[{"scopus_import":"1","article_processing_charge":"No","day":"01","article_type":"original","citation":{"short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.","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).” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.174302.","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). Physical Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302","apa":"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. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302","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),” Physical Review B, 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."},"publication":"Physical Review B","date_published":"2023-11-01T00:00:00Z","type":"journal_article","issue":"17","abstract":[{"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.","lang":"eng"}],"intvolume":" 108","status":"public","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14605","oa_version":"None","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"11","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.108.174302","article_number":"174302","ec_funded":1,"department":[{"_id":"BiCh"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","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.","volume":108,"date_updated":"2023-11-28T07:48:55Z","date_created":"2023-11-26T23:00:54Z","author":[{"full_name":"Ouyang, Niuchang","last_name":"Ouyang","first_name":"Niuchang"},{"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"},{"full_name":"Wang, Qi","first_name":"Qi","last_name":"Wang"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}]},{"quality_controlled":"1","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512"}],"main_file_link":[{"url":"https://eprint.iacr.org/2022/1389","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2023-08-09","location":"Anaheim, CA, United States","end_date":"2023-08-11","name":"USENIX Security Symposium"},"month":"08","publication_identifier":{"isbn":["9781713879497"]},"publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Usenix","year":"2023","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.","date_updated":"2023-11-28T09:17:38Z","date_created":"2023-11-26T23:00:55Z","volume":8,"author":[{"first_name":"Sourav","last_name":"Das","full_name":"Das, Sourav"},{"first_name":"Zhuolun","last_name":"Xiang","full_name":"Xiang, Zhuolun"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Ren, Ling","first_name":"Ling","last_name":"Ren"}],"file_date_updated":"2023-11-28T09:14:34Z","page":"5359-5376","publication":"32nd USENIX Security Symposium","citation":{"short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium, vol. 8, Usenix, 2023, pp. 5359–76.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: 32nd USENIX Security Symposium. Vol 8. Usenix; 2023:5359-5376.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in 32nd USENIX Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","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."},"date_published":"2023-08-15T00:00:00Z","scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","ddc":["000"],"status":"public","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","intvolume":" 8","_id":"14609","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","content_type":"application/pdf","file_size":704331,"access_level":"open_access","file_name":"2023_USENIX_Das.pdf","success":1,"checksum":"1a730765930138e23c6efd2575872641","date_created":"2023-11-28T09:14:34Z","date_updated":"2023-11-28T09:14:34Z","file_id":"14621","relation":"main_file"}],"oa_version":"Published Version","type":"conference","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."}]},{"citation":{"mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 2023;159(18). doi:10.1063/5.0173341","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,” Journal of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.","apa":"Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341"},"publication":"Journal of Chemical Physics","article_type":"original","date_published":"2023-11-14T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14603","intvolume":" 159","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","ddc":["530","540"],"status":"public","file":[{"file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","access_level":"open_access","creator":"dernst","file_size":6276059,"content_type":"application/pdf","file_id":"14620","relation":"main_file","date_updated":"2023-11-28T08:39:06Z","date_created":"2023-11-28T08:39:06Z","success":1,"checksum":"f668ee0d07096eef81159d05bc27aabc"}],"oa_version":"Published Version","type":"journal_article","issue":"18","abstract":[{"lang":"eng","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."}],"external_id":{"arxiv":["2308.10886"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1063/5.0173341","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"11","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.","year":"2023","publisher":"AIP Publishing","department":[{"_id":"BiCh"}],"publication_status":"published","related_material":{"record":[{"id":"14619","relation":"research_data","status":"public"}]},"author":[{"first_name":"Aleks","last_name":"Reinhardt","full_name":"Reinhardt, Aleks"},{"full_name":"Chew, Pin Yu","first_name":"Pin Yu","last_name":"Chew"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"}],"volume":159,"date_updated":"2023-11-28T08:39:23Z","date_created":"2023-11-26T23:00:54Z","article_number":"184110","file_date_updated":"2023-11-28T08:39:06Z","license":"https://creativecommons.org/licenses/by/4.0/"},{"month":"11","publication_identifier":{"eissn":["1558-5646"]},"doi":"10.1093/evolut/qpad169","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37738212"]},"quality_controlled":"1","file_date_updated":"2023-11-28T08:12:15Z","author":[{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/veryoldx"}],"record":[{"status":"public","relation":"research_data","id":"14616"},{"id":"14617","relation":"research_data","status":"public"}]},"date_updated":"2023-11-28T08:25:28Z","date_created":"2023-11-26T23:00:54Z","volume":77,"year":"2023","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.","pmid":1,"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","day":"02","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-11-02T00:00:00Z","publication":"Evolution","citation":{"ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpad169."},"article_type":"original","page":"2504-2511","abstract":[{"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.","lang":"eng"}],"issue":"11","type":"journal_article","file":[{"date_created":"2023-11-28T08:12:15Z","date_updated":"2023-11-28T08:12:15Z","success":1,"checksum":"b66dc10edae92d38918d534e64dda77c","file_id":"14618","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1399102,"file_name":"2023_Evolution_Toups.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14604","status":"public","title":"The X chromosome of insects likely predates the origin of class Insecta","ddc":["570"],"intvolume":" 77"},{"related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"oa_version":"Published Version","date_updated":"2023-11-28T08:17:31Z","date_created":"2023-11-28T08:01:53Z","_id":"14616","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","publisher":"Dryad","department":[{"_id":"BeVi"}],"status":"public","ddc":["570"],"title":"The X chromosome of insects likely predates the origin of Class Insecta","abstract":[{"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.","lang":"eng"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","date_published":"2023-09-15T00:00:00Z","doi":"10.5061/DRYAD.HX3FFBGKT","citation":{"chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.","short":"M.A. Toups, B. Vicoso, (2023).","mla":"Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","apa":"Toups, M. A., & Vicoso, B. (2023). 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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."}],"year":"2023","_id":"14617","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The X chromosome of insects likely predates the origin of Class Insecta","ddc":["570"],"status":"public","department":[{"_id":"BeVi"}],"publisher":"Zenodo","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-11-28T08:25:28Z","date_created":"2023-11-28T08:04:03Z","oa_version":"Published Version"},{"citation":{"chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.","mla":"Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.","short":"B. Cheng, (2023).","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8398094","open_access":"1"}],"oa":1,"doi":"10.5281/ZENODO.8398094","date_published":"2023-10-02T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"02","month":"10","_id":"14619","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BiCh"}],"publisher":"Zenodo","status":"public","ddc":["530"],"title":"BingqingCheng/solubility: V1.0","related_material":{"record":[{"id":"14603","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"oa_version":"Published Version","date_updated":"2023-11-28T08:39:22Z","date_created":"2023-11-28T08:32:18Z","type":"research_data_reference","abstract":[{"lang":"eng","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)."}]},{"scopus_import":"1","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Journal of Advances in Modeling Earth Systems","citation":{"mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:10.1029/2022ms003391.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems. American Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391.","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11. American Geophysical Union, 2023.","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. American Geophysical Union. https://doi.org/10.1029/2022ms003391"},"article_type":"original","date_published":"2023-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"issue":"11","_id":"14564","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","ddc":["550"],"status":"public","intvolume":" 15","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14582","checksum":"e30329dd985559de0ddc7021ca7382b4","success":1,"date_created":"2023-11-20T11:29:16Z","date_updated":"2023-11-20T11:29:16Z","access_level":"open_access","file_name":"2023_JAMES_Khoulder.pdf","file_size":6435697,"content_type":"application/pdf","creator":"dernst"}],"month":"11","publication_identifier":{"eissn":["1942-2466"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","doi":"10.1029/2022ms003391","language":[{"iso":"eng"}],"article_number":"e2022MS003391","file_date_updated":"2023-11-20T11:29:16Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","year":"2023","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"American Geophysical Union","author":[{"first_name":"B.","last_name":"Khouider","full_name":"Khouider, B."},{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","orcid":"0000-0001-8602-3083","first_name":"BIDYUT B","last_name":"GOSWAMI","full_name":"GOSWAMI, BIDYUT B"},{"full_name":"Phani, R.","last_name":"Phani","first_name":"R."},{"full_name":"Majda, A. J.","first_name":"A. J.","last_name":"Majda"}],"date_updated":"2023-11-28T12:04:42Z","date_created":"2023-11-20T09:18:21Z","volume":15},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14612","checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","success":1,"date_updated":"2023-11-27T09:51:48Z","date_created":"2023-11-27T09:51:48Z","access_level":"open_access","file_name":"PhysRevE.107.034901 (1).pdf","content_type":"application/pdf","file_size":1428631,"creator":"swaituka"}],"_id":"12789","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"title":"Accurate determination of the shapes of granular charge distributions","status":"public","intvolume":" 107","abstract":[{"text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2023-03-01T00:00:00Z","publication":"Physical Review E","citation":{"ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901","apa":"Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.034901","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” Physical Review E, vol. 107, no. 3. American Physical Society, 2023.","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901."},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Mujica","first_name":"Nicolás","full_name":"Mujica, Nicolás"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-11-28T09:22:25Z","volume":107,"acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. 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. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"file_date_updated":"2023-11-27T09:51:48Z","ec_funded":1,"article_number":"034901","doi":"10.1103/PhysRevE.107.034901","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000992142700001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"month":"03","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]}},{"quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.13459","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2204.13459"]},"language":[{"iso":"eng"}],"conference":{"name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2023-06-09","start_date":"2023-06-06","location":"Alcala de Henares, Spain"},"doi":"10.1007/978-3-031-32733-9_26","month":"05","publication_identifier":{"isbn":["9783031327322"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"},{"_id":"KrCh"}],"year":"2023","acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024.","date_updated":"2023-11-30T10:54:51Z","date_created":"2023-07-16T22:01:12Z","volume":13892,"author":[{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"last_name":"Svoboda","first_name":"Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"},{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"related_material":{"record":[{"id":"14506","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"page":"576-594","publication":"SIROCCO 2023: Structural Information and Communication Complexity ","citation":{"ista":"Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in SIROCCO 2023: Structural Information and Communication Complexity , Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.","apa":"Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In SIROCCO 2023: Structural Information and Communication Complexity (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26","ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023: Structural Information and Communication Complexity . Vol 13892. Springer Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26","chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In SIROCCO 2023: Structural Information and Communication Complexity , 13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94, doi:10.1007/978-3-031-32733-9_26.","short":"S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594."},"date_published":"2023-05-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"No","status":"public","title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","intvolume":" 13892","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13238","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."}]},{"day":"10","has_accepted_license":"1","article_processing_charge":"No","page":"162","citation":{"ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506","chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.","mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023."},"date_published":"2023-11-10T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"title":"Advances in efficiency and privacy in payment channel network analysis","ddc":["000"],"status":"public","_id":"14506","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"access_level":"closed","file_name":"thesis_yeo.zip","content_type":"application/x-zip-compressed","file_size":3037720,"creator":"cchlebak","relation":"source_file","file_id":"14598","checksum":"521c72818d720a52b377207b2ee87b6a","date_created":"2023-11-23T10:29:55Z","date_updated":"2023-11-23T10:29:55Z"},{"access_level":"open_access","file_name":"thesis_yeo.pdf","content_type":"application/pdf","file_size":2717256,"creator":"cchlebak","relation":"main_file","file_id":"14599","checksum":"0ed5d16899687aecf13d843c9878c9f2","success":1,"date_created":"2023-11-23T10:30:08Z","date_updated":"2023-11-23T10:30:08Z"}],"oa_version":"Published Version","month":"11","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"supervisor":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/14506","file_date_updated":"2023-11-23T10:30:08Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_created":"2023-11-10T08:10:43Z","date_updated":"2023-11-30T10:54:51Z","author":[{"full_name":"Yeo, Michelle X","last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"9969","status":"public","relation":"part_of_dissertation"},{"id":"13238","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14490"}]}},{"article_processing_charge":"No","day":"11","scopus_import":"1","date_published":"2023-10-11T00:00:00Z","citation":{"apa":"Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning creation games. In 43rd International Conference on Distributed Computing Systems (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037","ieee":"Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in 43rd International Conference on Distributed Computing Systems, Hong Kong, China, 2023, vol. 2023, pp. 603–613.","ista":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613.","ama":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: 43rd International Conference on Distributed Computing Systems. Vol 2023. IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037","chicago":"Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In 43rd International Conference on Distributed Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.","short":"Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.","mla":"Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13, doi:10.1109/ICDCS57875.2023.00037."},"publication":"43rd International Conference on Distributed Computing Systems","page":"603-613","abstract":[{"text":"Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"14490","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2023","status":"public","title":"Lightning creation games","publication_identifier":{"eissn":["2575-8411"],"isbn":["9798350339864"]},"month":"10","doi":"10.1109/ICDCS57875.2023.00037","conference":{"name":"ICDCS: International Conference on Distributed Computing Systems","start_date":"2023-07-18","location":"Hong Kong, China","end_date":"2023-07-21"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.16006","open_access":"1"}],"external_id":{"arxiv":["2306.16006"]},"oa":1,"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14506"}]},"author":[{"last_name":"Avarikioti","first_name":"Zeta","full_name":"Avarikioti, Zeta"},{"last_name":"Lizurej","first_name":"Tomasz","full_name":"Lizurej, Tomasz"},{"full_name":"Michalak, Tomasz","first_name":"Tomasz","last_name":"Michalak"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo"}],"volume":2023,"date_created":"2023-11-05T23:00:54Z","date_updated":"2023-11-30T10:54:51Z","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666.","year":"2023","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published"},{"date_published":"2023-03-23T00:00:00Z","citation":{"chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726"},"page":"260","has_accepted_license":"1","article_processing_charge":"No","day":"23","file":[{"file_id":"12745","relation":"main_file","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","date_updated":"2023-11-24T11:57:46Z","date_created":"2023-03-23T12:49:23Z","access_level":"closed","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":63734746},{"access_level":"closed","file_name":"Thesis_Riedl_2023_source.rar","embargo_to":"open_access","creator":"cchlebak","content_type":"application/octet-stream","file_size":339473651,"file_id":"12746","relation":"source_file","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","date_updated":"2023-09-24T22:30:03Z","date_created":"2023-03-23T12:54:34Z"}],"oa_version":"None","_id":"12726","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["530"],"title":"Synchronization in collectively moving active matter","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:12726","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["2663-337X"]},"month":"03","related_material":{"record":[{"id":"10703","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"id":"7932","relation":"part_of_dissertation","status":"public"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"id":"14530","relation":"new_edition","status":"public"}]},"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael"}],"date_created":"2023-03-15T13:22:13Z","date_updated":"2023-11-30T10:55:13Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2023-11-24T11:57:46Z"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14530","status":"public","title":"Synchronization in collectively moving active matter","ddc":["530","570"],"file":[{"access_level":"open_access","file_name":"Thesis_Riedl_2023_corr.pdf","file_size":36743942,"content_type":"application/pdf","creator":"mriedl","relation":"main_file","file_id":"14536","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","success":1,"date_created":"2023-11-15T09:52:54Z","date_updated":"2023-11-15T09:52:54Z"}],"oa_version":"Updated Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. "}],"citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530."},"page":"260","date_published":"2023-11-16T00:00:00Z","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"day":"16","article_processing_charge":"No","has_accepted_license":"1","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"10791","status":"public","relation":"part_of_dissertation"},{"id":"7932","relation":"part_of_dissertation","status":"public"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"old_edition","id":"12726"}]},"date_updated":"2023-11-30T10:55:13Z","date_created":"2023-11-15T09:59:03Z","file_date_updated":"2023-11-15T09:52:54Z","oa":1,"doi":"10.15479/14530","supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["2663 - 337X"]}},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"doi":"10.15479/14547","publication_identifier":{"issn":["2663 - 337X"]},"month":"11","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"publication_status":"published","year":"2023","date_updated":"2023-11-30T10:56:04Z","date_created":"2023-11-17T13:45:26Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10851"},{"status":"public","relation":"part_of_dissertation","id":"13264"}]},"author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-11-22T09:46:06Z","page":"80","citation":{"ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547."},"date_published":"2023-11-16T00:00:00Z","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"article_processing_charge":"No","has_accepted_license":"1","day":"16","status":"public","ddc":["530"],"title":"Resonant microwave spectroscopy of Al-InAs","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"14547","file":[{"checksum":"db0c37d213bc002125bd59690e9db246","date_updated":"2023-11-22T09:46:06Z","date_created":"2023-11-17T13:36:44Z","relation":"main_file","file_id":"14548","content_type":"application/pdf","file_size":34828019,"creator":"pduc","access_level":"open_access","file_name":"Phan_Thesis_pdfa.pdf"},{"checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","date_created":"2023-11-17T13:44:53Z","date_updated":"2023-11-17T13:47:54Z","file_id":"14549","relation":"source_file","creator":"pduc","file_size":279319709,"content_type":"application/zip","access_level":"closed","file_name":"dissertation_src.zip"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.","lang":"eng"}]},{"issue":"6","abstract":[{"text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 19","status":"public","title":"Gate-tunable superconductor-semiconductor parametric amplifier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13264","article_processing_charge":"No","day":"09","scopus_import":"1","date_published":"2023-06-09T00:00:00Z","article_type":"original","citation":{"apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.19.064032","ieee":"D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical Society, 2023.","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.19.064032.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:10.1103/PhysRevApplied.19.064032."},"publication":"Physical Review Applied","article_number":"064032","volume":19,"date_updated":"2023-11-30T10:56:03Z","date_created":"2023-07-23T22:01:12Z","related_material":{"record":[{"id":"14547","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"},{"first_name":"Paul","last_name":"Falthansl-Scheinecker","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","full_name":"Falthansl-Scheinecker, Paul"},{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","last_name":"Mishra","first_name":"Umang","full_name":"Mishra, Umang"},{"full_name":"Strickland, W. M.","last_name":"Strickland","first_name":"W. M."},{"first_name":"D.","last_name":"Langone","full_name":"Langone, D."},{"full_name":"Shabani, J.","last_name":"Shabani","first_name":"J."},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P"}],"publisher":"American Physical Society","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"publication_status":"published","year":"2023","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","publication_identifier":{"eissn":["2331-7019"]},"month":"06","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.1103/PhysRevApplied.19.064032","quality_controlled":"1","isi":1,"external_id":{"arxiv":["2206.05746"],"isi":["001012022600004"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.05746"}],"oa":1},{"related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Nagel, Marie-Kristin","last_name":"Nagel","first_name":"Marie-Kristin"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","last_name":"Hlavata","first_name":"Annamaria","full_name":"Hlavata, Annamaria"},{"first_name":"Erika","last_name":"Isono","full_name":"Isono, Erika"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"oa_version":"Preprint","date_created":"2023-11-22T10:17:49Z","date_updated":"2023-12-01T13:51:06Z","year":"2023","_id":"14591","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"publication_status":"submitted","status":"public","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","ec_funded":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"type":"preprint","date_published":"2023-10-10T00:00:00Z","doi":"10.1101/2023.10.09.561523","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2"}],"citation":{"ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523."},"oa":1,"publication":"bioRxiv","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"article_processing_charge":"No","day":"10","month":"10"},{"type":"journal_article","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”."}],"_id":"14639","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","intvolume":" 15","file":[{"file_size":14791081,"content_type":"application/pdf","creator":"dernst","file_name":"2023_GenomeMed_Lin.pdf","access_level":"open_access","date_created":"2023-12-04T08:15:43Z","date_updated":"2023-12-04T08:15:43Z","checksum":"279efd212005549aba817a487d56d363","success":1,"relation":"main_file","file_id":"14640"}],"oa_version":"Published Version","keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"day":"23","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Genome Medicine","citation":{"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. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4","ieee":"S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer Nature, 2023.","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.","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01258-4","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.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4.","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).","mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102, Springer Nature, 2023, doi:10.1186/s13073-023-01258-4."},"article_type":"original","date_published":"2023-11-23T00:00:00Z","article_number":"102","file_date_updated":"2023-12-04T08:15:43Z","extern":"1","year":"2023","publication_status":"published","publisher":"Springer Nature","author":[{"first_name":"Sheng-Jia","last_name":"Lin","full_name":"Lin, Sheng-Jia"},{"last_name":"Vona","first_name":"Barbara","full_name":"Vona, Barbara"},{"full_name":"Lau, Tracy","first_name":"Tracy","last_name":"Lau"},{"last_name":"Huang","first_name":"Kevin","orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin"},{"full_name":"Zaki, Maha S.","first_name":"Maha S.","last_name":"Zaki"},{"full_name":"Aldeen, Huda Shujaa","last_name":"Aldeen","first_name":"Huda Shujaa"},{"full_name":"Karimiani, Ehsan Ghayoor","first_name":"Ehsan Ghayoor","last_name":"Karimiani"},{"full_name":"Rocca, Clarissa","first_name":"Clarissa","last_name":"Rocca"},{"last_name":"Noureldeen","first_name":"Mahmoud M.","full_name":"Noureldeen, Mahmoud M."},{"first_name":"Ahmed K.","last_name":"Saad","full_name":"Saad, Ahmed K."},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"first_name":"Tobias","last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias"},{"full_name":"Abou Jamra, Rami","first_name":"Rami","last_name":"Abou Jamra"},{"full_name":"Zifarelli, Giovanni","last_name":"Zifarelli","first_name":"Giovanni"},{"last_name":"Gotkhindikar","first_name":"Aditi","full_name":"Gotkhindikar, Aditi"},{"first_name":"Ingrid M.","last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M."},{"full_name":"Liao, Mingjuan","first_name":"Mingjuan","last_name":"Liao"},{"full_name":"Cork, Emalyn Elise","last_name":"Cork","first_name":"Emalyn Elise"},{"last_name":"Varshney","first_name":"Pratishtha","full_name":"Varshney, Pratishtha"},{"full_name":"Hashemi, Narges","last_name":"Hashemi","first_name":"Narges"},{"full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan","last_name":"Mohammadi"},{"first_name":"Aboulfazl","last_name":"Rad","full_name":"Rad, Aboulfazl"},{"last_name":"Neira","first_name":"Juanita","full_name":"Neira, Juanita"},{"full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi","last_name":"Toosi"},{"full_name":"Knopp, Cordula","first_name":"Cordula","last_name":"Knopp"},{"full_name":"Kurth, Ingo","first_name":"Ingo","last_name":"Kurth"},{"last_name":"Challman","first_name":"Thomas D.","full_name":"Challman, Thomas D."},{"first_name":"Rebecca","last_name":"Smith","full_name":"Smith, Rebecca"},{"first_name":"Asmahan","last_name":"Abdalla","full_name":"Abdalla, Asmahan"},{"full_name":"Haaf, Thomas","first_name":"Thomas","last_name":"Haaf"},{"full_name":"Suri, Mohnish","first_name":"Mohnish","last_name":"Suri"},{"first_name":"Manali","last_name":"Joshi","full_name":"Joshi, Manali"},{"full_name":"Chung, Wendy K.","first_name":"Wendy K.","last_name":"Chung"},{"first_name":"Andres","last_name":"Moreno-De-Luca","full_name":"Moreno-De-Luca, Andres"},{"first_name":"Henry","last_name":"Houlden","full_name":"Houlden, Henry"},{"full_name":"Maroofian, Reza","last_name":"Maroofian","first_name":"Reza"},{"last_name":"Varshney","first_name":"Gaurav K.","full_name":"Varshney, Gaurav K."}],"date_created":"2023-12-04T08:10:55Z","date_updated":"2023-12-04T08:17:22Z","volume":15,"month":"11","publication_identifier":{"issn":["1756-994X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1186/s13073-023-01258-4","language":[{"iso":"eng"}]},{"type":"journal_article","issue":"5","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14628","intvolume":" 42","ddc":["531","006"],"title":"Procedural metamaterials: A unified procedural graph for metamaterial design","status":"public","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14630","date_created":"2023-11-29T15:16:01Z","date_updated":"2023-11-29T15:16:01Z","checksum":"0192f597d7a2ceaf89baddfd6190d4c8","success":1,"file_name":"tog-22-0089-File004.zip","access_level":"open_access","file_size":95467870,"content_type":"application/zip","creator":"yichen"},{"creator":"yichen","file_size":103731880,"content_type":"application/zip","access_level":"open_access","file_name":"tog-22-0089-File005.zip","success":1,"checksum":"7fb024963be81933494f38de191e4710","date_updated":"2023-11-29T15:16:01Z","date_created":"2023-11-29T15:16:01Z","file_id":"14631","relation":"main_file"},{"date_updated":"2023-12-04T08:04:14Z","date_created":"2023-12-04T08:04:14Z","checksum":"b7d6829ce396e21cac9fae0ec7130a6b","success":1,"relation":"main_file","file_id":"14638","file_size":57067476,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ACMToG_Makatura.pdf","access_level":"open_access"}],"keyword":["Computer Graphics and Computer-Aided Design"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","citation":{"mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","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.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389","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.","ieee":"L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","apa":"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. Association for Computing Machinery. https://doi.org/10.1145/3605389"},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2023-10-01T00:00:00Z","article_number":"168","file_date_updated":"2023-12-04T08:04:14Z","year":"2023","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.","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","author":[{"first_name":"Liane","last_name":"Makatura","full_name":"Makatura, Liane"},{"full_name":"Wang, Bohan","first_name":"Bohan","last_name":"Wang"},{"full_name":"Chen, Yi-Lu","last_name":"Chen","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"first_name":"Bolei","last_name":"Deng","full_name":"Deng, Bolei"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"}],"volume":42,"date_updated":"2023-12-04T08:09:05Z","date_created":"2023-11-29T15:02:03Z","publication_identifier":{"issn":["0730-0301","1557-7368"]},"month":"10","oa":1,"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"quality_controlled":"1","doi":"10.1145/3605389","language":[{"iso":"eng"}]},{"has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"05","project":[{"name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","grant_number":"P34185"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"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. https://doi.org/10.15479/AT:ISTA:14644.","mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_published":"2023-12-05T00:00:00Z","doi":"10.15479/AT:ISTA:14644","type":"preprint","file_date_updated":"2023-12-05T10:37:02Z","abstract":[{"lang":"eng","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."}],"department":[{"_id":"CaBe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"submitted","ddc":["572"],"status":"public","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","year":"2023","_id":"14644","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"14646","checksum":"c45608cb97ee36d7b50ba518db8e07b0","success":1,"date_created":"2023-12-05T10:37:02Z","date_updated":"2023-12-05T10:37:02Z","access_level":"open_access","file_name":"2023_Tluckova_etal_REx.pdf","content_type":"application/pdf","file_size":4892920,"creator":"dernst"}],"date_created":"2023-12-04T14:51:00Z","date_updated":"2023-12-05T10:37:28Z","author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Tluckova","full_name":"Tluckova, Katarina"},{"full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P","last_name":"Testa Salmazo"},{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"}]}]