[{"conference":{"location":"Amsterdam, The Netherlands","name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2019-08-29","start_date":"2019-08-27"},"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-0302-9661-2"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11514"}],"status":"public","type":"conference","_id":"7231","date_created":"2020-01-05T23:00:47Z","article_processing_charge":"No","volume":11750,"language":[{"iso":"eng"}],"month":"08","author":[{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","intvolume":" 11750","arxiv":1,"scopus_import":"1","doi":"10.1007/978-3-030-29662-9_8","year":"2019","page":"123-141","day":"13","oa":1,"title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","date_published":"2019-08-13T00:00:00Z","publisher":"Springer Nature","isi":1,"abstract":[{"text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature.","lang":"eng"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"external_id":{"isi":["000611677700008"],"arxiv":["1907.11514"]},"citation":{"ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8."},"date_updated":"2023-09-06T14:55:15Z","department":[{"_id":"ToHe"}]},{"language":[{"iso":"eng"}],"volume":11750,"article_processing_charge":"No","month":"08","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"None","conference":{"end_date":"2019-08-29","start_date":"2019-08-27","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","location":"Amsterdam, The Netherlands"},"status":"public","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["978-3-0302-9661-2"]},"date_created":"2020-01-05T23:00:48Z","type":"conference","_id":"7232","publisher":"Springer Nature","date_published":"2019-08-13T00:00:00Z","title":"Mixed-time signal temporal logic","publication_status":"published","abstract":[{"lang":"eng","text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. "}],"isi":1,"alternative_title":["LNCS"],"external_id":{"isi":["000611677700004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"date_updated":"2023-09-06T14:57:17Z","citation":{"ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4."},"intvolume":" 11750","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","scopus_import":"1","year":"2019","page":"59-75","doi":"10.1007/978-3-030-29662-9_4","day":"13"},{"abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"publication_status":"published","month":"07","article_number":"NM2A.5","date_published":"2019-07-15T00:00:00Z","publisher":"Optica Publishing Group","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","date_updated":"2023-10-17T12:14:46Z","department":[{"_id":"JoFi"}],"quality_controlled":"1","citation":{"ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019."},"oa_version":"None","author":[{"orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","conference":{"end_date":"2019-07-19","start_date":"2019-07-15","location":"Waikoloa Beach, Hawaii (HI), United States","name":"NLO: Nonlinear Optics"},"publication":"Nonlinear Optics, OSA Technical Digest","date_created":"2020-01-05T23:00:48Z","_id":"7233","type":"conference","doi":"10.1364/NLO.2019.NM2A.5","publication_identifier":{"isbn":["9781557528209"]},"status":"public","year":"2019","day":"15"},{"month":"08","has_accepted_license":"1","issue":"8","file":[{"access_level":"open_access","file_size":2888027,"file_id":"7424","checksum":"94d4cfb2ab0b4c90ef76a7f3cc811feb","creator":"dernst","relation":"main_file","file_name":"2019_EnergyEnvironScienc_Mourad.pdf","date_created":"2020-01-30T16:11:05Z","date_updated":"2020-07-14T12:47:55Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":12,"quality_controlled":"1","oa_version":"Published Version","author":[{"first_name":"Eléonore","last_name":"Mourad","full_name":"Mourad, Eléonore"},{"full_name":"Petit, Yann K.","first_name":"Yann K.","last_name":"Petit"},{"last_name":"Spezia","first_name":"Riccardo","full_name":"Spezia, Riccardo"},{"full_name":"Samojlov, Aleksej","last_name":"Samojlov","first_name":"Aleksej"},{"last_name":"Summa","first_name":"Francesco F.","full_name":"Summa, Francesco F."},{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"Leypold, Christian","first_name":"Christian","last_name":"Leypold"},{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"first_name":"Christian","last_name":"Slugovc","full_name":"Slugovc, Christian"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"}],"date_created":"2020-01-15T07:18:04Z","type":"journal_article","_id":"7275","article_type":"original","status":"public","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["1754-5692","1754-5706"]},"abstract":[{"text":"Aprotic alkali metal–oxygen batteries require reversible formation of metal superoxide or peroxide on cycling. Severe parasitic reactions cause poor rechargeability, efficiency, and cycle life and have been shown to be caused by singlet oxygen (1O2) that forms at all stages of cycling. However, its formation mechanism remains unclear. We show that disproportionation of superoxide, the product or intermediate on discharge and charge, to peroxide and oxygen is responsible for 1O2 formation. While the overall reaction is driven by the stability of peroxide and thus favored by stronger Lewis acidic cations such as Li+, the 1O2 fraction is enhanced by weak Lewis acids such as organic cations. Concurrently, the metal peroxide yield drops with increasing 1O2. The results explain a major parasitic pathway during cell cycling and the growing severity in K–, Na–, and Li–O2 cells based on the growing propensity for disproportionation. High capacities and rates with peroxides are now realized to require solution processes, which form peroxide or release O2via disproportionation. The results therefore establish the central dilemma that disproportionation is required for high capacity but also responsible for irreversible reactions. Highly reversible cell operation requires hence finding reaction routes that avoid disproportionation.","lang":"eng"}],"publication_status":"published","ddc":["530","541","540"],"date_published":"2019-08-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:55Z","publisher":"RSC","title":"Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries","date_updated":"2021-01-12T08:12:41Z","extern":"1","citation":{"ama":"Mourad E, Petit YK, Spezia R, et al. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. 2019;12(8):2559-2568. doi:10.1039/c9ee01453e","ista":"Mourad E, Petit YK, Spezia R, Samojlov A, Summa FF, Prehal C, Leypold C, Mahne N, Slugovc C, Fontaine O, Brutti S, Freunberger SA. 2019. Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. 12(8), 2559–2568.","chicago":"Mourad, Eléonore, Yann K. Petit, Riccardo Spezia, Aleksej Samojlov, Francesco F. Summa, Christian Prehal, Christian Leypold, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” Energy & Environmental Science. RSC, 2019. https://doi.org/10.1039/c9ee01453e.","apa":"Mourad, E., Petit, Y. K., Spezia, R., Samojlov, A., Summa, F. F., Prehal, C., … Freunberger, S. A. (2019). Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries. Energy & Environmental Science. RSC. https://doi.org/10.1039/c9ee01453e","ieee":"E. Mourad et al., “Singlet oxygen from cation driven superoxide disproportionation and consequences for aprotic metal–O2 batteries,” Energy & Environmental Science, vol. 12, no. 8. RSC, pp. 2559–2568, 2019.","mla":"Mourad, Eléonore, et al. “Singlet Oxygen from Cation Driven Superoxide Disproportionation and Consequences for Aprotic Metal–O2 Batteries.” Energy & Environmental Science, vol. 12, no. 8, RSC, 2019, pp. 2559–68, doi:10.1039/c9ee01453e.","short":"E. Mourad, Y.K. Petit, R. Spezia, A. Samojlov, F.F. Summa, C. Prehal, C. Leypold, N. Mahne, C. Slugovc, O. Fontaine, S. Brutti, S.A. Freunberger, Energy & Environmental Science 12 (2019) 2559–2568."},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 12","publication":"Energy & Environmental Science","oa":1,"day":"01","year":"2019","doi":"10.1039/c9ee01453e","page":"2559-2568"},{"quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Petit, Yann K.","first_name":"Yann K.","last_name":"Petit"},{"full_name":"Leypold, Christian","first_name":"Christian","last_name":"Leypold"},{"first_name":"Nika","last_name":"Mahne","full_name":"Mahne, Nika"},{"full_name":"Mourad, Eléonore","first_name":"Eléonore","last_name":"Mourad"},{"first_name":"Lukas","last_name":"Schafzahl","full_name":"Schafzahl, Lukas"},{"full_name":"Slugovc, Christian","last_name":"Slugovc","first_name":"Christian"},{"first_name":"Sergey M.","last_name":"Borisov","full_name":"Borisov, Sergey M."},{"first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"month":"05","has_accepted_license":"1","issue":"20","file":[{"file_name":"2019_AngewChemie_Petit.pdf","date_created":"2020-01-22T16:16:54Z","date_updated":"2020-07-14T12:47:55Z","content_type":"application/pdf","access_level":"open_access","file_size":952737,"file_id":"7356","checksum":"9620b6a511a910d7abe1f26c42dc7f83","creator":"dernst","relation":"main_file"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":58,"date_created":"2020-01-15T07:19:27Z","type":"journal_article","_id":"7276","article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","publication_identifier":{"issn":["1433-7851"]},"date_updated":"2021-01-12T08:12:42Z","extern":"1","citation":{"ieee":"Y. K. Petit et al., “DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells,” Angewandte Chemie International Edition, vol. 58, no. 20. Wiley, pp. 6535–6539, 2019.","ista":"Petit YK, Leypold C, Mahne N, Mourad E, Schafzahl L, Slugovc C, Borisov SM, Freunberger SA. 2019. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 58(20), 6535–6539.","ama":"Petit YK, Leypold C, Mahne N, et al. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 2019;58(20):6535-6539. doi:10.1002/anie.201901869","chicago":"Petit, Yann K., Christian Leypold, Nika Mahne, Eléonore Mourad, Lukas Schafzahl, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition. Wiley, 2019. https://doi.org/10.1002/anie.201901869.","apa":"Petit, Y. K., Leypold, C., Mahne, N., Mourad, E., Schafzahl, L., Slugovc, C., … Freunberger, S. A. (2019). DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201901869","short":"Y.K. Petit, C. Leypold, N. Mahne, E. Mourad, L. Schafzahl, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie International Edition 58 (2019) 6535–6539.","mla":"Petit, Yann K., et al. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition, vol. 58, no. 20, Wiley, 2019, pp. 6535–39, doi:10.1002/anie.201901869."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Singlet oxygen (1O2) causes a major fraction of the parasitic chemistry during the cycling of non‐aqueous alkali metal‐O2 batteries and also contributes to interfacial reactivity of transition‐metal oxide intercalation compounds. We introduce DABCOnium, the mono alkylated form of 1,4‐diazabicyclo[2.2.2]octane (DABCO), as an efficient 1O2 quencher with an unusually high oxidative stability of ca. 4.2 V vs. Li/Li+. Previous quenchers are strongly Lewis basic amines with too low oxidative stability. DABCOnium is an ionic liquid, non‐volatile, highly soluble in the electrolyte, stable against superoxide and peroxide, and compatible with lithium metal. The electrochemical stability covers the required range for metal–O2 batteries and greatly reduces 1O2 related parasitic chemistry as demonstrated for the Li–O2 cell.","lang":"eng"}],"publication_status":"published","ddc":["540"],"file_date_updated":"2020-07-14T12:47:55Z","publisher":"Wiley","date_published":"2019-05-13T00:00:00Z","title":"DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells","oa":1,"year":"2019","page":"6535-6539","doi":"10.1002/anie.201901869","day":"13","intvolume":" 58","publication":"Angewandte Chemie International Edition"},{"status":"public","publication_identifier":{"issn":["2041-1723"]},"date_created":"2020-01-15T12:12:26Z","type":"journal_article","_id":"7280","article_type":"original","author":[{"first_name":"Won-Jin","last_name":"Kwak","full_name":"Kwak, Won-Jin"},{"last_name":"Kim","first_name":"Hun","full_name":"Kim, Hun"},{"full_name":"Petit, Yann K.","first_name":"Yann K.","last_name":"Petit"},{"last_name":"Leypold","first_name":"Christian","full_name":"Leypold, Christian"},{"full_name":"Nguyen, Trung Thien","first_name":"Trung Thien","last_name":"Nguyen"},{"last_name":"Mahne","first_name":"Nika","full_name":"Mahne, Nika"},{"full_name":"Redfern, Paul","last_name":"Redfern","first_name":"Paul"},{"last_name":"Curtiss","first_name":"Larry A.","full_name":"Curtiss, Larry A."},{"last_name":"Jung","first_name":"Hun-Gi","full_name":"Jung, Hun-Gi"},{"last_name":"Borisov","first_name":"Sergey M.","full_name":"Borisov, Sergey M."},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Sun","first_name":"Yang-Kook","full_name":"Sun, Yang-Kook"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":10,"month":"03","has_accepted_license":"1","file":[{"file_name":"2019_NatureComm_Kwak.pdf","content_type":"application/pdf","date_created":"2020-01-22T15:58:54Z","date_updated":"2020-07-14T12:47:55Z","file_id":"7355","checksum":"123dd33e7f26761c82c74e10811a1e4d","creator":"dernst","access_level":"open_access","file_size":1003676,"relation":"main_file"}],"article_number":"1380","doi":"10.1038/s41467-019-09399-0","year":"2019","day":"26","oa":1,"intvolume":" 10","publication":"Nature Communications","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:44Z","extern":"1","citation":{"ieee":"W.-J. Kwak et al., “Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen,” Nature Communications, vol. 10. Springer Nature, 2019.","chicago":"Kwak, Won-Jin, Hun Kim, Yann K. Petit, Christian Leypold, Trung Thien Nguyen, Nika Mahne, Paul Redfern, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09399-0.","ista":"Kwak W-J, Kim H, Petit YK, Leypold C, Nguyen TT, Mahne N, Redfern P, Curtiss LA, Jung H-G, Borisov SM, Freunberger SA, Sun Y-K. 2019. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 10, 1380.","ama":"Kwak W-J, Kim H, Petit YK, et al. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 2019;10. doi:10.1038/s41467-019-09399-0","apa":"Kwak, W.-J., Kim, H., Petit, Y. K., Leypold, C., Nguyen, T. T., Mahne, N., … Sun, Y.-K. (2019). Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09399-0","mla":"Kwak, Won-Jin, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications, vol. 10, 1380, Springer Nature, 2019, doi:10.1038/s41467-019-09399-0.","short":"W.-J. Kwak, H. Kim, Y.K. Petit, C. Leypold, T.T. Nguyen, N. Mahne, P. Redfern, L.A. Curtiss, H.-G. Jung, S.M. Borisov, S.A. Freunberger, Y.-K. Sun, Nature Communications 10 (2019)."},"publisher":"Springer Nature","date_published":"2019-03-26T00:00:00Z","file_date_updated":"2020-07-14T12:47:55Z","title":"Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen","abstract":[{"text":"Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during discharge and oxidizing it during recharge. The significant problem of oxidizing the solid insulating lithium peroxide can greatly be facilitated by incorporating redox mediators that shuttle electron-holes between the porous substrate and lithium peroxide. Redox mediator stability is thus key for energy efficiency, reversibility, and cycle life. However, the gradual deactivation of redox mediators during repeated cycling has not conclusively been explained. Here, we show that organic redox mediators are predominantly decomposed by singlet oxygen that forms during cycling. Their reaction with superoxide, previously assumed to mainly trigger their degradation, peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced form of the mediator is markedly more reactive towards singlet oxygen than the oxidized form, from which we derive reaction mechanisms supported by density functional theory calculations. Redox mediators must thus be designed for stability against singlet oxygen.","lang":"eng"}],"publication_status":"published","ddc":["540"]},{"status":"public","publication_identifier":{"issn":["2155-5435"]},"_id":"7281","type":"journal_article","article_type":"original","date_created":"2020-01-15T12:12:40Z","article_processing_charge":"No","volume":9,"language":[{"iso":"eng"}],"issue":"11","file":[{"date_updated":"2020-07-14T12:47:55Z","date_created":"2020-06-29T15:19:30Z","content_type":"application/pdf","file_name":"Revised Manuscript.pdf","relation":"main_file","file_size":1199086,"access_level":"open_access","creator":"sfreunbe","checksum":"bbaebfe5ff0bcab6235821ba3460b7de","file_id":"8053"}],"month":"11","has_accepted_license":"1","author":[{"last_name":"Kwak","first_name":"Won-Jin","full_name":"Kwak, Won-Jin"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Hun","last_name":"Kim","full_name":"Kim, Hun"},{"last_name":"Park","first_name":"Jiwon","full_name":"Park, Jiwon"},{"first_name":"Trung Thien","last_name":"Nguyen","full_name":"Nguyen, Trung Thien"},{"full_name":"Jung, Hun-Gi","last_name":"Jung","first_name":"Hun-Gi"},{"last_name":"Byon","first_name":"Hye Ryung","full_name":"Byon, Hye Ryung"},{"full_name":"Sun, Yang-Kook","first_name":"Yang-Kook","last_name":"Sun"}],"oa_version":"Submitted Version","quality_controlled":"1","publication":"ACS Catalysis","intvolume":" 9","year":"2019","day":"01","doi":"10.1021/acscatal.9b01337","page":"9914-9922","oa":1,"title":"Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries","publisher":"ACS","file_date_updated":"2020-07-14T12:47:55Z","date_published":"2019-11-01T00:00:00Z","ddc":["540"],"abstract":[{"lang":"eng","text":"Li–O2 batteries are plagued by side reactions that cause poor rechargeability and efficiency. These reactions were recently revealed to be predominantly caused by singlet oxygen, which can be neutralized by chemical traps or physical quenchers. However, traps are irreversibly consumed and thus only active for a limited time, and so far identified quenchers lack oxidative stability to be suitable for typically required recharge potentials. Thus, reducing the charge potential within the stability limit of the quencher and/or finding more stable quenchers is required. Here, we show that dimethylphenazine as a redox mediator decreases the charge potential well within the stability limit of the quencher 1,4-diazabicyclo[2.2.2]octane. The quencher can thus mitigate the parasitic reactions without being oxidatively decomposed. At the same time the quencher protects the redox mediator from singlet oxygen attack. The mutual conservation of the redox mediator and the quencher is rational for stable and effective Li–O2 batteries."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kwak W-J, Freunberger SA, Kim H, et al. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 2019;9(11):9914-9922. doi:10.1021/acscatal.9b01337","chicago":"Kwak, Won-Jin, Stefan Alexander Freunberger, Hun Kim, Jiwon Park, Trung Thien Nguyen, Hun-Gi Jung, Hye Ryung Byon, and Yang-Kook Sun. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis. ACS, 2019. https://doi.org/10.1021/acscatal.9b01337.","ista":"Kwak W-J, Freunberger SA, Kim H, Park J, Nguyen TT, Jung H-G, Byon HR, Sun Y-K. 2019. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 9(11), 9914–9922.","apa":"Kwak, W.-J., Freunberger, S. A., Kim, H., Park, J., Nguyen, T. T., Jung, H.-G., … Sun, Y.-K. (2019). Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. ACS. https://doi.org/10.1021/acscatal.9b01337","ieee":"W.-J. Kwak et al., “Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries,” ACS Catalysis, vol. 9, no. 11. ACS, pp. 9914–9922, 2019.","short":"W.-J. Kwak, S.A. Freunberger, H. Kim, J. Park, T.T. Nguyen, H.-G. Jung, H.R. Byon, Y.-K. Sun, ACS Catalysis 9 (2019) 9914–9922.","mla":"Kwak, Won-Jin, et al. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis, vol. 9, no. 11, ACS, 2019, pp. 9914–22, doi:10.1021/acscatal.9b01337."},"date_updated":"2021-01-12T08:12:44Z","extern":"1"},{"publication_identifier":{"issn":["1755-4330","1755-4349"]},"status":"public","date_created":"2020-01-15T12:12:53Z","type":"journal_article","_id":"7282","article_type":"letter_note","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":11,"has_accepted_license":"1","month":"08","issue":"9","file":[{"file_size":286805,"access_level":"open_access","creator":"sfreunbe","file_id":"8054","checksum":"76806cff3d5b62f846499a8617cee7ef","relation":"main_file","file_name":"Freunberger on Eichhorn.pdf","date_updated":"2020-07-14T12:47:55Z","date_created":"2020-06-29T15:38:21Z","content_type":"application/pdf"}],"author":[{"first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"quality_controlled":"1","oa_version":"Submitted Version","intvolume":" 11","publication":"Nature Chemistry","year":"2019","doi":"10.1038/s41557-019-0311-0","page":"761-763","day":"19","oa":1,"file_date_updated":"2020-07-14T12:47:55Z","date_published":"2019-08-19T00:00:00Z","publisher":"Springer Nature","title":"Interphase identity crisis","abstract":[{"text":"Interphases that form on the anode surface of lithium-ion batteries are critical for performance and lifetime, but are poorly understood. Now, a decade-old misconception regarding a main component of the interphase has been revealed, which could potentially lead to improved devices.","lang":"eng"}],"publication_status":"published","ddc":["540","547"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:44Z","extern":"1","citation":{"short":"S.A. Freunberger, Nature Chemistry 11 (2019) 761–763.","mla":"Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry, vol. 11, no. 9, Springer Nature, 2019, pp. 761–63, doi:10.1038/s41557-019-0311-0.","ieee":"S. A. Freunberger, “Interphase identity crisis,” Nature Chemistry, vol. 11, no. 9. Springer Nature, pp. 761–763, 2019.","ama":"Freunberger SA. Interphase identity crisis. Nature Chemistry. 2019;11(9):761-763. doi:10.1038/s41557-019-0311-0","chicago":"Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry. Springer Nature, 2019. https://doi.org/10.1038/s41557-019-0311-0.","ista":"Freunberger SA. 2019. Interphase identity crisis. Nature Chemistry. 11(9), 761–763.","apa":"Freunberger, S. A. (2019). Interphase identity crisis. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-019-0311-0"}},{"doi":"10.1038/s41563-019-0313-8","year":"2019","day":"20","page":"301-302","oa":1,"intvolume":" 18","publication":"Nature Materials","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:12:45Z","citation":{"ama":"Petit YK, Freunberger SA. Thousands of cycles. Nature Materials. 2019;18(4):301-302. doi:10.1038/s41563-019-0313-8","ista":"Petit YK, Freunberger SA. 2019. Thousands of cycles. Nature Materials. 18(4), 301–302.","chicago":"Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials. Springer Nature, 2019. https://doi.org/10.1038/s41563-019-0313-8.","apa":"Petit, Y. K., & Freunberger, S. A. (2019). Thousands of cycles. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-019-0313-8","ieee":"Y. K. Petit and S. A. Freunberger, “Thousands of cycles,” Nature Materials, vol. 18, no. 4. Springer Nature, pp. 301–302, 2019.","short":"Y.K. Petit, S.A. Freunberger, Nature Materials 18 (2019) 301–302.","mla":"Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials, vol. 18, no. 4, Springer Nature, 2019, pp. 301–02, doi:10.1038/s41563-019-0313-8."},"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:55Z","date_published":"2019-03-20T00:00:00Z","title":"Thousands of cycles","publication_status":"published","abstract":[{"lang":"eng","text":"Potassium–air batteries, which suffer from oxygen cathode and potassium metal anode degradation, can be cycled thousands of times when an organic anode replaces the metal."}],"ddc":["540","541"],"status":"public","publication_identifier":{"issn":["1476-1122","1476-4660"]},"date_created":"2020-01-15T12:13:05Z","article_type":"letter_note","_id":"7283","type":"journal_article","author":[{"last_name":"Petit","first_name":"Yann K.","full_name":"Petit, Yann K."},{"last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":18,"article_processing_charge":"No","month":"03","has_accepted_license":"1","file":[{"checksum":"4c9a0314327028a22dd902bc109b8798","file_id":"8059","creator":"sfreunbe","access_level":"open_access","file_size":398123,"relation":"main_file","file_name":"NaV_final.pdf","content_type":"application/pdf","date_created":"2020-06-29T16:26:54Z","date_updated":"2020-07-14T12:47:55Z"}],"issue":"4"},{"volume":3,"article_processing_charge":"No","language":[{"iso":"eng"}],"issue":"2","month":"02","author":[{"full_name":"Prehal, Christian","last_name":"Prehal","first_name":"Christian"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","publication_identifier":{"issn":["2542-4351"]},"main_file_link":[{"url":"https://www.doi.org/10.1016/j.joule.2019.01.020","open_access":"1"}],"article_type":"review","type":"journal_article","_id":"7284","date_created":"2020-01-15T12:13:15Z","title":"Li-O2 cell-scale energy densities","publisher":"Elsevier","date_published":"2019-02-20T00:00:00Z","publication_status":"published","abstract":[{"text":"In this issue of Joule, Dongmin Im and coworkers from Samsung in South Korea describe a prototype lithium-O2 battery that reaches ∼700 Wh kg–1 and ∼600 Wh L–1 on the cell level. They cut all components to the minimum to reach this value. Difficulties filling the pores with discharge product and inhomogeneous cell utilization turn out to limit the achievable energy. Their work underlines the importance of reporting performance with respect to full cell weight and volume.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. Prehal and S. A. Freunberger, “Li-O2 cell-scale energy densities,” Joule, vol. 3, no. 2. Elsevier, pp. 321–323, 2019.","apa":"Prehal, C., & Freunberger, S. A. (2019). Li-O2 cell-scale energy densities. Joule. Elsevier. https://doi.org/10.1016/j.joule.2019.01.020","ista":"Prehal C, Freunberger SA. 2019. Li-O2 cell-scale energy densities. Joule. 3(2), 321–323.","ama":"Prehal C, Freunberger SA. Li-O2 cell-scale energy densities. Joule. 2019;3(2):321-323. doi:10.1016/j.joule.2019.01.020","chicago":"Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule. Elsevier, 2019. https://doi.org/10.1016/j.joule.2019.01.020.","mla":"Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule, vol. 3, no. 2, Elsevier, 2019, pp. 321–23, doi:10.1016/j.joule.2019.01.020.","short":"C. Prehal, S.A. Freunberger, Joule 3 (2019) 321–323."},"extern":"1","date_updated":"2021-01-12T08:12:45Z","publication":"Joule","intvolume":" 3","page":"321-323","doi":"10.1016/j.joule.2019.01.020","day":"20","year":"2019","oa":1},{"author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338"},{"first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior"}],"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":58,"article_processing_charge":"Yes (via OA deal)","month":"02","has_accepted_license":"1","file":[{"relation":"main_file","file_size":645565,"access_level":"open_access","creator":"dernst","checksum":"ba05ac2d69de4c58d2cd338b63512798","file_id":"5895","date_updated":"2020-07-14T12:47:55Z","date_created":"2019-01-28T15:37:11Z","content_type":"application/pdf","file_name":"2018_Calculus_Erbar.pdf"}],"article_number":"19","issue":"1","publication_identifier":{"issn":["09442669"]},"status":"public","date_created":"2018-12-11T11:44:29Z","article_type":"original","type":"journal_article","_id":"73","ec_funded":1,"external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"JaMa"}],"date_updated":"2023-09-13T09:12:35Z","citation":{"short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1.","ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1"},"file_date_updated":"2020-07-14T12:47:55Z","publisher":"Springer","date_published":"2019-02-01T00:00:00Z","title":"On the geometry of geodesics in discrete optimal transport","publication_status":"published","abstract":[{"text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest.","lang":"eng"}],"isi":1,"ddc":["510"],"year":"2019","day":"01","doi":"10.1007/s00526-018-1456-1","oa":1,"arxiv":1,"intvolume":" 58","publication":"Calculus of Variations and Partial Differential Equations","scopus_import":"1"},{"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","date_published":"2019-12-24T00:00:00Z","publisher":"eLife Sciences Publications","file_date_updated":"2020-11-19T11:37:41Z","pmid":1,"isi":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling."}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["31873072"],"isi":["000512303700001"]},"citation":{"mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793"},"date_updated":"2023-09-06T14:58:02Z","department":[{"_id":"MaDe"}],"publication":"eLife","intvolume":" 8","scopus_import":"1","day":"24","doi":"10.7554/eLife.50793","year":"2019","acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","oa":1,"article_processing_charge":"No","volume":8,"language":[{"iso":"eng"}],"article_number":"e50793","file":[{"file_name":"2019_eLife_AminWetzel.pdf","date_created":"2020-11-19T11:37:41Z","date_updated":"2020-11-19T11:37:41Z","content_type":"application/pdf","access_level":"open_access","file_size":4817384,"file_id":"8777","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","creator":"dernst","relation":"main_file","success":1}],"month":"12","has_accepted_license":"1","author":[{"full_name":"Amin-Wetzel, Niko Paresh","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","first_name":"Niko Paresh","last_name":"Amin-Wetzel"},{"full_name":"Neidhardt, Lisa","first_name":"Lisa","last_name":"Neidhardt"},{"full_name":"Yan, Yahui","first_name":"Yahui","last_name":"Yan"},{"first_name":"Matthias P.","last_name":"Mayer","full_name":"Mayer, Matthias P."},{"first_name":"David","last_name":"Ron","full_name":"Ron, David"}],"oa_version":"Published Version","quality_controlled":"1","publication_identifier":{"eissn":["2050084X"]},"status":"public","_id":"7340","type":"journal_article","article_type":"original","date_created":"2020-01-19T23:00:39Z"},{"day":"13","status":"public","year":"2019","doi":"10.1101/2019.12.13.875773","page":"75","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2019.12.13.875773"}],"date_created":"2020-01-23T09:53:40Z","oa":1,"type":"preprint","_id":"7358","publication":"bioRxiv","author":[{"first_name":"Momoko","last_name":"Watanabe","full_name":"Watanabe, Momoko"},{"first_name":"Jillian R.","last_name":"Haney","full_name":"Haney, Jillian R."},{"last_name":"Vishlaghi","first_name":"Neda","full_name":"Vishlaghi, Neda"},{"full_name":"Turcios, Felix","last_name":"Turcios","first_name":"Felix"},{"full_name":"Buth, Jessie E.","last_name":"Buth","first_name":"Jessie E."},{"full_name":"Gu, Wen","first_name":"Wen","last_name":"Gu"},{"full_name":"Collier, Amanda J.","first_name":"Amanda J.","last_name":"Collier"},{"orcid":"0000-0001-6618-6889","last_name":"Miranda","first_name":"Osvaldo","full_name":"Miranda, Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425"},{"first_name":"Di","last_name":"Chen","full_name":"Chen, Di"},{"first_name":"Shan","last_name":"Sabri","full_name":"Sabri, Shan"},{"first_name":"Amander T.","last_name":"Clark","full_name":"Clark, Amander T."},{"last_name":"Plath","first_name":"Kathrin","full_name":"Plath, Kathrin"},{"full_name":"Christofk, Heather R.","last_name":"Christofk","first_name":"Heather R."},{"last_name":"Gandal","first_name":"Michael J.","full_name":"Gandal, Michael J."},{"full_name":"Novitch, Bennett G.","last_name":"Novitch","first_name":"Bennett G."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2022-06-17T08:03:32Z","citation":{"mla":"Watanabe, Momoko, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv, Cold Spring Harbor Laboratory, 2019, doi:10.1101/2019.12.13.875773.","short":"M. Watanabe, J.R. Haney, N. Vishlaghi, F. Turcios, J.E. Buth, W. Gu, A.J. Collier, O. Miranda, D. Chen, S. Sabri, A.T. Clark, K. Plath, H.R. Christofk, M.J. Gandal, B.G. Novitch, BioRxiv (2019).","ieee":"M. Watanabe et al., “TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids,” bioRxiv. Cold Spring Harbor Laboratory, 2019.","apa":"Watanabe, M., Haney, J. R., Vishlaghi, N., Turcios, F., Buth, J. E., Gu, W., … Novitch, B. G. (2019). TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2019.12.13.875773","ista":"Watanabe M, Haney JR, Vishlaghi N, Turcios F, Buth JE, Gu W, Collier AJ, Miranda O, Chen D, Sabri S, Clark AT, Plath K, Christofk HR, Gandal MJ, Novitch BG. 2019. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv, 10.1101/2019.12.13.875773.","ama":"Watanabe M, Haney JR, Vishlaghi N, et al. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. 2019. doi:10.1101/2019.12.13.875773","chicago":"Watanabe, Momoko, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Jessie E. Buth, Wen Gu, Amanda J. Collier, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv. Cold Spring Harbor Laboratory, 2019. https://doi.org/10.1101/2019.12.13.875773."},"oa_version":"Preprint","date_published":"2019-12-13T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","title":"TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids","article_processing_charge":"No","publication_status":"published","month":"12","abstract":[{"lang":"eng","text":"Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSCs are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSCs compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily signaling pathways and increased expression of genes associated with naïve pluripotency. We further identify combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enable reproducible formation of brain structures suitable for disease modeling."}]},{"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"call_identifier":"H2020","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Tabata","first_name":"Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","full_name":"Tabata, Shigekazu"},{"id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","full_name":"Jevtic, Marijo","first_name":"Marijo","last_name":"Jevtic"},{"first_name":"Nobutaka","last_name":"Kurashige","full_name":"Kurashige, Nobutaka"},{"first_name":"Hirokazu","last_name":"Fuchida","full_name":"Fuchida, Hirokazu"},{"full_name":"Kido, Munetsugu","last_name":"Kido","first_name":"Munetsugu"},{"full_name":"Tani, Kazushi","first_name":"Kazushi","last_name":"Tani"},{"full_name":"Zenmyo, Naoki","first_name":"Naoki","last_name":"Zenmyo"},{"full_name":"Uchinomiya, Shohei","first_name":"Shohei","last_name":"Uchinomiya"},{"full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","last_name":"Harada","first_name":"Harumi"},{"first_name":"Makoto","last_name":"Itakura","full_name":"Itakura, Makoto"},{"full_name":"Hamachi, Itaru","first_name":"Itaru","last_name":"Hamachi"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Ojida, Akio","first_name":"Akio","last_name":"Ojida"}],"has_accepted_license":"1","month":"12","file":[{"access_level":"open_access","file_size":7197776,"checksum":"f3e90056a49f09b205b1c4f8c739ffd1","file_id":"7448","creator":"dernst","relation":"main_file","file_name":"2019_iScience_Tabata.pdf","date_created":"2020-02-04T10:48:36Z","date_updated":"2020-07-14T12:47:57Z","content_type":"application/pdf"}],"issue":"12","language":[{"iso":"eng"}],"volume":22,"article_processing_charge":"No","date_created":"2020-01-29T15:56:56Z","article_type":"original","_id":"7391","type":"journal_article","publication_identifier":{"issn":["2589-0042"]},"status":"public","ec_funded":1,"department":[{"_id":"RySh"}],"date_updated":"2024-03-25T23:30:07Z","citation":{"mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","ieee":"S. Tabata et al., “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268. doi:10.1016/j.isci.2019.11.025","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025"},"external_id":{"pmid":["31786521"],"isi":[":000504652000020"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","abstract":[{"text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM.","lang":"eng"}],"ddc":["570"],"pmid":1,"publisher":"Elsevier","date_published":"2019-12-20T00:00:00Z","file_date_updated":"2020-07-14T12:47:57Z","title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","oa":1,"year":"2019","day":"20","page":"256-268","doi":"10.1016/j.isci.2019.11.025","scopus_import":"1","related_material":{"record":[{"status":"public","id":"11393","relation":"dissertation_contains"}]},"intvolume":" 22","publication":"iScience"},{"has_accepted_license":"1","month":"12","issue":"12","file":[{"file_name":"2019_ScienceAdvances_Morales.pdf","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-03T13:33:25Z","content_type":"application/pdf","file_size":1869449,"access_level":"open_access","creator":"dernst","checksum":"af99a5dcdc66c6d6102051faf3be48d8","file_id":"7442","relation":"main_file"}],"article_number":"eaav9963","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":5,"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"oa_version":"Published Version","author":[{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"ec_funded":1,"date_created":"2020-01-29T15:58:27Z","type":"journal_article","_id":"7393","article_type":"original","status":"public","publication_identifier":{"issn":["2375-2548"]},"abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"publication_status":"published","ddc":["570"],"isi":1,"date_published":"2019-12-04T00:00:00Z","file_date_updated":"2020-07-14T12:47:57Z","publisher":"AAAS","pmid":1,"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","date_updated":"2023-09-06T15:35:56Z","department":[{"_id":"NiBa"}],"citation":{"apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"scopus_import":"1","intvolume":" 5","publication":"Science Advances","oa":1,"year":"2019","doi":"10.1126/sciadv.aav9963","day":"04"},{"author":[{"orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dagdas, Yasin","first_name":"Yasin","last_name":"Dagdas"}],"quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":52,"month":"12","issue":"12","status":"public","publication_identifier":{"issn":["1369-5266"]},"date_created":"2020-01-29T16:00:07Z","_id":"7394","type":"journal_article","article_type":"letter_note","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000502890600001"],"pmid":["31787165"]},"date_updated":"2023-09-07T14:56:55Z","department":[{"_id":"EvBe"}],"citation":{"short":"E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2.","mla":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology, vol. 52, no. 12, Elsevier, 2019, pp. A1–2, doi:10.1016/j.pbi.2019.11.002.","ieee":"E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of omics?,” Current Opinion in Plant Biology, vol. 52, no. 12. Elsevier, pp. A1–A2, 2019.","ista":"Benková E, Dagdas Y. 2019. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 52(12), A1–A2.","ama":"Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 2019;52(12):A1-A2. doi:10.1016/j.pbi.2019.11.002","chicago":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.11.002.","apa":"Benková, E., & Dagdas, Y. (2019). Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.11.002"},"publisher":"Elsevier","date_published":"2019-12-01T00:00:00Z","pmid":1,"title":"Editorial overview: Cell biology in the era of omics?","publication_status":"published","isi":1,"year":"2019","page":"A1-A2","doi":"10.1016/j.pbi.2019.11.002","day":"01","intvolume":" 52","publication":"Current Opinion in Plant Biology","scopus_import":"1"},{"file":[{"file_size":9654895,"access_level":"open_access","creator":"dernst","file_id":"7447","checksum":"5202f53a237d6650ece038fbf13bdcea","relation":"main_file","file_name":"2019_MolecularCell_Letts.pdf","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:37:28Z","content_type":"application/pdf"}],"issue":"6","has_accepted_license":"1","month":"09","volume":75,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"quality_controlled":"1","author":[{"full_name":"Letts, James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9864-3586","first_name":"James A","last_name":"Letts"},{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","first_name":"Karol","last_name":"Fiedorczuk"},{"full_name":"Degliesposti, Gianluca","first_name":"Gianluca","last_name":"Degliesposti"},{"first_name":"Mark","last_name":"Skehel","full_name":"Skehel, Mark"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A"}],"ec_funded":1,"article_type":"original","_id":"7395","type":"journal_article","date_created":"2020-01-29T16:02:33Z","publication_identifier":{"issn":["1097-2765"]},"status":"public","isi":1,"ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs."}],"title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","pmid":1,"file_date_updated":"2020-07-14T12:47:57Z","publisher":"Cell Press","date_published":"2019-09-19T00:00:00Z","citation":{"short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6.","mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022.","ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019."},"department":[{"_id":"LeSa"}],"date_updated":"2023-09-07T14:53:06Z","external_id":{"pmid":["31492636"],"isi":["000486614200006"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publication":"Molecular Cell","intvolume":" 75","oa":1,"year":"2019","page":"1131-1146.e6","doi":"10.1016/j.molcel.2019.07.022","day":"19"},{"intvolume":" 91","arxiv":1,"publication":"Reviews of Modern Physics","scopus_import":"1","year":"2019","doi":"10.1103/revmodphys.91.035005","day":"18","oa":1,"publisher":"American Physical Society","date_published":"2019-09-18T00:00:00Z","title":"Quantum control of molecular rotation","abstract":[{"text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting.","lang":"eng"}],"publication_status":"published","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000486661700001"],"arxiv":["1810.11338"]},"date_updated":"2024-02-28T13:15:33Z","department":[{"_id":"MiLe"}],"citation":{"mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:10.1103/revmodphys.91.035005.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).","apa":"Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.035005.","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005.","ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005","ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019."},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.11338"}],"publication_identifier":{"issn":["0034-6861"],"eissn":["1539-0756"]},"date_created":"2020-01-29T16:04:19Z","_id":"7396","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":91,"month":"09","issue":"3","article_number":"035005 ","author":[{"first_name":"Christiane P.","last_name":"Koch","full_name":"Koch, Christiane P."},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sugny, Dominique","first_name":"Dominique","last_name":"Sugny"}],"quality_controlled":"1","project":[{"name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF"}],"oa_version":"Preprint"},{"arxiv":1,"intvolume":" 874","publication":"Journal of Fluid Mechanics","scopus_import":"1","day":"10","doi":"10.1017/jfm.2019.486","page":"699-719","year":"2019","oa":1,"date_published":"2019-09-10T00:00:00Z","publisher":"CUP","title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","publication_status":"published","abstract":[{"text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT).","lang":"eng"}],"isi":1,"external_id":{"isi":["000475349900001"],"arxiv":["1808.04080"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BjHo"}],"date_updated":"2023-09-06T15:36:36Z","citation":{"chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.","ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719.","ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486","apa":"Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.","mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719."},"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"main_file_link":[{"url":"https://arxiv.org/abs/1808.04080","open_access":"1"}],"status":"public","date_created":"2020-01-29T16:05:19Z","article_type":"original","_id":"7397","type":"journal_article","language":[{"iso":"eng"}],"volume":874,"article_processing_charge":"No","month":"09","author":[{"orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso","first_name":"Jose M","full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"first_name":"George H","last_name":"Choueiri","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"quality_controlled":"1","oa_version":"Preprint"},{"status":"public","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_identifier":{"eissn":["1540-7748"],"issn":["0022-1295"]},"date_created":"2020-01-29T16:06:29Z","type":"journal_article","_id":"7398","article_type":"original","author":[{"full_name":"Erdem, Fatma Asli","last_name":"Erdem","first_name":"Fatma Asli"},{"last_name":"Ilic","first_name":"Marija","full_name":"Ilic, Marija"},{"full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner","first_name":"Peter"},{"first_name":"Jakub","last_name":"Gołacki","full_name":"Gołacki, Jakub"},{"full_name":"Lubec, Gert","first_name":"Gert","last_name":"Lubec"},{"last_name":"Freissmuth","first_name":"Michael","full_name":"Freissmuth, Michael"},{"last_name":"Sandtner","first_name":"Walter","full_name":"Sandtner, Walter"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":151,"month":"07","has_accepted_license":"1","issue":"8","file":[{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-05T07:20:32Z","content_type":"application/pdf","file_name":"2019_JGP_Erdem.pdf","relation":"main_file","file_size":2641297,"access_level":"open_access","creator":"dernst","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71","file_id":"7450"}],"page":"1035-1050","doi":"10.1085/jgp.201912318","year":"2019","day":"03","oa":1,"intvolume":" 151","publication":"The Journal of General Physiology","scopus_import":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000478792500008"],"pmid":["31270129"]},"date_updated":"2023-09-07T14:52:23Z","department":[{"_id":"RySh"}],"citation":{"ieee":"F. A. Erdem et al., “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” The Journal of General Physiology, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. Rockefeller University Press. https://doi.org/10.1085/jgp.201912318","ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318","chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318.","ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.","short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050."},"date_published":"2019-07-03T00:00:00Z","publisher":"Rockefeller University Press","file_date_updated":"2020-07-14T12:47:57Z","pmid":1,"title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","abstract":[{"text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation.","lang":"eng"}],"publication_status":"published","isi":1,"ddc":["570"]}]