[{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-08-24T13:31:53Z","success":1,"checksum":"b3656d14d5ddbb9d26e3074eea2d0c15","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":7320493,"creator":"cziletti","file_name":"2020_eLife_Steiner.pdf","date_created":"2020-08-24T13:31:53Z","file_id":"8289"}],"volume":9,"article_processing_charge":"No","has_accepted_license":"1","month":"07","pmid":1,"ddc":["570"],"file_date_updated":"2020-08-24T13:31:53Z","citation":{"apa":"Steiner, J., & Sazanov, L. A. (2020). Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.59407","ieee":"J. Steiner and L. A. Sazanov, “Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter,” eLife, vol. 9. eLife Sciences Publications, 2020.","ama":"Steiner J, Sazanov LA. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 2020;9. doi:10.7554/eLife.59407","short":"J. Steiner, L.A. Sazanov, ELife 9 (2020).","ista":"Steiner J, Sazanov LA. 2020. Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter. eLife. 9, e59407.","mla":"Steiner, Julia, and Leonid A. Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife, vol. 9, e59407, eLife Sciences Publications, 2020, doi:10.7554/eLife.59407.","chicago":"Steiner, Julia, and Leonid A Sazanov. “Structure and Mechanism of the Mrp Complex, an Ancient Cation/Proton Antiporter.” ELife. eLife Sciences Publications, 2020. https://doi.org/10.7554/eLife.59407."},"day":"31","oa_version":"Published Version","project":[{"_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741","name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I"}],"publication_identifier":{"eissn":["2050084X"]},"status":"public","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank Dr Victor-Valentin Hodirnau and Daniel Johann Gütl from IST Austria for assistance with collecting cryo-EM data. We thank Prof. Masahiro Ito (Graduate School of Life Sciences, Toyo University, Japan) for a kind provision of plasmid DNA encoding Mrp from A. flavithermus WK1. JS is a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria.","publication_status":"published","_id":"8284","title":"Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter","author":[{"orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Steiner, Julia","last_name":"Steiner"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989"}],"doi":"10.7554/eLife.59407","abstract":[{"text":"Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.","lang":"eng"}],"publisher":"eLife Sciences Publications","intvolume":" 9","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LeSa"}],"date_created":"2020-08-24T06:24:04Z","scopus_import":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"external_id":{"isi":["000562123600001"],"pmid":["32735215"]},"date_published":"2020-07-31T00:00:00Z","date_updated":"2023-09-07T13:14:08Z","publication":"eLife","article_number":"e59407","article_type":"original","related_material":{"record":[{"id":"8353","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"oa":1,"year":"2020"},{"oa_version":"Preprint","day":"24","citation":{"chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202.","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202"},"month":"07","pmid":1,"volume":125,"article_processing_charge":"No","arxiv":1,"issue":"4","abstract":[{"text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.","lang":"eng"}],"doi":"10.1103/PhysRevLett.125.043202","author":[{"first_name":"Benjamin K.","last_name":"Malia","full_name":"Malia, Benjamin K."},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"first_name":"Yunfan","last_name":"Wu","full_name":"Wu, Yunfan"},{"orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","_id":"8285","publication_status":"published","status":"public","acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"date_published":"2020-07-24T00:00:00Z","external_id":{"isi":["000552227400008"],"arxiv":["1912.10218"],"pmid":["32794788"]},"scopus_import":"1","date_created":"2020-08-24T06:24:04Z","department":[{"_id":"OnHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":" 125","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"publisher":"American Physical Society","year":"2020","oa":1,"article_type":"original","article_number":"043202","publication":"Physical Review Letters","date_updated":"2023-10-18T08:38:35Z"},{"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"8288","date_created":"2020-08-24T12:53:15Z","success":1,"date_updated":"2020-08-24T12:53:15Z","access_level":"open_access","content_type":"application/pdf","checksum":"d19e97d0f8a3a441dc078ec812297d75","file_name":"2020EMSOFT.pdf","creator":"cschilli","relation":"main_file","file_size":696384}],"arxiv":1,"oa_version":"Preprint","conference":{"name":"EMSOFT: International Conference on Embedded Software","location":"Virtual ","start_date":"2020-09-20","end_date":"2020-09-25"},"file_date_updated":"2020-08-24T12:53:15Z","ddc":["000"],"citation":{"chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” In Proceedings of the International Conference on Embedded Software, 2020.","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” Proceedings of the International Conference on Embedded Software, 2020.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. In: Proceedings of the International Conference on Embedded Software. ; 2020.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the International Conference on Embedded Software, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. Proceedings of the International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. In Proceedings of the International Conference on Embedded Software. Virtual .","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” in Proceedings of the International Conference on Embedded Software, Virtual , 2020."},"ec_funded":1,"publication_status":"published","status":"public","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"abstract":[{"text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.","lang":"eng"}],"_id":"8287","title":"Reachability analysis of linear hybrid systems via block decomposition","author":[{"first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"first_name":"Marcelo","full_name":"Forets, Marcelo","last_name":"Forets"},{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"first_name":"Kostiantyn","full_name":"Potomkin, Kostiantyn","last_name":"Potomkin"},{"orcid":"0000-0003-3658-1065","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","full_name":"Schilling, Christian"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","date_created":"2020-08-24T12:56:20Z","date_published":"2020-01-01T00:00:00Z","external_id":{"arxiv":["1905.02458"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"ToHe"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"8790"}]},"date_updated":"2023-08-22T13:27:32Z","publication":"Proceedings of the International Conference on Embedded Software","keyword":["reachability","hybrid systems","decomposition"],"year":"2020","oa":1},{"_id":"8294","title":"RGtracker","oa":1,"author":[{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"}],"doi":"10.15479/AT:ISTA:8294","abstract":[{"text":"Automated root growth analysis and tracking of root tips. ","lang":"eng"}],"year":"2020","date_updated":"2021-01-12T08:17:56Z","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","file_date_updated":"2020-09-08T14:26:33Z","citation":{"mla":"Hauschild, Robert. RGtracker. IST Austria, 2020, doi:10.15479/AT:ISTA:8294.","chicago":"Hauschild, Robert. “RGtracker.” IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:8294.","apa":"Hauschild, R. (2020). RGtracker. IST Austria. https://doi.org/10.15479/AT:ISTA:8294","ieee":"R. Hauschild, “RGtracker.” IST Austria, 2020.","short":"R. Hauschild, (2020).","ama":"Hauschild R. RGtracker. 2020. doi:10.15479/AT:ISTA:8294","ista":"Hauschild R. 2020. RGtracker, IST Austria, 10.15479/AT:ISTA:8294."},"department":[{"_id":"Bio"}],"day":"10","date_created":"2020-08-25T12:52:48Z","license":"https://opensource.org/licenses/BSD-3-Clause","date_published":"2020-09-10T00:00:00Z","publisher":"IST Austria","file":[{"date_updated":"2020-09-08T14:26:31Z","success":1,"checksum":"108352149987ac6f066e4925bd56e35e","content_type":"text/plain","access_level":"open_access","relation":"main_file","file_size":882,"creator":"rhauschild","file_name":"readme.txt","date_created":"2020-09-08T14:26:31Z","file_id":"8346"},{"file_id":"8347","date_created":"2020-09-08T14:26:33Z","access_level":"open_access","checksum":"ffd6c643b28e0cc7c6d0060a18a7e8ea","content_type":"application/octet-stream","success":1,"date_updated":"2020-09-08T14:26:33Z","file_name":"RGtracker.mlappinstall","creator":"rhauschild","file_size":246121,"relation":"main_file"}],"tmp":{"legal_code_url":"https://opensource.org/licenses/BSD-3-Clause","short":"3-Clause BSD","name":"The 3-Clause BSD License"},"type":"software","has_accepted_license":"1"},{"year":"2020","oa":1,"article_number":"060202(R)","article_type":"original","related_material":{"record":[{"id":"12732","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-08-24T14:20:21Z","publication":"Physical Review B","date_created":"2020-08-26T19:27:42Z","scopus_import":"1","date_published":"2020-08-26T00:00:00Z","external_id":{"isi":["000562628300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"American Physical Society","intvolume":" 102","doi":"10.1103/physrevb.102.060202","abstract":[{"lang":"eng","text":"Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model."}],"issue":"6","_id":"8308","title":"Stability of mobility edges in disordered interacting systems","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publication_status":"published","acknowledgement":"Acknowledgments. We acknowledge useful discussions with W. De Roeck and A. Michailidis. P.B. was supported by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 665385. D.A. was supported by the Swiss National Science Foundation. M.S. was supported by European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant Agreement No. 850899). This work benefited from visits to KITP, supported by the National Science Foundation under Grant No. NSF PHY-1748958 and from the program “Thermalization, Many Body Localization and Hydrodynamics” at International Centre for Theoretical Sciences (Code: ICTS/hydrodynamics2019/11).","status":"public","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa_version":"None","file_date_updated":"2020-08-26T19:29:00Z","ddc":["530"],"month":"08","citation":{"chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/physrevb.102.060202.","mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” Physical Review B, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:10.1103/physrevb.102.060202.","ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. Physical Review B. 2020;102(6). doi:10.1103/physrevb.102.060202","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","apa":"Brighi, P., Abanin, D. A., & Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.102.060202","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” Physical Review B, vol. 102, no. 6. American Physical Society, 2020."},"day":"26","article_processing_charge":"No","volume":102,"has_accepted_license":"1","file":[{"file_id":"8309","date_created":"2020-08-26T19:28:55Z","file_name":"PhysRevB.102.060202.pdf","creator":"mserbyn","relation":"main_file","file_size":488825,"success":1,"date_updated":"2020-08-26T19:28:55Z","access_level":"open_access","content_type":"application/pdf","checksum":"716442fa7861323fcc80b93718ca009c"},{"date_updated":"2020-08-26T19:29:00Z","success":1,"content_type":"application/pdf","checksum":"be0abdc8f60fe065ea6dc92e08487122","access_level":"open_access","creator":"mserbyn","relation":"main_file","file_size":711405,"file_name":"Supplementary-mbme.pdf","date_created":"2020-08-26T19:29:00Z","file_id":"8310"}]},{"file":[{"file_id":"8326","date_created":"2020-08-31T13:40:00Z","file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","relation":"main_file","creator":"cziletti","file_size":7527373,"access_level":"open_access","checksum":"52b96f41d7d0db9728064c08da00d030","content_type":"application/pdf","success":1,"date_updated":"2020-08-31T13:40:00Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"file_date_updated":"2020-08-31T13:40:00Z","pmid":1,"month":"08","day":"18","citation":{"apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","ista":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, Baradaran R, Tambalo M, Gallagher DT, Sazanov LA. 2020. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 11(1), 4135.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0.","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0."},"oa_version":"Published Version","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","status":"public","acknowledgement":"This work was funded by the Medical Research Council, UK and IST Austria. We thank the European Synchrotron Radiation Facility and the Diamond Light Source for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29, ID23-2 (ESRF, Grenoble, France) and I03 (Diamond Light Source, Didcot, UK) for assistance. Data processing was performed at the IST high-performance computing cluster.","_id":"8318","author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","full_name":"Gutierrez-Fernandez, Javier","last_name":"Gutierrez-Fernandez"},{"full_name":"Kaszuba, Karol","last_name":"Kaszuba","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","first_name":"Karol"},{"first_name":"Gurdeep S.","full_name":"Minhas, Gurdeep S.","last_name":"Minhas"},{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","first_name":"Margherita","full_name":"Tambalo, Margherita","last_name":"Tambalo"},{"first_name":"David T.","full_name":"Gallagher, David T.","last_name":"Gallagher"},{"orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"title":"Key role of quinone in the mechanism of respiratory complex I","doi":"10.1038/s41467-020-17957-0","issue":"1","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}],"intvolume":" 11","publisher":"Springer Nature","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LeSa"}],"scopus_import":"1","date_created":"2020-08-30T22:01:10Z","date_published":"2020-08-18T00:00:00Z","external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"date_updated":"2023-08-22T09:03:00Z","publication":"Nature Communications","article_type":"original","article_number":"4135","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage"}]},"oa":1,"year":"2020"},{"external_id":{"isi":["000555104200011"],"arxiv":["1912.08334"]},"date_published":"2020-07-30T00:00:00Z","scopus_import":"1","date_created":"2020-08-30T22:01:10Z","department":[{"_id":"OnHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1912.08334","open_access":"1"}],"intvolume":" 102","publisher":"American Physical Society","year":"2020","oa":1,"article_type":"original","article_number":"012224","publication":"Physical Review A","date_updated":"2024-02-28T13:11:28Z","oa_version":"Preprint","day":"30","citation":{"apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224."},"month":"07","article_processing_charge":"No","volume":102,"arxiv":1,"issue":"1","abstract":[{"lang":"eng","text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated."}],"doi":"10.1103/PhysRevA.102.012224","author":[{"full_name":"Wu, Yunfan","last_name":"Wu","first_name":"Yunfan"},{"first_name":"Rajiv","full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar"},{"last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián","first_name":"Julián"},{"first_name":"Benjamin K.","last_name":"Malia","full_name":"Malia, Benjamin K."},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","full_name":"Hosten, Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X"},{"last_name":"Kasevich","full_name":"Kasevich, Mark A.","first_name":"Mark A."}],"title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","_id":"8319","publication_status":"published","acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","status":"public","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]}},{"year":"2020","article_type":"original","page":"475-484","related_material":{"record":[{"status":"public","relation":"original","id":"8321"}]},"date_updated":"2023-08-22T09:01:03Z","publication":"Molecular Biology","scopus_import":"1","date_created":"2020-08-30T22:01:11Z","external_id":{"isi":["000562110300001"]},"date_published":"2020-08-19T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":" 54","publisher":"Springer Nature","doi":"10.1134/S0026893320040111","issue":"4","abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"_id":"8320","author":[{"first_name":"S. A.","full_name":"Mukba, S. A.","last_name":"Mukba"},{"last_name":"Vlasov","full_name":"Vlasov, Petr","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolosov","full_name":"Kolosov, P. M.","first_name":"P. M."},{"first_name":"E. Y.","full_name":"Shuvalova, E. Y.","last_name":"Shuvalova"},{"last_name":"Egorova","full_name":"Egorova, T. V.","first_name":"T. V."},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","status":"public","publication_status":"published","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","publication_identifier":{"issn":["00268933"],"eissn":["16083245"]},"oa_version":"None","month":"08","day":"19","citation":{"mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020."},"volume":54,"article_processing_charge":"No"},{"year":"2020","related_material":{"record":[{"id":"8320","status":"public","relation":"translation"}]},"page":"531-541","article_type":"original","publication":"Molekuliarnaia biologiia","date_updated":"2023-08-22T09:01:02Z","date_published":"2020-07-01T00:00:00Z","external_id":{"pmid":["32799218"]},"date_created":"2020-08-30T22:01:11Z","scopus_import":"1","department":[{"_id":"FyKo"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"rus"}],"quality_controlled":"1","type":"journal_article","publisher":"Russian Academy of Sciences","intvolume":" 54","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"issue":"4","doi":"10.31857/S0026898420040126","title":"Expanding the genetic code: Unnatural base pairs in biological systems","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","full_name":"Vlasov, Petr","last_name":"Vlasov"},{"first_name":"P. M.","full_name":"Kolosov, P. M.","last_name":"Kolosov"},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z.","first_name":"E. Z."}],"_id":"8321","status":"public","publication_status":"published","publication_identifier":{"issn":["00268984"]},"oa_version":"None","citation":{"ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126."},"day":"01","pmid":1,"month":"07","article_processing_charge":"No","volume":54},{"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030568795"],"eissn":["16113349"]},"ec_funded":1,"status":"public","acknowledgement":"We would like to thank the anonymous reviewers for their helpful comments and suggestions. The work was initiated while the first author was in IIT Madras, India. Part of this work was done while the author was visiting the University of Warsaw. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT) and from the Foundation for Polish Science under grant TEAM/2016-1/4 founded within the UE 2014–2020 Smart Growth Operational Program. The last author was supported by the Independent Research Fund Denmark project BETHE and the Concordium Blockchain Research Center, Aarhus University, Denmark.","publication_status":"published","_id":"8322","title":"Reverse firewalls for actively secure MPCs","author":[{"last_name":"Chakraborty","full_name":"Chakraborty, Suvradip","first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"last_name":"Dziembowski","full_name":"Dziembowski, Stefan","first_name":"Stefan"},{"first_name":"Jesper Buus","full_name":"Nielsen, Jesper Buus","last_name":"Nielsen"}],"doi":"10.1007/978-3-030-56880-1_26","abstract":[{"lang":"eng","text":"Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.\r\nIn this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.\r\nOur core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001)."}],"article_processing_charge":"No","volume":12171,"month":"08","citation":{"short":"S. Chakraborty, S. Dziembowski, J.B. Nielsen, in:, Advances in Cryptology – CRYPTO 2020, Springer Nature, 2020, pp. 732–762.","ama":"Chakraborty S, Dziembowski S, Nielsen JB. Reverse firewalls for actively secure MPCs. In: Advances in Cryptology – CRYPTO 2020. Vol 12171. Springer Nature; 2020:732-762. doi:10.1007/978-3-030-56880-1_26","ista":"Chakraborty S, Dziembowski S, Nielsen JB. 2020. Reverse firewalls for actively secure MPCs. Advances in Cryptology – CRYPTO 2020. CRYPTO: Annual International Cryptology Conference, LNCS, vol. 12171, 732–762.","ieee":"S. Chakraborty, S. Dziembowski, and J. B. Nielsen, “Reverse firewalls for actively secure MPCs,” in Advances in Cryptology – CRYPTO 2020, Santa Barbara, CA, United States, 2020, vol. 12171, pp. 732–762.","apa":"Chakraborty, S., Dziembowski, S., & Nielsen, J. B. (2020). Reverse firewalls for actively secure MPCs. In Advances in Cryptology – CRYPTO 2020 (Vol. 12171, pp. 732–762). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-56880-1_26","mla":"Chakraborty, Suvradip, et al. “Reverse Firewalls for Actively Secure MPCs.” Advances in Cryptology – CRYPTO 2020, vol. 12171, Springer Nature, 2020, pp. 732–62, doi:10.1007/978-3-030-56880-1_26.","chicago":"Chakraborty, Suvradip, Stefan Dziembowski, and Jesper Buus Nielsen. “Reverse Firewalls for Actively Secure MPCs.” In Advances in Cryptology – CRYPTO 2020, 12171:732–62. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-56880-1_26."},"day":"10","oa_version":"Preprint","conference":{"name":"CRYPTO: Annual International Cryptology Conference","location":"Santa Barbara, CA, United States","start_date":"2020-08-17","end_date":"2020-08-21"},"date_updated":"2021-01-12T08:18:08Z","publication":"Advances in Cryptology – CRYPTO 2020","page":"732-762","oa":1,"year":"2020","alternative_title":["LNCS"],"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1317"}],"intvolume":" 12171","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"date_created":"2020-08-30T22:01:12Z","scopus_import":"1","date_published":"2020-08-10T00:00:00Z"},{"language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":" 64","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00237-5"}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2020-08-30T22:01:12Z","external_id":{"isi":["000561483500001"]},"date_published":"2020-10-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"HeEd"}],"article_type":"letter_note","page":"571-574","date_updated":"2023-08-22T09:05:04Z","publication":"Discrete and Computational Geometry","year":"2020","oa":1,"article_processing_charge":"No","volume":64,"oa_version":"None","month":"10","day":"01","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020."},"status":"public","publication_status":"published","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"doi":"10.1007/s00454-020-00237-5","_id":"8323","author":[{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"title":"A farewell to Ricky Pollack"},{"year":"2020","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.3533633","relation":"software"}]},"article_number":"25","publication":"Proceedings of the ACM on Programming Languages","date_updated":"2024-02-22T15:16:45Z","date_published":"2020-01-01T00:00:00Z","external_id":{"arxiv":["1902.04744"]},"date_created":"2020-08-30T22:01:12Z","scopus_import":"1","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"ACM","intvolume":" 4","abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"issue":"POPL","doi":"10.1145/3371093","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","author":[{"last_name":"Wang","full_name":"Wang, Peixin","first_name":"Peixin"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Yuxin","last_name":"Deng","full_name":"Deng, Yuxin"},{"last_name":"Xu","full_name":"Xu, Ming","first_name":"Ming"}],"_id":"8324","acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","publication_status":"published","status":"public","publication_identifier":{"eissn":["2475-1421"]},"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"oa_version":"Published Version","citation":{"mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25."},"day":"01","ddc":["004"],"file_date_updated":"2020-09-01T11:12:58Z","month":"01","has_accepted_license":"1","article_processing_charge":"No","volume":4,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"success":1,"date_updated":"2020-09-01T11:12:58Z","access_level":"open_access","content_type":"application/pdf","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","file_name":"2019_ACM_POPL_Wang.pdf","file_size":564151,"creator":"cziletti","relation":"main_file","file_id":"8328","date_created":"2020-09-01T11:12:58Z"}]},{"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"intvolume":" 378","date_created":"2020-08-30T22:01:13Z","scopus_import":"1","external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"date_published":"2020-09-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"TaHa"}],"page":"1649-1675","article_type":"original","date_updated":"2023-08-22T09:00:03Z","publication":"Communications in Mathematical Physics","year":"2020","oa":1,"article_processing_charge":"No","volume":378,"arxiv":1,"oa_version":"Preprint","month":"09","citation":{"ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8."},"day":"01","ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We thank Andrea Sportiello for sharing his insights on perturbative regimes of the Abelian sandpile model which was the starting point of our work. We also thank Grigory Mikhalkin, who encouraged us to approach this problem. We thank an anonymous referee. Also we thank Misha Khristoforov and Sergey Lanzat who participated on the initial state of this project, when we had nothing except the computer simulation and pictures. We thank Mikhail Raskin for providing us the code on Golly for faster simulations. Ilia Zharkov, Ilia Itenberg, Kristin Shaw, Max Karev, Lionel Levine, Ernesto Lupercio, Pavol Ševera, Yulieth Prieto, Michael Polyak, Danila Cherkashin asked us a lot of questions and listened to us; not all of their questions found answers here, but we are going to treat them in subsequent papers.","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"doi":"10.1007/s00220-020-03828-8","abstract":[{"lang":"eng","text":"Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. "}],"issue":"9","_id":"8325","title":"Sandpile solitons via smoothing of superharmonic functions","author":[{"first_name":"Nikita","full_name":"Kalinin, Nikita","last_name":"Kalinin"},{"orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov"}]},{"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Wiley","main_file_link":[{"url":"https://doi.org/10.1002/anie.202008253","open_access":"1"}],"intvolume":" 59","date_created":"2020-09-03T16:10:56Z","scopus_import":"1","date_published":"2020-12-14T00:00:00Z","external_id":{"isi":["000576148700001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"StFr"}],"page":"22943-22946","article_type":"original","related_material":{"record":[{"id":"9780","relation":"research_data","status":"public"}]},"date_updated":"2023-09-05T16:03:47Z","publication":"Angewandte Chemie International Edition","year":"2020","oa":1,"article_processing_charge":"No","volume":59,"oa_version":"Published Version","month":"12","citation":{"mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:10.1002/anie.202008253.","chicago":"Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, Roland Fischer, Stefan Alexander Freunberger, Wolfgang Kern, and Stefan Spirk. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” Angewandte Chemie International Edition. Wiley, 2020. https://doi.org/10.1002/anie.202008253.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 2020;59(51):22943-22946. doi:10.1002/anie.202008253","short":"W. Schlemmer, P. Nothdurft, A. Petzold, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, Angewandte Chemie International Edition 59 (2020) 22943–22946.","ista":"Schlemmer W, Nothdurft P, Petzold A, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. 59(51), 22943–22946.","apa":"Schlemmer, W., Nothdurft, P., Petzold, A., Frühwirt, P., Schmallegger, M., Gescheidt-Demner, G., … Spirk, S. (2020). 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202008253","ieee":"W. Schlemmer et al., “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” Angewandte Chemie International Edition, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020."},"day":"14","status":"public","publication_status":"published","acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"doi":"10.1002/anie.202008253","abstract":[{"text":"We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles.","lang":"eng"}],"issue":"51","_id":"8329","title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","author":[{"full_name":"Schlemmer, Werner","last_name":"Schlemmer","first_name":"Werner"},{"last_name":"Nothdurft","full_name":"Nothdurft, Philipp","first_name":"Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"first_name":"Philipp","full_name":"Frühwirt, Philipp","last_name":"Frühwirt"},{"first_name":"Max","full_name":"Schmallegger, Max","last_name":"Schmallegger"},{"last_name":"Gescheidt-Demner","full_name":"Gescheidt-Demner, Georg","first_name":"Georg"},{"last_name":"Fischer","full_name":"Fischer, Roland","first_name":"Roland"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319"},{"first_name":"Wolfgang","full_name":"Kern, Wolfgang","last_name":"Kern"},{"first_name":"Stefan","full_name":"Spirk, Stefan","last_name":"Spirk"}]},{"date_published":"2020-09-03T00:00:00Z","date_created":"2020-09-04T12:24:12Z","department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","year":"2020","alternative_title":["ISTA Thesis"],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"133"},{"id":"8012","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8195"},{"id":"160","status":"public","relation":"part_of_dissertation"}]},"page":"120","date_updated":"2023-09-13T08:45:08Z","oa_version":"Published Version","citation":{"mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria."},"day":"03","month":"09","ddc":["000"],"file_date_updated":"2020-09-04T13:00:17Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"date_updated":"2020-09-04T12:17:47Z","access_level":"open_access","checksum":"26fe261550f691280bda4c454bf015c7","content_type":"application/pdf","file_name":"kragl-thesis.pdf","creator":"bkragl","relation":"main_file","file_size":1348815,"file_id":"8333","date_created":"2020-09-04T12:17:47Z"},{"creator":"bkragl","relation":"source_file","file_size":372312,"file_name":"kragl-thesis.zip","checksum":"b9694ce092b7c55557122adba8337ebc","content_type":"application/zip","access_level":"closed","date_updated":"2020-09-04T13:00:17Z","date_created":"2020-09-04T13:00:17Z","file_id":"8335"}],"abstract":[{"lang":"eng","text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step."}],"doi":"10.15479/AT:ISTA:8332","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","supervisor":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117"}],"_id":"8332","publication_status":"published","status":"public","publication_identifier":{"issn":["2663-337X"]}},{"oa":1,"year":"2020","date_updated":"2023-08-22T09:09:06Z","publication":"Nature Communications","article_type":"original","article_number":"4285","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"EvBe"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2020-09-06T22:01:12Z","external_id":{"pmid":["32855390"],"isi":["000567931000002"]},"date_published":"2020-08-27T00:00:00Z","intvolume":" 11","publisher":"Springer Nature","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"8336","author":[{"orcid":"0000-0001-5630-9419","last_name":"Kubiasova","full_name":"Kubiasova, Karolina","first_name":"Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E"},{"last_name":"Montesinos López","full_name":"Montesinos López, Juan C","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099"},{"first_name":"Olga","full_name":"Šamajová, Olga","last_name":"Šamajová"},{"first_name":"Jaroslav","full_name":"Nisler, Jaroslav","last_name":"Nisler"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"full_name":"Semeradova, Hana","last_name":"Semeradova","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana"},{"last_name":"Plíhalová","full_name":"Plíhalová, Lucie","first_name":"Lucie"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"orcid":"0000-0001-5227-5741","last_name":"Marhavý","full_name":"Marhavý, Peter","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cavallari","full_name":"Cavallari, Nicola","first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Zalabák, David","last_name":"Zalabák"},{"first_name":"Karel","last_name":"Berka","full_name":"Berka, Karel"},{"first_name":"Karel","last_name":"Doležal","full_name":"Doležal, Karel"},{"first_name":"Petr","last_name":"Galuszka","full_name":"Galuszka, Petr"},{"last_name":"Šamaj","full_name":"Šamaj, Jozef","first_name":"Jozef"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"full_name":"Spíchal, Lukáš","last_name":"Spíchal","first_name":"Lukáš"}],"title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","doi":"10.1038/s41467-020-17949-0","abstract":[{"lang":"eng","text":"Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER."}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746","_id":"261821BC-B435-11E9-9278-68D0E5697425"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"}],"publication_identifier":{"eissn":["20411723"]},"ec_funded":1,"publication_status":"published","acknowledgement":"This paper is dedicated to deceased P. Galuszka for his support and contribution to the project. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and by Centre of the Region Haná (CRH), Palacký University. We thank Lucia Hlusková, Zuzana Pěkná and Martin Hönig for technical assistance, and Fernando Aniento, Rashed Abualia and Andrej Hurný for sharing material. The work was supported from ERDF project “Plants as a tool for sustainable global development” (No. CZ.02.1.01/0.0/0.0/16_019/0000827), from Czech Science Foundation via projects 16-04184S (O.P., K.K. and K.D.), 18-23972Y (D.Z., K.K.), 17-21122S (K.B.), Erasmus+ (K.K.), Endowment Fund of Palacký University (K.K.) and EMBO Long-Term Fellowship, ALTF number 710-2016 (J.C.M.); People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734] (N.C.); DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria (H.S.).","status":"public","ddc":["580"],"file_date_updated":"2020-09-10T08:05:19Z","month":"08","pmid":1,"day":"27","citation":{"mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications, vol. 11, 4285, Springer Nature, 2020, doi:10.1038/s41467-020-17949-0.","chicago":"Kubiasova, Karolina, Juan C Montesinos López, Olga Šamajová, Jaroslav Nisler, Václav Mik, Hana Semerádová, Lucie Plíhalová, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17949-0.","ista":"Kubiasova K, Montesinos López JC, Šamajová O, Nisler J, Mik V, Semerádová H, Plíhalová L, Novák O, Marhavý P, Cavallari N, Zalabák D, Berka K, Doležal K, Galuszka P, Šamaj J, Strnad M, Benková E, Plíhal O, Spíchal L. 2020. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 11, 4285.","short":"K. Kubiasova, J.C. Montesinos López, O. Šamajová, J. Nisler, V. Mik, H. Semerádová, L. Plíhalová, O. Novák, P. Marhavý, N. Cavallari, D. Zalabák, K. Berka, K. Doležal, P. Galuszka, J. Šamaj, M. Strnad, E. Benková, O. Plíhal, L. Spíchal, Nature Communications 11 (2020).","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. 2020;11. doi:10.1038/s41467-020-17949-0","ieee":"K. Kubiasova et al., “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” Nature Communications, vol. 11. Springer Nature, 2020.","apa":"Kubiasova, K., Montesinos López, J. C., Šamajová, O., Nisler, J., Mik, V., Semerádová, H., … Spíchal, L. (2020). Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17949-0"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-09-10T08:05:19Z","success":1,"file_size":3455704,"relation":"main_file","creator":"dernst","file_name":"2020_NatureComm_Kubiasova.pdf","date_created":"2020-09-10T08:05:19Z","file_id":"8357"}],"article_processing_charge":"No","volume":11,"has_accepted_license":"1"},{"ec_funded":1,"acknowledgement":"We thank Bruno Müller and Aaron Rashotte for critical discussions and provision of plant lines used in this work, Roger Granbom and Tamara Hernández Verdeja (UPSC, Umeå, Sweden) for technical assistance and providing materials, Zuzana Pěkná and Karolina Wojewodová (CRH, Palacký University, Olomouc, Czech Republic) for help with cytokinin receptor binding assays, and David Zalabák (CRH, Palacký University, Olomouc, Czech Republic) for provision of vector pINIIIΔEH expressing CRE1/AHK4. The bioimaging facility of IST Austria, the Swedish Metabolomics Centre and the IST Austria Bio-Imaging facility are acknowledged for support. The work was funded by the European Molecular Biology Organization (EMBO ASTF 297-2013) (I.A.), Development—The Company of Biologists (DEVTF2012) (I.A.; C.T.), Plant Fellows (the International Post doc Fellowship Programme in Plant Sciences, 267423) (I.A.; K.L.), the Swedish Research Council (621-2014-4514) (K.L.), UPSC Berzelii Center for Forest Biotechnology (Vinnova 2012-01560), Kempestiftelserna (JCK-2711) (K.L.) and (JCK-1811) (E.-M.B., K.L.). The Ministry of Education, Youth and Sports of the Czech Republic via the European Regional Development Fund-Project “Plants as a tool for sustainable global development” (CZ.02.1.01/0.0/0.0/16_019/0000827) (O.N., O.P., R.S., V.M., L.P., K.D.) and project CEITEC 2020 (LQ1601) (M.P., J.H.) provided support, as did the Czech Science Foundation via projects GP14-30004P (M.P.) and 16-04184S (O.P., K.D., O.N.), Vetenskapsrådet and Vinnova (Verket för Innovationssystem) (T.V., S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” grant number 2012.0050. A.J. was supported by the Austria Science Fund (FWF): I03630 to J.F. The research leading to these results received funding from European Union’s Horizon 2020 programme (ERC grant no. 742985) and FWO-FWF joint project G0E5718N to J.F.","publication_status":"published","status":"public","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-020-17700-9","abstract":[{"text":"Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.","lang":"eng"}],"_id":"8337","title":"Cell-surface receptors enable perception of extracellular cytokinins","author":[{"last_name":"Antoniadi","full_name":"Antoniadi, Ioanna","first_name":"Ioanna"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","first_name":"Zuzana"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"full_name":"Plíhal, Ondřej","last_name":"Plíhal","first_name":"Ondřej"},{"last_name":"Simerský","full_name":"Simerský, Radim","first_name":"Radim"},{"last_name":"Mik","full_name":"Mik, Václav","first_name":"Václav"},{"first_name":"Thomas","last_name":"Vain","full_name":"Vain, Thomas"},{"full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí","first_name":"Eduardo"},{"last_name":"Karady","full_name":"Karady, Michal","first_name":"Michal"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"last_name":"Plačková","full_name":"Plačková, Lenka","first_name":"Lenka"},{"full_name":"Opassathian, Korawit","last_name":"Opassathian","first_name":"Korawit"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Karel","last_name":"Doležal","full_name":"Doležal, Karel"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"full_name":"Turnbull, Colin","last_name":"Turnbull","first_name":"Colin"}],"volume":11,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"8936","date_created":"2020-12-10T12:23:56Z","file_name":"2020_NatureComm_Antoniadi.pdf","relation":"main_file","file_size":3526415,"creator":"dernst","success":1,"date_updated":"2020-12-10T12:23:56Z","access_level":"open_access","content_type":"application/pdf","checksum":"5b96f39b598de7510cfefefb819b9a6d"}],"oa_version":"Published Version","file_date_updated":"2020-12-10T12:23:56Z","month":"08","ddc":["580"],"citation":{"ista":"Antoniadi I, Novák O, Gelová Z, Johnson AJ, Plíhal O, Simerský R, Mik V, Vain T, Mateo-Bonmatí E, Karady M, Pernisová M, Plačková L, Opassathian K, Hejátko J, Robert S, Friml J, Doležal K, Ljung K, Turnbull C. 2020. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 11, 4284.","short":"I. Antoniadi, O. Novák, Z. Gelová, A.J. Johnson, O. Plíhal, R. Simerský, V. Mik, T. Vain, E. Mateo-Bonmatí, M. Karady, M. Pernisová, L. Plačková, K. Opassathian, J. Hejátko, S. Robert, J. Friml, K. Doležal, K. Ljung, C. Turnbull, Nature Communications 11 (2020).","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. 2020;11. doi:10.1038/s41467-020-17700-9","apa":"Antoniadi, I., Novák, O., Gelová, Z., Johnson, A. J., Plíhal, O., Simerský, R., … Turnbull, C. (2020). Cell-surface receptors enable perception of extracellular cytokinins. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17700-9","ieee":"I. Antoniadi et al., “Cell-surface receptors enable perception of extracellular cytokinins,” Nature Communications, vol. 11. Springer Nature, 2020.","chicago":"Antoniadi, Ioanna, Ondřej Novák, Zuzana Gelová, Alexander J Johnson, Ondřej Plíhal, Radim Simerský, Václav Mik, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17700-9.","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” Nature Communications, vol. 11, 4284, Springer Nature, 2020, doi:10.1038/s41467-020-17700-9."},"day":"27","article_number":"4284","article_type":"original","date_updated":"2023-08-22T09:10:32Z","publication":"Nature Communications","year":"2020","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer Nature","intvolume":" 11","date_created":"2020-09-06T22:01:13Z","scopus_import":"1","acknowledged_ssus":[{"_id":"Bio"}],"date_published":"2020-08-27T00:00:00Z","external_id":{"isi":["000567931000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}]},{"date_created":"2020-09-06T22:01:13Z","scopus_import":"1","date_published":"2020-05-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"Springer Nature","intvolume":" 12110","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/337"}],"year":"2020","alternative_title":["LNCS"],"oa":1,"page":"623-651","date_updated":"2023-02-23T13:31:06Z","publication":"23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography","oa_version":"Preprint","conference":{"end_date":"2020-05-07","start_date":"2020-05-04","location":"Edinburgh, United Kingdom","name":"PKC: Public-Key Cryptography"},"month":"05","citation":{"short":"N. Genise, D. Micciancio, C. Peikert, M. Walter, in:, 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, Springer Nature, 2020, pp. 623–651.","ama":"Genise N, Micciancio D, Peikert C, Walter M. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In: 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography. Vol 12110. Springer Nature; 2020:623-651. doi:10.1007/978-3-030-45374-9_21","ista":"Genise N, Micciancio D, Peikert C, Walter M. 2020. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography. PKC: Public-Key Cryptography, LNCS, vol. 12110, 623–651.","ieee":"N. Genise, D. Micciancio, C. Peikert, and M. Walter, “Improved discrete Gaussian and subgaussian analysis for lattice cryptography,” in 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, Edinburgh, United Kingdom, 2020, vol. 12110, pp. 623–651.","apa":"Genise, N., Micciancio, D., Peikert, C., & Walter, M. (2020). Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography (Vol. 12110, pp. 623–651). Edinburgh, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-45374-9_21","chicago":"Genise, Nicholas, Daniele Micciancio, Chris Peikert, and Michael Walter. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” In 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, 12110:623–51. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-45374-9_21.","mla":"Genise, Nicholas, et al. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography, vol. 12110, Springer Nature, 2020, pp. 623–51, doi:10.1007/978-3-030-45374-9_21."},"day":"15","volume":12110,"article_processing_charge":"No","doi":"10.1007/978-3-030-45374-9_21","abstract":[{"text":"Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend.\r\nIn this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach.\r\nAs a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems.","lang":"eng"}],"_id":"8339","title":"Improved discrete Gaussian and subgaussian analysis for lattice cryptography","author":[{"full_name":"Genise, Nicholas","last_name":"Genise","first_name":"Nicholas"},{"first_name":"Daniele","full_name":"Micciancio, Daniele","last_name":"Micciancio"},{"first_name":"Chris","last_name":"Peikert","full_name":"Peikert, Chris"},{"orcid":"0000-0003-3186-2482","last_name":"Walter","full_name":"Walter, Michael","first_name":"Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030453732"],"eissn":["16113349"]}},{"page":"242","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6848"}]},"date_updated":"2023-09-07T13:26:17Z","year":"2020","alternative_title":["ISTA Thesis"],"oa":1,"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2020-09-07T18:42:23Z","date_published":"2020-09-09T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"LeSa"}],"ec_funded":1,"publication_status":"published","acknowledgement":"I acknowledge the support of IST facilities, especially the Electron Miscroscopy facility for providing training and resources. Special thanks also go to cryo-EM specialists who helped me to collect the data present here: Dr Valentin Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni. of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","status":"public","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-3-99078-008-4"],"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:8340","abstract":[{"text":"Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.","lang":"eng"}],"_id":"8340","author":[{"full_name":"Kampjut, Domen","last_name":"Kampjut","id":"37233050-F248-11E8-B48F-1D18A9856A87","first_name":"Domen"}],"supervisor":[{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"title":"Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"ThesisFull20200908.docx","relation":"source_file","creator":"dkampjut","file_size":166146359,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"dd270baf82121eb4472ad19d77bf227c","date_updated":"2021-09-11T22:30:04Z","embargo_to":"open_access","file_id":"8345","date_created":"2020-09-08T13:32:06Z"},{"access_level":"open_access","content_type":"application/pdf","checksum":"82fce6f95ffa47ecc4ebca67ea2cc38c","date_updated":"2021-09-11T22:30:04Z","file_name":"2020_Thesis_Kampjut.pdf","creator":"dernst","relation":"main_file","file_size":13873769,"embargo":"2021-09-10","file_id":"8393","date_created":"2020-09-14T15:02:20Z"}],"degree_awarded":"PhD","oa_version":"None","month":"09","ddc":["572"],"file_date_updated":"2021-09-11T22:30:04Z","day":"09","citation":{"chicago":"Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.","mla":"Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.","ista":"Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria.","ama":"Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. 2020. doi:10.15479/AT:ISTA:8340","short":"D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping Enzymes, Institute of Science and Technology Austria, 2020.","apa":"Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340","ieee":"D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes,” Institute of Science and Technology Austria, 2020."}},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","day":"08","citation":{"ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:10.15479/AT:ISTA:8341","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","apa":"Bezeljak, U. (2020). In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8341","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8341.","mla":"Bezeljak, Urban. In Vitro Reconstitution of a Rab Activation Switch. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8341."},"file_date_updated":"2021-09-16T12:49:12Z","month":"09","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"date_created":"2020-09-08T09:00:29Z","file_id":"8342","date_updated":"2021-09-16T12:49:12Z","checksum":"70871b335a595252a66c6bbf0824fb02","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_size":65246782,"creator":"dernst","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip"},{"file_id":"8343","date_created":"2020-09-08T09:00:27Z","file_name":"2020_Urban_Bezeljak_Thesis.pdf","relation":"main_file","file_size":31259058,"creator":"dernst","date_updated":"2021-09-16T12:49:12Z","access_level":"open_access","content_type":"application/pdf","checksum":"59a62275088b00b7241e6ff4136434c7"}],"abstract":[{"lang":"eng","text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level."}],"doi":"10.15479/AT:ISTA:8341","author":[{"orcid":"0000-0003-1365-5631","last_name":"Bezeljak","full_name":"Bezeljak, Urban","first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"}],"title":"In vitro reconstitution of a Rab activation switch","supervisor":[{"full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"_id":"8341","status":"public","publication_status":"published","acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","publication_identifier":{"issn":["2663-337X"]},"date_published":"2020-09-08T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"date_created":"2020-09-08T08:53:53Z","department":[{"_id":"MaLo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2020","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7580"}]},"page":"215","date_updated":"2023-09-07T13:17:06Z"}]