[{"abstract":[{"lang":"eng","text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"month":"03","intvolume":" 107","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":107,"issue":"3","_id":"12819","article_type":"letter_note","type":"journal_article","status":"public","date_updated":"2023-08-01T14:06:05Z","department":[{"_id":"JoFi"}],"acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2023","day":"22","publication":"Physical Review A","date_published":"2023-03-22T00:00:00Z","doi":"10.1103/PhysRevA.107.L031701","date_created":"2023-04-09T22:01:00Z","article_number":"L031701","citation":{"chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L031701.","ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701.","mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.","ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical Society, 2023.","short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L031701"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Sokolova, Alesya","orcid":"0000-0002-8308-4144","last_name":"Sokolova","first_name":"Alesya","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a"},{"first_name":"D. A.","last_name":"Kalacheva","full_name":"Kalacheva, D. A."},{"first_name":"G. P.","full_name":"Fedorov, G. P.","last_name":"Fedorov"},{"first_name":"O. V.","full_name":"Astafiev, O. V.","last_name":"Astafiev"}],"external_id":{"isi":["000957799000006"],"arxiv":["2209.05165"]},"article_processing_charge":"No","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling"},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations.","lang":"eng"}],"intvolume":" 14","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","file_id":"12868","success":1,"creator":"dernst","date_updated":"2023-04-25T09:13:53Z","file_size":1786475,"date_created":"2023-04-25T09:13:53Z","file_name":"2023_NatureComm_Schmid.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"volume":14,"_id":"12861","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2023-08-01T14:15:57Z","department":[{"_id":"KrCh"}],"file_date_updated":"2023-04-25T09:13:53Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","day":"12","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-04-23T22:01:03Z","date_published":"2023-04-12T00:00:00Z","doi":"10.1038/s41467-023-37817-x","article_number":"2086","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer Nature, 2023, doi:10.1038/s41467-023-37817-x.","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","apa":"Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 2023;14. doi:10.1038/s41467-023-37817-x","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086."},"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","article_processing_charge":"No","external_id":{"pmid":["37045828"],"isi":["001003644100020"]},"author":[{"last_name":"Schmid","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Farbod","last_name":"Ekbatani","full_name":"Ekbatani, Farbod"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}]},{"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","date_created":"2023-04-23T22:01:03Z","date_published":"2023-04-01T00:00:00Z","doi":"10.1371/journal.pcbi.1010983","publication":"PLoS Computational Biology","day":"01","year":"2023","has_accepted_license":"1","isi":1,"article_number":"e1010983","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","external_id":{"isi":["000962668700002"]},"article_processing_charge":"No","author":[{"first_name":"Shervin","full_name":"Safavi, Shervin","last_name":"Safavi"},{"last_name":"Panagiotaropoulos","full_name":"Panagiotaropoulos, Theofanis I.","first_name":"Theofanis I."},{"first_name":"Vishal","full_name":"Kapoor, Vishal","last_name":"Kapoor"},{"id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F","last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."},{"first_name":"Michel","full_name":"Besserve, Michel","last_name":"Besserve"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol. 19, no. 4. Public Library of Science, 2023.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983."},"intvolume":" 19","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"issue":"4","related_material":{"link":[{"url":"https://github.com/shervinsafavi/gpla.git","relation":"software"}]},"volume":19,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"12867","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_PLoSCompBio_Safavi.pdf","date_created":"2023-04-25T08:59:18Z","file_size":4737671,"date_updated":"2023-04-25T08:59:18Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1553-7358"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"12862","department":[{"_id":"JoCs"}],"file_date_updated":"2023-04-25T08:59:18Z","ddc":["570"],"date_updated":"2023-08-01T14:15:16Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.","ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d3sc00841j","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” Chemical Science. Royal Society of Chemistry, 2023.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science."},"title":"Physics-inspired machine learning of localized intensive properties","author":[{"id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","first_name":"Ke","last_name":"Chen","full_name":"Chen, Ke"},{"last_name":"Kunkel","full_name":"Kunkel, Christian","first_name":"Christian"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"last_name":"Reuter","full_name":"Reuter, Karsten","first_name":"Karsten"},{"last_name":"Margraf","full_name":"Margraf, Johannes T.","first_name":"Johannes T."}],"external_id":{"isi":["000971508100001"]},"article_processing_charge":"No","day":"10","publication":"Chemical Science","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-04-10T00:00:00Z","doi":"10.1039/d3sc00841j","date_created":"2023-04-30T22:01:06Z","acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"ddc":["000","540"],"date_updated":"2023-08-01T14:18:10Z","department":[{"_id":"BiCh"}],"file_date_updated":"2023-05-02T07:17:05Z","_id":"12879","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"file":[{"file_id":"12883","checksum":"5eeec69a51e192dcd94b955d84423836","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-02T07:17:05Z","file_name":"2023_ChemialScience_Chen.pdf","date_updated":"2023-05-02T07:17:05Z","file_size":1515446,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"publication_status":"published","license":"https://creativecommons.org/licenses/by/3.0/","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations."}],"month":"04","scopus_import":"1"},{"citation":{"ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal. Wiley, 2023. https://doi.org/10.1111/tpj.16218.","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","ieee":"L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 2023;115(1):155-174. doi:10.1111/tpj.16218","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218","mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"author":[{"first_name":"Lihui","full_name":"Jiang, Lihui","last_name":"Jiang"},{"first_name":"Baolin","last_name":"Yao","full_name":"Yao, Baolin"},{"full_name":"Zhang, Xiaoyan","last_name":"Zhang","first_name":"Xiaoyan"},{"first_name":"Lixia","last_name":"Wu","full_name":"Wu, Lixia"},{"first_name":"Qijing","full_name":"Fu, Qijing","last_name":"Fu"},{"last_name":"Zhao","full_name":"Zhao, Yiting","first_name":"Yiting"},{"last_name":"Cao","full_name":"Cao, Yuxin","first_name":"Yuxin"},{"full_name":"Zhu, Ruomeng","last_name":"Zhu","first_name":"Ruomeng"},{"full_name":"Lu, Xinqi","last_name":"Lu","first_name":"Xinqi"},{"first_name":"Wuying","full_name":"Huang, Wuying","last_name":"Huang"},{"last_name":"Zhao","full_name":"Zhao, Jianping","first_name":"Jianping"},{"first_name":"Kuixiu","last_name":"Li","full_name":"Li, Kuixiu"},{"full_name":"Zhao, Shuanglu","last_name":"Zhao","first_name":"Shuanglu"},{"last_name":"Han","full_name":"Han, Li","first_name":"Li"},{"first_name":"Xuan","last_name":"Zhou","full_name":"Zhou, Xuan"},{"full_name":"Luo, Chongyu","last_name":"Luo","first_name":"Chongyu"},{"first_name":"Haiyan","full_name":"Zhu, Haiyan","last_name":"Zhu"},{"first_name":"Jing","full_name":"Yang, Jing","last_name":"Yang"},{"last_name":"Huang","full_name":"Huang, Huichuan","first_name":"Huichuan"},{"full_name":"Zhu, Zhengge","last_name":"Zhu","first_name":"Zhengge"},{"first_name":"Xiahong","last_name":"He","full_name":"He, Xiahong"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Zhang, Zhongkai","last_name":"Zhang","first_name":"Zhongkai"},{"full_name":"Liu, Changning","last_name":"Liu","first_name":"Changning"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"}],"title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","publisher":"Wiley","quality_controlled":"1","year":"2023","isi":1,"publication":"Plant Journal","day":"01","page":"155-174","date_created":"2023-04-30T22:01:06Z","doi":"10.1111/tpj.16218","date_published":"2023-07-01T00:00:00Z","_id":"12878","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-01T14:16:33Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 115","month":"07","publication_status":"published","publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"language":[{"iso":"eng"}],"issue":"1","volume":115},{"acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","quality_controlled":"1","publisher":"Oxford Academic","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"03","publication":"Bioinformatics","doi":"10.1093/bioinformatics/btad158","date_published":"2023-04-03T00:00:00Z","date_created":"2023-04-30T22:01:05Z","article_number":"btad158","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"citation":{"mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 2023;39(4). doi:10.1093/bioinformatics/btad158","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Nikola","full_name":"Beneš, Nikola","last_name":"Beneš"},{"first_name":"Luboš","full_name":"Brim, Luboš","last_name":"Brim"},{"last_name":"Huvar","full_name":"Huvar, Ondřej","first_name":"Ondřej"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","full_name":"Pastva, Samuel","last_name":"Pastva"},{"last_name":"Šafránek","full_name":"Šafránek, David","first_name":"David"}],"external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"article_processing_charge":"No","title":"Boolean network sketches: A unifying framework for logical model inference","abstract":[{"text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 39","publication_identifier":{"eissn":["1367-4811"]},"publication_status":"published","file":[{"date_updated":"2023-05-02T07:39:04Z","file_size":478740,"creator":"dernst","date_created":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12886","checksum":"2cb90ddf781baefddf47eac4b54e2a03","success":1}],"language":[{"iso":"eng"}],"issue":"4","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"volume":39,"ec_funded":1,"_id":"12876","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-01T14:27:28Z","ddc":["000"],"file_date_updated":"2023-05-02T07:39:04Z","department":[{"_id":"ToHe"}]},{"ddc":["570"],"date_updated":"2023-08-01T14:18:46Z","department":[{"_id":"MaHe"}],"file_date_updated":"2023-05-02T07:24:55Z","_id":"12880","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-02T07:24:55Z","file_size":3811113,"date_created":"2023-05-02T07:24:55Z","file_name":"2023_Nucleus_Kaneshiro.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8e707eda84f64dbad7f03545ae0a83ef","file_id":"12884","success":1}],"publication_status":"published","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"volume":14,"issue":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"intvolume":" 14","month":"04","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548.","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” Nucleus, vol. 14, no. 1. Taylor & Francis, 2023.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","apa":"Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. Taylor & Francis. https://doi.org/10.1080/19491034.2023.2202548","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548"},"title":"Lamin B1 overexpression alters chromatin organization and gene expression","article_processing_charge":"No","external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"author":[{"first_name":"Jeanae M.","last_name":"Kaneshiro","full_name":"Kaneshiro, Jeanae M."},{"last_name":"Capitanio","full_name":"Capitanio, Juliana S.","first_name":"Juliana S."},{"last_name":"Hetzer","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"article_number":"2202548","publication":"Nucleus","day":"18","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-04-30T22:01:06Z","date_published":"2023-04-18T00:00:00Z","doi":"10.1080/19491034.2023.2202548","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","oa":1,"quality_controlled":"1","publisher":"Taylor & Francis"},{"date_updated":"2023-08-01T14:33:21Z","department":[{"_id":"MiLe"}],"_id":"12914","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"4","volume":107,"abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.13130"}],"scopus_import":"1","intvolume":" 107","month":"04","citation":{"ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216.","apa":"Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023.","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000975799300006"],"arxiv":["2207.13130"]},"author":[{"last_name":"Suzuki","orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","first_name":"Fumika"},{"last_name":"Unruh","full_name":"Unruh, William G.","first_name":"William G."}],"title":"Numerical quantum clock simulations for measuring tunneling times","article_number":"042216","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"year":"2023","isi":1,"publication":"Physical Review A","day":"20","date_created":"2023-05-07T22:01:03Z","doi":"10.1103/PhysRevA.107.042216","date_published":"2023-04-20T00:00:00Z","acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"scopus_import":"1","intvolume":" 14","month":"04","abstract":[{"lang":"eng","text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices."}],"pmid":1,"oa_version":"Published Version","volume":14,"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"file_id":"12917","checksum":"a778105665c10beb2354c92d2b295115","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-08T07:26:40Z","file_name":"2023_NatureComm_DiezMerida.pdf","creator":"dernst","date_updated":"2023-05-08T07:26:40Z","file_size":1405588}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"12913","file_date_updated":"2023-05-08T07:26:40Z","department":[{"_id":"AnHi"}],"date_updated":"2023-08-01T14:34:00Z","ddc":["530"],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","date_created":"2023-05-07T22:01:03Z","doi":"10.1038/s41467-023-38005-7","date_published":"2023-04-26T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"26","article_number":"2396","external_id":{"pmid":["37100775"],"isi":["000979744000004"]},"article_processing_charge":"No","author":[{"full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida","first_name":"J."},{"full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón","first_name":"A."},{"full_name":"Yang, S. Y.","last_name":"Yang","first_name":"S. Y."},{"first_name":"Y. M.","full_name":"Xie, Y. M.","last_name":"Xie"},{"full_name":"Gao, X. J.","last_name":"Gao","first_name":"X. J."},{"last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"X.","full_name":"Lu, X.","last_name":"Lu"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"},{"first_name":"K. T.","last_name":"Law","full_name":"Law, K. T."},{"full_name":"Efetov, Dmitri K.","last_name":"Efetov","first_name":"Dmitri K."}],"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","citation":{"chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications, vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.","ieee":"J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 2023;14. doi:10.1038/s41467-023-38005-7","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38005-7"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","author":[{"first_name":"Klemens","full_name":"Fellner, Klemens","last_name":"Fellner"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael","last_name":"Kniely"},{"first_name":"Bao Quoc","full_name":"Tang, Bao Quoc","last_name":"Tang"}],"article_processing_charge":"No","external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w.","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66."},"article_number":"66","date_published":"2023-06-07T00:00:00Z","doi":"10.1007/s00332-023-09926-w","date_created":"2021-12-16T12:15:35Z","day":"07","publication":"Journal of Nonlinear Science","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","department":[{"_id":"JuFi"}],"file_date_updated":"2023-06-19T07:33:53Z","ddc":["510"],"date_updated":"2023-08-01T14:40:33Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10550","volume":33,"file":[{"file_name":"2023_JourNonlinearScience_Fellner.pdf","date_created":"2023-06-19T07:33:53Z","creator":"dernst","file_size":742315,"date_updated":"2023-06-19T07:33:53Z","success":1,"file_id":"13149","checksum":"f3f0f0886098e31c81116cff8183750b","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-1467"],"issn":["0938-8974"]},"publication_status":"published","month":"06","intvolume":" 33","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.","lang":"eng"}]},{"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484","apa":"Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS Press, pp. 37–107, 2023.","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.","ista":"Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023. https://doi.org/10.4171/IFB/484."},"title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","article_processing_charge":"No","external_id":{"arxiv":["2108.01733"],"isi":["000975817300002"]},"author":[{"last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"acknowledgement":"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. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","oa":1,"quality_controlled":"1","publisher":"EMS Press","publication":"Interfaces and Free Boundaries","day":"20","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-05-21T22:01:06Z","date_published":"2023-04-20T00:00:00Z","doi":"10.4171/IFB/484","page":"37-107","_id":"13043","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-08-01T14:43:29Z","department":[{"_id":"JuFi"}],"file_date_updated":"2023-05-22T07:24:13Z","oa_version":"Published Version","abstract":[{"text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions.","lang":"eng"}],"intvolume":" 25","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-22T07:24:13Z","file_name":"2023_Interfaces_Hensel.pdf","creator":"dernst","date_updated":"2023-05-22T07:24:13Z","file_size":867876,"file_id":"13045","checksum":"622422484810441e48f613e968c7e7a4","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"ec_funded":1,"volume":25,"related_material":{"record":[{"status":"public","id":"10013","relation":"earlier_version"}]},"issue":"1"},{"department":[{"_id":"BiCh"}],"file_date_updated":"2023-05-08T07:44:49Z","ddc":["540"],"date_updated":"2023-08-01T14:34:49Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12912","volume":158,"issue":"16","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/mu-adsorption"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"file":[{"file_name":"2023_JourChemicalPhysics_Schmid.pdf","date_created":"2023-05-08T07:44:49Z","creator":"dernst","file_size":6499468,"date_updated":"2023-05-08T07:44:49Z","success":1,"checksum":"4ab8c965f2fa4e17920bfa846847f137","file_id":"12918","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"]},"publication_status":"published","month":"04","intvolume":" 158","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"title":"Computing chemical potentials of adsorbed or confined fluids","author":[{"first_name":"Rochus","last_name":"Schmid","full_name":"Schmid, Rochus"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"}],"article_processing_charge":"No","external_id":{"arxiv":["2302.01297"],"pmid":["37093149"],"isi":["001010676000010"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:10.1063/5.0146711.","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing, 2023.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711","apa":"Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0146711.","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101."},"article_number":"161101 ","doi":"10.1063/5.0146711","date_published":"2023-04-24T00:00:00Z","date_created":"2023-05-07T22:01:03Z","day":"24","publication":"The Journal of Chemical Physics","has_accepted_license":"1","isi":1,"year":"2023","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the 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."},{"title":"Directionality-aware design of embroidery patterns","author":[{"last_name":"Liu","full_name":"Liu, Zhenyuan","orcid":"0000-0001-9200-5690","first_name":"Zhenyuan","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19"},{"first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","last_name":"Piovarci"},{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Charrondiere, Raphael","last_name":"Charrondiere","first_name":"Raphael","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["001000062600033"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .","apa":"Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ","ama":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409. doi:10.1111/cgf.14770 ","ieee":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2. Wiley, pp. 397–409, 2023.","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409.","chicago":"Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere, and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770 .","ista":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409."},"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2023-05-08T00:00:00Z","doi":"10.1111/cgf.14770 ","date_created":"2023-05-16T08:47:25Z","page":"397-409","day":"08","publication":"Computer Graphics Forum","isi":1,"has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and Paola Mejia for proofreading; everyone in the visual computing group at ISTA for inspiring lunch and coffee breaks; Thibault Tricard for help producing the results of Phasor Noise.","department":[{"_id":"BeBi"}],"file_date_updated":"2023-05-16T08:28:37Z","ddc":["004"],"date_updated":"2023-08-01T14:47:05Z","status":"public","keyword":["embroidery","design","directionality","density","image"],"type":"journal_article","article_type":"original","conference":{"name":"EG: Eurographics","location":"Saarbrucken, Germany","end_date":"2023-05-12","start_date":"2023-05-08"},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"12972","volume":42,"issue":"2","ec_funded":1,"file":[{"checksum":"4c188c2be4745467a8790bbf5d6491aa","file_id":"12974","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-16T08:28:37Z","file_name":"Zhenyuan2023.pdf","date_updated":"2023-05-16T08:28:37Z","file_size":24003702,"creator":"mpiovarc"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1467-8659"]},"publication_status":"published","month":"05","intvolume":" 42","oa_version":"Published Version","abstract":[{"text":"Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths.","lang":"eng"}]},{"ddc":["570"],"date_updated":"2023-08-01T14:46:06Z","file_date_updated":"2023-05-22T07:57:37Z","department":[{"_id":"Bio"}],"_id":"13033","status":"public","keyword":["Multidisciplinary"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"success":1,"file_id":"13047","checksum":"8c1b769693ff4288df8376e59ad1176d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_ScientificReports_Zavadakova.pdf","date_created":"2023-05-22T07:57:37Z","file_size":3055077,"date_updated":"2023-05-22T07:57:37Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","issue":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"volume":13,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases."}],"month":"05","intvolume":" 13","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z."},"title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","author":[{"first_name":"Anna","full_name":"Zavadakova, Anna","last_name":"Zavadakova"},{"full_name":"Vistejnova, Lucie","last_name":"Vistejnova","first_name":"Lucie"},{"last_name":"Belinova","full_name":"Belinova, Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","first_name":"Tereza"},{"full_name":"Tichanek, Filip","last_name":"Tichanek","first_name":"Filip"},{"first_name":"Dagmar","last_name":"Bilikova","full_name":"Bilikova, Dagmar"},{"first_name":"Peter R.","last_name":"Mouton","full_name":"Mouton, Peter R."}],"external_id":{"isi":["000995271600104"]},"article_processing_charge":"No","article_number":"7959","day":"17","publication":"Scientific Reports","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1038/s41598-023-35162-z","date_published":"2023-05-17T00:00:00Z","date_created":"2023-05-19T11:12:25Z","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13095","department":[{"_id":"PaSc"}],"file_date_updated":"2023-05-30T07:05:28Z","date_updated":"2023-08-01T14:48:09Z","ddc":["540"],"scopus_import":"1","intvolume":" 145","month":"05","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"12820","relation":"research_data"}]},"volume":145,"issue":"19","publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"language":[{"iso":"eng"}],"file":[{"file_id":"13098","checksum":"0758a930ef21c62fc91b14e657479f83","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-30T07:05:28Z","file_name":"2023_JACS_Troussicot.pdf","creator":"dernst","date_updated":"2023-05-30T07:05:28Z","file_size":6719299}],"article_processing_charge":"No","external_id":{"isi":["000985907400001"],"pmid":["37140345"]},"author":[{"first_name":"Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","full_name":"Troussicot, Laura","last_name":"Troussicot"},{"first_name":"Alicia","full_name":"Vallet, Alicia","last_name":"Vallet"},{"full_name":"Molin, Mikael","last_name":"Molin","first_name":"Mikael"},{"first_name":"Björn M.","full_name":"Burmann, Björn M.","last_name":"Burmann"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","citation":{"chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200","ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","page":"10700–10711","date_created":"2023-05-28T22:01:04Z","doi":"10.1021/jacs.3c01200","date_published":"2023-05-04T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Journal of the American Chemical Society","day":"04"},{"volume":30,"issue":"2","publication_identifier":{"eissn":["1077-8926"]},"publication_status":"published","file":[{"file_name":"2023_JourCombinatorics_Anastos.pdf","date_created":"2023-05-22T07:43:19Z","creator":"dernst","file_size":448736,"date_updated":"2023-05-22T07:43:19Z","success":1,"file_id":"13046","checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 30","abstract":[{"lang":"eng","text":"Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞."}],"oa_version":"Published Version","department":[{"_id":"MaKw"}],"file_date_updated":"2023-05-22T07:43:19Z","date_updated":"2023-08-01T14:44:52Z","ddc":["510"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13042","date_published":"2023-05-05T00:00:00Z","doi":"10.37236/11471","date_created":"2023-05-21T22:01:05Z","isi":1,"has_accepted_license":"1","year":"2023","day":"05","publication":"Electronic Journal of Combinatorics","quality_controlled":"1","publisher":"Electronic Journal of Combinatorics","oa":1,"acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"}],"article_processing_charge":"No","external_id":{"arxiv":["2105.13828"],"isi":["000988285500001"]},"title":"A note on long cycles in sparse random graphs","citation":{"ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21.","chicago":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471.","ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471","apa":"Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471","ieee":"M. Anastos, “A note on long cycles in sparse random graphs,” Electronic Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023.","short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","mla":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:10.37236/11471."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"P2.21"},{"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-01T14:48:08Z","citation":{"chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","short":"P. Schanda, (2023)."},"title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","file_date_updated":"2023-04-14T09:39:58Z","department":[{"_id":"PaSc"}],"author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"article_processing_charge":"No","_id":"12820","status":"public","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"day":"18","file":[{"file_name":"data_deposition.zip","date_created":"2023-04-14T09:39:33Z","creator":"pschanda","file_size":54184807,"date_updated":"2023-04-14T09:39:33Z","success":1,"checksum":"54a619605e44c871214fb0e07b05c6bf","file_id":"12823","relation":"main_file","access_level":"open_access","content_type":"application/zip"},{"date_created":"2023-04-14T09:39:58Z","file_name":"README","date_updated":"2023-04-14T09:39:58Z","file_size":4978,"creator":"pschanda","checksum":"8dede9fc78399d13144eb05c62bf5750","file_id":"12824","success":1,"content_type":"application/octet-stream","access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","year":"2023","date_published":"2023-04-18T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"13095","status":"public"}]},"doi":"10.15479/AT:ISTA:12820","contributor":[{"contributor_type":"researcher","first_name":"Laura","last_name":"Troussicot"},{"contributor_type":"researcher","first_name":"Björn M.","last_name":"Burmann"}],"date_created":"2023-04-10T05:55:56Z","oa_version":"Published Version","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}],"month":"04","publisher":"Institute of Science and Technology Austria","oa":1},{"publication":"Physical Review B","day":"01","year":"2023","isi":1,"date_created":"2023-05-21T22:01:04Z","doi":"10.1103/PhysRevB.107.134109","date_published":"2023-04-01T00:00:00Z","acknowledgement":"We thank R. Redmer for helpful discussions. M.F. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge support form the French National Research Agency (ANR) through the projects POMPEI (Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The ab initio calculations were performed at the NorthGerman Supercomputing Alliance (HLRN) facilities. ","publisher":"American Physical Society","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation of the reflectivity of molecular fluids under shock compression,” Physical Review B, vol. 107, no. 13. American Physical Society, 2023.","short":"M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B 107 (2023).","ama":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 2023;107(13). doi:10.1103/PhysRevB.107.134109","apa":"French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109","mla":"French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109, American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109.","ista":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 107(13), 134109.","chicago":"French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.134109."},"title":"Ab initio calculation of the reflectivity of molecular fluids under shock compression","article_processing_charge":"No","external_id":{"isi":["000974672600001"]},"author":[{"full_name":"French, Martin","last_name":"French","first_name":"Martin"},{"full_name":"Bethkenhagen, Mandy","orcid":"0000-0002-1838-2129","last_name":"Bethkenhagen","first_name":"Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"},{"full_name":"Ravasio, Alessandra","last_name":"Ravasio","first_name":"Alessandra"},{"first_name":"Jean Alexis","last_name":"Hernandez","full_name":"Hernandez, Jean Alexis"}],"article_number":"134109","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"volume":107,"issue":"13","oa_version":"None","abstract":[{"text":"We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression.","lang":"eng"}],"intvolume":" 107","month":"04","scopus_import":"1","date_updated":"2023-08-01T14:45:25Z","department":[{"_id":"BiCh"}],"_id":"13039","status":"public","type":"journal_article","article_type":"original"},{"publication_status":"published","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":5640829,"date_updated":"2023-05-30T07:38:44Z","file_name":"2023_ACSAppliedMaterials_Nan.pdf","date_created":"2023-05-30T07:38:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"13099","checksum":"23893be46763c4c78daacddd019de821"}],"issue":"19","volume":15,"abstract":[{"text":"There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 15","month":"05","date_updated":"2023-08-01T14:50:09Z","ddc":["540"],"file_date_updated":"2023-05-30T07:38:44Z","department":[{"_id":"MaIb"}],"_id":"13092","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","year":"2023","isi":1,"has_accepted_license":"1","publication":"ACS Applied Materials and Interfaces","day":"04","page":"23380–23389","date_created":"2023-05-28T22:01:03Z","doi":"10.1021/acsami.3c00625","date_published":"2023-05-04T00:00:00Z","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria.","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","citation":{"ama":"Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389. doi:10.1021/acsami.3c00625","apa":"Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625","short":"B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.","ieee":"B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,” ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023.","mla":"Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625.","ista":"Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389.","chicago":"Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["37141543"],"isi":["000985497900001"]},"article_processing_charge":"No","author":[{"last_name":"Nan","full_name":"Nan, Bingfei","first_name":"Bingfei"},{"first_name":"Xuan","last_name":"Song","full_name":"Song, Xuan"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Linlin","full_name":"Yang, Linlin","last_name":"Yang"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","full_name":"Horta, Sharona","last_name":"Horta"},{"last_name":"Li","full_name":"Li, Junshan","first_name":"Junshan"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"title":"Bottom-up synthesis of SnTe-based thermoelectric composites","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}]},{"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"citation":{"mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ali","full_name":"Azadbakht, Ali","last_name":"Azadbakht"},{"first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie"},{"first_name":"Thijs","last_name":"Varkevisser","full_name":"Varkevisser, Thijs"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Kraft","full_name":"Kraft, Daniela J.","first_name":"Daniela J."}],"article_processing_charge":"No","external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"04","publication":"Nano Letters","page":"4267–4273","doi":"10.1021/acs.nanolett.3c00375","date_published":"2023-05-04T00:00:00Z","date_created":"2023-05-28T22:01:03Z","_id":"13094","article_type":"letter_note","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-01T14:51:25Z","ddc":["540"],"file_date_updated":"2023-05-30T07:55:31Z","department":[{"_id":"AnSa"}],"abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 23","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13100","checksum":"9734d4c617bab3578ef62916b764547a","file_size":3654910,"date_updated":"2023-05-30T07:55:31Z","creator":"dernst","file_name":"2023_NanoLetters_Azadbakht.pdf","date_created":"2023-05-30T07:55:31Z"}],"language":[{"iso":"eng"}],"volume":23,"issue":"10","ec_funded":1},{"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["2637-6113"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated."}],"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaelm.3c00055"}],"scopus_import":"1","date_updated":"2023-08-01T14:50:48Z","department":[{"_id":"MaIb"}],"_id":"13093","status":"public","article_type":"original","type":"journal_article","publication":"ACS Applied Electronic Materials","day":"05","year":"2023","isi":1,"date_created":"2023-05-28T22:01:03Z","date_published":"2023-05-05T00:00:00Z","doi":"10.1021/acsaelm.3c00055","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). B.N., M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457 and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/. ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges support from the National Natural Science Foundation of China (22208293). This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials.","chicago":"Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang, Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055.","ieee":"B. Nan et al., “Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature,” ACS Applied Electronic Materials. American Chemical Society, 2023.","short":"B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J. Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials (2023).","ama":"Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055","apa":"Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023). Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. American Chemical Society. https://doi.org/10.1021/acsaelm.3c00055","mla":"Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055."},"title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature","article_processing_charge":"No","external_id":{"isi":["000986859000001"]},"author":[{"first_name":"Bingfei","full_name":"Nan, Bingfei","last_name":"Nan"},{"first_name":"Mengyao","full_name":"Li, Mengyao","last_name":"Li"},{"first_name":"Yu","last_name":"Zhang","full_name":"Zhang, Yu"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang","first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Han","full_name":"Han, Xu","first_name":"Xu"},{"first_name":"Yong","full_name":"Zuo, Yong","last_name":"Zuo"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"first_name":"Jordi","full_name":"Arbiol, Jordi","last_name":"Arbiol"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}]},{"citation":{"chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719.","ista":"Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 17(3), 719–748.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.","apa":"Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719","ama":"Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719","ieee":"T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical Sciences Publishers, pp. 719–748, 2023.","short":"T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["1810.06882"],"isi":["000996014700004"]},"author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}],"title":"Free rational curves on low degree hypersurfaces and the circle method","project":[{"name":"Between rational and integral points","grant_number":"EP-P026710-2","_id":"26A8D266-B435-11E9-9278-68D0E5697425"}],"year":"2023","has_accepted_license":"1","isi":1,"publication":"Algebra and Number Theory","day":"12","page":"719-748","date_created":"2023-05-28T22:01:02Z","doi":"10.2140/ant.2023.17.719","date_published":"2023-04-12T00:00:00Z","acknowledgement":"The authors are grateful to Paul Nelson, Per Salberger and Jason Starr for useful comments. While working on this paper the first author was supported by EPRSC grant EP/P026710/1. The research was partially conducted during the period the second author served as a Clay Research Fellow, and partially conducted during the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zurich Foundation.","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","date_updated":"2023-08-01T14:51:57Z","ddc":["510"],"file_date_updated":"2023-05-30T08:05:22Z","department":[{"_id":"TiBr"}],"_id":"13091","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1944-7833"],"issn":["1937-0652"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-30T08:05:22Z","file_name":"2023_AlgebraNumberTheory_Browning.pdf","date_updated":"2023-05-30T08:05:22Z","file_size":1430719,"creator":"dernst","checksum":"5d5d67b235905650e33cf7065d7583b4","file_id":"13101","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"volume":17,"issue":"3","abstract":[{"text":"We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 17","month":"04"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"13117","file_date_updated":"2023-06-06T07:31:20Z","department":[{"_id":"JoFi"}],"ddc":["530"],"date_updated":"2023-08-02T06:10:26Z","intvolume":" 14","month":"05","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"ec_funded":1,"volume":14,"related_material":{"record":[{"status":"public","id":"13124","relation":"research_data"}]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1654389,"date_updated":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","date_created":"2023-06-06T07:31:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a857df40f0882859c48a1ff1e2001ec2","file_id":"13123"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"project":[{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"article_number":"2998","title":"Tunable directional photon scattering from a pair of superconducting qubits","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"]},"article_processing_charge":"No","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V."},{"last_name":"Sett","full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6"},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","date_created":"2023-06-04T22:01:02Z","doi":"10.1038/s41467-023-38761-6","date_published":"2023-05-24T00:00:00Z","publication":"Nature Communications","day":"24","year":"2023","isi":1,"has_accepted_license":"1"},{"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"citation":{"mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:10.1126/science.adg3812.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","ieee":"R. Sahu et al., “Entangling microwaves with light,” Science, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science. 2023;380(6646):718-721. doi:10.1126/science.adg3812","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves with light. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267","last_name":"Qiu","first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"last_name":"Hease","full_name":"Hease, William J","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","full_name":"Arnold, Georg M","last_name":"Arnold"},{"last_name":"Minoguchi","full_name":"Minoguchi, Y.","first_name":"Y."},{"first_name":"P.","last_name":"Rabl","full_name":"Rabl, P."},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.03315"],"isi":["000996515200004"]},"title":"Entangling microwaves with light","acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"isi":1,"year":"2023","day":"18","publication":"Science","page":"718-721","date_published":"2023-05-18T00:00:00Z","doi":"10.1126/science.adg3812","date_created":"2023-05-31T11:39:24Z","_id":"13106","article_type":"original","type":"journal_article","status":"public","keyword":["Multidisciplinary"],"date_updated":"2023-08-02T06:08:57Z","department":[{"_id":"JoFi"}],"abstract":[{"text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"month":"05","intvolume":" 380","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","description":"News on ISTA Website"}],"record":[{"status":"public","id":"13122","relation":"research_data"}]},"issue":"6646","volume":380,"ec_funded":1},{"title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","author":[{"first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","last_name":"Clozeau","full_name":"Clozeau, Nicolas"},{"first_name":"Marc","full_name":"Josien, Marc","last_name":"Josien"},{"full_name":"Otto, Felix","last_name":"Otto","first_name":"Felix"},{"last_name":"Xu","full_name":"Xu, Qiang","first_name":"Qiang"}],"external_id":{"isi":["000999623100001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.","apa":"Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” Foundations of Computational Mathematics. Springer Nature, 2023.","chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.","ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics."},"date_published":"2023-05-30T00:00:00Z","doi":"10.1007/s10208-023-09613-y","date_created":"2023-06-11T22:00:40Z","day":"30","publication":"Foundations of Computational Mathematics","has_accepted_license":"1","isi":1,"year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","department":[{"_id":"JuFi"}],"ddc":["510"],"date_updated":"2023-08-02T06:12:39Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"13129","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"publication_status":"epub_ahead","month":"05","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10208-023-09613-y","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.","lang":"eng"}]},{"date_created":"2023-06-06T07:36:50Z","doi":"10.5281/ZENODO.7858567","related_material":{"record":[{"id":"13117","status":"public","relation":"used_in_publication"}]},"date_published":"2023-04-28T00:00:00Z","year":"2023","day":"28","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"publisher":"Zenodo","month":"04","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","full_name":"Redchenko, Elena"},{"first_name":"Alexander","last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander"},{"last_name":"Sett","full_name":"Sett, Riya","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Poddubny","full_name":"Poddubny, Alexander"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","department":[{"_id":"JoFi"}],"citation":{"ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567."},"date_updated":"2023-08-02T06:10:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","status":"public","_id":"13124"},{"type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13122","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"}],"article_processing_charge":"No","title":"Entangling microwaves with light","department":[{"_id":"JoFi"}],"citation":{"mla":"Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417.","short":"R. Sahu, (2023).","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417."},"date_updated":"2023-08-02T06:08:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"month":"03","abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"oa_version":"Published Version","doi":"10.5281/ZENODO.7789417","related_material":{"record":[{"id":"13106","status":"public","relation":"used_in_publication"}]},"date_published":"2023-03-31T00:00:00Z","date_created":"2023-06-06T06:46:16Z","year":"2023","day":"31"},{"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"article_processing_charge":"No","author":[{"last_name":"Vetrova","full_name":"Vetrova, Alexandra A.","first_name":"Alexandra A."},{"first_name":"Daria M.","full_name":"Kupaeva, Daria M.","last_name":"Kupaeva"},{"last_name":"Kizenko","full_name":"Kizenko, Alena","first_name":"Alena","id":"a521c60b-0815-11ed-9b02-b8bd522477c8"},{"last_name":"Lebedeva","full_name":"Lebedeva, Tatiana S.","first_name":"Tatiana S."},{"full_name":"Walentek, Peter","last_name":"Walentek","first_name":"Peter"},{"last_name":"Tsikolia","full_name":"Tsikolia, Nikoloz","first_name":"Nikoloz"},{"first_name":"Stanislav V.","full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8."},"article_number":"9382","date_created":"2023-06-25T22:00:46Z","date_published":"2023-06-09T00:00:00Z","doi":"10.1038/s41598-023-35979-8","publication":"Scientific Reports","day":"09","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","department":[{"_id":"GradSch"}],"file_date_updated":"2023-06-26T09:58:53Z","ddc":["570"],"date_updated":"2023-08-02T06:17:18Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"13166","volume":13,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_ScientificReports_Vetrova.pdf","date_created":"2023-06-26T09:58:53Z","file_size":4844149,"date_updated":"2023-06-26T09:58:53Z","creator":"dernst","success":1,"checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","file_id":"13170","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["2045-2322"]},"intvolume":" 13","month":"06","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.","lang":"eng"}]},{"acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2023","isi":1,"publication":"Physical Review B","day":"01","date_created":"2023-06-18T22:00:46Z","date_published":"2023-05-01T00:00:00Z","doi":"10.1103/PhysRevB.107.184312","article_number":"184312","citation":{"apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["001003686900004"],"arxiv":["2303.00729"]},"article_processing_charge":"No","author":[{"full_name":"Orlov, Pavel","last_name":"Orlov","first_name":"Pavel"},{"full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina","first_name":"Anastasiia"},{"full_name":"Sharipov, Rustem","last_name":"Sharipov","first_name":"Rustem"},{"first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","full_name":"Petrova, Elena"},{"last_name":"Gritsev","full_name":"Gritsev, Vladimir","first_name":"Vladimir"},{"full_name":"Kurlov, Denis V.","last_name":"Kurlov","first_name":"Denis V."}],"title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","abstract":[{"text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.00729","open_access":"1"}],"scopus_import":"1","intvolume":" 107","month":"05","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"issue":"18","volume":107,"_id":"13138","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-02T06:16:02Z","department":[{"_id":"GradSch"}]},{"title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","external_id":{"isi":["000971795800001"],"pmid":["37010107"]},"article_processing_charge":"No","author":[{"first_name":"C","last_name":"Chen","full_name":"Chen, C"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"full_name":"Cai, J","last_name":"Cai","first_name":"J"},{"last_name":"Qiu","full_name":"Qiu, Y","first_name":"Y"},{"first_name":"L","last_name":"Li","full_name":"Li, L"},{"last_name":"Gao","full_name":"Gao, C","first_name":"C"},{"last_name":"Gao","full_name":"Gao, Y","first_name":"Y"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"first_name":"S","last_name":"Wu","full_name":"Wu, S"},{"first_name":"C","full_name":"Wei, C","last_name":"Wei"},{"full_name":"Chen, J","last_name":"Chen","first_name":"J"},{"full_name":"Xu, T","last_name":"Xu","first_name":"T"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"J","last_name":"Wang","full_name":"Wang, J"},{"first_name":"R","full_name":"Li, R","last_name":"Li"},{"full_name":"Chao, D","last_name":"Chao","first_name":"D"},{"full_name":"Zhang, B","last_name":"Zhang","first_name":"B"},{"first_name":"X","full_name":"Chen, X","last_name":"Chen"},{"first_name":"Z","last_name":"Gao","full_name":"Gao, Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.","ieee":"C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207","apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207"},"date_created":"2023-07-12T07:32:58Z","date_published":"2023-07-01T00:00:00Z","doi":"10.1093/plphys/kiad207","page":"2243-2260","publication":"Plant Physiology","day":"01","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"American Society of Plant Biologists","quality_controlled":"1","acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","department":[{"_id":"JiFr"}],"file_date_updated":"2023-07-13T13:26:33Z","ddc":["575"],"date_updated":"2023-08-02T06:27:55Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13213","volume":192,"issue":"3","language":[{"iso":"eng"}],"file":[{"file_id":"13220","checksum":"5492e1d18ac3eaf202633d210fa0fb75","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-07-13T13:26:33Z","file_name":"2023_PlantPhys_Chen.pdf","date_updated":"2023-07-13T13:26:33Z","file_size":2076977,"creator":"cchlebak"}],"publication_status":"published","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"intvolume":" 192","month":"07","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth.","lang":"eng"}]},{"article_number":"1049255","citation":{"mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255.","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1049255","ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255","short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255.","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 14, 1049255."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"last_name":"Bruneaux","full_name":"Bruneaux, L","first_name":"L"},{"last_name":"Oikonomou","full_name":"Oikonomou, P","first_name":"P"},{"first_name":"M","last_name":"Aldana","full_name":"Aldana, M"},{"first_name":"P","full_name":"Cluzel, P","last_name":"Cluzel"}],"external_id":{"pmid":["37485524"],"isi":["001030002600001"]},"article_processing_charge":"Yes","title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression","acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.","quality_controlled":"1","publisher":"Frontiers","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"20","publication":"Frontiers in Microbiology","doi":"10.3389/fmicb.2023.1049255","date_published":"2023-06-20T00:00:00Z","date_created":"2023-02-02T08:13:28Z","_id":"12478","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-02T06:25:04Z","ddc":["570"],"department":[{"_id":"CaGu"}],"file_date_updated":"2023-07-31T07:16:34Z","abstract":[{"text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 14","publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","file":[{"file_name":"2023_FrontiersMicrobiology_Guet.pdf","date_created":"2023-07-31T07:16:34Z","creator":"dernst","file_size":6452841,"date_updated":"2023-07-31T07:16:34Z","success":1,"file_id":"13322","checksum":"7dd322347512afaa5daf72a0154f2f07","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":14},{"author":[{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"first_name":"Daoyuan","last_name":"Qian","full_name":"Qian, Daoyuan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}],"article_processing_charge":"No","external_id":{"isi":["001017539800001"]},"title":"Amyloid formation as a protein phase transition","citation":{"apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., & Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397. doi:10.1038/s42254-023-00598-9","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 379–397, 2023.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","page":"379–397","doi":"10.1038/s42254-023-00598-9","date_published":"2023-07-01T00:00:00Z","date_created":"2023-07-16T22:01:12Z","isi":1,"year":"2023","day":"01","publication":"Nature Reviews Physics","article_type":"original","type":"journal_article","status":"public","_id":"13237","department":[{"_id":"AnSa"}],"date_updated":"2023-08-02T06:28:38Z","scopus_import":"1","month":"07","intvolume":" 5","abstract":[{"text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.","lang":"eng"}],"oa_version":"None","volume":5,"publication_identifier":{"eissn":["2522-5820"]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","external_id":{"pmid":["37289834"],"isi":["001003199100005"]},"article_processing_charge":"No","author":[{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031","first_name":"Laura","last_name":"Hofmann","full_name":"Hofmann, Laura"},{"first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","full_name":"Steccari, Irene"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","last_name":"Kardos","full_name":"Kardos, Roland"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146."},"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_created":"2023-07-16T22:01:09Z","doi":"10.1371/journal.pbio.3002146","date_published":"2023-06-08T00:00:00Z","page":"e3002146","publication":"PLoS Biology","day":"08","year":"2023","has_accepted_license":"1","isi":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"13229","department":[{"_id":"CaHe"}],"file_date_updated":"2023-07-18T07:59:58Z","ddc":["570"],"date_updated":"2023-08-02T06:33:14Z","intvolume":" 21","month":"06","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"ec_funded":1,"issue":"6","volume":21,"language":[{"iso":"eng"}],"file":[{"file_id":"13246","checksum":"8e88cb0e5a6433a2f1939a9030bed384","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-07-18T07:59:58Z","file_name":"2023_PloSBiology_Shamipour.pdf","creator":"dernst","date_updated":"2023-07-18T07:59:58Z","file_size":4431723}],"publication_status":"published","publication_identifier":{"eissn":["1545-7885"]}},{"isi":1,"has_accepted_license":"1","year":"2023","day":"13","publication":"Physical Review Materials","doi":"10.1103/physrevmaterials.7.065601","date_published":"2023-06-13T00:00:00Z","date_created":"2023-07-07T12:48:01Z","acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","quality_controlled":"1","publisher":"American Physical Society","oa":1,"citation":{"mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.","ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601.","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Grosjean","full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","first_name":"Galien M"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"external_id":{"arxiv":["2304.12861"],"isi":["001019565900002"]},"article_processing_charge":"No","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","article_number":"065601","project":[{"grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication_identifier":{"issn":["2475-9953"]},"publication_status":"published","file":[{"success":1,"file_id":"13198","checksum":"75584730d9cdd50eeccb4c52c509776d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Mosaic_asymmetries.pdf","date_created":"2023-07-07T12:49:51Z","file_size":1127040,"date_updated":"2023-07-07T12:49:51Z","creator":"ggrosjea"}],"language":[{"iso":"eng"}],"volume":7,"issue":"6","ec_funded":1,"abstract":[{"lang":"eng","text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally."}],"oa_version":"Submitted Version","month":"06","intvolume":" 7","date_updated":"2023-08-02T06:34:47Z","ddc":["537"],"department":[{"_id":"ScWa"}],"file_date_updated":"2023-07-07T12:49:51Z","_id":"13197","article_type":"original","type":"journal_article","status":"public","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"]},{"day":"08","publication":"PLoS Computational Biology","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-06-08T00:00:00Z","doi":"10.1371/journal.pcbi.1011104","date_created":"2023-07-16T22:01:09Z","acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104.","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104"},"title":"Environmental dynamics shape perceptual decision bias","author":[{"first_name":"Julie A.","full_name":"Charlton, Julie A.","last_name":"Charlton"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"first_name":"Yoon H.","last_name":"Bai","full_name":"Bai, Yoon H."},{"first_name":"Ann M.","full_name":"Hermundstad, Ann M.","last_name":"Hermundstad"},{"first_name":"Robbe L.T.","full_name":"Goris, Robbe L.T.","last_name":"Goris"}],"article_processing_charge":"No","external_id":{"pmid":["37289753"],"isi":["001003410200003"]},"article_number":"e1011104","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"800761fa2c647fabd6ad034589bc526e","file_id":"13247","file_size":2281868,"date_updated":"2023-07-18T08:07:59Z","creator":"dernst","file_name":"2023_PloSCompBio_Charlton.pdf","date_created":"2023-07-18T08:07:59Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"publication_status":"published","issue":"6","volume":19,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals."}],"month":"06","intvolume":" 19","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-02T06:33:50Z","file_date_updated":"2023-07-18T08:07:59Z","department":[{"_id":"MaJö"}],"_id":"13230","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"date_updated":"2023-08-02T06:31:19Z","ddc":["570"],"department":[{"_id":"LeSa"}],"file_date_updated":"2023-07-18T07:25:43Z","_id":"13232","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2076-393X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","file_id":"13244","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-07-18T07:25:43Z","file_name":"2023_Vaccines_Dormeshkin.pdf","date_updated":"2023-07-18T07:25:43Z","file_size":2339746,"creator":"dernst"}],"volume":11,"issue":"6","abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 11","month":"06","citation":{"chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["001017740000001"]},"article_processing_charge":"No","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"last_name":"Katsin","full_name":"Katsin, Mikalai","first_name":"Mikalai"},{"first_name":"Maria","last_name":"Stegantseva","full_name":"Stegantseva, Maria"},{"first_name":"Sergey","full_name":"Golenchenko, Sergey","last_name":"Golenchenko"},{"last_name":"Shapira","full_name":"Shapira, Michail","first_name":"Michail"},{"first_name":"Simon","last_name":"Dubovik","full_name":"Dubovik, Simon"},{"last_name":"Lutskovich","full_name":"Lutskovich, Dzmitry","first_name":"Dzmitry"},{"first_name":"Anton","id":"62304f89-eb97-11eb-a6c2-8903dd183976","last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton"},{"full_name":"Meleshko, Alexander","last_name":"Meleshko","first_name":"Alexander"}],"title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","article_number":"1014","year":"2023","has_accepted_license":"1","isi":1,"publication":"Vaccines","day":"01","date_created":"2023-07-16T22:01:10Z","date_published":"2023-06-01T00:00:00Z","doi":"10.3390/vaccines11061014","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"quality_controlled":"1","publisher":"American Chemical Society","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","date_created":"2023-07-16T22:01:11Z","date_published":"2023-06-13T00:00:00Z","doi":"10.1021/acsnano.3c03541","page":"11923–11934","publication":"ACS Nano","day":"13","year":"2023","isi":1,"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","article_processing_charge":"No","external_id":{"isi":["001008564800001"],"pmid":["37310395"]},"author":[{"orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mingquan","last_name":"Li","full_name":"Li, Mingquan"},{"first_name":"Shanhong","full_name":"Wan, Shanhong","last_name":"Wan"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hong, Min","last_name":"Hong","first_name":"Min"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.3c03541.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” ACS Nano, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:10.1021/acsnano.3c03541.","short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","ieee":"Y. Liu et al., “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” ACS Nano, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 2023;17(12):11923–11934. doi:10.1021/acsnano.3c03541","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c03541"},"intvolume":" 17","month":"06","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications.","lang":"eng"}],"issue":"12","volume":17,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"status":"public","type":"journal_article","article_type":"original","_id":"13235","department":[{"_id":"MaIb"}],"date_updated":"2023-08-02T06:29:55Z"},{"article_number":"065207","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","ieee":"M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207."},"title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","author":[{"full_name":"Schörner, Maximilian","last_name":"Schörner","first_name":"Maximilian"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","first_name":"Mandy","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"},{"last_name":"Döppner","full_name":"Döppner, Tilo","first_name":"Tilo"},{"first_name":"Dominik","full_name":"Kraus, Dominik","last_name":"Kraus"},{"first_name":"Luke B.","full_name":"Fletcher, Luke B.","last_name":"Fletcher"},{"first_name":"Siegfried H.","last_name":"Glenzer","full_name":"Glenzer, Siegfried H."},{"first_name":"Ronald","full_name":"Redmer, Ronald","last_name":"Redmer"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"]},"acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"14","publication":"Physical Review E","isi":1,"year":"2023","date_published":"2023-06-14T00:00:00Z","doi":"10.1103/PhysRevE.107.065207","date_created":"2023-07-16T22:01:10Z","_id":"13231","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-02T06:30:46Z","department":[{"_id":"BiCh"}],"oa_version":"Preprint","abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"month":"06","intvolume":" 107","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"publication_status":"published","issue":"6","volume":107},{"oa_version":"Preprint","abstract":[{"text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.","lang":"eng"}],"month":"06","intvolume":" 107","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.01022","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"publication_status":"published","issue":"6","volume":107,"ec_funded":1,"_id":"13233","status":"public","type":"journal_article","article_type":"letter_note","date_updated":"2023-08-02T06:31:52Z","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"day":"20","publication":"Physical Review A","isi":1,"year":"2023","doi":"10.1103/PhysRevA.107.L061304","date_published":"2023-06-20T00:00:00Z","date_created":"2023-07-16T22:01:10Z","article_number":"L061304","project":[{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304"},"title":"Finite-range bias in fitting three-body loss to the zero-range model","author":[{"full_name":"Agafonova, Sofya","last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"external_id":{"arxiv":["2302.01022"],"isi":["001019748000005"]},"article_processing_charge":"No"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5."},"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","article_processing_charge":"Yes","external_id":{"isi":["001024920300002"]},"author":[{"id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","full_name":"Goswami, Bidyut B","last_name":"Goswami"},{"first_name":"Soon Il","last_name":"An","full_name":"An, Soon Il"}],"article_number":"82","publication":"npj Climate and Atmospheric Science","day":"08","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-07-23T22:01:10Z","doi":"10.1038/s41612-023-00411-5","date_published":"2023-07-08T00:00:00Z","acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","ddc":["550"],"date_updated":"2023-08-02T06:38:07Z","file_date_updated":"2023-07-31T08:00:01Z","department":[{"_id":"CaMu"}],"_id":"13256","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"e9967d436a83b8ffcc6f58782e1f7500","file_id":"13326","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_npjclimate_Goswami.pdf","date_created":"2023-07-31T08:00:01Z","creator":"dernst","file_size":1750712,"date_updated":"2023-07-31T08:00:01Z"}],"publication_status":"published","publication_identifier":{"eissn":["2397-3722"]},"volume":6,"oa_version":"Published Version","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"intvolume":" 6","month":"07","scopus_import":"1"},{"publication":"Genome biology and evolution","day":"01","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-07-23T22:01:11Z","date_published":"2023-07-01T00:00:00Z","doi":"10.1093/gbe/evad113","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","oa":1,"quality_controlled":"1","publisher":"Oxford Academic","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023."},"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"article_processing_charge":"Yes","author":[{"last_name":"De Castro Barbosa Rodrigues Barata","full_name":"De Castro Barbosa Rodrigues Barata, Carolina","first_name":"Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef"},{"first_name":"Rhonda R.","last_name":"Snook","full_name":"Snook, Rhonda R."},{"first_name":"Michael G.","last_name":"Ritchie","full_name":"Ritchie, Michael G."},{"first_name":"Carolin","last_name":"Kosiol","full_name":"Kosiol, Carolin"}],"article_number":"evad113","language":[{"iso":"eng"}],"file":[{"file_id":"13339","checksum":"70de3c4878de6efe00dc56de2df8812f","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-01T06:58:34Z","file_name":"2023_GBE_Barata.pdf","creator":"dernst","date_updated":"2023-08-01T06:58:34Z","file_size":2382587}],"publication_status":"published","publication_identifier":{"eissn":["1759-6653"]},"volume":15,"issue":"7","related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"intvolume":" 15","month":"07","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-02T06:42:35Z","department":[{"_id":"BeVi"}],"file_date_updated":"2023-08-01T06:58:34Z","_id":"13260","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"_id":"13346","type":"journal_article","article_type":"original","keyword":["General Physics and Astronomy","General Engineering","General Materials Science"],"status":"public","date_updated":"2023-08-02T06:51:15Z","extern":"1","abstract":[{"text":"The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.2c07558","open_access":"1"}],"scopus_import":"1","intvolume":" 17","month":"01","publication_status":"published","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"language":[{"iso":"eng"}],"volume":17,"issue":"1","citation":{"mla":"Lionello, Chiara, et al. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano, vol. 17, no. 1, American Chemical Society, 2023, pp. 275–87, doi:10.1021/acsnano.2c07558.","ama":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 2023;17(1):275-287. doi:10.1021/acsnano.2c07558","apa":"Lionello, C., Perego, C., Gardin, A., Klajn, R., & Pavan, G. M. (2023). Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.2c07558","short":"C. Lionello, C. Perego, A. Gardin, R. Klajn, G.M. Pavan, ACS Nano 17 (2023) 275–287.","ieee":"C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. M. Pavan, “Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices,” ACS Nano, vol. 17, no. 1. American Chemical Society, pp. 275–287, 2023.","chicago":"Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni M. Pavan. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” ACS Nano. American Chemical Society, 2023. https://doi.org/10.1021/acsnano.2c07558.","ista":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. 2023. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 17(1), 275–287."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Lionello","full_name":"Lionello, Chiara","first_name":"Chiara"},{"full_name":"Perego, Claudio","last_name":"Perego","first_name":"Claudio"},{"full_name":"Gardin, Andrea","last_name":"Gardin","first_name":"Andrea"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"last_name":"Pavan","full_name":"Pavan, Giovanni M.","first_name":"Giovanni M."}],"title":"Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","year":"2023","publication":"ACS Nano","day":"10","page":"275-287","date_created":"2023-08-01T09:30:29Z","doi":"10.1021/acsnano.2c07558","date_published":"2023-01-10T00:00:00Z"},{"title":"Asteroseismology with the Roman galactic bulge time-domain survey","department":[{"_id":"LiBu"}],"article_processing_charge":"No","external_id":{"arxiv":["2307.03237"]},"author":[{"first_name":"Daniel","full_name":"Huber, Daniel","last_name":"Huber"},{"last_name":"Pinsonneault","full_name":"Pinsonneault, Marc","first_name":"Marc"},{"last_name":"Beck","full_name":"Beck, Paul","first_name":"Paul"},{"first_name":"Timothy R.","last_name":"Bedding","full_name":"Bedding, Timothy R."},{"first_name":"Joss Bland-Hawthorn","full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn","last_name":"Joss Bland-Hawthorn"},{"last_name":"Breton","full_name":"Breton, Sylvain N.","first_name":"Sylvain N."},{"first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet"},{"last_name":"Chaplin","full_name":"Chaplin, William J.","first_name":"William J."},{"first_name":"Rafael A.","last_name":"Garcia","full_name":"Garcia, Rafael A."},{"last_name":"Grunblatt","full_name":"Grunblatt, Samuel K.","first_name":"Samuel K."},{"last_name":"Guzik","full_name":"Guzik, Joyce A.","first_name":"Joyce A."},{"last_name":"Hekker","full_name":"Hekker, Saskia","first_name":"Saskia"},{"last_name":"Kawaler","full_name":"Kawaler, Steven D.","first_name":"Steven D."},{"first_name":"Stephane","last_name":"Mathis","full_name":"Mathis, Stephane"},{"first_name":"Savita","last_name":"Mathur","full_name":"Mathur, Savita"},{"full_name":"Metcalfe, Travis","last_name":"Metcalfe","first_name":"Travis"},{"last_name":"Mosser","full_name":"Mosser, Benoit","first_name":"Benoit"},{"first_name":"Melissa K.","full_name":"Ness, Melissa K.","last_name":"Ness"},{"first_name":"Anthony L.","full_name":"Piro, Anthony L.","last_name":"Piro"},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"first_name":"Sanjib","full_name":"Sharma, Sanjib","last_name":"Sharma"},{"last_name":"Soderblom","full_name":"Soderblom, David R.","first_name":"David R."},{"first_name":"Keivan G.","full_name":"Stassun, Keivan G.","last_name":"Stassun"},{"full_name":"Stello, Dennis","last_name":"Stello","first_name":"Dennis"},{"first_name":"Jamie","last_name":"Tayar","full_name":"Tayar, Jamie"},{"first_name":"Gerard T. van","full_name":"Belle, Gerard T. van","last_name":"Belle"},{"first_name":"Joel C.","full_name":"Zinn, Joel C.","last_name":"Zinn"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.","chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.","ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237."},"date_updated":"2023-08-02T07:36:00Z","status":"public","type":"preprint","article_number":"2307.03237","_id":"13447","date_created":"2023-08-02T07:30:43Z","date_published":"2023-07-06T00:00:00Z","doi":"10.48550/arXiv.2307.03237","language":[{"iso":"eng"}],"publication":"arXiv","day":"06","year":"2023","publication_status":"submitted","month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.03237"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing."}]},{"_id":"13354","article_type":"original","type":"journal_article","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_updated":"2023-08-02T10:44:22Z","extern":"1","abstract":[{"text":"Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c11973"}],"month":"02","intvolume":" 145","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"7","volume":145,"citation":{"chicago":"Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.2c11973.","ista":"Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108.","mla":"Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” Journal of the American Chemical Society, vol. 145, no. 7, American Chemical Society, 2023, pp. 4098–108, doi:10.1021/jacs.2c11973.","ieee":"J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive nanoparticle aggregates,” Journal of the American Chemical Society, vol. 145, no. 7. American Chemical Society, pp. 4098–4108, 2023.","short":"J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145 (2023) 4098–4108.","apa":"Wang, J., Peled, T. S., & Klajn, R. (2023). Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.2c11973","ama":"Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 2023;145(7):4098-4108. doi:10.1021/jacs.2c11973"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jinhua","full_name":"Wang, Jinhua","last_name":"Wang"},{"last_name":"Peled","full_name":"Peled, Tzuf Shay","first_name":"Tzuf Shay"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["36757850"]},"article_processing_charge":"No","title":"Photocleavable anionic glues for light-responsive nanoparticle aggregates","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"year":"2023","day":"09","publication":"Journal of the American Chemical Society","page":"4098-4108","doi":"10.1021/jacs.2c11973","date_published":"2023-02-09T00:00:00Z","date_created":"2023-08-01T09:33:08Z"},{"_id":"12781","status":"public","type":"dissertation","ddc":["570","572"],"date_updated":"2023-08-04T08:54:51Z","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A"}],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"file_date_updated":"2023-04-20T07:02:59Z","oa_version":"Published Version","abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"03","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"closed","embargo_to":"local","content_type":"application/pdf","embargo":"2024-04-20","file_id":"12852","checksum":"5ebb6345cb4119f93460c81310265a6d","creator":"vkravchu","file_size":6071553,"date_updated":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_created":"2023-04-19T14:33:41Z"},{"embargo":"2024-04-20","file_id":"12853","checksum":"c12055c48411d030d2afa51de2166221","relation":"source_file","access_level":"closed","embargo_to":"local","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","date_created":"2023-04-19T14:33:52Z","creator":"vkravchu","file_size":19468766,"date_updated":"2023-04-20T07:02:59Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"12138","relation":"part_of_dissertation"}]},"project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","name":"Structural characterization of E. coli complex I: an important mechanistic model","grant_number":"25541"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781."},"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","article_processing_charge":"No","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav"}],"publisher":"Institute of Science and Technology Austria","day":"23","year":"2023","has_accepted_license":"1","date_created":"2023-03-31T12:24:42Z","doi":"10.15479/at:ista:12781","date_published":"2023-03-23T00:00:00Z","page":"127"},{"_id":"13074","status":"public","type":"dissertation","ddc":["000"],"date_updated":"2023-08-04T10:33:27Z","supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"file_date_updated":"2023-05-24T16:12:59Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"month":"05","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-24T16:11:16Z","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","date_updated":"2023-05-24T16:11:16Z","file_size":2152072,"creator":"epeste","checksum":"6b3354968403cb9d48cc5a83611fb571","file_id":"13087","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/zip","relation":"source_file","access_level":"closed","file_id":"13088","checksum":"8d0df94bbcf4db72c991f22503b3fd60","file_size":1658293,"date_updated":"2023-05-24T16:12:59Z","creator":"epeste","file_name":"PhD_Thesis_APeste.zip","date_created":"2023-05-24T16:12:59Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11458"},{"relation":"part_of_dissertation","id":"13053","status":"public"},{"status":"public","id":"12299","relation":"part_of_dissertation"}]},"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria."},"title":"Efficiency and generalization of sparse neural networks","article_processing_charge":"No","author":[{"last_name":"Peste","full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"23","year":"2023","has_accepted_license":"1","date_created":"2023-05-23T17:07:53Z","date_published":"2023-05-23T00:00:00Z","doi":"10.15479/at:ista:13074","page":"147"},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-17T13:39:54Z","file_name":"thesis_boocock.pdf","creator":"dboocock","date_updated":"2023-05-19T07:04:25Z","file_size":40414730,"file_id":"12988","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","embargo":"2024-05-17","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access"},{"creator":"dboocock","file_size":34338567,"date_updated":"2023-05-17T14:35:13Z","file_name":"thesis_boocock.zip","date_created":"2023-05-17T13:39:53Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"12989","checksum":"581a2313ffeb40fe77e8a122a25a7795"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"8602","status":"public"}]},"abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","date_updated":"2023-08-04T11:02:40Z","supervisor":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"file_date_updated":"2023-05-19T07:04:25Z","_id":"12964","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","year":"2023","has_accepted_license":"1","day":"17","page":"146","date_created":"2023-05-15T14:52:36Z","date_published":"2023-05-17T00:00:00Z","doi":"10.15479/at:ista:12964","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","last_name":"Boocock"}],"title":"Mechanochemical pattern formation across biological scales","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}]},{"scopus_import":"1","intvolume":" 108","month":"08","abstract":[{"lang":"eng","text":"The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons."}],"oa_version":"Published Version","ec_funded":1,"issue":"5","volume":108,"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-08-07T09:48:08Z","file_size":3051398,"creator":"dernst","date_created":"2023-08-07T09:48:08Z","file_name":"2023_PhysRevB_Brighi.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f763000339b5fd543c14377109920690","file_id":"13981","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13963","file_date_updated":"2023-08-07T09:48:08Z","department":[{"_id":"MaSe"}],"date_updated":"2023-08-07T09:51:39Z","ddc":["530"],"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60].","date_created":"2023-08-05T18:25:22Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1103/physrevb.108.054201","year":"2023","has_accepted_license":"1","publication":"Physical Review B","day":"01","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"054201","article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2303.16876"]},"author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","last_name":"Brighi"},{"first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","full_name":"Ljubotina, Marko"},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"title":"Many-body localization proximity effect in a two-species bosonic Hubbard model","citation":{"mla":"Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201.","ama":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201","apa":"Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201","ieee":"P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023.","short":"P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).","chicago":"Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.","ista":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams."}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12666","open_access":"1"}],"scopus_import":"1","intvolume":" 108","month":"07","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":108,"issue":"4","_id":"13966","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T08:41:29Z","department":[{"_id":"MiLe"},{"_id":"TaHa"}],"acknowledgement":"We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2023","publication":"Physical Review B","day":"15","date_created":"2023-08-06T22:01:10Z","doi":"10.1103/PhysRevB.108.045115","date_published":"2023-07-15T00:00:00Z","article_number":"045115","project":[{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities"},{"call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","name":"Algebro-Geometric Applications of Factorization Homology","grant_number":"M02751"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"citation":{"chicago":"Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115.","ista":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.","ama":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115","apa":"Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115","short":"G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).","ieee":"G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2203.12666"]},"author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"last_name":"Ho","full_name":"Ho, Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Tscherbul, T. V.","last_name":"Tscherbul","first_name":"T. V."}],"title":"Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling"},{"volume":100,"publication_identifier":{"eissn":["2333-3553"],"issn":["0078-6209"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15227/orgsyn.100.0271"}],"month":"07","intvolume":" 100","oa_version":"Published Version","department":[{"_id":"BaPi"}],"date_updated":"2023-08-07T08:21:45Z","article_type":"original","type":"journal_article","status":"public","_id":"13970","page":"271-286","doi":"10.15227/orgsyn.100.0271","date_published":"2023-07-01T00:00:00Z","date_created":"2023-08-06T22:01:11Z","year":"2023","day":"01","publication":"Organic Syntheses","quality_controlled":"1","publisher":"Organic Syntheses","oa":1,"author":[{"first_name":"Amiera","full_name":"Madani, Amiera","last_name":"Madani"},{"last_name":"Sletten","full_name":"Sletten, Eric T.","first_name":"Eric T."},{"full_name":"Cavedon, Cristian","last_name":"Cavedon","first_name":"Cristian"},{"last_name":"Seeberger","full_name":"Seeberger, Peter H.","first_name":"Peter H."},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"}],"article_processing_charge":"No","title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose","citation":{"ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.","short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271","mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.","ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]