1","article_processing_charge":"Yes","status":"public","has_accepted_license":"1","intvolume":"        15","doi":"10.1186/s13073-023-01258-4"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"file":[{"content_type":"application/pdf","success":1,"file_id":"14646","file_name":"2023_Tluckova_etal_REx.pdf","checksum":"c45608cb97ee36d7b50ba518db8e07b0","creator":"dernst","date_updated":"2023-12-05T10:37:02Z","relation":"main_file","file_size":4892920,"access_level":"open_access","date_created":"2023-12-05T10:37:02Z"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.","lang":"eng"}],"language":[{"iso":"eng"}],"corr_author":"1","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","day":"05","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-12-05T00:00:00Z","month":"12","ddc":["572"],"date_created":"2023-12-04T14:51:00Z","date_updated":"2025-11-20T10:28:37Z","citation":{"short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","apa":"Tluckova, K., Testa Salmazo, A. P., &#38; Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">https://doi.org/10.15479/AT:ISTA:14644</a>.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","mla":"Tluckova, Katarina, et al. <i>Mechanism of Mammalian Transcriptional Repression by Noncoding RNA</i>. Institute of Science and Technology Austria, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <a href=\"https://doi.org/10.15479/AT:ISTA:14644\">10.15479/AT:ISTA:14644</a>."},"project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA"}],"file_date_updated":"2023-12-05T10:37:02Z","oa":1,"_id":"14644","oa_version":"Submitted Version","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"has_accepted_license":"1","status":"public","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","doi":"10.15479/AT:ISTA:14644","author":[{"first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","full_name":"Tluckova, Katarina","last_name":"Tluckova"},{"last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P"},{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"}],"publication_status":"draft","type":"preprint","related_material":{"record":[{"relation":"later_version","id":"18778","status":"public"}]},"article_processing_charge":"No"},{"issue":"6","status":"public","has_accepted_license":"1","acknowledgement":"We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247.","isi":1,"intvolume":"        15","doi":"10.21468/scipostphys.15.6.232","author":[{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","last_name":"Bighin"},{"last_name":"Santos","first_name":"Luis","full_name":"Santos, Luis"},{"first_name":"Luisllu A.","full_name":"Peña Ardila, Luisllu A.","last_name":"Peña Ardila"}],"publication_status":"published","type":"journal_article","article_number":"232","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"MiLe"}],"citation":{"ieee":"A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” <i>SciPost Physics</i>, vol. 15, no. 6. SciPost Foundation, 2023.","mla":"Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>.","ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","short":"A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023).","apa":"Volosniev, A., Bighin, G., Santos, L., &#38; Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>","ama":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. <i>SciPost Physics</i>. 2023;15(6). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">10.21468/scipostphys.15.6.232</a>","chicago":"Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.6.232\">https://doi.org/10.21468/scipostphys.15.6.232</a>."},"project":[{"_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","call_identifier":"FWF","name":"A path-integral approach to composite impurities"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"volume":15,"file_date_updated":"2023-12-11T07:42:04Z","oa_version":"Published Version","_id":"14650","oa":1,"publisher":"SciPost Foundation","external_id":{"isi":["001121864100003"],"arxiv":["2305.17969"]},"arxiv":1,"title":"Non-equilibrium dynamics of dipolar polarons","day":"07","scopus_import":"1","article_type":"original","year":"2023","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-12-07T00:00:00Z","ec_funded":1,"month":"12","ddc":["530"],"date_created":"2023-12-10T13:03:07Z","publication":"SciPost Physics","date_updated":"2025-09-09T13:34:34Z","keyword":["General Physics and Astronomy"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"relation":"main_file","file_size":3543541,"date_updated":"2023-12-11T07:42:04Z","access_level":"open_access","date_created":"2023-12-11T07:42:04Z","content_type":"application/pdf","success":1,"file_id":"14669","file_name":"2023_SciPostPhysics_Volosniev.pdf","checksum":"e664372a1fe9d628a9bb1d135ebab7d8","creator":"dernst"}],"abstract":[{"lang":"eng","text":"We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures."}],"publication_identifier":{"issn":["2542-4653"]},"language":[{"iso":"eng"}],"corr_author":"1"},{"scopus_import":"1","year":"2023","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Assessing memory in convection schemes using idealized tests","day":"01","ddc":["550"],"date_updated":"2025-09-09T13:35:40Z","publication":"Journal of Advances in Modeling Earth Systems","date_created":"2023-12-10T23:00:57Z","date_published":"2023-12-01T00:00:00Z","month":"12","ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"corr_author":"1","file":[{"date_updated":"2023-12-11T08:08:44Z","file_size":2783677,"relation":"main_file","date_created":"2023-12-11T08:08:44Z","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14670","file_name":"2023_JAMES_Hwong.pdf","checksum":"4d060b293da3d203de8769e398edf711","creator":"dernst"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions."}],"publication_identifier":{"eissn":["1942-2466"]},"isi":1,"doi":"10.1029/2023MS003726","intvolume":"        15","status":"public","issue":"12","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. CJM gratefully acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). YLH and SCS were supported by the Australian Research Council (FL150100035). The authors thank Brian Mapes, David Fuchs and Siwon Song for stimulating and helpful discussions. MC warmly thanks the LMD team in Paris for their assistance with the LMDZ model. We thank the two anonymous reviewers for their constructive comments that greatly improved this manuscript.","has_accepted_license":"1","article_number":"e2023MS003726","related_material":{"record":[{"relation":"research_data","status":"public","id":"14991"}]},"article_processing_charge":"Yes","quality_controlled":"1","author":[{"last_name":"Hwong","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22"},{"last_name":"Colin","first_name":"M.","full_name":"Colin, M."},{"last_name":"Aglas","full_name":"Aglas, Philipp","first_name":"Philipp","id":"02eace56-97fc-11ee-b81a-f0939ca85a77"},{"last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"first_name":"S. C.","full_name":"Sherwood, S. C.","last_name":"Sherwood"}],"publication_status":"published","type":"journal_article","volume":15,"file_date_updated":"2023-12-11T08:08:44Z","_id":"14654","oa":1,"oa_version":"Published Version","project":[{"name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"department":[{"_id":"CaMu"}],"citation":{"short":"Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, Journal of Advances in Modeling Earth Systems 15 (2023).","ama":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. 2023;15(12). doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>","apa":"Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., &#38; Sherwood, S. C. (2023). Assessing memory in convection schemes using idealized tests. <i>Journal of Advances in Modeling Earth Systems</i>. Wiley. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>","chicago":"Hwong, Yi-Ling, M. Colin, Philipp Aglas, Caroline J Muller, and S. C. Sherwood. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>. Wiley, 2023. <a href=\"https://doi.org/10.1029/2023MS003726\">https://doi.org/10.1029/2023MS003726</a>.","ieee":"Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Assessing memory in convection schemes using idealized tests,” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12. Wiley, 2023.","ista":"Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. 15(12), e2023MS003726.","mla":"Hwong, Yi-Ling, et al. “Assessing Memory in Convection Schemes Using Idealized Tests.” <i>Journal of Advances in Modeling Earth Systems</i>, vol. 15, no. 12, e2023MS003726, Wiley, 2023, doi:<a href=\"https://doi.org/10.1029/2023MS003726\">10.1029/2023MS003726</a>."},"external_id":{"isi":["001110801100001"]},"publisher":"Wiley"},{"language":[{"iso":"eng"}],"corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.03088","open_access":"1"}],"abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_created":"2023-12-10T23:00:57Z","publication":"Physical Review Letters","date_updated":"2025-09-09T13:35:06Z","date_published":"2023-12-01T00:00:00Z","month":"12","year":"2023","article_type":"original","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Transverse fluctuations control the assembly of semiflexible filaments","day":"01","arxiv":1,"publisher":"American Physical Society","external_id":{"isi":["001163810200008"],"arxiv":["2303.03088"],"pmid":["38101392"]},"volume":131,"_id":"14655","oa":1,"oa_version":"Preprint","citation":{"mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>.","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” <i>Physical Review Letters</i>, vol. 131, no. 22. American Physical Society, 2023.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>.","short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","apa":"Sorichetti, V., &#38; Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. 2023;131(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>"},"department":[{"_id":"AnSa"}],"article_number":"228401","quality_controlled":"1","article_processing_charge":"No","pmid":1,"author":[{"full_name":"Sorichetti, Valerio","orcid":"0000-0002-9645-6576","first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti"},{"last_name":"Lenz","first_name":"Martin","full_name":"Lenz, Martin"}],"publication_status":"published","type":"journal_article","isi":1,"intvolume":"       131","doi":"10.1103/PhysRevLett.131.228401","issue":"22","status":"public","acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066)."},{"external_id":{"isi":["001124419300002"],"pmid":["38016637"]},"publisher":"The Royal Society","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"citation":{"ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” <i>Journal of the Royal Society, Interface</i>, vol. 20, no. 208. The Royal Society, 2023.","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 20(208), 20230355.","mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society, Interface</i>, vol. 20, no. 208, 20230355, The Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>.","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society, Interface 20 (2023).","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society, Interface</i>. 2023;20(208). doi:<a href=\"https://doi.org/10.1098/rsif.2023.0355\">10.1098/rsif.2023.0355</a>","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., &#38; Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. <i>Journal of the Royal Society, Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>","chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” <i>Journal of the Royal Society, Interface</i>. The Royal Society, 2023. <a href=\"https://doi.org/10.1098/rsif.2023.0355\">https://doi.org/10.1098/rsif.2023.0355</a>."},"department":[{"_id":"KrCh"}],"oa":1,"_id":"14657","oa_version":"Published Version","volume":20,"file_date_updated":"2023-12-11T11:10:32Z","type":"journal_article","publication_status":"published","author":[{"last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"first_name":"Kamran","full_name":"Kaveh, Kamran","last_name":"Kaveh"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"pmid":1,"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","article_number":"20230355","status":"public","has_accepted_license":"1","acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","issue":"208","doi":"10.1098/rsif.2023.0355","intvolume":"        20","isi":1,"abstract":[{"text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.","lang":"eng"}],"publication_identifier":{"eissn":["1742-5662"]},"file":[{"date_created":"2023-12-11T11:10:32Z","access_level":"open_access","file_size":1720243,"date_updated":"2023-12-11T11:10:32Z","relation":"main_file","file_name":"2023_RoyalInterface_Tkadlec.pdf","creator":"dernst","checksum":"2eefab13127c7786dbd33303c482a004","file_id":"14673","success":1,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"11","ec_funded":1,"date_published":"2023-11-29T00:00:00Z","publication":"Journal of the Royal Society, Interface","date_updated":"2025-09-09T13:37:01Z","date_created":"2023-12-10T23:00:58Z","ddc":["000","570"],"day":"29","title":"Evolutionary dynamics of mutants that modify population structure","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","year":"2023","article_type":"original"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"date_updated":"2023-12-11T10:49:07Z","relation":"main_file","file_size":2362158,"date_created":"2023-12-11T10:49:07Z","access_level":"open_access","content_type":"application/pdf","file_id":"14672","success":1,"checksum":"ee31c0d0de5d1b65591990ae6705a601","creator":"dernst","file_name":"2023_PhysReviewResearch_Becker.pdf"}],"abstract":[{"lang":"eng","text":"We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom."}],"publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"corr_author":"1","title":"Spin-charge correlations in finite one-dimensional multiband Fermi systems","day":"12","year":"2023","scopus_import":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-12T00:00:00Z","ec_funded":1,"month":"10","ddc":["530"],"date_created":"2023-12-10T23:00:58Z","date_updated":"2025-04-14T07:54:54Z","publication":"Physical Review Research","department":[{"_id":"MiLe"}],"citation":{"chicago":"Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” <i>Physical Review Research</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">https://doi.org/10.1103/PhysRevResearch.5.043039</a>.","apa":"Becker, J. M., Koutentakis, G., &#38; Schmelcher, P. (2023). Spin-charge correlations in finite one-dimensional multiband Fermi systems. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">https://doi.org/10.1103/PhysRevResearch.5.043039</a>","ama":"Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite one-dimensional multiband Fermi systems. <i>Physical Review Research</i>. 2023;5(4). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">10.1103/PhysRevResearch.5.043039</a>","short":"J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023).","mla":"Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” <i>Physical Review Research</i>, vol. 5, no. 4, 043039, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.5.043039\">10.1103/PhysRevResearch.5.043039</a>.","ista":"Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4), 043039.","ieee":"J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations in finite one-dimensional multiband Fermi systems,” <i>Physical Review Research</i>, vol. 5, no. 4. American Physical Society, 2023."},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"volume":5,"file_date_updated":"2023-12-11T10:49:07Z","_id":"14658","oa_version":"Published Version","oa":1,"publisher":"American Physical Society","external_id":{"arxiv":["2305.09529"]},"arxiv":1,"has_accepted_license":"1","status":"public","issue":"4","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","intvolume":"         5","doi":"10.1103/PhysRevResearch.5.043039","author":[{"full_name":"Becker, J. M.","first_name":"J. M.","last_name":"Becker"},{"first_name":"Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","full_name":"Koutentakis, Georgios","last_name":"Koutentakis"},{"full_name":"Schmelcher, P.","first_name":"P.","last_name":"Schmelcher"}],"publication_status":"published","type":"journal_article","article_number":"043039","quality_controlled":"1","article_processing_charge":"Yes"},{"date_updated":"2025-09-09T13:36:16Z","publication":"Nature Geoscience","date_created":"2023-12-10T23:00:58Z","page":"1120-1127","ddc":["550"],"month":"12","date_published":"2023-12-04T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","year":"2023","article_type":"original","day":"04","title":"Local cooling and drying induced by Himalayan glaciers under global warming","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment."}],"publication_identifier":{"issn":["1752-0894"],"eissn":["1752-0908"]},"file":[{"date_created":"2023-12-11T10:11:19Z","access_level":"open_access","relation":"main_file","date_updated":"2023-12-11T10:11:19Z","file_size":6072603,"creator":"dernst","checksum":"d5ae0d17069eebc6f454c8608cf83e21","file_name":"2023_NatureGeoscience_Salerno.pdf","success":1,"file_id":"14671","content_type":"application/pdf"}],"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","related_material":{"link":[{"url":"https://ista.ac.at/en/news/wind-of-climate-change/","relation":"press_release","description":"News on ISTA website"}]},"OA_place":"publisher","type":"journal_article","publication_status":"published","author":[{"full_name":"Salerno, Franco","first_name":"Franco","last_name":"Salerno"},{"last_name":"Guyennon","first_name":"Nicolas","full_name":"Guyennon, Nicolas"},{"full_name":"Yang, Kun","first_name":"Kun","last_name":"Yang"},{"last_name":"Shaw","first_name":"Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","full_name":"Shaw, Thomas","orcid":"0000-0001-7640-6152"},{"last_name":"Lin","first_name":"Changgui","full_name":"Lin, Changgui"},{"last_name":"Colombo","full_name":"Colombo, Nicola","first_name":"Nicola"},{"last_name":"Romano","full_name":"Romano, Emanuele","first_name":"Emanuele"},{"first_name":"Stephan","full_name":"Gruber, Stephan","last_name":"Gruber"},{"last_name":"Bolch","first_name":"Tobias","full_name":"Bolch, Tobias"},{"last_name":"Alessandri","first_name":"Andrea","full_name":"Alessandri, Andrea"},{"first_name":"Paolo","full_name":"Cristofanelli, Paolo","last_name":"Cristofanelli"},{"last_name":"Putero","first_name":"Davide","full_name":"Putero, Davide"},{"last_name":"Diolaiuti","full_name":"Diolaiuti, Guglielmina","first_name":"Guglielmina"},{"last_name":"Tartari","full_name":"Tartari, Gianni","first_name":"Gianni"},{"first_name":"Gianpietro","full_name":"Verza, Gianpietro","last_name":"Verza"},{"full_name":"Thakuri, Sudeep","first_name":"Sudeep","last_name":"Thakuri"},{"last_name":"Balsamo","first_name":"Gianpaolo","full_name":"Balsamo, Gianpaolo"},{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"doi":"10.1038/s41561-023-01331-y","intvolume":"        16","APC_amount":"4800 EUR","isi":1,"has_accepted_license":"1","status":"public","acknowledgement":"This work was carried out within the framework of the EV-K2-CNR and Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C. was supported by the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no. ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058. F.P. has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN, ‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’ (grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 101004156 (CONFESS project) and by the European Union’s Horizon Europe research and innovation program under grant agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant for the whole globe.","external_id":{"isi":["001112839700003"]},"publisher":"Springer Nature","_id":"14659","oa_version":"Published Version","oa":1,"volume":16,"file_date_updated":"2023-12-11T10:11:19Z","department":[{"_id":"FrPe"}],"citation":{"chicago":"Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin, Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” <i>Nature Geoscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41561-023-01331-y\">https://doi.org/10.1038/s41561-023-01331-y</a>.","apa":"Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti, F. (2023). Local cooling and drying induced by Himalayan glaciers under global warming. <i>Nature Geoscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41561-023-01331-y\">https://doi.org/10.1038/s41561-023-01331-y</a>","ama":"Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan glaciers under global warming. <i>Nature Geoscience</i>. 2023;16:1120-1127. doi:<a href=\"https://doi.org/10.1038/s41561-023-01331-y\">10.1038/s41561-023-01331-y</a>","short":"F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano, S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti, G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature Geoscience 16 (2023) 1120–1127.","ista":"Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127.","mla":"Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” <i>Nature Geoscience</i>, vol. 16, Springer Nature, 2023, pp. 1120–27, doi:<a href=\"https://doi.org/10.1038/s41561-023-01331-y\">10.1038/s41561-023-01331-y</a>.","ieee":"F. Salerno <i>et al.</i>, “Local cooling and drying induced by Himalayan glaciers under global warming,” <i>Nature Geoscience</i>, vol. 16. Springer Nature, pp. 1120–1127, 2023."}},{"type":"journal_article","author":[{"last_name":"Carioni","full_name":"Carioni, Marcello","first_name":"Marcello"},{"last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"first_name":"Anja","full_name":"Schlömerkemper, Anja","last_name":"Schlömerkemper"}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","status":"public","issue":"1","intvolume":"        30","isi":1,"external_id":{"arxiv":["1811.09857"],"isi":["001115503400013"]},"publisher":"Heldermann Verlag","arxiv":1,"department":[{"_id":"JuFi"}],"citation":{"chicago":"Carioni, Marcello, Julian L Fischer, and Anja Schlömerkemper. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” <i>Journal of Convex Analysis</i>. Heldermann Verlag, 2023.","short":"M. Carioni, J.L. Fischer, A. Schlömerkemper, Journal of Convex Analysis 30 (2023) 217–247.","ama":"Carioni M, Fischer JL, Schlömerkemper A. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. <i>Journal of Convex Analysis</i>. 2023;30(1):217-247.","apa":"Carioni, M., Fischer, J. L., &#38; Schlömerkemper, A. (2023). External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. <i>Journal of Convex Analysis</i>. Heldermann Verlag.","mla":"Carioni, Marcello, et al. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” <i>Journal of Convex Analysis</i>, vol. 30, no. 1, Heldermann Verlag, 2023, pp. 217–47.","ista":"Carioni M, Fischer JL, Schlömerkemper A. 2023. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 30(1), 217–247.","ieee":"M. Carioni, J. L. Fischer, and A. Schlömerkemper, “External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development,” <i>Journal of Convex Analysis</i>, vol. 30, no. 1. Heldermann Verlag, pp. 217–247, 2023."},"oa_version":"Preprint","_id":"14661","oa":1,"volume":30,"month":"01","date_published":"2023-01-01T00:00:00Z","date_updated":"2024-10-09T21:07:35Z","publication":"Journal of Convex Analysis","date_created":"2023-12-10T23:00:59Z","page":"217-247","day":"01","title":"External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","scopus_import":"1","year":"2023","publication_identifier":{"eissn":["2363-6394"],"issn":["0944-6532"]},"abstract":[{"text":"This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are \"close to\" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.09857"}],"corr_author":"1","language":[{"iso":"eng"}]},{"month":"11","date_published":"2023-11-25T00:00:00Z","date_updated":"2025-09-09T13:40:33Z","publication":"Journal of Spectral Theory","date_created":"2023-12-10T23:00:59Z","page":"1045-1055","ddc":["510"],"day":"25","title":"Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","year":"2023","article_type":"original","abstract":[{"lang":"eng","text":"We consider a class of polaron models, including the Fröhlich model, at zero total momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below the essential spectrum."}],"publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"file":[{"content_type":"application/pdf","success":1,"file_id":"14677","checksum":"9ce96ca87d56ea9a70d2eb9a32839f8d","creator":"dernst","file_name":"2023_JST_Seiringer.pdf","file_size":201513,"relation":"main_file","date_updated":"2023-12-11T12:03:12Z","date_created":"2023-12-11T12:03:12Z","access_level":"open_access"}],"OA_type":"diamond","corr_author":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"DOAJ_listed":"1","type":"journal_article","author":[{"last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"publication_status":"published","article_processing_charge":"Yes","quality_controlled":"1","OA_place":"publisher","status":"public","issue":"3","has_accepted_license":"1","doi":"10.4171/JST/469","intvolume":"        13","isi":1,"external_id":{"arxiv":["2210.17123"],"isi":["001127467700008"]},"publisher":"EMS Press","arxiv":1,"citation":{"chicago":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” <i>Journal of Spectral Theory</i>. EMS Press, 2023. <a href=\"https://doi.org/10.4171/JST/469\">https://doi.org/10.4171/JST/469</a>.","short":"R. Seiringer, Journal of Spectral Theory 13 (2023) 1045–1055.","apa":"Seiringer, R. (2023). Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. <i>Journal of Spectral Theory</i>. EMS Press. <a href=\"https://doi.org/10.4171/JST/469\">https://doi.org/10.4171/JST/469</a>","ama":"Seiringer R. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. <i>Journal of Spectral Theory</i>. 2023;13(3):1045-1055. doi:<a href=\"https://doi.org/10.4171/JST/469\">10.4171/JST/469</a>","ista":"Seiringer R. 2023. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 13(3), 1045–1055.","mla":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” <i>Journal of Spectral Theory</i>, vol. 13, no. 3, EMS Press, 2023, pp. 1045–55, doi:<a href=\"https://doi.org/10.4171/JST/469\">10.4171/JST/469</a>.","ieee":"R. Seiringer, “Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling,” <i>Journal of Spectral Theory</i>, vol. 13, no. 3. EMS Press, pp. 1045–1055, 2023."},"department":[{"_id":"RoSe"}],"_id":"14662","oa_version":"Published Version","oa":1,"file_date_updated":"2023-12-11T12:03:12Z","volume":13}]