[{"article_type":"original","page":"1649-1675","publication":"Communications in Mathematical Physics","citation":{"chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-020-03828-8.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Sandpile Solitons via Smoothing of Superharmonic Functions.” Communications in Mathematical Physics, vol. 378, no. 9, Springer Nature, 2020, pp. 1649–75, doi:10.1007/s00220-020-03828-8.","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.","apa":"Kalinin, N., & Shkolnikov, M. (2020). Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-020-03828-8","ieee":"N. Kalinin and M. Shkolnikov, “Sandpile solitons via smoothing of superharmonic functions,” Communications in Mathematical Physics, vol. 378, no. 9. Springer Nature, pp. 1649–1675, 2020.","ama":"Kalinin N, Shkolnikov M. Sandpile solitons via smoothing of superharmonic functions. Communications in Mathematical Physics. 2020;378(9):1649-1675. doi:10.1007/s00220-020-03828-8"},"date_published":"2020-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Sandpile solitons via smoothing of superharmonic functions","status":"public","intvolume":" 378","_id":"8325","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"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. ","lang":"eng"}],"issue":"9","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"external_id":{"arxiv":["1711.04285"],"isi":["000560620600001"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.04285"}],"language":[{"iso":"eng"}],"doi":"10.1007/s00220-020-03828-8","month":"09","publication_identifier":{"eissn":["14320916"],"issn":["00103616"]},"publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","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.","year":"2020","date_created":"2020-08-30T22:01:13Z","date_updated":"2023-08-22T09:00:03Z","volume":378,"author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"full_name":"Shkolnikov, Mikhail","first_name":"Mikhail","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"}],"ec_funded":1},{"publication_identifier":{"eissn":["20411723"]},"month":"08","doi":"10.1038/s41467-020-17957-0","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000607072900001"],"pmid":["32811817"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-08-31T13:40:00Z","article_number":"4135","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/mystery-of-giant-proton-pump-solved/"}]},"author":[{"full_name":"Gutierrez-Fernandez, Javier","id":"3D9511BA-F248-11E8-B48F-1D18A9856A87","first_name":"Javier","last_name":"Gutierrez-Fernandez"},{"last_name":"Kaszuba","first_name":"Karol","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87","full_name":"Kaszuba, Karol"},{"full_name":"Minhas, Gurdeep S.","first_name":"Gurdeep S.","last_name":"Minhas"},{"first_name":"Rozbeh","last_name":"Baradaran","full_name":"Baradaran, Rozbeh"},{"id":"4187dfe4-ec23-11ea-ae46-f08ab378313a","last_name":"Tambalo","first_name":"Margherita","full_name":"Tambalo, Margherita"},{"full_name":"Gallagher, David T.","last_name":"Gallagher","first_name":"David T."},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"volume":11,"date_created":"2020-08-30T22:01:10Z","date_updated":"2023-08-22T09:03:00Z","pmid":1,"year":"2020","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.","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","date_published":"2020-08-18T00:00:00Z","citation":{"ama":"Gutierrez-Fernandez J, Kaszuba K, Minhas GS, et al. Key role of quinone in the mechanism of respiratory complex I. Nature Communications. 2020;11(1). doi:10.1038/s41467-020-17957-0","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.","apa":"Gutierrez-Fernandez, J., Kaszuba, K., Minhas, G. S., Baradaran, R., Tambalo, M., Gallagher, D. T., & Sazanov, L. A. (2020). Key role of quinone in the mechanism of respiratory complex I. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-17957-0","ieee":"J. Gutierrez-Fernandez et al., “Key role of quinone in the mechanism of respiratory complex I,” Nature Communications, vol. 11, no. 1. Springer Nature, 2020.","mla":"Gutierrez-Fernandez, Javier, et al. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications, vol. 11, no. 1, 4135, Springer Nature, 2020, doi:10.1038/s41467-020-17957-0.","short":"J. Gutierrez-Fernandez, K. Kaszuba, G.S. Minhas, R. Baradaran, M. Tambalo, D.T. Gallagher, L.A. Sazanov, Nature Communications 11 (2020).","chicago":"Gutierrez-Fernandez, Javier, Karol Kaszuba, Gurdeep S. Minhas, Rozbeh Baradaran, Margherita Tambalo, David T. Gallagher, and Leonid A Sazanov. “Key Role of Quinone in the Mechanism of Respiratory Complex I.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17957-0."},"publication":"Nature Communications","article_type":"original","issue":"1","abstract":[{"text":"Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8326","date_updated":"2020-08-31T13:40:00Z","date_created":"2020-08-31T13:40:00Z","checksum":"52b96f41d7d0db9728064c08da00d030","success":1,"file_name":"2020_NatComm_Gutierrez-Fernandez.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7527373,"creator":"cziletti"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8318","intvolume":" 11","title":"Key role of quinone in the mechanism of respiratory complex I","ddc":["570"],"status":"public"},{"day":"19","article_processing_charge":"No","scopus_import":"1","date_published":"2020-08-19T00:00:00Z","publication":"Molecular Biology","citation":{"ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:10.1134/S0026893320040111.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 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.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111."},"article_type":"original","page":"475-484","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"issue":"4","type":"journal_article","oa_version":"None","_id":"8320","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Expanding the genetic code: Unnatural base pairs in biological systems","intvolume":" 54","month":"08","publication_identifier":{"eissn":["16083245"],"issn":["00268933"]},"doi":"10.1134/S0026893320040111","language":[{"iso":"eng"}],"external_id":{"isi":["000562110300001"]},"quality_controlled":"1","isi":1,"author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"full_name":"Vlasov, Petr","first_name":"Petr","last_name":"Vlasov","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolosov","first_name":"P. M.","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."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"related_material":{"record":[{"status":"public","relation":"original","id":"8321"}]},"date_updated":"2023-08-22T09:01:03Z","date_created":"2020-08-30T22:01:11Z","volume":54,"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.","year":"2020","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Springer Nature"},{"abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"issue":"4","type":"journal_article","oa_version":"None","_id":"8321","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","title":"Expanding the genetic code: Unnatural base pairs in biological systems","intvolume":" 54","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2020-07-01T00:00:00Z","publication":"Molekuliarnaia biologiia","citation":{"mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.","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.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420040126.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126","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.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020.","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., & Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences. https://doi.org/10.31857/S0026898420040126"},"article_type":"original","page":"531-541","author":[{"full_name":"Mukba, S. A.","first_name":"S. A.","last_name":"Mukba"},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","first_name":"Petr"},{"full_name":"Kolosov, P. M.","last_name":"Kolosov","first_name":"P. M."},{"last_name":"Shuvalova","first_name":"E. Y.","full_name":"Shuvalova, E. Y."},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}],"related_material":{"record":[{"status":"public","relation":"translation","id":"8320"}]},"date_updated":"2023-08-22T09:01:02Z","date_created":"2020-08-30T22:01:11Z","volume":54,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Russian Academy of Sciences","month":"07","publication_identifier":{"issn":["00268984"]},"doi":"10.31857/S0026898420040126","language":[{"iso":"rus"}],"external_id":{"pmid":["32799218"]},"quality_controlled":"1"},{"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","year":"2020","date_created":"2020-08-30T22:01:12Z","date_updated":"2023-08-22T09:05:04Z","volume":64,"author":[{"full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach","first_name":"János"}],"isi":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00237-5","open_access":"1"}],"external_id":{"isi":["000561483500001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00237-5","month":"10","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"title":"A farewell to Ricky Pollack","status":"public","intvolume":" 64","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8323","oa_version":"None","type":"journal_article","article_type":"letter_note","page":"571-574","publication":"Discrete and Computational Geometry","citation":{"chicago":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry. Springer Nature, 2020. https://doi.org/10.1007/s00454-020-00237-5.","mla":"Pach, János. “A Farewell to Ricky Pollack.” Discrete and Computational Geometry, vol. 64, Springer Nature, 2020, pp. 571–74, doi:10.1007/s00454-020-00237-5.","short":"J. Pach, Discrete and Computational Geometry 64 (2020) 571–574.","ista":"Pach J. 2020. A farewell to Ricky Pollack. Discrete and Computational Geometry. 64, 571–574.","ieee":"J. Pach, “A farewell to Ricky Pollack,” Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 571–574, 2020.","apa":"Pach, J. (2020). A farewell to Ricky Pollack. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00237-5","ama":"Pach J. A farewell to Ricky Pollack. Discrete and Computational Geometry. 2020;64:571-574. doi:10.1007/s00454-020-00237-5"},"date_published":"2020-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"}]