[{"related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"OA_place":"repository","article_type":"original","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).","corr_author":"1","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"file_date_updated":"2020-08-26T19:29:00Z","language":[{"iso":"eng"}],"date_created":"2020-08-26T19:27:42Z","day":"26","publication":"Physical Review B","month":"08","ddc":["530"],"date_published":"2020-08-26T00:00:00Z","status":"public","department":[{"_id":"MaSe"}],"has_accepted_license":"1","type":"journal_article","issue":"6","date_updated":"2026-04-07T13:26:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/physrevb.102.060202","volume":102,"quality_controlled":"1","citation":{"mla":"Brighi, Pietro, et al. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>, vol. 102, no. 6, 060202(R), American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>.","ama":"Brighi P, Abanin DA, Serbyn M. Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. 2020;102(6). doi:<a href=\"https://doi.org/10.1103/physrevb.102.060202\">10.1103/physrevb.102.060202</a>","apa":"Brighi, P., Abanin, D. A., &#38; Serbyn, M. (2020). Stability of mobility edges in disordered interacting systems. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>","chicago":"Brighi, Pietro, Dmitry A. Abanin, and Maksym Serbyn. “Stability of Mobility Edges in Disordered Interacting Systems.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.060202\">https://doi.org/10.1103/physrevb.102.060202</a>.","short":"P. Brighi, D.A. Abanin, M. Serbyn, Physical Review B 102 (2020).","ista":"Brighi P, Abanin DA, Serbyn M. 2020. Stability of mobility edges in disordered interacting systems. Physical Review B. 102(6), 060202(R).","ieee":"P. Brighi, D. A. Abanin, and M. Serbyn, “Stability of mobility edges in disordered interacting systems,” <i>Physical Review B</i>, vol. 102, no. 6. American Physical Society, 2020."},"article_processing_charge":"No","file":[{"success":1,"file_name":"PhysRevB.102.060202.pdf","relation":"main_file","date_created":"2020-08-26T19:28:55Z","access_level":"open_access","file_id":"8309","content_type":"application/pdf","file_size":488825,"creator":"mserbyn","checksum":"716442fa7861323fcc80b93718ca009c","date_updated":"2020-08-26T19:28:55Z"},{"creator":"mserbyn","checksum":"be0abdc8f60fe065ea6dc92e08487122","date_updated":"2020-08-26T19:29:00Z","file_id":"8310","content_type":"application/pdf","file_size":711405,"date_created":"2020-08-26T19:29:00Z","access_level":"open_access","relation":"main_file","file_name":"Supplementary-mbme.pdf","success":1}],"isi":1,"scopus_import":"1","OA_type":"green","abstract":[{"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.","lang":"eng"}],"year":"2020","arxiv":1,"oa":1,"ec_funded":1,"intvolume":"       102","oa_version":"Preprint","title":"Stability of mobility edges in disordered interacting systems","_id":"8308","publication_status":"published","publisher":"American Physical Society","article_number":"060202(R)","external_id":{"arxiv":["2005.02999"],"isi":["000562628300001"]},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1038/s41467-020-17957-0","citation":{"apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., &#38; Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>","ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. <i>Nature Communications</i>. 2020;11(1). doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” <i>Nature Communications</i>, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17957-0\">10.1038/s41467-020-17957-0</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17957-0\">https://doi.org/10.1038/s41467-020-17957-0</a>.","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).","ieee":"J. Gutierrez-Fernandez <i>et al.</i>, “Key role of quinone in the mechanism of respiratory complex I,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, 2020."},"quality_controlled":"1","volume":11,"file":[{"date_created":"2020-08-31T13:40:00Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","date_updated":"2020-08-31T13:40:00Z","creator":"cziletti","checksum":"52b96f41d7d0db9728064c08da00d030","file_size":7527373,"content_type":"application/pdf","file_id":"8326"}],"article_processing_charge":"No","isi":1,"scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/","description":"News on IST Homepage","relation":"press_release"}]},"article_type":"original","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.","author":[{"id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","last_name":"Gutierrez-Fernandez","first_name":"Javier","full_name":"Gutierrez-Fernandez, Javier"},{"first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","last_name":"Kaszuba","full_name":"Kaszuba, Karol"},{"full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S.","last_name":"Minhas"},{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh"},{"full_name":"Tambalo, Margherita","id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita"},{"full_name":"Gallagher, David T.","last_name":"Gallagher","first_name":"David T."},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"day":"18","date_created":"2020-08-30T22:01:10Z","language":[{"iso":"eng"}],"file_date_updated":"2020-08-31T13:40:00Z","month":"08","ddc":["570"],"date_published":"2020-08-18T00:00:00Z","publication":"Nature Communications","status":"public","type":"journal_article","issue":"1","department":[{"_id":"LeSa"}],"has_accepted_license":"1","date_updated":"2026-04-02T14:36:31Z","publisher":"Springer Nature","article_number":"4135","external_id":{"pmid":["32811817"],"isi":["000607072900001"]},"publication_identifier":{"eissn":["2041-1723"]},"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"},"year":"2020","abstract":[{"lang":"eng","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."}],"intvolume":"        11","oa":1,"pmid":1,"oa_version":"Published Version","_id":"8318","publication_status":"published","title":"Key role of quinone in the mechanism of respiratory complex I"},{"author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"full_name":"Vlasov, Petr","first_name":"Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov"},{"last_name":"Kolosov","first_name":"P. M.","full_name":"Kolosov, P. M."},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"date_created":"2020-08-30T22:01:11Z","day":"19","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"original","id":"8321","status":"public"}]},"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.","article_type":"original","department":[{"_id":"FyKo"}],"issue":"4","type":"journal_article","date_updated":"2025-07-10T11:57:02Z","publication":"Molecular Biology","date_published":"2020-08-19T00:00:00Z","month":"08","page":"475-484","status":"public","volume":54,"citation":{"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,” <i>Molecular Biology</i>, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","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.","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.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. 2020;54(4):475-484. doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>"},"quality_controlled":"1","doi":"10.1134/S0026893320040111","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","isi":1,"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"}],"year":"2020","oa_version":"None","title":"Expanding the genetic code: Unnatural base pairs in biological systems","publication_status":"published","_id":"8320","intvolume":"        54","publisher":"Springer Nature","external_id":{"isi":["000562110300001"]},"publication_identifier":{"eissn":["1608-3245"],"issn":["0026-8933"]}},{"publication_identifier":{"issn":["0026-8984"]},"external_id":{"pmid":["32799218"]},"publisher":"Russian Academy of Sciences","pmid":1,"intvolume":"        54","title":"Expanding the genetic code: Unnatural base pairs in biological systems","_id":"8321","publication_status":"published","oa_version":"None","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."}],"year":"2020","article_processing_charge":"No","scopus_import":"1","doi":"10.31857/S0026898420040126","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":54,"quality_controlled":"1","citation":{"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,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","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.","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.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. 2020;54(4):531-541. doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>"},"page":"531-541","status":"public","publication":"Molekuliarnaia biologiia","date_published":"2020-07-01T00:00:00Z","month":"07","date_updated":"2025-07-10T11:57:03Z","department":[{"_id":"FyKo"}],"issue":"4","type":"journal_article","article_type":"original","related_material":{"record":[{"status":"public","id":"8320","relation":"translation"}]},"day":"01","language":[{"iso":"rus"}],"date_created":"2020-08-30T22:01:11Z","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr"},{"first_name":"P. M.","last_name":"Kolosov","full_name":"Kolosov, P. M."},{"last_name":"Shuvalova","first_name":"E. Y.","full_name":"Shuvalova, E. Y."},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}]},{"status":"public","page":"571-574","date_published":"2020-10-01T00:00:00Z","month":"10","publication":"Discrete and Computational Geometry","date_updated":"2024-10-09T20:59:55Z","type":"journal_article","department":[{"_id":"HeEd"}],"corr_author":"1","article_type":"letter_note","date_created":"2020-08-30T22:01:12Z","language":[{"iso":"eng"}],"day":"01","author":[{"full_name":"Pach, János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János"}],"isi":1,"article_processing_charge":"No","scopus_import":"1","doi":"10.1007/s00454-020-00237-5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>, vol. 64, Springer Nature, 2020, pp. 571–74, doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>","ama":"Pach J. A farewell to Ricky Pollack. <i>Discrete and Computational Geometry</i>. 2020;64:571-574. doi:<a href=\"https://doi.org/10.1007/s00454-020-00237-5\">10.1007/s00454-020-00237-5</a>","chicago":"Pach, János. “A Farewell to Ricky Pollack.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00454-020-00237-5\">https://doi.org/10.1007/s00454-020-00237-5</a>.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ieee":"J. Pach, “A farewell to Ricky Pollack,” <i>Discrete and Computational Geometry</i>, vol. 64. Springer Nature, pp. 571–574, 2020."},"volume":64,"intvolume":"        64","oa":1,"_id":"8323","publication_status":"published","title":"A farewell to Ricky Pollack","oa_version":"None","year":"2020","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00237-5"}],"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"external_id":{"isi":["000561483500001"]},"publisher":"Springer Nature"},{"scopus_import":"1","file":[{"file_name":"2019_ACM_POPL_Wang.pdf","success":1,"access_level":"open_access","date_created":"2020-09-01T11:12:58Z","relation":"main_file","content_type":"application/pdf","file_size":564151,"file_id":"8328","date_updated":"2020-09-01T11:12:58Z","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","creator":"cziletti"}],"article_processing_charge":"No","citation":{"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 <i>Proceedings of the ACM on Programming Languages</i>, Vol. 4. ACM, 2020. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>.","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: <i>Proceedings of the ACM on Programming Languages</i>. Vol 4. ACM; 2020. doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., &#38; Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In <i>Proceedings of the ACM on Programming Languages</i> (Vol. 4). ACM. <a href=\"https://doi.org/10.1145/3371093\">https://doi.org/10.1145/3371093</a>","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 4, no. POPL, 25, ACM, 2020, doi:<a href=\"https://doi.org/10.1145/3371093\">10.1145/3371093</a>.","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 <i>Proceedings of the ACM on Programming Languages</i>, 2020, vol. 4, no. POPL.","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.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020."},"quality_controlled":"1","volume":4,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3371093","date_updated":"2025-04-15T06:30:10Z","type":"conference","issue":"POPL","department":[{"_id":"KrCh"}],"has_accepted_license":"1","status":"public","month":"01","ddc":["004"],"date_published":"2020-01-01T00:00:00Z","publication":"Proceedings of the ACM on Programming Languages","day":"01","date_created":"2020-08-30T22:01:12Z","language":[{"iso":"eng"}],"file_date_updated":"2020-09-01T11:12:58Z","author":[{"last_name":"Wang","first_name":"Peixin","full_name":"Wang, Peixin"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Deng","first_name":"Yuxin","full_name":"Deng, Yuxin"},{"full_name":"Xu, Ming","last_name":"Xu","first_name":"Ming"}],"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.","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"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"},"project":[{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"}],"publication_identifier":{"eissn":["2475-1421"]},"external_id":{"arxiv":["1902.04744"]},"article_number":"25","publisher":"ACM","_id":"8324","publication_status":"published","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","oa_version":"Published Version","intvolume":"         4","oa":1,"arxiv":1,"year":"2020","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."}]},{"external_id":{"isi":["000560620600001"],"arxiv":["1711.04285"]},"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publisher":"Springer Nature","oa":1,"ec_funded":1,"intvolume":"       378","oa_version":"Preprint","title":"Sandpile solitons via smoothing of superharmonic functions","publication_status":"published","_id":"8325","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"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. "}],"year":"2020","arxiv":1,"article_processing_charge":"No","isi":1,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00220-020-03828-8","volume":378,"citation":{"ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. 2020;378(9):1649-1675. doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>","apa":"Kalinin, N., &#38; Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:<a href=\"https://doi.org/10.1007/s00220-020-03828-8\">10.1007/s00220-020-03828-8</a>.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-020-03828-8\">https://doi.org/10.1007/s00220-020-03828-8</a>.","short":"N. Kalinin, M. Shkolnikov, Communications in Mathematical Physics 378 (2020) 1649–1675.","ista":"Kalinin N, Shkolnikov M. 2020. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 378(9), 1649–1675.","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” <i>Communications in Mathematical Physics</i>, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020."},"quality_controlled":"1","publication":"Communications in Mathematical Physics","date_published":"2020-09-01T00:00:00Z","month":"09","page":"1649-1675","status":"public","department":[{"_id":"TaHa"}],"type":"journal_article","issue":"9","date_updated":"2025-07-10T11:57:03Z","article_type":"original","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.","author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"}],"date_created":"2020-08-30T22:01:13Z","language":[{"iso":"eng"}],"day":"01"},{"date_updated":"2026-06-18T19:32:35Z","department":[{"_id":"StFr"}],"issue":"51","type":"journal_article","page":"22943-22946","status":"public","publication":"Angewandte Chemie International Edition","month":"12","date_published":"2020-12-14T00:00:00Z","ddc":["540"],"date_created":"2020-09-03T16:10:56Z","language":[{"iso":"eng"}],"day":"14","author":[{"last_name":"Schlemmer","first_name":"Werner","full_name":"Schlemmer, Werner"},{"first_name":"Philipp","last_name":"Nothdurft","full_name":"Nothdurft, Philipp"},{"first_name":"Alina","last_name":"Petzold","full_name":"Petzold, Alina"},{"first_name":"Philipp","last_name":"Frühwirt","full_name":"Frühwirt, Philipp"},{"full_name":"Schmallegger, Max","first_name":"Max","last_name":"Schmallegger"},{"last_name":"Gescheidt-Demner","first_name":"Georg","full_name":"Gescheidt-Demner, Georg"},{"full_name":"Fischer, Roland","first_name":"Roland","last_name":"Fischer"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Kern, Wolfgang","first_name":"Wolfgang","last_name":"Kern"},{"last_name":"Spirk","first_name":"Stefan","full_name":"Spirk, Stefan"}],"acknowledgement":"The Austrian Research Promotion Agency (FFG) is gratefully acknowledged for financial support of the project LignoBatt (860429).","article_type":"original","related_material":{"record":[{"relation":"research_data","status":"public","id":"9780"}]},"scopus_import":"1","isi":1,"article_processing_charge":"No","volume":59,"citation":{"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.” <i>Angewandte Chemie International Edition</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/anie.202008253\">https://doi.org/10.1002/anie.202008253</a>.","ama":"Schlemmer W, Nothdurft P, Petzold A, et al. 2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries. <i>Angewandte Chemie International Edition</i>. 2020;59(51):22943-22946. doi:<a href=\"https://doi.org/10.1002/anie.202008253\">10.1002/anie.202008253</a>","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. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202008253\">https://doi.org/10.1002/anie.202008253</a>","mla":"Schlemmer, Werner, et al. “2‐methoxyhydroquinone from Vanillin for Aqueous Redox‐flow Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 51, Wiley, 2020, pp. 22943–46, doi:<a href=\"https://doi.org/10.1002/anie.202008253\">10.1002/anie.202008253</a>.","ieee":"W. Schlemmer <i>et al.</i>, “2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries,” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 51. Wiley, pp. 22943–22946, 2020.","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."},"quality_controlled":"1","doi":"10.1002/anie.202008253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries","publication_status":"published","_id":"8329","oa_version":"Published Version","oa":1,"intvolume":"        59","abstract":[{"lang":"eng","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."}],"year":"2020","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202008253"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"external_id":{"isi":["000576148700001"]},"publisher":"Wiley"},{"year":"2020","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."}],"oa":1,"publication_status":"published","_id":"8332","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"corr_author":"1","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"8195","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"133"},{"relation":"part_of_dissertation","id":"160","status":"public"},{"status":"public","id":"8012","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"day":"03","date_created":"2020-09-04T12:24:12Z","file_date_updated":"2020-09-04T13:00:17Z","author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard"}],"status":"public","page":"120","date_published":"2020-09-03T00:00:00Z","month":"09","ddc":["000"],"date_updated":"2026-06-18T19:29:42Z","degree_awarded":"PhD","type":"dissertation","has_accepted_license":"1","department":[{"_id":"ToHe"}],"doi":"10.15479/AT:ISTA:8332","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","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.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8332\">https://doi.org/10.15479/AT:ISTA:8332</a>.","apa":"Kragl, B. (2020). <i>Verifying concurrent programs: Refinement, synchronization, sequentialization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8332\">https://doi.org/10.15479/AT:ISTA:8332</a>","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8332\">10.15479/AT:ISTA:8332</a>","mla":"Kragl, Bernhard. <i>Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8332\">10.15479/AT:ISTA:8332</a>."},"file":[{"relation":"main_file","date_created":"2020-09-04T12:17:47Z","access_level":"open_access","file_name":"kragl-thesis.pdf","date_updated":"2020-09-04T12:17:47Z","creator":"bkragl","checksum":"26fe261550f691280bda4c454bf015c7","content_type":"application/pdf","file_size":1348815,"file_id":"8333"},{"file_id":"8335","file_size":372312,"content_type":"application/zip","creator":"bkragl","checksum":"b9694ce092b7c55557122adba8337ebc","date_updated":"2020-09-04T13:00:17Z","file_name":"kragl-thesis.zip","access_level":"closed","date_created":"2020-09-04T13:00:17Z","relation":"source_file"}],"article_processing_charge":"No"},{"article_type":"original","corr_author":"1","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.).","language":[{"iso":"eng"}],"day":"27","date_created":"2020-09-06T22:01:12Z","file_date_updated":"2020-09-10T08:05:19Z","author":[{"orcid":"0000-0001-5630-9419","full_name":"Kubiasova, Karolina","first_name":"Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","last_name":"Kubiasova"},{"id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López","first_name":"Juan C","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"full_name":"Nisler, Jaroslav","first_name":"Jaroslav","last_name":"Nisler"},{"first_name":"Václav","last_name":"Mik","full_name":"Mik, Václav"},{"full_name":"Semeradova, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","last_name":"Semeradova","first_name":"Hana"},{"last_name":"Plíhalová","first_name":"Lucie","full_name":"Plíhalová, Lucie"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter","first_name":"Peter","last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","full_name":"Cavallari, Nicola"},{"full_name":"Zalabák, David","last_name":"Zalabák","first_name":"David"},{"full_name":"Berka, Karel","last_name":"Berka","first_name":"Karel"},{"last_name":"Doležal","first_name":"Karel","full_name":"Doležal, Karel"},{"last_name":"Galuszka","first_name":"Petr","full_name":"Galuszka, Petr"},{"first_name":"Jozef","last_name":"Šamaj","full_name":"Šamaj, Jozef"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"first_name":"Ondřej","last_name":"Plíhal","full_name":"Plíhal, Ondřej"},{"full_name":"Spíchal, Lukáš","first_name":"Lukáš","last_name":"Spíchal"}],"status":"public","date_published":"2020-08-27T00:00:00Z","month":"08","ddc":["580"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication":"Nature Communications","date_updated":"2026-04-02T14:35:13Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"EvBe"}],"doi":"10.1038/s41467-020-17949-0","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","citation":{"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.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>.","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17949-0\">https://doi.org/10.1038/s41467-020-17949-0</a>","ama":"Kubiasova K, Montesinos López JC, Šamajová O, et al. Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>","mla":"Kubiasova, Karolina, et al. “Cytokinin Fluoroprobe Reveals Multiple Sites of Cytokinin Perception at Plasma Membrane and Endoplasmic Reticulum.” <i>Nature Communications</i>, vol. 11, 4285, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17949-0\">10.1038/s41467-020-17949-0</a>.","ieee":"K. Kubiasova <i>et al.</i>, “Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","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).","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."},"volume":11,"isi":1,"file":[{"relation":"main_file","access_level":"open_access","date_created":"2020-09-10T08:05:19Z","file_name":"2020_NatureComm_Kubiasova.pdf","success":1,"checksum":"7494b7665b3d2bf2d8edb13e4f12b92d","creator":"dernst","date_updated":"2020-09-10T08:05:19Z","file_id":"8357","content_type":"application/pdf","file_size":3455704}],"article_processing_charge":"No","scopus_import":"1","year":"2020","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."}],"pmid":1,"intvolume":"        11","ec_funded":1,"oa":1,"_id":"8336","publication_status":"published","title":"Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum","oa_version":"Published Version","publisher":"Springer Nature","article_number":"4285","publication_identifier":{"eissn":["2041-1723"]},"external_id":{"isi":["000567931000002"],"pmid":["32855390"]},"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"},"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis","_id":"261821BC-B435-11E9-9278-68D0E5697425","grant_number":"24746"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","grant_number":"ALTF710-2016"}]},{"article_processing_charge":"No","file":[{"checksum":"5b96f39b598de7510cfefefb819b9a6d","creator":"dernst","date_updated":"2020-12-10T12:23:56Z","file_id":"8936","file_size":3526415,"content_type":"application/pdf","access_level":"open_access","date_created":"2020-12-10T12:23:56Z","relation":"main_file","file_name":"2020_NatureComm_Antoniadi.pdf","success":1}],"isi":1,"scopus_import":"1","doi":"10.1038/s41467-020-17700-9","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","volume":11,"quality_controlled":"1","citation":{"ieee":"I. Antoniadi <i>et al.</i>, “Cell-surface receptors enable perception of extracellular cytokinins,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","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).","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.","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.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>.","ama":"Antoniadi I, Novák O, Gelová Z, et al. Cell-surface receptors enable perception of extracellular cytokinins. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17700-9\">https://doi.org/10.1038/s41467-020-17700-9</a>","mla":"Antoniadi, Ioanna, et al. “Cell-Surface Receptors Enable Perception of Extracellular Cytokinins.” <i>Nature Communications</i>, vol. 11, 4284, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-17700-9\">10.1038/s41467-020-17700-9</a>."},"publication":"Nature Communications","month":"08","acknowledged_ssus":[{"_id":"Bio"}],"ddc":["580"],"date_published":"2020-08-27T00:00:00Z","status":"public","department":[{"_id":"JiFr"}],"has_accepted_license":"1","type":"journal_article","date_updated":"2026-04-03T09:25:48Z","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.","article_type":"original","author":[{"last_name":"Antoniadi","first_name":"Ioanna","full_name":"Antoniadi, Ioanna"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","last_name":"Gelová","first_name":"Zuzana","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752"},{"first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"full_name":"Plíhal, Ondřej","first_name":"Ondřej","last_name":"Plíhal"},{"full_name":"Simerský, Radim","last_name":"Simerský","first_name":"Radim"},{"full_name":"Mik, Václav","last_name":"Mik","first_name":"Václav"},{"full_name":"Vain, Thomas","first_name":"Thomas","last_name":"Vain"},{"full_name":"Mateo-Bonmatí, Eduardo","last_name":"Mateo-Bonmatí","first_name":"Eduardo"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"first_name":"Lenka","last_name":"Plačková","full_name":"Plačková, Lenka"},{"full_name":"Opassathian, Korawit","first_name":"Korawit","last_name":"Opassathian"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doležal, Karel","first_name":"Karel","last_name":"Doležal"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"full_name":"Turnbull, Colin","first_name":"Colin","last_name":"Turnbull"}],"file_date_updated":"2020-12-10T12:23:56Z","day":"27","date_created":"2020-09-06T22:01:13Z","language":[{"iso":"eng"}],"external_id":{"isi":["000567931000001"],"pmid":["32855409"]},"publication_identifier":{"eissn":["2041-1723"]},"project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"}],"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"},"publisher":"Springer Nature","article_number":"4284","oa":1,"ec_funded":1,"intvolume":"        11","pmid":1,"oa_version":"Published Version","title":"Cell-surface receptors enable perception of extracellular cytokinins","_id":"8337","publication_status":"published","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"}],"year":"2020"},{"date_created":"2020-09-06T22:01:13Z","day":"15","language":[{"iso":"eng"}],"author":[{"first_name":"Nicholas","last_name":"Genise","full_name":"Genise, Nicholas"},{"full_name":"Micciancio, Daniele","last_name":"Micciancio","first_name":"Daniele"},{"first_name":"Chris","last_name":"Peikert","full_name":"Peikert, Chris"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"date_updated":"2026-04-16T09:32:27Z","department":[{"_id":"KrPi"}],"type":"conference","page":"623-651","status":"public","publication":"23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography","month":"05","date_published":"2020-05-15T00:00:00Z","volume":12110,"quality_controlled":"1","citation":{"ieee":"N. Genise, D. Micciancio, C. Peikert, and M. Walter, “Improved discrete Gaussian and subgaussian analysis for lattice cryptography,” in <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, Edinburgh, United Kingdom, 2020, vol. 12110, pp. 623–651.","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.","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.","chicago":"Genise, Nicholas, Daniele Micciancio, Chris Peikert, and Michael Walter. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, 12110:623–51. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>.","mla":"Genise, Nicholas, et al. “Improved Discrete Gaussian and Subgaussian Analysis for Lattice Cryptography.” <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>, vol. 12110, Springer Nature, 2020, pp. 623–51, doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>.","ama":"Genise N, Micciancio D, Peikert C, Walter M. Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In: <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i>. Vol 12110. Springer Nature; 2020:623-651. doi:<a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">10.1007/978-3-030-45374-9_21</a>","apa":"Genise, N., Micciancio, D., Peikert, C., &#38; Walter, M. (2020). Improved discrete Gaussian and subgaussian analysis for lattice cryptography. In <i>23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography</i> (Vol. 12110, pp. 623–651). Edinburgh, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-45374-9_21\">https://doi.org/10.1007/978-3-030-45374-9_21</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/978-3-030-45374-9_21","scopus_import":"1","isi":1,"article_processing_charge":"No","conference":{"start_date":"2020-05-04","location":"Edinburgh, United Kingdom","end_date":"2020-05-07","name":"PKC: Public-Key Cryptography"},"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"}],"year":"2020","main_file_link":[{"url":"https://eprint.iacr.org/2020/337","open_access":"1"}],"title":"Improved discrete Gaussian and subgaussian analysis for lattice cryptography","_id":"8339","publication_status":"published","oa_version":"Preprint","oa":1,"ec_funded":1,"intvolume":"     12110","publisher":"Springer Nature","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030453732"]},"alternative_title":["LNCS"],"external_id":{"isi":["001299210200021"]}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"supervisor":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"}],"publisher":"Institute of Science and Technology Austria","title":"In vitro reconstitution of a Rab activation switch","_id":"8341","publication_status":"published","oa_version":"Published Version","oa":1,"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."}],"year":"2020","article_processing_charge":"No","file":[{"relation":"source_file","date_created":"2020-09-08T09:00:29Z","access_level":"closed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","checksum":"70871b335a595252a66c6bbf0824fb02","creator":"dernst","date_updated":"2021-09-16T12:49:12Z","file_id":"8342","file_size":65246782,"content_type":"application/x-zip-compressed"},{"file_name":"2020_Urban_Bezeljak_Thesis.pdf","date_created":"2020-09-08T09:00:27Z","access_level":"open_access","relation":"main_file","file_id":"8343","content_type":"application/pdf","file_size":31259058,"checksum":"59a62275088b00b7241e6ff4136434c7","creator":"dernst","date_updated":"2021-09-16T12:49:12Z"}],"citation":{"apa":"Bezeljak, U. (2020). <i>In vitro reconstitution of a Rab activation switch</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>","mla":"Bezeljak, Urban. <i>In Vitro Reconstitution of a Rab Activation Switch</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>.","chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT:ISTA:8341","degree_awarded":"PhD","date_updated":"2026-04-08T07:24:56Z","department":[{"_id":"MaLo"}],"has_accepted_license":"1","type":"dissertation","page":"215","status":"public","month":"09","ddc":["570"],"date_published":"2020-09-08T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"file_date_updated":"2021-09-16T12:49:12Z","day":"08","language":[{"iso":"eng"}],"date_created":"2020-09-08T08:53:53Z","author":[{"orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","first_name":"Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"}],"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.","corr_author":"1","OA_place":"publisher","related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]}},{"citation":{"ista":"Steiner J. 2020. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. Institute of Science and Technology Austria.","short":"J. Steiner, Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I, Institute of Science and Technology Austria, 2020.","ieee":"J. Steiner, “Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I,” Institute of Science and Technology Austria, 2020.","mla":"Steiner, Julia. <i>Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>.","ama":"Steiner J. Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8353\">10.15479/AT:ISTA:8353</a>","apa":"Steiner, J. (2020). <i>Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>","chicago":"Steiner, Julia. “Biochemical and Structural Investigation of the Mrp Antiporter, an Ancestor of Complex I.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8353\">https://doi.org/10.15479/AT:ISTA:8353</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT:ISTA:8353","file":[{"creator":"jsteiner","checksum":"2388d7e6e7a4d364c096fa89f305c3de","date_updated":"2021-09-16T12:40:56Z","file_id":"8354","content_type":"application/pdf","file_size":117547589,"relation":"main_file","date_created":"2020-09-09T14:22:35Z","access_level":"open_access","file_name":"Thesis_Julia_Steiner_pdfA.pdf"},{"access_level":"closed","date_created":"2020-09-09T14:23:25Z","relation":"source_file","file_name":"Thesis_Julia_Steiner.docx","date_updated":"2020-09-15T08:48:37Z","creator":"jsteiner","checksum":"ba112f957b7145462d0ab79044873ee9","file_size":223328668,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8355"}],"article_processing_charge":"No","author":[{"last_name":"Steiner","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Steiner, Julia","orcid":"0000-0003-0493-3775"}],"day":"09","date_created":"2020-09-09T14:27:01Z","language":[{"iso":"eng"}],"file_date_updated":"2021-09-16T12:40:56Z","related_material":{"record":[{"id":"8284","status":"public","relation":"part_of_dissertation"}]},"OA_place":"publisher","acknowledgement":"I acknowledge the scientific service units of the IST Austria for providing resources by the Life Science Facility, the Electron Microscopy Facility and the high-performance computer cluster. Special thanks to the cryo-EM specialists Valentin Hodirnau and Daniel Johann Gütl for spending many hours with me in front of the microscope and for supporting me to collect the data presented here. I also want to thank Professor Masahiro Ito for providing plasmid DNA\r\nencoding Mrp from Anoxybacillus flavithermus WK1. I am a recipient of a DOC Fellowship of the Austrian Academy of Sciences.","corr_author":"1","type":"dissertation","has_accepted_license":"1","department":[{"_id":"LeSa"}],"date_updated":"2026-04-08T07:23:36Z","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"}],"ddc":["572"],"date_published":"2020-09-09T00:00:00Z","month":"09","status":"public","page":"191","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","project":[{"name":"Revealing the functional mechanism of Mrp antiporter, an ancestor of complex I","_id":"26169496-B435-11E9-9278-68D0E5697425","grant_number":"24741"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"year":"2020","abstract":[{"lang":"eng","text":"Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent\r\nprofile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest\r\nand homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these\r\nelectrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner."}],"oa_version":"None","_id":"8353","publication_status":"published","title":"Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I","oa":1},{"doi":"10.15479/AT:ISTA:8358","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>.","mla":"Dos Santos Caldas, Paulo R. <i>Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>","apa":"Dos Santos Caldas, P. R. (2020). <i>Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020."},"file":[{"date_updated":"2020-09-10T12:11:29Z","checksum":"882f93fe9c351962120e2669b84bf088","creator":"pcaldas","content_type":"application/pdf","file_size":141602462,"file_id":"8364","date_created":"2020-09-10T12:11:29Z","access_level":"open_access","relation":"main_file","file_name":"phd_thesis_pcaldas.pdf","success":1},{"checksum":"70cc9e399c4e41e6e6ac445ae55e8558","creator":"pcaldas","date_updated":"2020-09-11T07:48:10Z","file_id":"8365","content_type":"application/x-zip-compressed","file_size":450437458,"access_level":"closed","date_created":"2020-09-10T12:18:17Z","relation":"source_file","file_name":"phd_thesis_latex_pcaldas.zip"}],"article_processing_charge":"No","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"7197","relation":"part_of_dissertation"},{"id":"7572","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","corr_author":"1","author":[{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R"}],"date_created":"2020-09-10T09:26:49Z","language":[{"iso":"eng"}],"day":"10","file_date_updated":"2020-09-11T07:48:10Z","month":"09","ddc":["572"],"date_published":"2020-09-10T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"}],"status":"public","page":"135","type":"dissertation","department":[{"_id":"MaLo"}],"has_accepted_license":"1","date_updated":"2026-04-08T07:26:30Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"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"},"year":"2020","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n"}],"oa":1,"oa_version":"Published Version","publication_status":"published","_id":"8358","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers"},{"intvolume":"       480","oa":1,"_id":"8361","publication_status":"published","title":"Current status and future perspectives of lithium metal batteries","oa_version":"Published Version","year":"2020","abstract":[{"lang":"eng","text":"With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7."}],"main_file_link":[{"url":"https://doi.org/10.1016/j.jpowsour.2020.228803","open_access":"1"}],"publication_identifier":{"issn":["0378-7753"]},"external_id":{"isi":["000593857300001"]},"publisher":"Elsevier","article_number":"228803","status":"public","ddc":["540"],"date_published":"2020-12-31T00:00:00Z","month":"12","publication":"Journal of Power Sources","date_updated":"2026-06-18T19:33:06Z","issue":"12","type":"journal_article","department":[{"_id":"StFr"}],"acknowledgement":"A.V. and K.T. acknowledge, respectively, the financial support of the Helmholtz Association and BMW AG. J.H. acknowledges the collabo-ration project “Accordo di Collaborazione Quadro 2015” between Uni-versity of  Ferrara (Department of  Chemical and Pharmaceutical Sciences) and Sapienza University of Rome (Department of Chemistry). S.D., H.A. and S.K. thank the Fraunhofer Gesellschaft, Technische Uni-versit ̈at  Dresden and would like to  acknowledge European Union’s Horizon 2020 research and innovation programme under grant agree-ment No 814471. S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 636069) and IST Austria.","article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"8067","status":"public"}]},"date_created":"2020-09-10T10:48:40Z","language":[{"iso":"eng"}],"day":"31","author":[{"last_name":"Varzi","first_name":"Alberto","full_name":"Varzi, Alberto","orcid":"0000-0001-5069-0589"},{"full_name":"Thanner, Katharina","orcid":"0000-0001-5394-2323","last_name":"Thanner","first_name":"Katharina"},{"last_name":"Scipioni","first_name":"Roberto","full_name":"Scipioni, Roberto","orcid":"0000-0003-1926-421X"},{"full_name":"Di Lecce, Daniele","last_name":"Di Lecce","first_name":"Daniele"},{"full_name":"Hassoun, Jusef","last_name":"Hassoun","first_name":"Jusef"},{"full_name":"Dörfler, Susanne","first_name":"Susanne","last_name":"Dörfler"},{"full_name":"Altheus, Holger","first_name":"Holger","last_name":"Altheus"},{"full_name":"Kaskel, Stefan","last_name":"Kaskel","first_name":"Stefan"},{"orcid":"0000-0003-0654-0940","full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander"}],"isi":1,"article_processing_charge":"No","scopus_import":"1","doi":"10.1016/j.jpowsour.2020.228803","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Varzi, Alberto, Katharina Thanner, Roberto Scipioni, Daniele Di Lecce, Jusef Hassoun, Susanne Dörfler, Holger Altheus, Stefan Kaskel, Christian Prehal, and Stefan Alexander Freunberger. “Current Status and Future Perspectives of Lithium Metal Batteries.” <i>Journal of Power Sources</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">https://doi.org/10.1016/j.jpowsour.2020.228803</a>.","apa":"Varzi, A., Thanner, K., Scipioni, R., Di Lecce, D., Hassoun, J., Dörfler, S., … Freunberger, S. A. (2020). Current status and future perspectives of lithium metal batteries. <i>Journal of Power Sources</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">https://doi.org/10.1016/j.jpowsour.2020.228803</a>","ama":"Varzi A, Thanner K, Scipioni R, et al. Current status and future perspectives of lithium metal batteries. <i>Journal of Power Sources</i>. 2020;480(12). doi:<a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">10.1016/j.jpowsour.2020.228803</a>","mla":"Varzi, Alberto, et al. “Current Status and Future Perspectives of Lithium Metal Batteries.” <i>Journal of Power Sources</i>, vol. 480, no. 12, 228803, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.jpowsour.2020.228803\">10.1016/j.jpowsour.2020.228803</a>.","ieee":"A. Varzi <i>et al.</i>, “Current status and future perspectives of lithium metal batteries,” <i>Journal of Power Sources</i>, vol. 480, no. 12. Elsevier, 2020.","ista":"Varzi A, Thanner K, Scipioni R, Di Lecce D, Hassoun J, Dörfler S, Altheus H, Kaskel S, Prehal C, Freunberger SA. 2020. Current status and future perspectives of lithium metal batteries. Journal of Power Sources. 480(12), 228803.","short":"A. Varzi, K. Thanner, R. Scipioni, D. Di Lecce, J. Hassoun, S. Dörfler, H. Altheus, S. Kaskel, C. Prehal, S.A. Freunberger, Journal of Power Sources 480 (2020)."},"quality_controlled":"1","volume":480},{"article_processing_charge":"No","file":[{"relation":"main_file","access_level":"open_access","date_created":"2020-09-10T16:11:49Z","file_name":"thesis_rguseinov.pdf","success":1,"checksum":"f8da89553da36037296b0a80f14ebf50","creator":"rguseino","date_updated":"2020-09-10T16:11:49Z","file_id":"8367","content_type":"application/pdf","file_size":70950442},{"file_id":"8374","file_size":76207597,"content_type":"application/x-zip-compressed","creator":"rguseino","checksum":"e8fd944c960c20e0e27e6548af69121d","date_updated":"2020-09-16T15:11:01Z","file_name":"thesis_source.zip","date_created":"2020-09-11T09:39:48Z","access_level":"closed","relation":"source_file"}],"citation":{"mla":"Guseinov, Ruslan. <i>Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>.","apa":"Guseinov, R. (2020). <i>Computational design of curved thin shells: From glass façades to programmable matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8366\">10.15479/AT:ISTA:8366</a>","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8366\">https://doi.org/10.15479/AT:ISTA:8366</a>.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria.","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT:ISTA:8366","degree_awarded":"PhD","date_updated":"2026-04-08T07:25:22Z","has_accepted_license":"1","department":[{"_id":"BeBi"}],"type":"dissertation","page":"118","status":"public","month":"09","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"date_published":"2020-09-21T00:00:00Z","ddc":["000"],"file_date_updated":"2020-09-16T15:11:01Z","date_created":"2020-09-10T16:19:55Z","language":[{"iso":"eng"}],"day":"21","author":[{"first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan"}],"acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","corr_author":"1","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8562"},{"status":"public","id":"8375","relation":"research_data"},{"status":"deleted","id":"7151","relation":"research_data"},{"relation":"part_of_dissertation","id":"1001","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7262"}]},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"alternative_title":["ISTA Thesis"],"supervisor":[{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"publisher":"Institute of Science and Technology Austria","title":"Computational design of curved thin shells: From glass façades to programmable matter","publication_status":"published","_id":"8366","oa_version":"Published Version","oa":1,"ec_funded":1,"abstract":[{"text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop.","lang":"eng"}],"keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"year":"2020"},{"file":[{"file_id":"8376","content_type":"video/mp4","file_size":29214988,"checksum":"4029ffd65fb82ef2366b2fc2a4908e16","creator":"rguseino","date_updated":"2020-09-11T09:45:21Z","file_name":"supplementary_movie_1.mp4","success":1,"relation":"main_file","access_level":"open_access","date_created":"2020-09-11T09:45:21Z"},{"date_updated":"2020-09-11T09:45:25Z","checksum":"8ed03b04d80f1a4e622cb22e6100afd8","creator":"rguseino","content_type":"video/mp4","file_size":28449475,"file_id":"8377","relation":"main_file","access_level":"open_access","date_created":"2020-09-11T09:45:25Z","success":1,"file_name":"supplementary_movie_2.mp4"},{"creator":"rguseino","checksum":"ad6864afb5e694e5c52a88fba4e02eea","date_updated":"2020-09-11T09:45:28Z","file_id":"8378","content_type":"video/mp4","file_size":26315853,"relation":"main_file","date_created":"2020-09-11T09:45:28Z","access_level":"open_access","success":1,"file_name":"supplementary_movie_3.mp4"},{"content_type":"video/mp4","file_size":25198755,"file_id":"8379","date_updated":"2020-09-11T09:45:33Z","creator":"rguseino","checksum":"b079cef7871fe1afb69af0e2b099f3b1","file_name":"supplementary_movie_4.mp4","success":1,"access_level":"open_access","date_created":"2020-09-11T09:45:33Z","relation":"main_file"},{"checksum":"9d1d48a8ed5c109a999c51b044ee523d","creator":"rguseino","date_updated":"2020-09-11T09:45:36Z","file_id":"8380","file_size":29011354,"content_type":"video/mp4","relation":"main_file","access_level":"open_access","date_created":"2020-09-11T09:45:36Z","file_name":"supplementary_movie_5.mp4","success":1},{"date_created":"2020-09-11T09:52:36Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"readme.txt","date_updated":"2020-09-11T09:52:36Z","creator":"rguseino","checksum":"d414d0059e982d752d218756b3c3ce05","content_type":"text/plain","file_size":586,"file_id":"8381"}],"contributor":[{"first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Connor","last_name":"McMahan"},{"first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","contributor_type":"researcher"},{"last_name":"Daraio","first_name":"Chiara","contributor_type":"researcher"},{"orcid":"0000-0001-6511-9385","contributor_type":"researcher","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"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"},"doi":"10.15479/AT:ISTA:8375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","citation":{"ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","short":"R. Guseinov, (2020).","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>.","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">https://doi.org/10.15479/AT:ISTA:8375</a>.","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8375\">https://doi.org/10.15479/AT:ISTA:8375</a>","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8375\">10.15479/AT:ISTA:8375</a>."},"date_published":"2020-09-21T00:00:00Z","ddc":["000"],"month":"09","oa":1,"ec_funded":1,"status":"public","type":"research_data","has_accepted_license":"1","oa_version":"Published Version","department":[{"_id":"BeBi"}],"_id":"8375","date_updated":"2026-04-08T07:25:22Z","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","related_material":{"record":[{"id":"8366","status":"public","relation":"used_in_publication"}]},"year":"2020","corr_author":"1","abstract":[{"text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape.","lang":"eng"}],"author":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan"}],"date_created":"2020-09-11T09:52:54Z","day":"21","file_date_updated":"2020-09-11T09:52:36Z"},{"author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Aspnes","first_name":"James","full_name":"Aspnes, James"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Zhu, Leqi","first_name":"Leqi","last_name":"Zhu"}],"conference":{"start_date":"2020-08-03","end_date":"2020-08-07","name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy"},"date_created":"2020-09-13T22:01:18Z","day":"31","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"year":"2020","department":[{"_id":"DaAl"}],"oa_version":"None","type":"conference","title":"Brief Announcement: Why Extension-Based Proofs Fail","_id":"8383","date_updated":"2025-09-10T10:26:32Z","publication_status":"published","publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","date_published":"2020-07-31T00:00:00Z","month":"07","page":"54-56","status":"public","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, 54–56. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3382734.3405743\">https://doi.org/10.1145/3382734.3405743</a>.","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs Fail.” <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2020, pp. 54–56, doi:<a href=\"https://doi.org/10.1145/3382734.3405743\">10.1145/3382734.3405743</a>.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement: Why Extension-Based Proofs Fail. In: <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2020:54-56. doi:<a href=\"https://doi.org/10.1145/3382734.3405743\">10.1145/3382734.3405743</a>","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2020). Brief Announcement: Why Extension-Based Proofs Fail. In <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i> (pp. 54–56). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3382734.3405743\">https://doi.org/10.1145/3382734.3405743</a>","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement: Why Extension-Based Proofs Fail,” in <i>Proceedings of the 39th Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2020, pp. 54–56.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement: Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56."},"quality_controlled":"1","doi":"10.1145/3382734.3405743","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Association for Computing Machinery","scopus_import":"1","article_processing_charge":"No","external_id":{"isi":["001436693500007"]},"isi":1,"publication_identifier":{"isbn":["9781450375825"]}},{"oa":1,"ec_funded":1,"intvolume":"        39","oa_version":"Submitted Version","title":"A model for soap film dynamics with evolving thickness","_id":"8384","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3386569.3392405"}],"abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"year":"2020","external_id":{"isi":["000583700300004"]},"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"}],"publisher":"Association for Computing Machinery","article_number":"31","publication":"ACM Transactions on Graphics","date_published":"2020-07-08T00:00:00Z","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["000"],"status":"public","has_accepted_license":"1","department":[{"_id":"ChWo"}],"type":"journal_article","issue":"4","date_updated":"2026-04-16T08:29:36Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19630"}]},"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","article_type":"original","author":[{"orcid":"0000-0002-3121-3100","full_name":"Ishida, Sadashige","first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida"},{"id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","first_name":"Peter","full_name":"Synak, Peter"},{"first_name":"Fumiya","last_name":"Narita","full_name":"Narita, Fumiya"},{"last_name":"Hachisuka","first_name":"Toshiya","full_name":"Hachisuka, Toshiya"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"file_date_updated":"2020-11-23T09:03:19Z","date_created":"2020-09-13T22:01:18Z","language":[{"iso":"eng"}],"day":"08","article_processing_charge":"No","file":[{"access_level":"open_access","date_created":"2020-11-23T09:03:19Z","relation":"main_file","file_name":"2020_soapfilm_submitted.pdf","success":1,"checksum":"813831ca91319d794d9748c276b24578","creator":"dernst","date_updated":"2020-11-23T09:03:19Z","file_id":"8795","content_type":"application/pdf","file_size":14935529}],"isi":1,"scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1145/3386569.3392405","volume":39,"citation":{"ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4. Association for Computing Machinery, 2020.","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. 2020;39(4). doi:<a href=\"https://doi.org/10.1145/3386569.3392405\">10.1145/3386569.3392405</a>","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., &#38; Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>","chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3386569.3392405\">https://doi.org/10.1145/3386569.3392405</a>."},"quality_controlled":"1"}]