[{"volume":107,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","month":"03","intvolume":" 107","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"oa_version":"Preprint","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."}],"department":[{"_id":"JoFi"}],"date_updated":"2023-08-01T14:06:05Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"12819","date_published":"2023-03-22T00:00:00Z","doi":"10.1103/PhysRevA.107.L031701","date_created":"2023-04-09T22:01:00Z","day":"22","publication":"Physical Review A","isi":1,"year":"2023","quality_controlled":"1","publisher":"American Physical Society","oa":1,"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.","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","author":[{"full_name":"Sokolova, Alesya","orcid":"0000-0002-8308-4144","last_name":"Sokolova","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","first_name":"Alesya"},{"first_name":"D. A.","last_name":"Kalacheva","full_name":"Kalacheva, D. A."},{"first_name":"G. P.","full_name":"Fedorov, G. P.","last_name":"Fedorov"},{"full_name":"Astafiev, O. V.","last_name":"Astafiev","first_name":"O. V."}],"article_processing_charge":"No","external_id":{"arxiv":["2209.05165"],"isi":["000957799000006"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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).","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","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","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."},"article_number":"L031701"},{"abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 14","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12868","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","file_size":1786475,"date_updated":"2023-04-25T09:13:53Z","creator":"dernst","file_name":"2023_NatureComm_Schmid.pdf","date_created":"2023-04-25T09:13:53Z"}],"language":[{"iso":"eng"}],"volume":14,"ec_funded":1,"_id":"12861","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","date_updated":"2023-08-01T14:15:57Z","ddc":["000"],"file_date_updated":"2023-04-25T09:13:53Z","department":[{"_id":"KrCh"}],"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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"12","publication":"Nature Communications","date_published":"2023-04-12T00:00:00Z","doi":"10.1038/s41467-023-37817-x","date_created":"2023-04-23T22:01:03Z","article_number":"2086","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","last_name":"Schmid","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"last_name":"Ekbatani","full_name":"Ekbatani, Farbod","first_name":"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","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"article_processing_charge":"No","title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information"},{"publication_status":"published","publication_identifier":{"eissn":["1553-7358"]},"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"}],"issue":"4","related_material":{"link":[{"url":"https://github.com/shervinsafavi/gpla.git","relation":"software"}]},"volume":19,"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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"04","date_updated":"2023-08-01T14:15:16Z","ddc":["570"],"file_date_updated":"2023-04-25T08:59:18Z","department":[{"_id":"JoCs"}],"_id":"12862","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","year":"2023","has_accepted_license":"1","isi":1,"publication":"PLoS Computational Biology","day":"01","date_created":"2023-04-23T22:01:03Z","date_published":"2023-04-01T00:00:00Z","doi":"10.1371/journal.pcbi.1010983","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. ","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","citation":{"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.","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","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.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000962668700002"]},"author":[{"last_name":"Safavi","full_name":"Safavi, Shervin","first_name":"Shervin"},{"first_name":"Theofanis I.","full_name":"Panagiotaropoulos, Theofanis I.","last_name":"Panagiotaropoulos"},{"first_name":"Vishal","last_name":"Kapoor","full_name":"Kapoor, Vishal"},{"last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."},{"last_name":"Besserve","full_name":"Besserve, Michel","first_name":"Michel"}],"title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","article_number":"e1010983"},{"citation":{"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.","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Chen, Ke","last_name":"Chen","first_name":"Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d"},{"last_name":"Kunkel","full_name":"Kunkel, Christian","first_name":"Christian"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"first_name":"Karsten","full_name":"Reuter, Karsten","last_name":"Reuter"},{"first_name":"Johannes T.","full_name":"Margraf, Johannes T.","last_name":"Margraf"}],"external_id":{"isi":["000971508100001"]},"article_processing_charge":"No","title":"Physics-inspired machine learning of localized intensive properties","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.","publisher":"Royal Society of Chemistry","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"10","publication":"Chemical Science","doi":"10.1039/d3sc00841j","date_published":"2023-04-10T00:00:00Z","date_created":"2023-04-30T22:01:06Z","_id":"12879","type":"journal_article","article_type":"original","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)"},"status":"public","date_updated":"2023-08-01T14:18:10Z","ddc":["000","540"],"file_date_updated":"2023-05-02T07:17:05Z","department":[{"_id":"BiCh"}],"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."}],"oa_version":"Published Version","scopus_import":"1","month":"04","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"publication_status":"published","file":[{"checksum":"5eeec69a51e192dcd94b955d84423836","file_id":"12883","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-02T07:17:05Z","file_name":"2023_ChemialScience_Chen.pdf","creator":"dernst","date_updated":"2023-05-02T07:17:05Z","file_size":1515446}],"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by/3.0/"},{"isi":1,"year":"2023","day":"01","publication":"Plant Journal","page":"155-174","date_published":"2023-07-01T00:00:00Z","doi":"10.1111/tpj.16218","date_created":"2023-04-30T22:01:06Z","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","citation":{"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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Lihui","last_name":"Jiang","full_name":"Jiang, Lihui"},{"first_name":"Baolin","last_name":"Yao","full_name":"Yao, Baolin"},{"last_name":"Zhang","full_name":"Zhang, Xiaoyan","first_name":"Xiaoyan"},{"first_name":"Lixia","last_name":"Wu","full_name":"Wu, Lixia"},{"last_name":"Fu","full_name":"Fu, Qijing","first_name":"Qijing"},{"first_name":"Yiting","last_name":"Zhao","full_name":"Zhao, Yiting"},{"full_name":"Cao, Yuxin","last_name":"Cao","first_name":"Yuxin"},{"full_name":"Zhu, Ruomeng","last_name":"Zhu","first_name":"Ruomeng"},{"full_name":"Lu, Xinqi","last_name":"Lu","first_name":"Xinqi"},{"full_name":"Huang, Wuying","last_name":"Huang","first_name":"Wuying"},{"first_name":"Jianping","last_name":"Zhao","full_name":"Zhao, Jianping"},{"full_name":"Li, Kuixiu","last_name":"Li","first_name":"Kuixiu"},{"first_name":"Shuanglu","last_name":"Zhao","full_name":"Zhao, Shuanglu"},{"first_name":"Li","full_name":"Han, Li","last_name":"Han"},{"full_name":"Zhou, Xuan","last_name":"Zhou","first_name":"Xuan"},{"full_name":"Luo, Chongyu","last_name":"Luo","first_name":"Chongyu"},{"first_name":"Haiyan","last_name":"Zhu","full_name":"Zhu, Haiyan"},{"full_name":"Yang, Jing","last_name":"Yang","first_name":"Jing"},{"first_name":"Huichuan","full_name":"Huang, Huichuan","last_name":"Huang"},{"full_name":"Zhu, Zhengge","last_name":"Zhu","first_name":"Zhengge"},{"last_name":"He","full_name":"He, Xiahong","first_name":"Xiahong"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Zhang, Zhongkai","last_name":"Zhang","first_name":"Zhongkai"},{"first_name":"Changning","last_name":"Liu","full_name":"Liu, Changning"},{"first_name":"Yunlong","full_name":"Du, Yunlong","last_name":"Du"}],"article_processing_charge":"No","external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":115,"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","month":"07","intvolume":" 115","date_updated":"2023-08-01T14:16:33Z","department":[{"_id":"JiFr"}],"_id":"12878","type":"journal_article","article_type":"original","status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."},"title":"Boolean network sketches: A unifying framework for logical model inference","external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"article_processing_charge":"No","author":[{"first_name":"Nikola","last_name":"Beneš","full_name":"Beneš, Nikola"},{"first_name":"Luboš","full_name":"Brim, Luboš","last_name":"Brim"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"full_name":"Pastva, Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel"},{"first_name":"David","full_name":"Šafránek, David","last_name":"Šafránek"}],"article_number":"btad158","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"publication":"Bioinformatics","day":"03","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-04-30T22:01:05Z","doi":"10.1093/bioinformatics/btad158","date_published":"2023-04-03T00:00:00Z","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.].","oa":1,"quality_controlled":"1","publisher":"Oxford Academic","ddc":["000"],"date_updated":"2023-08-01T14:27:28Z","file_date_updated":"2023-05-02T07:39:04Z","department":[{"_id":"ToHe"}],"_id":"12876","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","language":[{"iso":"eng"}],"file":[{"date_created":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","creator":"dernst","date_updated":"2023-05-02T07:39:04Z","file_size":478740,"checksum":"2cb90ddf781baefddf47eac4b54e2a03","file_id":"12886","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1367-4811"]},"ec_funded":1,"issue":"4","volume":39,"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"oa_version":"Published Version","pmid":1,"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"}],"intvolume":" 39","month":"04","scopus_import":"1"},{"status":"public","type":"journal_article","article_type":"original","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)"},"_id":"12880","file_date_updated":"2023-05-02T07:24:55Z","department":[{"_id":"MaHe"}],"ddc":["570"],"date_updated":"2023-08-01T14:18:46Z","month":"04","intvolume":" 14","scopus_import":"1","oa_version":"Published Version","pmid":1,"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"}],"volume":14,"issue":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","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}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"publication_status":"published","article_number":"2202548","title":"Lamin B1 overexpression alters chromatin organization and gene expression","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"first_name":"Juliana S.","last_name":"Capitanio","full_name":"Capitanio, Juliana S."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W","last_name":"Hetzer"}],"external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","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.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","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.","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","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."},"publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"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.","doi":"10.1080/19491034.2023.2202548","date_published":"2023-04-18T00:00:00Z","date_created":"2023-04-30T22:01:06Z","day":"18","publication":"Nucleus","isi":1,"has_accepted_license":"1","year":"2023"},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"042216","title":"Numerical quantum clock simulations for measuring tunneling times","external_id":{"arxiv":["2207.13130"],"isi":["000975799300006"]},"article_processing_charge":"No","author":[{"id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","first_name":"Fumika","last_name":"Suzuki","full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970"},{"first_name":"William G.","last_name":"Unruh","full_name":"Unruh, William G."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","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."},"oa":1,"quality_controlled":"1","publisher":"American Physical Society","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.","date_created":"2023-05-07T22:01:03Z","doi":"10.1103/PhysRevA.107.042216","date_published":"2023-04-20T00:00:00Z","publication":"Physical Review A","day":"20","year":"2023","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"12914","department":[{"_id":"MiLe"}],"date_updated":"2023-08-01T14:33:21Z","intvolume":" 107","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.13130"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"ec_funded":1,"issue":"4","volume":107,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]}},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12917","checksum":"a778105665c10beb2354c92d2b295115","success":1,"date_updated":"2023-05-08T07:26:40Z","file_size":1405588,"creator":"dernst","date_created":"2023-05-08T07:26:40Z","file_name":"2023_NatureComm_DiezMerida.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"volume":14,"pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 14","month":"04","scopus_import":"1","ddc":["530"],"date_updated":"2023-08-01T14:34:00Z","file_date_updated":"2023-05-08T07:26:40Z","department":[{"_id":"AnHi"}],"_id":"12913","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","publication":"Nature Communications","day":"26","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-05-07T22:01:03Z","date_published":"2023-04-26T00:00:00Z","doi":"10.1038/s41467-023-38005-7","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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","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.","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."},"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"article_processing_charge":"No","author":[{"full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida","first_name":"J."},{"last_name":"Díez-Carlón","full_name":"Díez-Carlón, A.","first_name":"A."},{"full_name":"Yang, S. Y.","last_name":"Yang","first_name":"S. Y."},{"last_name":"Xie","full_name":"Xie, Y. M.","first_name":"Y. M."},{"first_name":"X. J.","last_name":"Gao","full_name":"Gao, X. J."},{"full_name":"Senior, Jorden L","last_name":"Senior","first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"first_name":"X.","full_name":"Lu, X.","last_name":"Lu"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Law","full_name":"Law, K. T.","first_name":"K. T."},{"last_name":"Efetov","full_name":"Efetov, Dmitri K.","first_name":"Dmitri K."}],"article_number":"2396"},{"department":[{"_id":"JuFi"}],"file_date_updated":"2023-06-19T07:33:53Z","ddc":["510"],"date_updated":"2023-08-01T14:40:33Z","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":"10550","volume":33,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"13149","checksum":"f3f0f0886098e31c81116cff8183750b","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_JourNonlinearScience_Fellner.pdf","date_created":"2023-06-19T07:33:53Z","file_size":742315,"date_updated":"2023-06-19T07:33:53Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"intvolume":" 33","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"article_processing_charge":"No","author":[{"first_name":"Klemens","full_name":"Fellner, Klemens","last_name":"Fellner"},{"last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kniely","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tang, Bao Quoc","last_name":"Tang","first_name":"Bao Quoc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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"},"article_number":"66","date_created":"2021-12-16T12:15:35Z","doi":"10.1007/s00332-023-09926-w","date_published":"2023-06-07T00:00:00Z","publication":"Journal of Nonlinear Science","day":"07","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","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."},{"date_updated":"2023-08-01T14:43:29Z","ddc":["510"],"department":[{"_id":"JuFi"}],"file_date_updated":"2023-05-22T07:24:13Z","_id":"13043","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","publication_status":"published","publication_identifier":{"eissn":["1463-9971"],"issn":["1463-9963"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-22T07:24:13Z","file_size":867876,"date_created":"2023-05-22T07:24:13Z","file_name":"2023_Interfaces_Hensel.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"622422484810441e48f613e968c7e7a4","file_id":"13045","success":1}],"ec_funded":1,"volume":25,"related_material":{"record":[{"id":"10013","status":"public","relation":"earlier_version"}]},"issue":"1","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"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 25","month":"04","citation":{"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.","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.","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.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2108.01733"],"isi":["000975817300002"]},"article_processing_charge":"No","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020"}],"year":"2023","has_accepted_license":"1","isi":1,"publication":"Interfaces and Free Boundaries","day":"20","page":"37-107","date_created":"2023-05-21T22:01:06Z","date_published":"2023-04-20T00:00:00Z","doi":"10.4171/IFB/484","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,"publisher":"EMS Press","quality_controlled":"1"},{"article_number":"161101 ","article_processing_charge":"No","external_id":{"pmid":["37093149"],"isi":["001010676000010"],"arxiv":["2302.01297"]},"author":[{"first_name":"Rochus","full_name":"Schmid, Rochus","last_name":"Schmid"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"title":"Computing chemical potentials of adsorbed or confined fluids","citation":{"ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","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.","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","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","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","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.","date_created":"2023-05-07T22:01:03Z","date_published":"2023-04-24T00:00:00Z","doi":"10.1063/5.0146711","year":"2023","isi":1,"has_accepted_license":"1","publication":"The Journal of Chemical Physics","day":"24","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":"12912","file_date_updated":"2023-05-08T07:44:49Z","department":[{"_id":"BiCh"}],"date_updated":"2023-08-01T14:34:49Z","ddc":["540"],"scopus_import":"1","intvolume":" 158","month":"04","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"issue":"16","related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"url":"https://github.com/BingqingCheng/S0","relation":"software"}]},"volume":158,"publication_status":"published","publication_identifier":{"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"4ab8c965f2fa4e17920bfa846847f137","file_id":"12918","relation":"main_file","access_level":"open_access","content_type":"application/pdf","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"}]},{"citation":{"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.","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 ","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 .","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.","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 ."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["001000062600033"]},"article_processing_charge":"No","author":[{"last_name":"Liu","full_name":"Liu, Zhenyuan","orcid":"0000-0001-9200-5690","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","first_name":"Zhenyuan"},{"last_name":"Piovarci","full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael"},{"last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1","first_name":"Raphael","full_name":"Charrondiere, Raphael","last_name":"Charrondiere"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"title":"Directionality-aware design of embroidery patterns","project":[{"name":"Perception-Aware Appearance Fabrication","grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027"},{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"year":"2023","has_accepted_license":"1","isi":1,"publication":"Computer Graphics Forum","day":"08","page":"397-409","date_created":"2023-05-16T08:47:25Z","date_published":"2023-05-08T00:00:00Z","doi":"10.1111/cgf.14770 ","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.","oa":1,"quality_controlled":"1","publisher":"Wiley","date_updated":"2023-08-01T14:47:05Z","ddc":["004"],"department":[{"_id":"BeBi"}],"file_date_updated":"2023-05-16T08:28:37Z","_id":"12972","conference":{"name":"EG: Eurographics","end_date":"2023-05-12","location":"Saarbrucken, Germany","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"},"type":"journal_article","article_type":"original","keyword":["embroidery","design","directionality","density","image"],"status":"public","publication_status":"published","publication_identifier":{"issn":["1467-8659"]},"language":[{"iso":"eng"}],"file":[{"checksum":"4c188c2be4745467a8790bbf5d6491aa","file_id":"12974","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-16T08:28:37Z","file_name":"Zhenyuan2023.pdf","creator":"mpiovarc","date_updated":"2023-05-16T08:28:37Z","file_size":24003702}],"ec_funded":1,"volume":42,"issue":"2","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"}],"oa_version":"Published Version","intvolume":" 42","month":"05"},{"page":"10700–10711","doi":"10.1021/jacs.3c01200","date_published":"2023-05-04T00:00:00Z","date_created":"2023-05-28T22:01:04Z","isi":1,"has_accepted_license":"1","year":"2023","day":"04","publication":"Journal of the American Chemical Society","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"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. ","author":[{"first_name":"Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","full_name":"Troussicot, Laura","last_name":"Troussicot"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"first_name":"Mikael","last_name":"Molin","full_name":"Molin, Mikael"},{"first_name":"Björn M.","last_name":"Burmann","full_name":"Burmann, Björn M."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","citation":{"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.","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.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":145,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12820"}]},"issue":"19","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0758a930ef21c62fc91b14e657479f83","file_id":"13098","success":1,"date_updated":"2023-05-30T07:05:28Z","file_size":6719299,"creator":"dernst","date_created":"2023-05-30T07:05:28Z","file_name":"2023_JACS_Troussicot.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 145","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","department":[{"_id":"PaSc"}],"file_date_updated":"2023-05-30T07:05:28Z","date_updated":"2023-08-01T14:48:09Z","ddc":["540"],"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":"13095"},{"publication_identifier":{"eissn":["1077-8926"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13046","checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","success":1,"creator":"dernst","date_updated":"2023-05-22T07:43:19Z","file_size":448736,"date_created":"2023-05-22T07:43:19Z","file_name":"2023_JourCombinatorics_Anastos.pdf"}],"language":[{"iso":"eng"}],"volume":30,"issue":"2","abstract":[{"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→∞.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 30","date_updated":"2023-08-01T14:44:52Z","ddc":["510"],"file_date_updated":"2023-05-22T07:43:19Z","department":[{"_id":"MaKw"}],"_id":"13042","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","isi":1,"has_accepted_license":"1","year":"2023","day":"05","publication":"Electronic Journal of Combinatorics","doi":"10.37236/11471","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-21T22:01:05Z","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","quality_controlled":"1","publisher":"Electronic Journal of Combinatorics","oa":1,"citation":{"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.","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","ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi: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).","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.","ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","full_name":"Anastos, Michael","last_name":"Anastos"}],"article_processing_charge":"No","external_id":{"isi":["000988285500001"],"arxiv":["2105.13828"]},"title":"A note on long cycles in sparse random graphs","article_number":"P2.21"},{"_id":"12820","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)"},"status":"public","date_updated":"2023-08-01T14:48:08Z","citation":{"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.","short":"P. Schanda, (2023).","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.","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","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."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","file_date_updated":"2023-04-14T09:39:58Z","department":[{"_id":"PaSc"}],"title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","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"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"04","has_accepted_license":"1","year":"2023","day":"18","file":[{"file_size":54184807,"date_updated":"2023-04-14T09:39:33Z","creator":"pschanda","file_name":"data_deposition.zip","date_created":"2023-04-14T09:39:33Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","success":1,"file_id":"12823","checksum":"54a619605e44c871214fb0e07b05c6bf"},{"checksum":"8dede9fc78399d13144eb05c62bf5750","file_id":"12824","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2023-04-14T09:39:58Z","file_name":"README","creator":"pschanda","date_updated":"2023-04-14T09:39:58Z","file_size":4978}],"related_material":{"record":[{"status":"public","id":"13095","relation":"used_in_publication"}]},"date_published":"2023-04-18T00:00:00Z","doi":"10.15479/AT:ISTA:12820","contributor":[{"last_name":"Troussicot","contributor_type":"researcher","first_name":"Laura"},{"contributor_type":"researcher","first_name":"Björn M.","last_name":"Burmann"}],"date_created":"2023-04-10T05:55:56Z"},{"_id":"13039","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-01T14:45:25Z","department":[{"_id":"BiCh"}],"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"}],"month":"04","intvolume":" 107","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","volume":107,"issue":"13","article_number":"134109","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","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.","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."},"title":"Ab initio calculation of the reflectivity of molecular fluids under shock compression","author":[{"first_name":"Martin","last_name":"French","full_name":"French, Martin"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","first_name":"Mandy","full_name":"Bethkenhagen, Mandy","orcid":"0000-0002-1838-2129","last_name":"Bethkenhagen"},{"full_name":"Ravasio, Alessandra","last_name":"Ravasio","first_name":"Alessandra"},{"first_name":"Jean Alexis","last_name":"Hernandez","full_name":"Hernandez, Jean Alexis"}],"external_id":{"isi":["000974672600001"]},"article_processing_charge":"No","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","day":"01","publication":"Physical Review B","isi":1,"year":"2023","date_published":"2023-04-01T00:00:00Z","doi":"10.1103/PhysRevB.107.134109","date_created":"2023-05-21T22:01:04Z"},{"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","publication":"ACS Applied Materials and Interfaces","day":"04","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-05-28T22:01:03Z","date_published":"2023-05-04T00:00:00Z","doi":"10.1021/acsami.3c00625","page":"23380–23389","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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."},"title":"Bottom-up synthesis of SnTe-based thermoelectric composites","article_processing_charge":"No","external_id":{"isi":["000985497900001"],"pmid":["37141543"]},"author":[{"first_name":"Bingfei","full_name":"Nan, Bingfei","last_name":"Nan"},{"first_name":"Xuan","last_name":"Song","full_name":"Song, Xuan"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"full_name":"Yang, Linlin","last_name":"Yang","first_name":"Linlin"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona","last_name":"Horta","full_name":"Horta, Sharona"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 15","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13099","checksum":"23893be46763c4c78daacddd019de821","success":1,"date_updated":"2023-05-30T07:38:44Z","file_size":5640829,"creator":"dernst","date_created":"2023-05-30T07:38:44Z","file_name":"2023_ACSAppliedMaterials_Nan.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1944-8252"],"issn":["1944-8244"]},"volume":15,"issue":"19","_id":"13092","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":["540"],"date_updated":"2023-08-01T14:50:09Z","file_date_updated":"2023-05-30T07:38:44Z","department":[{"_id":"MaIb"}]},{"month":"05","intvolume":" 23","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"volume":23,"issue":"10","ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"13100","checksum":"9734d4c617bab3578ef62916b764547a","creator":"dernst","file_size":3654910,"date_updated":"2023-05-30T07:55:31Z","file_name":"2023_NanoLetters_Azadbakht.pdf","date_created":"2023-05-30T07:55:31Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","status":"public","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)"},"_id":"13094","file_date_updated":"2023-05-30T07:55:31Z","department":[{"_id":"AnSa"}],"ddc":["540"],"date_updated":"2023-08-01T14:51:25Z","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"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).","doi":"10.1021/acs.nanolett.3c00375","date_published":"2023-05-04T00:00:00Z","date_created":"2023-05-28T22:01:03Z","page":"4267–4273","day":"04","publication":"Nano Letters","has_accepted_license":"1","isi":1,"year":"2023","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","author":[{"first_name":"Ali","last_name":"Azadbakht","full_name":"Azadbakht, Ali"},{"first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie"},{"last_name":"Varkevisser","full_name":"Varkevisser, Thijs","first_name":"Thijs"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"last_name":"Kraft","full_name":"Kraft, Daniela J.","first_name":"Daniela J."}],"external_id":{"isi":["000985481400001"],"pmid":["37141427"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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."}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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).","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.","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"},"title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature","author":[{"full_name":"Nan, Bingfei","last_name":"Nan","first_name":"Bingfei"},{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"first_name":"Ke","full_name":"Xiao, Ke","last_name":"Xiao"},{"last_name":"Lim","full_name":"Lim, Khak Ho","first_name":"Khak Ho"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","last_name":"Chang"},{"first_name":"Xu","full_name":"Han, Xu","last_name":"Han"},{"first_name":"Yong","last_name":"Zuo","full_name":"Zuo, Yong"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"external_id":{"isi":["000986859000001"]},"article_processing_charge":"No","project":[{"grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"day":"05","publication":"ACS Applied Electronic Materials","isi":1,"year":"2023","doi":"10.1021/acsaelm.3c00055","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-28T22:01:03Z","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.","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"date_updated":"2023-08-01T14:50:48Z","department":[{"_id":"MaIb"}],"_id":"13093","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2637-6113"]},"publication_status":"epub_ahead","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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaelm.3c00055"}]}]