[{"date_published":"2023-03-16T00:00:00Z","citation":{"short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689","ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689."},"publication":"PLoS ONE","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"16","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":856625,"content_type":"application/pdf","creator":"dernst","file_name":"2023_PLoSOne_Pak.pdf","access_level":"open_access","date_updated":"2023-03-27T07:09:08Z","date_created":"2023-03-27T07:09:08Z","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","success":1,"relation":"main_file","file_id":"12771"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12758","intvolume":" 18","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","ddc":["570"],"status":"public","issue":"3","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"type":"journal_article","doi":"10.1371/journal.pone.0282689","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":["000985134400106"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1932-6203"]},"month":"03","author":[{"last_name":"Pak","first_name":"Marina A.","full_name":"Pak, Marina A."},{"full_name":"Markhieva, Karina A.","last_name":"Markhieva","first_name":"Karina A."},{"last_name":"Novikova","first_name":"Mariia S.","full_name":"Novikova, Mariia S."},{"first_name":"Dmitry S.","last_name":"Petrov","full_name":"Petrov, Dmitry S."},{"full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev","first_name":"Ilya S."},{"full_name":"Maksimova, Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","last_name":"Maksimova","first_name":"Ekaterina"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ivankov, Dmitry N.","first_name":"Dmitry N.","last_name":"Ivankov"}],"volume":18,"date_updated":"2023-08-01T13:47:14Z","date_created":"2023-03-26T22:01:07Z","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","year":"2023","publisher":"Public Library of Science","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publication_status":"published","file_date_updated":"2023-03-27T07:09:08Z","article_number":"e0282689"},{"publication":"The Biochemical Journal","citation":{"ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285."},"article_type":"review","page":"319-333","date_published":"2023-03-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12757","ddc":["570"],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","status":"public","intvolume":" 480","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"issue":"5","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"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"external_id":{"isi":["000957065700001"],"pmid":["36920092"]},"quality_controlled":"1","isi":1,"doi":"10.1042/BCJ20210285","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Portland Press","author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"date_updated":"2023-08-01T13:45:12Z","date_created":"2023-03-26T22:01:06Z","volume":480},{"file_date_updated":"2023-04-03T06:25:29Z","ec_funded":1,"article_number":"20220685","date_updated":"2023-08-01T13:58:34Z","date_created":"2023-04-02T22:01:09Z","volume":479,"author":[{"full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"related_material":{"link":[{"relation":"research_data","url":"https://doi.org/10.6084/m9.figshare.21261771.v1"}]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"KrCh"}],"year":"2023","acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","month":"03","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"language":[{"iso":"eng"}],"doi":"10.1098/rspa.2022.0685","isi":1,"quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"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":["000957125500002"]},"oa":1,"abstract":[{"text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results.","lang":"eng"}],"issue":"2271","type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","creator":"dernst","content_type":"application/pdf","file_size":827784,"file_id":"12796","relation":"main_file","success":1,"checksum":"13953d349fbefcb5d21ccc6b303297eb","date_created":"2023-04-03T06:25:29Z","date_updated":"2023-04-03T06:25:29Z"}],"oa_version":"Published Version","status":"public","ddc":["000"],"title":"Coexistence times in the Moran process with environmental heterogeneity","intvolume":" 479","_id":"12787","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"29","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-29T00:00:00Z","article_type":"original","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685","chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685."}},{"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.07067","open_access":"1"}],"oa":1,"external_id":{"isi":["000957635500003"],"arxiv":["2206.07067"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.130.103202","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","volume":130,"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T14:02:06Z","related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"author":[{"full_name":"Karle, Volker","last_name":"Karle","first_name":"Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425"},{"full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"article_number":"103202","ec_funded":1,"article_type":"original","citation":{"ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023)."},"publication":"Physical Review Letters","date_published":"2023-03-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","intvolume":" 130","title":"Topological charges of periodically kicked molecules","status":"public","_id":"12788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}]},{"related_material":{"link":[{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/"}]},"author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"volume":107,"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T13:59:29Z","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2023","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","article_number":"104502","doi":"10.1103/PhysRevB.107.104502","language":[{"iso":"eng"}],"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.02492","open_access":"1"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"03","oa_version":"Preprint","_id":"12790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 107","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","status":"public","issue":"10","abstract":[{"lang":"eng","text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity."}],"type":"journal_article","date_published":"2023-03-01T00:00:00Z","citation":{"short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502."},"publication":"Physical Review B","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"citation":{"ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9."},"publication":"The European Physical Journal E","article_type":"original","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"20","_id":"12791","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 46","status":"public","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra."}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2301.07769","open_access":"1"}],"external_id":{"isi":["000956387200001"],"arxiv":["2301.07769"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"month":"03","year":"2023","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","publisher":"Springer Nature","department":[{"_id":"CaMu"}],"publication_status":"published","author":[{"full_name":"Clark Di Leoni, Patricio","first_name":"Patricio","last_name":"Clark Di Leoni"},{"full_name":"Agasthya, Lokahith N","last_name":"Agasthya","first_name":"Lokahith N","id":"cd100965-0804-11ed-9c55-f4878ff4e877"},{"full_name":"Buzzicotti, Michele","last_name":"Buzzicotti","first_name":"Michele"},{"first_name":"Luca","last_name":"Biferale","full_name":"Biferale, Luca"}],"volume":46,"date_created":"2023-04-02T22:01:11Z","date_updated":"2023-08-01T14:03:47Z","article_number":"16"},{"article_type":"original","page":"582-596.e7","publication":"Developmental Cell","citation":{"ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016."},"date_published":"2023-04-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","ddc":["570"],"status":"public","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","intvolume":" 58","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12830","oa_version":"Published Version","file":[{"file_size":7925886,"content_type":"application/pdf","creator":"dernst","file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","date_updated":"2023-04-17T07:41:25Z","date_created":"2023-04-17T07:41:25Z","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","success":1,"relation":"main_file","file_id":"12842"}],"type":"journal_article","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"issue":"7","isi":1,"quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","_id":"26520D1E-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 850-2017"},{"name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","grant_number":"LT000429"}],"external_id":{"isi":["000982111800001"]},"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"},"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2023.02.016","month":"04","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"Bio"}],"year":"2023","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","date_updated":"2023-08-01T14:10:38Z","date_created":"2023-04-16T22:01:07Z","volume":58,"author":[{"full_name":"Huljev, Karla","last_name":"Huljev","first_name":"Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"last_name":"Nunes Pinheiro","first_name":"Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C"},{"first_name":"Friedrich","last_name":"Preusser","full_name":"Preusser, Friedrich"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari","full_name":"Steccari, Irene"},{"last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"first_name":"Suyash","last_name":"Naik","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"file_date_updated":"2023-04-17T07:41:25Z","ec_funded":1},{"day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-04-07T00:00:00Z","publication":"The Journal of Chemical Physics","citation":{"short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893.","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893.","ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023.","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301."},"article_type":"original","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"issue":"13","type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"8d801babea4df48e08895c76571bb19e","date_updated":"2023-04-17T07:28:38Z","date_created":"2023-04-17T07:28:38Z","file_id":"12841","relation":"main_file","creator":"dernst","file_size":7388057,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_JourChemicalPhysics_Zeng.pdf"}],"_id":"12831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["530"],"title":"Variational theory of angulons and their rotational spectroscopy","status":"public","intvolume":" 158","month":"04","publication_identifier":{"eissn":["1089-7690"]},"doi":"10.1063/5.0135893","language":[{"iso":"eng"}],"external_id":{"isi":["000970038800001"],"arxiv":["2211.08070"]},"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"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"file_date_updated":"2023-04-17T07:28:38Z","ec_funded":1,"article_number":"134301","author":[{"last_name":"Zeng","first_name":"Zhongda","full_name":"Zeng, Zhongda"},{"first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shi, Tao","first_name":"Tao","last_name":"Shi"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"date_created":"2023-04-16T22:01:07Z","date_updated":"2023-08-01T14:08:47Z","volume":158,"year":"2023","acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Institute of Physics"},{"publication_identifier":{"eissn":["2160-3308"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevX.13.011033","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"quality_controlled":"1","isi":1,"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":["000957625700001"]},"oa":1,"ec_funded":1,"file_date_updated":"2023-04-17T08:36:53Z","article_number":"011033","volume":13,"date_created":"2023-04-16T22:01:09Z","date_updated":"2023-08-01T14:11:28Z","author":[{"full_name":"Ljubotina, Marko","first_name":"Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"full_name":"Desaules, Jean Yves","last_name":"Desaules","first_name":"Jean Yves"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","year":"2023","has_accepted_license":"1","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2023-03-07T00:00:00Z","article_type":"original","citation":{"chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033.","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033","ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033"},"publication":"Physical Review X","issue":"1","abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_PhysReviewX_Ljubotina.pdf","content_type":"application/pdf","file_size":1958523,"creator":"dernst","relation":"main_file","file_id":"12845","checksum":"ee060cea609af79bba7af74b1ce28078","success":1,"date_created":"2023-04-17T08:36:53Z","date_updated":"2023-04-17T08:36:53Z"}],"oa_version":"Published Version","intvolume":" 13","title":"Superdiffusive energy transport in kinetically constrained models","ddc":["530"],"status":"public","_id":"12839","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-01-01T00:00:00Z","article_type":"original","publication":"Advanced Intelligent Systems","citation":{"ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","apa":"Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. Wiley. https://doi.org/10.1002/aisy.202200129","ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” Advanced Intelligent Systems, vol. 5, no. 1. Wiley, 2023.","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129, Wiley, 2023, doi:10.1002/aisy.202200129.","short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).","chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129."},"abstract":[{"lang":"eng","text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","file_size":2414125,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12840","checksum":"d48fc41d39892e7fa0d44cb352dd46aa","success":1,"date_updated":"2023-04-17T06:44:17Z","date_created":"2023-04-17T06:44:17Z"}],"status":"public","ddc":["530"],"title":"Rotation control, interlocking, and self‐positioning of active cogwheels","intvolume":" 5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12822","month":"01","publication_identifier":{"issn":["2640-4567"]},"language":[{"iso":"eng"}],"doi":"10.1002/aisy.202200129","isi":1,"quality_controlled":"1","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"},"oa":1,"external_id":{"arxiv":["2201.03333"],"isi":["000852291200001"]},"file_date_updated":"2023-04-17T06:44:17Z","article_number":"2200129","date_created":"2023-04-12T08:30:03Z","date_updated":"2023-08-01T14:06:50Z","volume":5,"author":[{"full_name":"Martinet, Quentin","first_name":"Quentin","last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"publication_status":"published","department":[{"_id":"JePa"}],"publisher":"Wiley","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","year":"2023"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37054-2","isi":1,"quality_controlled":"1","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"},"oa":1,"external_id":{"pmid":["36964141"],"isi":["000959887700008"]},"month":"03","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2023-08-01T14:05:30Z","date_created":"2023-04-09T22:01:00Z","volume":14,"author":[{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"full_name":"Han, Yu Long","last_name":"Han","first_name":"Yu Long"},{"last_name":"Alert","first_name":"Ricard","full_name":"Alert, Ricard"},{"full_name":"Guo, Ming","last_name":"Guo","first_name":"Ming"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"year":"2023","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","pmid":1,"file_date_updated":"2023-04-11T06:27:00Z","article_number":"1643","date_published":"2023-03-24T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023."},"day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2023_NatureComm_Brandstaetter.pdf","content_type":"application/pdf","file_size":4146777,"creator":"dernst","relation":"main_file","file_id":"12821","checksum":"54f06f9eee11d43bab253f3492c983ba","success":1,"date_updated":"2023-04-11T06:27:00Z","date_created":"2023-04-11T06:27:00Z"}],"oa_version":"Published Version","title":"Curvature induces active velocity waves in rotating spherical tissues","status":"public","ddc":["570"],"intvolume":" 14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12818","abstract":[{"text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues.","lang":"eng"}],"type":"journal_article"},{"year":"2023","acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Sokolova, Alesya","orcid":"0000-0002-8308-4144","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","last_name":"Sokolova","first_name":"Alesya"},{"full_name":"Kalacheva, D. A.","last_name":"Kalacheva","first_name":"D. A."},{"full_name":"Fedorov, G. P.","first_name":"G. P.","last_name":"Fedorov"},{"last_name":"Astafiev","first_name":"O. V.","full_name":"Astafiev, O. V."}],"volume":107,"date_created":"2023-04-09T22:01:00Z","date_updated":"2023-08-01T14:06:05Z","article_number":"L031701","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"external_id":{"arxiv":["2209.05165"],"isi":["000957799000006"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevA.107.L031701","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"month":"03","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12819","intvolume":" 107","status":"public","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds."}],"citation":{"mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.","short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L031701.","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701","ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701.","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L031701","ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical Society, 2023."},"publication":"Physical Review A","article_type":"letter_note","date_published":"2023-03-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22"},{"abstract":[{"lang":"eng","text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations."}],"type":"journal_article","file":[{"date_updated":"2023-04-25T09:13:53Z","date_created":"2023-04-25T09:13:53Z","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","success":1,"relation":"main_file","file_id":"12868","file_size":1786475,"content_type":"application/pdf","creator":"dernst","file_name":"2023_NatureComm_Schmid.pdf","access_level":"open_access"}],"oa_version":"Published Version","title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","status":"public","ddc":["000"],"intvolume":" 14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12861","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-04-12T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 2023;14. doi:10.1038/s41467-023-37817-x","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer Nature, 2023, doi:10.1038/s41467-023-37817-x.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023)."},"file_date_updated":"2023-04-25T09:13:53Z","ec_funded":1,"article_number":"2086","date_updated":"2023-08-01T14:15:57Z","date_created":"2023-04-23T22:01:03Z","volume":14,"author":[{"full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329","first_name":"Laura","last_name":"Schmid"},{"first_name":"Farbod","last_name":"Ekbatani","full_name":"Ekbatani, Farbod"},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","pmid":1,"month":"04","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37817-x","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"external_id":{"pmid":["37045828"],"isi":["001003644100020"]},"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"},"oa":1},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"PLoS Computational Biology","citation":{"chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol. 19, no. 4. Public Library of Science, 2023.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983"},"article_type":"original","date_published":"2023-04-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12862","status":"public","ddc":["570"],"title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","intvolume":" 19","file":[{"date_created":"2023-04-25T08:59:18Z","date_updated":"2023-04-25T08:59:18Z","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","success":1,"relation":"main_file","file_id":"12867","file_size":4737671,"content_type":"application/pdf","creator":"dernst","file_name":"2023_PLoSCompBio_Safavi.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"04","publication_identifier":{"eissn":["1553-7358"]},"oa":1,"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":["000962668700002"]},"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pcbi.1010983","language":[{"iso":"eng"}],"article_number":"e1010983","file_date_updated":"2023-04-25T08:59:18Z","year":"2023","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Public Library of Science","author":[{"full_name":"Safavi, Shervin","first_name":"Shervin","last_name":"Safavi"},{"first_name":"Theofanis I.","last_name":"Panagiotaropoulos","full_name":"Panagiotaropoulos, Theofanis I."},{"full_name":"Kapoor, Vishal","last_name":"Kapoor","first_name":"Vishal"},{"last_name":"Ramirez Villegas","first_name":"Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","full_name":"Ramirez Villegas, Juan F"},{"first_name":"Nikos K.","last_name":"Logothetis","full_name":"Logothetis, Nikos K."},{"first_name":"Michel","last_name":"Besserve","full_name":"Besserve, Michel"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"date_updated":"2023-08-01T14:15:16Z","date_created":"2023-04-23T22:01:03Z","volume":19},{"abstract":[{"lang":"eng","text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12883","relation":"main_file","success":1,"checksum":"5eeec69a51e192dcd94b955d84423836","date_created":"2023-05-02T07:17:05Z","date_updated":"2023-05-02T07:17:05Z","access_level":"open_access","file_name":"2023_ChemialScience_Chen.pdf","creator":"dernst","file_size":1515446,"content_type":"application/pdf"}],"title":"Physics-inspired machine learning of localized intensive properties","ddc":["000","540"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12879","article_processing_charge":"No","has_accepted_license":"1","day":"10","scopus_import":"1","date_published":"2023-04-10T00:00:00Z","article_type":"original","citation":{"ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” Chemical Science. Royal Society of Chemistry, 2023.","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d3sc00841j","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j."},"publication":"Chemical Science","license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2023-05-02T07:17:05Z","date_updated":"2023-08-01T14:18:10Z","date_created":"2023-04-30T22:01:06Z","author":[{"full_name":"Chen, Ke","first_name":"Ke","last_name":"Chen","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d"},{"full_name":"Kunkel, Christian","last_name":"Kunkel","first_name":"Christian"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"},{"full_name":"Reuter, Karsten","last_name":"Reuter","first_name":"Karsten"},{"full_name":"Margraf, Johannes T.","first_name":"Johannes T.","last_name":"Margraf"}],"department":[{"_id":"BiCh"}],"publisher":"Royal Society of Chemistry","publication_status":"published","acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","year":"2023","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1039/d3sc00841j","quality_controlled":"1","isi":1,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000971508100001"]}},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":478740,"creator":"dernst","file_name":"2023_Bioinformatics_Benes.pdf","access_level":"open_access","date_created":"2023-05-02T07:39:04Z","date_updated":"2023-05-02T07:39:04Z","checksum":"2cb90ddf781baefddf47eac4b54e2a03","success":1,"relation":"main_file","file_id":"12886"}],"_id":"12876","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 39","title":"Boolean network sketches: A unifying framework for logical model inference","ddc":["000"],"status":"public","issue":"4","abstract":[{"text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.","lang":"eng"}],"type":"journal_article","date_published":"2023-04-03T00:00:00Z","citation":{"apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 2023;39(4). doi:10.1093/bioinformatics/btad158","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158."},"publication":"Bioinformatics","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"03","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7688740"}]},"author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"last_name":"Brim","first_name":"Luboš","full_name":"Brim, Luboš"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","first_name":"Samuel","full_name":"Pastva, Samuel"},{"first_name":"David","last_name":"Šafránek","full_name":"Šafránek, David"}],"volume":39,"date_updated":"2023-08-01T14:27:28Z","date_created":"2023-04-30T22:01:05Z","pmid":1,"year":"2023","acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","publisher":"Oxford Academic","department":[{"_id":"ToHe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-05-02T07:39:04Z","article_number":"btad158","doi":"10.1093/bioinformatics/btad158","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"},"oa":1,"external_id":{"isi":["000976610800001"],"pmid":["37004199"]},"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1367-4811"]},"month":"04"},{"publication_identifier":{"eissn":["1949-1042"],"issn":["1949-1034"]},"month":"04","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"language":[{"iso":"eng"}],"doi":"10.1080/19491034.2023.2202548","article_number":"2202548","file_date_updated":"2023-05-02T07:24:55Z","department":[{"_id":"MaHe"}],"publisher":"Taylor & Francis","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","volume":14,"date_created":"2023-04-30T22:01:06Z","date_updated":"2023-08-01T14:18:46Z","author":[{"full_name":"Kaneshiro, Jeanae M.","first_name":"Jeanae M.","last_name":"Kaneshiro"},{"full_name":"Capitanio, Juliana S.","first_name":"Juliana S.","last_name":"Capitanio"},{"full_name":"Hetzer, Martin W","first_name":"Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","article_type":"original","citation":{"mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” Nucleus, vol. 14, no. 1. Taylor & Francis, 2023.","apa":"Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. Taylor & Francis. https://doi.org/10.1080/19491034.2023.2202548"},"publication":"Nucleus","date_published":"2023-04-18T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"intvolume":" 14","ddc":["570"],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","status":"public","_id":"12880","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":3811113,"content_type":"application/pdf","creator":"dernst","file_name":"2023_Nucleus_Kaneshiro.pdf","access_level":"open_access","date_updated":"2023-05-02T07:24:55Z","date_created":"2023-05-02T07:24:55Z","checksum":"8e707eda84f64dbad7f03545ae0a83ef","success":1,"relation":"main_file","file_id":"12884"}]},{"abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"issue":"4","type":"journal_article","oa_version":"Preprint","status":"public","title":"Numerical quantum clock simulations for measuring tunneling times","intvolume":" 107","_id":"12914","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-20T00:00:00Z","article_type":"original","publication":"Physical Review A","citation":{"chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.","apa":"Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023.","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216"},"ec_funded":1,"article_number":"042216","date_updated":"2023-08-01T14:33:21Z","date_created":"2023-05-07T22:01:03Z","volume":107,"author":[{"orcid":"0000-0003-4982-5970","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","last_name":"Suzuki","first_name":"Fumika","full_name":"Suzuki, Fumika"},{"last_name":"Unruh","first_name":"William G.","full_name":"Unruh, William G."}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","year":"2023","month":"04","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.042216","quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"isi":["000975799300006"],"arxiv":["2207.13130"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}]},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12917","checksum":"a778105665c10beb2354c92d2b295115","success":1,"date_created":"2023-05-08T07:26:40Z","date_updated":"2023-05-08T07:26:40Z","access_level":"open_access","file_name":"2023_NatureComm_DiezMerida.pdf","file_size":1405588,"content_type":"application/pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12913","intvolume":" 14","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","status":"public","ddc":["530"],"abstract":[{"lang":"eng","text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices."}],"type":"journal_article","date_published":"2023-04-26T00:00:00Z","citation":{"short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications, vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 2023;14. doi:10.1038/s41467-023-38005-7","ieee":"J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38005-7","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396."},"publication":"Nature Communications","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","author":[{"full_name":"Díez-Mérida, J.","first_name":"J.","last_name":"Díez-Mérida"},{"last_name":"Díez-Carlón","first_name":"A.","full_name":"Díez-Carlón, A."},{"full_name":"Yang, S. Y.","last_name":"Yang","first_name":"S. Y."},{"last_name":"Xie","first_name":"Y. M.","full_name":"Xie, Y. M."},{"full_name":"Gao, X. J.","first_name":"X. J.","last_name":"Gao"},{"full_name":"Senior, Jorden L","first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"full_name":"Lu, X.","last_name":"Lu","first_name":"X."},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"full_name":"Law, K. T.","first_name":"K. T.","last_name":"Law"},{"last_name":"Efetov","first_name":"Dmitri K.","full_name":"Efetov, Dmitri K."}],"volume":14,"date_created":"2023-05-07T22:01:03Z","date_updated":"2023-08-01T14:34:00Z","pmid":1,"acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","year":"2023","publisher":"Springer Nature","department":[{"_id":"AnHi"}],"publication_status":"published","file_date_updated":"2023-05-08T07:26:40Z","article_number":"2396","doi":"10.1038/s41467-023-38005-7","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":{"pmid":["37100775"],"isi":["000979744000004"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"04"},{"article_number":"66","file_date_updated":"2023-06-19T07:33:53Z","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","year":"2023","date_updated":"2023-08-01T14:40:33Z","date_created":"2021-12-16T12:15:35Z","volume":33,"author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"},{"last_name":"Kniely","first_name":"Michael","orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael"},{"first_name":"Bao Quoc","last_name":"Tang","full_name":"Tang, Bao Quoc"}],"month":"06","publication_identifier":{"eissn":["1432-1467"],"issn":["0938-8974"]},"isi":1,"quality_controlled":"1","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"},"oa":1,"external_id":{"isi":["001002343400002"],"arxiv":["2109.12019"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00332-023-09926-w","type":"journal_article","abstract":[{"text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.","lang":"eng"}],"status":"public","ddc":["510"],"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","intvolume":" 33","_id":"10550","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":742315,"creator":"dernst","access_level":"open_access","file_name":"2023_JourNonlinearScience_Fellner.pdf","checksum":"f3f0f0886098e31c81116cff8183750b","success":1,"date_updated":"2023-06-19T07:33:53Z","date_created":"2023-06-19T07:33:53Z","relation":"main_file","file_id":"13149"}],"oa_version":"Published Version","scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Journal of Nonlinear Science","citation":{"ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66.","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w."},"date_published":"2023-06-07T00:00:00Z"}]