[{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"16","article_type":"original","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","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","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.","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","date_published":"2023-03-16T00:00:00Z","type":"journal_article","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."}],"intvolume":" 18","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12758","oa_version":"Published Version","file":[{"file_name":"2023_PLoSOne_Pak.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":856625,"file_id":"12771","relation":"main_file","date_created":"2023-03-27T07:09:08Z","date_updated":"2023-03-27T07:09:08Z","success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6"}],"publication_identifier":{"eissn":["1932-6203"]},"month":"03","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"},"external_id":{"isi":["000985134400106"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0282689","article_number":"e0282689","file_date_updated":"2023-03-27T07:09:08Z","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2023","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.","volume":18,"date_updated":"2023-08-01T13:47:14Z","date_created":"2023-03-26T22:01:07Z","author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"first_name":"Karina A.","last_name":"Markhieva","full_name":"Markhieva, Karina A."},{"last_name":"Novikova","first_name":"Mariia S.","full_name":"Novikova, Mariia S."},{"last_name":"Petrov","first_name":"Dmitry S.","full_name":"Petrov, Dmitry S."},{"last_name":"Vorobyev","first_name":"Ilya S.","full_name":"Vorobyev, Ilya S."},{"first_name":"Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","full_name":"Maksimova, Ekaterina"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry N.","last_name":"Ivankov","full_name":"Ivankov, Dmitry N."}]},{"oa_version":"Published Version","_id":"12757","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","intvolume":" 480","abstract":[{"lang":"eng","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."}],"issue":"5","type":"journal_article","date_published":"2023-03-15T00:00:00Z","publication":"The Biochemical Journal","citation":{"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.","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.","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","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","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.","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.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333."},"article_type":"review","page":"319-333","day":"15","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"date_created":"2023-03-26T22:01:06Z","date_updated":"2023-08-01T13:45:12Z","volume":480,"year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Portland Press","doi":"10.1042/BCJ20210285","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,"main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"external_id":{"isi":["000957065700001"],"pmid":["36920092"]},"quality_controlled":"1","isi":1,"month":"03","publication_identifier":{"eissn":["1470-8728"],"issn":["0264-6021"]}},{"day":"29","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-29T00:00:00Z","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"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.","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.","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","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","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.","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."},"article_type":"original","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","oa_version":"Published Version","file":[{"file_size":827784,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","checksum":"13953d349fbefcb5d21ccc6b303297eb","success":1,"date_created":"2023-04-03T06:25:29Z","date_updated":"2023-04-03T06:25:29Z","relation":"main_file","file_id":"12796"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12787","status":"public","ddc":["000"],"title":"Coexistence times in the Moran process with environmental heterogeneity","intvolume":" 479","month":"03","publication_identifier":{"issn":["1364-5021"],"eissn":["1471-2946"]},"doi":"10.1098/rspa.2022.0685","language":[{"iso":"eng"}],"external_id":{"isi":["000957125500002"]},"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":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"file_date_updated":"2023-04-03T06:25:29Z","ec_funded":1,"article_number":"20220685","author":[{"first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.21261771.v1","relation":"research_data"}]},"date_created":"2023-04-02T22:01:09Z","date_updated":"2023-08-01T13:58:34Z","volume":479,"acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","year":"2023","publication_status":"published","publisher":"The Royal Society","department":[{"_id":"KrCh"}]},{"date_published":"2023-03-10T00:00:00Z","article_type":"original","publication":"Physical Review Letters","citation":{"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.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","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.","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","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 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"},"day":"10","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Topological charges of periodically kicked molecules","status":"public","intvolume":" 130","_id":"12788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","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."}],"issue":"10","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.130.103202","quality_controlled":"1","isi":1,"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"external_id":{"isi":["000957635500003"],"arxiv":["2206.07067"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.07067","open_access":"1"}],"month":"03","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"date_updated":"2023-08-01T14:02:06Z","date_created":"2023-04-02T22:01:10Z","volume":130,"author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","last_name":"Karle","full_name":"Karle, Volker"},{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","ec_funded":1,"article_number":"103202"},{"author":[{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"last_name":"Holder","first_name":"Tobias","full_name":"Holder, Tobias"},{"full_name":"Berg, Erez","first_name":"Erez","last_name":"Berg"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/","relation":"press_release","description":"News on the ISTA website"}]},"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T13:59:29Z","volume":107,"year":"2023","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.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"},{"_id":"MiLe"}],"article_number":"104502","doi":"10.1103/PhysRevB.107.104502","language":[{"iso":"eng"}],"external_id":{"isi":["000945526400003"],"arxiv":["2211.02492"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.02492","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"oa_version":"Preprint","_id":"12790","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","intvolume":" 107","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."}],"issue":"10","type":"journal_article","date_published":"2023-03-01T00:00:00Z","publication":"Physical Review B","citation":{"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","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.","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","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.","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.","short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","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."},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1"},{"_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":[{"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.","lang":"eng"}],"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","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.","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.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (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.","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","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))","year":"2023","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Clark Di Leoni, Patricio","first_name":"Patricio","last_name":"Clark Di Leoni"},{"full_name":"Agasthya, Lokahith N","first_name":"Lokahith N","last_name":"Agasthya","id":"cd100965-0804-11ed-9c55-f4878ff4e877"},{"full_name":"Buzzicotti, Michele","last_name":"Buzzicotti","first_name":"Michele"},{"full_name":"Biferale, Luca","first_name":"Luca","last_name":"Biferale"}],"volume":46,"date_created":"2023-04-02T22:01:11Z","date_updated":"2023-08-01T14:03:47Z","article_number":"16","external_id":{"isi":["000956387200001"],"arxiv":["2301.07769"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2301.07769"}],"isi":1,"quality_controlled":"1","doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"month":"03"},{"month":"04","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"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":["000982111800001"]},"quality_controlled":"1","isi":1,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"doi":"10.1016/j.devcel.2023.02.016","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"file_date_updated":"2023-04-17T07:41:25Z","ec_funded":1,"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.","year":"2023","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"Elsevier","author":[{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","last_name":"Nunes Pinheiro","first_name":"Diana C"},{"first_name":"Friedrich","last_name":"Preusser","full_name":"Preusser, Friedrich"},{"last_name":"Steccari","first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"full_name":"Naik, Suyash","last_name":"Naik","first_name":"Suyash","orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2023-04-16T22:01:07Z","date_updated":"2023-08-01T14:10:38Z","volume":58,"scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Developmental Cell","citation":{"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.","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.","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.","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.","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","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.","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"},"article_type":"original","page":"582-596.e7","date_published":"2023-04-10T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12830","ddc":["570"],"title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","status":"public","intvolume":" 58","oa_version":"Published Version","file":[{"file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","file_size":7925886,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12842","date_created":"2023-04-17T07:41:25Z","date_updated":"2023-04-17T07:41:25Z","checksum":"c80ca2ebc241232aacdb5aa4b4c80957","success":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":{"arxiv":["2211.08070"],"isi":["000970038800001"]},"oa":1,"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1063/5.0135893","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"]},"month":"04","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).","department":[{"_id":"MiLe"}],"publisher":"American Institute of Physics","publication_status":"published","author":[{"first_name":"Zhongda","last_name":"Zeng","full_name":"Zeng, Zhongda"},{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"last_name":"Shi","first_name":"Tao","full_name":"Shi, Tao"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"}],"volume":158,"date_updated":"2023-08-01T14:08:47Z","date_created":"2023-04-16T22:01:07Z","article_number":"134301","ec_funded":1,"file_date_updated":"2023-04-17T07:28:38Z","citation":{"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.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","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","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.","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."},"publication":"The Journal of Chemical Physics","article_type":"original","date_published":"2023-04-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","_id":"12831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 158","title":"Variational theory of angulons and their rotational spectroscopy","ddc":["530"],"status":"public","oa_version":"Published Version","file":[{"creator":"dernst","file_size":7388057,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_JourChemicalPhysics_Zeng.pdf","success":1,"checksum":"8d801babea4df48e08895c76571bb19e","date_created":"2023-04-17T07:28:38Z","date_updated":"2023-04-17T07:28:38Z","file_id":"12841","relation":"main_file"}],"type":"journal_article","issue":"13","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."}]},{"ec_funded":1,"file_date_updated":"2023-04-17T08:36:53Z","article_number":"011033","author":[{"first_name":"Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko"},{"last_name":"Desaules","first_name":"Jean Yves","full_name":"Desaules, Jean Yves"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"volume":13,"date_created":"2023-04-16T22:01:09Z","date_updated":"2023-08-01T14:11:28Z","year":"2023","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].","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","publication_identifier":{"eissn":["2160-3308"]},"month":"03","doi":"10.1103/PhysRevX.13.011033","language":[{"iso":"eng"}],"external_id":{"isi":["000957625700001"]},"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,"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"isi":1,"quality_controlled":"1","issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1958523,"creator":"dernst","access_level":"open_access","file_name":"2023_PhysReviewX_Ljubotina.pdf","checksum":"ee060cea609af79bba7af74b1ce28078","success":1,"date_created":"2023-04-17T08:36:53Z","date_updated":"2023-04-17T08:36:53Z","relation":"main_file","file_id":"12845"}],"_id":"12839","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13","ddc":["530"],"status":"public","title":"Superdiffusive energy transport in kinetically constrained models","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","date_published":"2023-03-07T00:00:00Z","citation":{"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","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.","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 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","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.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","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."},"publication":"Physical Review X","article_type":"original"},{"article_number":"2200129","file_date_updated":"2023-04-17T06:44:17Z","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","year":"2023","department":[{"_id":"JePa"}],"publisher":"Wiley","publication_status":"published","author":[{"last_name":"Martinet","first_name":"Quentin","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin"},{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"full_name":"Palacci, Jérémie A","first_name":"Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"}],"volume":5,"date_updated":"2023-08-01T14:06:50Z","date_created":"2023-04-12T08:30:03Z","publication_identifier":{"issn":["2640-4567"]},"month":"01","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":{"arxiv":["2201.03333"],"isi":["000852291200001"]},"quality_controlled":"1","isi":1,"doi":"10.1002/aisy.202200129","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","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."}],"_id":"12822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 5","status":"public","ddc":["530"],"title":"Rotation control, interlocking, and self‐positioning of active cogwheels","file":[{"file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","access_level":"open_access","file_size":2414125,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12840","date_updated":"2023-04-17T06:44:17Z","date_created":"2023-04-17T06:44:17Z","checksum":"d48fc41d39892e7fa0d44cb352dd46aa","success":1}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (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.","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.","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","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.","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","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129."},"publication":"Advanced Intelligent Systems","article_type":"original","date_published":"2023-01-01T00:00:00Z"},{"month":"03","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","isi":1,"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":{"pmid":["36964141"],"isi":["000959887700008"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37054-2","article_number":"1643","file_date_updated":"2023-04-11T06:27:00Z","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"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.","year":"2023","pmid":1,"date_updated":"2023-08-01T14:05:30Z","date_created":"2023-04-09T22:01:00Z","volume":14,"author":[{"full_name":"Brandstätter, Tom","last_name":"Brandstätter","first_name":"Tom"},{"full_name":"Brückner, David","last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"first_name":"Yu Long","last_name":"Han","full_name":"Han, Yu Long"},{"last_name":"Alert","first_name":"Ricard","full_name":"Alert, Ricard"},{"full_name":"Guo, Ming","first_name":"Ming","last_name":"Guo"},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."}],"scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Nature Communications","citation":{"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","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.","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","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.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","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.","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."},"date_published":"2023-03-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","title":"Curvature induces active velocity waves in rotating spherical tissues","ddc":["570"],"intvolume":" 14","_id":"12818","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"12821","relation":"main_file","date_updated":"2023-04-11T06:27:00Z","date_created":"2023-04-11T06:27:00Z","success":1,"checksum":"54f06f9eee11d43bab253f3492c983ba","file_name":"2023_NatureComm_Brandstaetter.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4146777}]},{"month":"03","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"external_id":{"isi":["000957799000006"],"arxiv":["2209.05165"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.L031701","article_number":"L031701","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"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.","date_updated":"2023-08-01T14:06:05Z","date_created":"2023-04-09T22:01:00Z","volume":107,"author":[{"full_name":"Sokolova, Alesya","first_name":"Alesya","last_name":"Sokolova","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","orcid":"0000-0002-8308-4144"},{"full_name":"Kalacheva, D. A.","last_name":"Kalacheva","first_name":"D. A."},{"full_name":"Fedorov, G. P.","last_name":"Fedorov","first_name":"G. P."},{"first_name":"O. V.","last_name":"Astafiev","full_name":"Astafiev, O. V."}],"scopus_import":"1","day":"22","article_processing_charge":"No","article_type":"letter_note","publication":"Physical Review A","citation":{"short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","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.","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","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.","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."},"date_published":"2023-03-22T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","status":"public","title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12819","oa_version":"Preprint"},{"file_date_updated":"2023-04-25T09:13:53Z","ec_funded":1,"article_number":"2086","author":[{"last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura"},{"full_name":"Ekbatani, Farbod","first_name":"Farbod","last_name":"Ekbatani"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-01T14:15:57Z","date_created":"2023-04-23T22:01:03Z","volume":14,"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,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"month":"04","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-37817-x","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":["001003644100020"],"pmid":["37045828"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"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":[{"access_level":"open_access","file_name":"2023_NatureComm_Schmid.pdf","creator":"dernst","file_size":1786475,"content_type":"application/pdf","file_id":"12868","relation":"main_file","success":1,"checksum":"a4b3b7b36fbef068cabf4fb99501fef6","date_updated":"2023-04-25T09:13:53Z","date_created":"2023-04-25T09:13:53Z"}],"oa_version":"Published Version","_id":"12861","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","ddc":["000"],"intvolume":" 14","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-12T00:00:00Z","publication":"Nature Communications","citation":{"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).","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","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","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.","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"},"article_type":"original"},{"file":[{"relation":"main_file","file_id":"12867","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","success":1,"date_updated":"2023-04-25T08:59:18Z","date_created":"2023-04-25T08:59:18Z","access_level":"open_access","file_name":"2023_PLoSCompBio_Safavi.pdf","content_type":"application/pdf","file_size":4737671,"creator":"dernst"}],"oa_version":"Published Version","_id":"12862","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 19","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","status":"public","ddc":["570"],"issue":"4","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2023-04-01T00:00:00Z","citation":{"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.","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","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.","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","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.","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.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023)."},"publication":"PLoS Computational Biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"author":[{"last_name":"Safavi","first_name":"Shervin","full_name":"Safavi, Shervin"},{"full_name":"Panagiotaropoulos, Theofanis I.","last_name":"Panagiotaropoulos","first_name":"Theofanis I."},{"full_name":"Kapoor, Vishal","first_name":"Vishal","last_name":"Kapoor"},{"first_name":"Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","full_name":"Ramirez Villegas, Juan F"},{"full_name":"Logothetis, Nikos K.","first_name":"Nikos K.","last_name":"Logothetis"},{"full_name":"Besserve, Michel","first_name":"Michel","last_name":"Besserve"}],"volume":19,"date_created":"2023-04-23T22:01:03Z","date_updated":"2023-08-01T14:15:16Z","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. ","year":"2023","publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"publication_status":"published","file_date_updated":"2023-04-25T08:59:18Z","article_number":"e1010983","doi":"10.1371/journal.pcbi.1010983","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":["000962668700002"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1553-7358"]},"month":"04"},{"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-04-10T00:00:00Z","article_type":"original","publication":"Chemical Science","citation":{"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","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","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.","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)."},"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","file":[{"relation":"main_file","file_id":"12883","date_updated":"2023-05-02T07:17:05Z","date_created":"2023-05-02T07:17:05Z","checksum":"5eeec69a51e192dcd94b955d84423836","success":1,"file_name":"2023_ChemialScience_Chen.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1515446,"creator":"dernst"}],"oa_version":"Published Version","title":"Physics-inspired machine learning of localized intensive properties","status":"public","ddc":["000","540"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12879","month":"04","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"language":[{"iso":"eng"}],"doi":"10.1039/d3sc00841j","isi":1,"quality_controlled":"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"},"oa":1,"external_id":{"isi":["000971508100001"]},"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":[{"last_name":"Chen","first_name":"Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","full_name":"Chen, Ke"},{"full_name":"Kunkel, Christian","last_name":"Kunkel","first_name":"Christian"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing"},{"full_name":"Reuter, Karsten","last_name":"Reuter","first_name":"Karsten"},{"last_name":"Margraf","first_name":"Johannes T.","full_name":"Margraf, Johannes T."}],"publication_status":"published","publisher":"Royal Society of Chemistry","department":[{"_id":"BiCh"}],"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"},{"day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-03T00:00:00Z","article_type":"original","publication":"Bioinformatics","citation":{"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.","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.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (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.","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.","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"},"abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"12886","relation":"main_file","date_created":"2023-05-02T07:39:04Z","date_updated":"2023-05-02T07:39:04Z","success":1,"checksum":"2cb90ddf781baefddf47eac4b54e2a03","file_name":"2023_Bioinformatics_Benes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":478740}],"ddc":["000"],"status":"public","title":"Boolean network sketches: A unifying framework for logical model inference","intvolume":" 39","_id":"12876","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","publication_identifier":{"eissn":["1367-4811"]},"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btad158","isi":1,"quality_controlled":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"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":["000976610800001"],"pmid":["37004199"]},"oa":1,"file_date_updated":"2023-05-02T07:39:04Z","ec_funded":1,"article_number":"btad158","date_updated":"2023-08-01T14:27:28Z","date_created":"2023-04-30T22:01:05Z","volume":39,"author":[{"last_name":"Beneš","first_name":"Nikola","full_name":"Beneš, Nikola"},{"last_name":"Brim","first_name":"Luboš","full_name":"Brim, Luboš"},{"first_name":"Ondřej","last_name":"Huvar","full_name":"Huvar, Ondřej"},{"full_name":"Pastva, Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","last_name":"Pastva"},{"last_name":"Šafránek","first_name":"David","full_name":"Šafránek, David"}],"related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7688740"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Oxford Academic","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.].","pmid":1},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"1","_id":"12880","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","intvolume":" 14","file":[{"file_name":"2023_Nucleus_Kaneshiro.pdf","access_level":"open_access","file_size":3811113,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12884","date_created":"2023-05-02T07:24:55Z","date_updated":"2023-05-02T07:24:55Z","checksum":"8e707eda84f64dbad7f03545ae0a83ef","success":1}],"oa_version":"Published Version","scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","publication":"Nucleus","citation":{"ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","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","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.","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","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.","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)."},"article_type":"original","date_published":"2023-04-18T00:00:00Z","article_number":"2202548","file_date_updated":"2023-05-02T07:24:55Z","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.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"MaHe"}],"publisher":"Taylor & Francis","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"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"}],"date_created":"2023-04-30T22:01:06Z","date_updated":"2023-08-01T14:18:46Z","volume":14,"month":"04","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"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)"},"oa":1,"external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"isi":1,"quality_controlled":"1","doi":"10.1080/19491034.2023.2202548","language":[{"iso":"eng"}]},{"day":"20","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-20T00:00:00Z","article_type":"original","publication":"Physical Review A","citation":{"ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 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.","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","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","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.","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.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023)."},"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","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12914","month":"04","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.042216","isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2207.13130"],"isi":["000975799300006"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}],"ec_funded":1,"article_number":"042216","date_updated":"2023-08-01T14:33:21Z","date_created":"2023-05-07T22:01:03Z","volume":107,"author":[{"last_name":"Suzuki","first_name":"Fumika","orcid":"0000-0003-4982-5970","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","full_name":"Suzuki, Fumika"},{"full_name":"Unruh, William G.","first_name":"William G.","last_name":"Unruh"}],"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"},{"intvolume":" 14","ddc":["530"],"status":"public","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12913","file":[{"success":1,"checksum":"a778105665c10beb2354c92d2b295115","date_updated":"2023-05-08T07:26:40Z","date_created":"2023-05-08T07:26:40Z","file_id":"12917","relation":"main_file","creator":"dernst","file_size":1405588,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_NatureComm_DiezMerida.pdf"}],"oa_version":"Published Version","type":"journal_article","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."}],"article_type":"original","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","date_published":"2023-04-26T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","publisher":"Springer Nature","department":[{"_id":"AnHi"}],"publication_status":"published","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","volume":14,"date_created":"2023-05-07T22:01:03Z","date_updated":"2023-08-01T14:34:00Z","author":[{"last_name":"Díez-Mérida","first_name":"J.","full_name":"Díez-Mérida, J."},{"full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón","first_name":"A."},{"full_name":"Yang, S. Y.","first_name":"S. Y.","last_name":"Yang"},{"last_name":"Xie","first_name":"Y. M.","full_name":"Xie, Y. M."},{"last_name":"Gao","first_name":"X. J.","full_name":"Gao, X. J."},{"full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","first_name":"Jorden L"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"full_name":"Lu, X.","last_name":"Lu","first_name":"X."},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"},{"full_name":"Law, K. T.","first_name":"K. T.","last_name":"Law"},{"full_name":"Efetov, Dmitri K.","first_name":"Dmitri K.","last_name":"Efetov"}],"article_number":"2396","file_date_updated":"2023-05-08T07:26:40Z","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"},"oa":1,"external_id":{"pmid":["37100775"],"isi":["000979744000004"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-38005-7","publication_identifier":{"eissn":["2041-1723"]},"month":"04"},{"type":"journal_article","abstract":[{"lang":"eng","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."}],"_id":"10550","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 33","status":"public","title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","ddc":["510"],"file":[{"content_type":"application/pdf","file_size":742315,"creator":"dernst","file_name":"2023_JourNonlinearScience_Fellner.pdf","access_level":"open_access","date_updated":"2023-06-19T07:33:53Z","date_created":"2023-06-19T07:33:53Z","checksum":"f3f0f0886098e31c81116cff8183750b","success":1,"relation":"main_file","file_id":"13149"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"07","citation":{"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.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (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.","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.","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.","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"},"publication":"Journal of Nonlinear Science","article_type":"original","date_published":"2023-06-07T00:00:00Z","article_number":"66","file_date_updated":"2023-06-19T07:33:53Z","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","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"published","author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"first_name":"Michael","last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael"},{"first_name":"Bao Quoc","last_name":"Tang","full_name":"Tang, Bao Quoc"}],"volume":33,"date_updated":"2023-08-01T14:40:33Z","date_created":"2021-12-16T12:15:35Z","publication_identifier":{"eissn":["1432-1467"],"issn":["0938-8974"]},"month":"06","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":["2109.12019"],"isi":["001002343400002"]},"isi":1,"quality_controlled":"1","doi":"10.1007/s00332-023-09926-w","language":[{"iso":"eng"}]},{"day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-20T00:00:00Z","article_type":"original","page":"37-107","publication":"Interfaces and Free Boundaries","citation":{"ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS Press, pp. 37–107, 2023.","apa":"Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484","ista":"Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023. https://doi.org/10.4171/IFB/484."},"abstract":[{"text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_Interfaces_Hensel.pdf","access_level":"open_access","file_size":867876,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13045","date_updated":"2023-05-22T07:24:13Z","date_created":"2023-05-22T07:24:13Z","checksum":"622422484810441e48f613e968c7e7a4","success":1}],"ddc":["510"],"title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","status":"public","intvolume":" 25","_id":"13043","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"language":[{"iso":"eng"}],"doi":"10.4171/IFB/484","quality_controlled":"1","isi":1,"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020"}],"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":["2108.01733"],"isi":["000975817300002"]},"file_date_updated":"2023-05-22T07:24:13Z","ec_funded":1,"date_created":"2023-05-21T22:01:06Z","date_updated":"2023-08-01T14:43:29Z","volume":25,"author":[{"orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","last_name":"Hensel","first_name":"Sebastian","full_name":"Hensel, Sebastian"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10013"}]},"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"EMS Press","year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813."},{"month":"04","publication_identifier":{"eissn":["1089-7690"]},"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"},"oa":1,"external_id":{"arxiv":["2302.01297"],"isi":["001010676000010"],"pmid":["37093149"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0146711","article_number":"161101 ","file_date_updated":"2023-05-08T07:44:49Z","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"BiCh"}],"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.","year":"2023","pmid":1,"date_updated":"2023-08-01T14:34:49Z","date_created":"2023-05-07T22:01:03Z","volume":158,"author":[{"full_name":"Schmid, Rochus","last_name":"Schmid","first_name":"Rochus"},{"orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/mu-adsorption"},{"url":"https://github.com/BingqingCheng/S0","relation":"software"}]},"scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"The Journal of Chemical Physics","citation":{"mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:10.1063/5.0146711.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0146711.","ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","apa":"Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing, 2023."},"date_published":"2023-04-24T00:00:00Z","type":"journal_article","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"issue":"16","title":"Computing chemical potentials of adsorbed or confined fluids","ddc":["540"],"status":"public","intvolume":" 158","_id":"12912","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":6499468,"creator":"dernst","file_name":"2023_JourChemicalPhysics_Schmid.pdf","access_level":"open_access","date_updated":"2023-05-08T07:44:49Z","date_created":"2023-05-08T07:44:49Z","checksum":"4ab8c965f2fa4e17920bfa846847f137","success":1,"relation":"main_file","file_id":"12918"}],"oa_version":"Published Version"},{"keyword":["embroidery","design","directionality","density","image"],"day":"08","has_accepted_license":"1","article_processing_charge":"No","publication":"Computer Graphics Forum","citation":{"mla":"Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409.","chicago":"Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere, and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770 .","ama":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409. doi:10.1111/cgf.14770 ","ista":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409.","apa":"Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ","ieee":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2. Wiley, pp. 397–409, 2023."},"article_type":"original","page":"397-409","date_published":"2023-05-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths.","lang":"eng"}],"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12972","status":"public","title":"Directionality-aware design of embroidery patterns","ddc":["004"],"intvolume":" 42","file":[{"access_level":"open_access","file_name":"Zhenyuan2023.pdf","creator":"mpiovarc","file_size":24003702,"content_type":"application/pdf","file_id":"12974","relation":"main_file","success":1,"checksum":"4c188c2be4745467a8790bbf5d6491aa","date_updated":"2023-05-16T08:28:37Z","date_created":"2023-05-16T08:28:37Z"}],"oa_version":"Published Version","month":"05","publication_identifier":{"issn":["1467-8659"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["001000062600033"]},"isi":1,"quality_controlled":"1","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2023-05-12","start_date":"2023-05-08","location":"Saarbrucken, Germany","name":"EG: Eurographics"},"doi":"10.1111/cgf.14770 ","language":[{"iso":"eng"}],"file_date_updated":"2023-05-16T08:28:37Z","ec_funded":1,"year":"2023","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and Paola Mejia for proofreading; everyone in the visual computing group at ISTA for inspiring lunch and coffee breaks; Thibault Tricard for help producing the results of Phasor Noise.","publication_status":"published","publisher":"Wiley","department":[{"_id":"BeBi"}],"author":[{"full_name":"Liu, Zhenyuan","first_name":"Zhenyuan","last_name":"Liu","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","orcid":"0000-0001-9200-5690"},{"last_name":"Piovarci","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael"},{"first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"full_name":"Charrondiere, Raphael","last_name":"Charrondiere","first_name":"Raphael","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"}],"date_created":"2023-05-16T08:47:25Z","date_updated":"2023-08-01T14:47:05Z","volume":42},{"file_date_updated":"2023-05-22T07:57:37Z","article_number":"7959","related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"author":[{"full_name":"Zavadakova, Anna","first_name":"Anna","last_name":"Zavadakova"},{"last_name":"Vistejnova","first_name":"Lucie","full_name":"Vistejnova, Lucie"},{"first_name":"Tereza","last_name":"Belinova","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","full_name":"Belinova, Tereza"},{"last_name":"Tichanek","first_name":"Filip","full_name":"Tichanek, Filip"},{"last_name":"Bilikova","first_name":"Dagmar","full_name":"Bilikova, Dagmar"},{"full_name":"Mouton, Peter R.","first_name":"Peter R.","last_name":"Mouton"}],"volume":13,"date_created":"2023-05-19T11:12:25Z","date_updated":"2023-08-01T14:46:06Z","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","year":"2023","department":[{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"month":"05","doi":"10.1038/s41598-023-35162-z","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":["000995271600104"]},"isi":1,"quality_controlled":"1","issue":"1","abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3055077,"file_name":"2023_ScientificReports_Zavadakova.pdf","access_level":"open_access","date_updated":"2023-05-22T07:57:37Z","date_created":"2023-05-22T07:57:37Z","success":1,"checksum":"8c1b769693ff4288df8376e59ad1176d","file_id":"13047","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13033","intvolume":" 13","ddc":["570"],"status":"public","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","keyword":["Multidisciplinary"],"date_published":"2023-05-17T00:00:00Z","citation":{"chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z"},"publication":"Scientific Reports","article_type":"original"},{"department":[{"_id":"PaSc"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","volume":145,"date_updated":"2023-08-01T14:48:09Z","date_created":"2023-05-28T22:01:04Z","related_material":{"record":[{"id":"12820","status":"public","relation":"research_data"}]},"author":[{"full_name":"Troussicot, Laura","first_name":"Laura","last_name":"Troussicot","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3"},{"first_name":"Alicia","last_name":"Vallet","full_name":"Vallet, Alicia"},{"first_name":"Mikael","last_name":"Molin","full_name":"Molin, Mikael"},{"last_name":"Burmann","first_name":"Björn M.","full_name":"Burmann, Björn M."},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"file_date_updated":"2023-05-30T07:05:28Z","quality_controlled":"1","isi":1,"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":{"pmid":["37140345"],"isi":["000985907400001"]},"language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c01200","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"month":"05","intvolume":" 145","status":"public","title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","ddc":["540"],"_id":"13095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"13098","relation":"main_file","date_created":"2023-05-30T07:05:28Z","date_updated":"2023-05-30T07:05:28Z","success":1,"checksum":"0758a930ef21c62fc91b14e657479f83","file_name":"2023_JACS_Troussicot.pdf","access_level":"open_access","creator":"dernst","file_size":6719299,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"19","abstract":[{"lang":"eng","text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts."}],"page":"10700–10711","article_type":"original","citation":{"ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023.","ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200","chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.","mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711."},"publication":"Journal of the American Chemical Society","date_published":"2023-05-04T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"04"},{"date_updated":"2023-08-01T14:44:52Z","date_created":"2023-05-21T22:01:05Z","volume":30,"author":[{"full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos","first_name":"Michael"}],"publication_status":"published","department":[{"_id":"MaKw"}],"publisher":"Electronic Journal of Combinatorics","year":"2023","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","file_date_updated":"2023-05-22T07:43:19Z","article_number":"P2.21","language":[{"iso":"eng"}],"doi":"10.37236/11471","isi":1,"quality_controlled":"1","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":{"arxiv":["2105.13828"],"isi":["000988285500001"]},"month":"05","publication_identifier":{"eissn":["1077-8926"]},"file":[{"checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","success":1,"date_created":"2023-05-22T07:43:19Z","date_updated":"2023-05-22T07:43:19Z","relation":"main_file","file_id":"13046","content_type":"application/pdf","file_size":448736,"creator":"dernst","access_level":"open_access","file_name":"2023_JourCombinatorics_Anastos.pdf"}],"oa_version":"Published Version","status":"public","ddc":["510"],"title":"A note on long cycles in sparse random graphs","intvolume":" 30","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13042","abstract":[{"text":"Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2023-05-05T00:00:00Z","article_type":"original","publication":"Electronic Journal of Combinatorics","citation":{"short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","mla":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:10.37236/11471.","chicago":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471.","ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471","ieee":"M. Anastos, “A note on long cycles in sparse random graphs,” Electronic Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023.","apa":"Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471","ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21."},"day":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"status":"public","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","ddc":["570"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"PaSc"}],"year":"2023","_id":"12820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-01T14:48:08Z","date_created":"2023-04-10T05:55:56Z","file":[{"content_type":"application/zip","file_size":54184807,"creator":"pschanda","access_level":"open_access","file_name":"data_deposition.zip","checksum":"54a619605e44c871214fb0e07b05c6bf","success":1,"date_updated":"2023-04-14T09:39:33Z","date_created":"2023-04-14T09:39:33Z","relation":"main_file","file_id":"12823"},{"file_name":"README","access_level":"open_access","file_size":4978,"content_type":"application/octet-stream","creator":"pschanda","relation":"main_file","file_id":"12824","date_created":"2023-04-14T09:39:58Z","date_updated":"2023-04-14T09:39:58Z","checksum":"8dede9fc78399d13144eb05c62bf5750","success":1}],"oa_version":"Published Version","author":[{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"}],"contributor":[{"first_name":"Laura","last_name":"Troussicot","contributor_type":"researcher"},{"last_name":"Burmann","contributor_type":"researcher","first_name":"Björn M."}],"related_material":{"record":[{"id":"13095","relation":"used_in_publication","status":"public"}]},"type":"research_data","file_date_updated":"2023-04-14T09:39:58Z","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}],"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)"},"oa":1,"citation":{"ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820","chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.","short":"P. Schanda, (2023)."},"doi":"10.15479/AT:ISTA:12820","date_published":"2023-04-18T00:00:00Z","day":"18","month":"04","article_processing_charge":"No","has_accepted_license":"1"},{"file":[{"access_level":"open_access","file_name":"2023_ACSAppliedMaterials_Nan.pdf","file_size":5640829,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13099","checksum":"23893be46763c4c78daacddd019de821","success":1,"date_created":"2023-05-30T07:38:44Z","date_updated":"2023-05-30T07:38:44Z"}],"oa_version":"Published Version","ddc":["540"],"status":"public","title":"Bottom-up synthesis of SnTe-based thermoelectric composites","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13092","abstract":[{"lang":"eng","text":"There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe."}],"issue":"19","type":"journal_article","date_published":"2023-05-04T00:00:00Z","article_type":"original","page":"23380–23389","publication":"ACS Applied Materials and Interfaces","citation":{"ieee":"B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,” ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023.","apa":"Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625","ista":"Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389.","ama":"Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389. doi:10.1021/acsami.3c00625","chicago":"Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625.","short":"B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.","mla":"Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625."},"day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-01T14:50:09Z","date_created":"2023-05-28T22:01:03Z","volume":15,"author":[{"last_name":"Nan","first_name":"Bingfei","full_name":"Nan, Bingfei"},{"last_name":"Song","first_name":"Xuan","full_name":"Song, Xuan"},{"full_name":"Chang, Cheng","first_name":"Cheng","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"last_name":"Lim","first_name":"Khak Ho","full_name":"Lim, Khak Ho"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"publication_status":"published","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","year":"2023","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria.","pmid":1,"file_date_updated":"2023-05-30T07:38:44Z","language":[{"iso":"eng"}],"doi":"10.1021/acsami.3c00625","quality_controlled":"1","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"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":["37141543"],"isi":["000985497900001"]},"oa":1,"month":"05","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]}},{"year":"2023","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","pmid":1,"publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"American Chemical Society","author":[{"full_name":"Azadbakht, Ali","first_name":"Ali","last_name":"Azadbakht"},{"full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"full_name":"Varkevisser, Thijs","first_name":"Thijs","last_name":"Varkevisser"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Kraft, Daniela J.","first_name":"Daniela J.","last_name":"Kraft"}],"date_created":"2023-05-28T22:01:03Z","date_updated":"2023-08-01T14:51:25Z","volume":23,"file_date_updated":"2023-05-30T07:55:31Z","ec_funded":1,"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":["000985481400001"],"pmid":["37141427"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"doi":"10.1021/acs.nanolett.3c00375","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"_id":"13094","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["540"],"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","intvolume":" 23","file":[{"file_id":"13100","relation":"main_file","date_updated":"2023-05-30T07:55:31Z","date_created":"2023-05-30T07:55:31Z","success":1,"checksum":"9734d4c617bab3578ef62916b764547a","file_name":"2023_NanoLetters_Azadbakht.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3654910}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"issue":"10","publication":"Nano Letters","citation":{"chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375"},"article_type":"letter_note","page":"4267–4273","date_published":"2023-05-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No"},{"department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","publication_status":"epub_ahead","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). B.N., M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457 and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/. ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges support from the National Natural Science Foundation of China (22208293). This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.","year":"2023","date_created":"2023-05-28T22:01:03Z","date_updated":"2023-08-01T14:50:48Z","author":[{"full_name":"Nan, Bingfei","first_name":"Bingfei","last_name":"Nan"},{"last_name":"Li","first_name":"Mengyao","full_name":"Li, Mengyao"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","first_name":"Cheng"},{"last_name":"Han","first_name":"Xu","full_name":"Han, Xu"},{"full_name":"Zuo, Yong","first_name":"Yong","last_name":"Zuo"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"},{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000986859000001"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1021/acsaelm.3c00055","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1021/acsaelm.3c00055","publication_identifier":{"eissn":["2637-6113"]},"month":"05","status":"public","title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13093","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated."}],"article_type":"original","citation":{"ama":"Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055","ista":"Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials.","apa":"Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023). Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. American Chemical Society. https://doi.org/10.1021/acsaelm.3c00055","ieee":"B. Nan et al., “Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature,” ACS Applied Electronic Materials. American Chemical Society, 2023.","mla":"Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055.","short":"B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J. Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials (2023).","chicago":"Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang, Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055."},"publication":"ACS Applied Electronic Materials","date_published":"2023-05-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"05"},{"date_published":"2023-04-12T00:00:00Z","publication":"Algebra and Number Theory","citation":{"ama":"Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719","ista":"Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 17(3), 719–748.","ieee":"T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical Sciences Publishers, pp. 719–748, 2023.","apa":"Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.","short":"T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719."},"article_type":"original","page":"719-748","day":"12","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1430719,"access_level":"open_access","file_name":"2023_AlgebraNumberTheory_Browning.pdf","success":1,"checksum":"5d5d67b235905650e33cf7065d7583b4","date_updated":"2023-05-30T08:05:22Z","date_created":"2023-05-30T08:05:22Z","file_id":"13101","relation":"main_file"}],"_id":"13091","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Free rational curves on low degree hypersurfaces and the circle method","status":"public","ddc":["510"],"intvolume":" 17","abstract":[{"lang":"eng","text":"We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle."}],"issue":"3","type":"journal_article","doi":"10.2140/ant.2023.17.719","language":[{"iso":"eng"}],"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":["000996014700004"],"arxiv":["1810.06882"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"EP-P026710-2","_id":"26A8D266-B435-11E9-9278-68D0E5697425","name":"Between rational and integral points"}],"month":"04","publication_identifier":{"eissn":["1944-7833"],"issn":["1937-0652"]},"author":[{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"date_updated":"2023-08-01T14:51:57Z","date_created":"2023-05-28T22:01:02Z","volume":17,"year":"2023","acknowledgement":"The authors are grateful to Paul Nelson, Per Salberger and Jason Starr for useful comments. While working on this paper the first author was supported by EPRSC grant EP/P026710/1. The research was partially conducted during the period the second author served as a Clay Research Fellow, and partially conducted during the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zurich Foundation.","publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Mathematical Sciences Publishers","file_date_updated":"2023-05-30T08:05:22Z"},{"ec_funded":1,"file_date_updated":"2023-06-06T07:31:20Z","article_number":"2998","related_material":{"record":[{"relation":"research_data","status":"public","id":"13124"}]},"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V.","last_name":"Poshakinskiy"},{"full_name":"Sett, Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","first_name":"Riya","last_name":"Sett"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"volume":14,"date_updated":"2023-08-02T06:10:26Z","date_created":"2023-06-04T22:01:02Z","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","year":"2023","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"month":"05","doi":"10.1038/s41467-023-38761-6","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"isi":["001001099700002"],"arxiv":["2205.03293"]},"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,"project":[{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"quality_controlled":"1","isi":1,"abstract":[{"text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2023-06-06T07:31:20Z","date_updated":"2023-06-06T07:31:20Z","success":1,"checksum":"a857df40f0882859c48a1ff1e2001ec2","file_id":"13123","relation":"main_file","creator":"dernst","file_size":1654389,"content_type":"application/pdf","file_name":"2023_NaturePhysics_Redchenko.pdf","access_level":"open_access"}],"_id":"13117","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","ddc":["530"],"article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","date_published":"2023-05-24T00:00:00Z","citation":{"mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023."},"publication":"Nature Communications","article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1126/science.adg3812","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"call_identifier":"FWF","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105"},{"name":"Quantum readout techniques and technologies","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"oa":1,"external_id":{"isi":["000996515200004"],"arxiv":["2301.03315"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.03315","open_access":"1"}],"month":"05","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"date_updated":"2023-08-02T06:08:57Z","date_created":"2023-05-31T11:39:24Z","volume":380,"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu"},{"orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu","full_name":"Qiu, Liu"},{"last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"full_name":"Minoguchi, Y.","first_name":"Y.","last_name":"Minoguchi"},{"first_name":"P.","last_name":"Rabl","full_name":"Rabl, P."},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"relation":"research_data","status":"public","id":"13122"}]},"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Association for the Advancement of Science","acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","year":"2023","ec_funded":1,"date_published":"2023-05-18T00:00:00Z","article_type":"original","page":"718-721","publication":"Science","citation":{"ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves with light. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812","ieee":"R. Sahu et al., “Entangling microwaves with light,” Science, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science. 2023;380(6646):718-721. doi:10.1126/science.adg3812","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.","mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:10.1126/science.adg3812.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721."},"day":"18","article_processing_charge":"No","keyword":["Multidisciplinary"],"oa_version":"Preprint","status":"public","title":"Entangling microwaves with light","intvolume":" 380","_id":"13106","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification."}],"issue":"6646","type":"journal_article"},{"type":"journal_article","abstract":[{"text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13129","title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","status":"public","ddc":["510"],"oa_version":"Published Version","scopus_import":"1","day":"30","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Foundations of Computational Mathematics","citation":{"mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y","ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.","apa":"Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” Foundations of Computational Mathematics. Springer Nature, 2023."},"article_type":"original","date_published":"2023-05-30T00:00:00Z","year":"2023","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"author":[{"first_name":"Nicolas","last_name":"Clozeau","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas"},{"first_name":"Marc","last_name":"Josien","full_name":"Josien, Marc"},{"full_name":"Otto, Felix","first_name":"Felix","last_name":"Otto"},{"full_name":"Xu, Qiang","last_name":"Xu","first_name":"Qiang"}],"date_created":"2023-06-11T22:00:40Z","date_updated":"2023-08-02T06:12:39Z","month":"05","publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"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":["000999623100001"]},"main_file_link":[{"url":"https://doi.org/10.1007/s10208-023-09613-y","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s10208-023-09613-y","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request."}],"type":"research_data_reference","date_created":"2023-06-06T07:36:50Z","date_updated":"2023-08-02T06:10:25Z","oa_version":"Published Version","author":[{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"last_name":"Poshakinskiy","first_name":"Alexander","full_name":"Poshakinskiy, Alexander"},{"last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin"},{"first_name":"Alexander","last_name":"Poddubny","full_name":"Poddubny, Alexander"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"related_material":{"record":[{"id":"13117","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Tunable directional photon scattering from a pair of superconducting qubits","ddc":["530"],"publisher":"Zenodo","department":[{"_id":"JoFi"}],"_id":"13124","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","month":"04","day":"28","article_processing_charge":"No","date_published":"2023-04-28T00:00:00Z","doi":"10.5281/ZENODO.7858567","citation":{"chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567.","mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567"},"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":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}]},{"day":"31","month":"03","article_processing_charge":"No","doi":"10.5281/ZENODO.7789417","date_published":"2023-03-31T00:00:00Z","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"},"citation":{"apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.","short":"R. Sahu, (2023).","mla":"Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417."},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"oa":1,"abstract":[{"lang":"eng","text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1"}],"type":"research_data_reference","author":[{"orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh","full_name":"Sahu, Rishabh"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13106"}]},"date_updated":"2023-08-02T06:08:56Z","date_created":"2023-06-06T06:46:16Z","oa_version":"Published Version","_id":"13122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","status":"public","title":"Entangling microwaves with light","publisher":"Zenodo","department":[{"_id":"JoFi"}]},{"date_published":"2023-06-09T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8"},"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"date_updated":"2023-06-26T09:58:53Z","date_created":"2023-06-26T09:58:53Z","success":1,"checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","file_id":"13170","relation":"main_file","creator":"dernst","file_size":4844149,"content_type":"application/pdf","file_name":"2023_ScientificReports_Vetrova.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["570"],"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","status":"public","intvolume":" 13","_id":"13166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41598-023-35979-8","quality_controlled":"1","isi":1,"external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"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,"month":"06","publication_identifier":{"eissn":["2045-2322"]},"date_updated":"2023-08-02T06:17:18Z","date_created":"2023-06-25T22:00:46Z","volume":13,"author":[{"first_name":"Alexandra A.","last_name":"Vetrova","full_name":"Vetrova, Alexandra A."},{"full_name":"Kupaeva, Daria M.","first_name":"Daria M.","last_name":"Kupaeva"},{"full_name":"Kizenko, Alena","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","last_name":"Kizenko","first_name":"Alena"},{"full_name":"Lebedeva, Tatiana S.","last_name":"Lebedeva","first_name":"Tatiana S."},{"full_name":"Walentek, Peter","last_name":"Walentek","first_name":"Peter"},{"last_name":"Tsikolia","first_name":"Nikoloz","full_name":"Tsikolia, Nikoloz"},{"full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov","first_name":"Stanislav V."}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"}],"year":"2023","acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","pmid":1,"file_date_updated":"2023-06-26T09:58:53Z","article_number":"9382"},{"article_number":"184312","author":[{"full_name":"Orlov, Pavel","last_name":"Orlov","first_name":"Pavel"},{"full_name":"Tiutiakina, Anastasiia","first_name":"Anastasiia","last_name":"Tiutiakina"},{"last_name":"Sharipov","first_name":"Rustem","full_name":"Sharipov, Rustem"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","first_name":"Elena","full_name":"Petrova, Elena"},{"full_name":"Gritsev, Vladimir","last_name":"Gritsev","first_name":"Vladimir"},{"first_name":"Denis V.","last_name":"Kurlov","full_name":"Kurlov, Denis V."}],"volume":107,"date_updated":"2023-08-02T06:16:02Z","date_created":"2023-06-18T22:00:46Z","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","year":"2023","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"05","doi":"10.1103/PhysRevB.107.184312","language":[{"iso":"eng"}],"external_id":{"arxiv":["2303.00729"],"isi":["001003686900004"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"oa":1,"quality_controlled":"1","isi":1,"issue":"18","abstract":[{"lang":"eng","text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain."}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13138","intvolume":" 107","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","citation":{"ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023)."},"publication":"Physical Review B","article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1093/plphys/kiad207","isi":1,"quality_controlled":"1","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":{"pmid":["37010107"],"isi":["000971795800001"]},"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"07","volume":192,"date_created":"2023-07-12T07:32:58Z","date_updated":"2023-08-02T06:27:55Z","author":[{"last_name":"Chen","first_name":"C","full_name":"Chen, C"},{"full_name":"Zhang, Y","first_name":"Y","last_name":"Zhang"},{"full_name":"Cai, J","first_name":"J","last_name":"Cai"},{"first_name":"Y","last_name":"Qiu","full_name":"Qiu, Y"},{"last_name":"Li","first_name":"L","full_name":"Li, L"},{"first_name":"C","last_name":"Gao","full_name":"Gao, C"},{"last_name":"Gao","first_name":"Y","full_name":"Gao, Y"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"last_name":"Wu","first_name":"S","full_name":"Wu, S"},{"full_name":"Wei, C","last_name":"Wei","first_name":"C"},{"full_name":"Chen, J","last_name":"Chen","first_name":"J"},{"last_name":"Xu","first_name":"T","full_name":"Xu, T"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Wang, J","first_name":"J","last_name":"Wang"},{"last_name":"Li","first_name":"R","full_name":"Li, R"},{"full_name":"Chao, D","last_name":"Chao","first_name":"D"},{"full_name":"Zhang, B","first_name":"B","last_name":"Zhang"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"},{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"}],"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","year":"2023","file_date_updated":"2023-07-13T13:26:33Z","date_published":"2023-07-01T00:00:00Z","page":"2243-2260","article_type":"original","citation":{"ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207","apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207","ieee":"C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.","chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207."},"publication":"Plant Physiology","article_processing_charge":"No","has_accepted_license":"1","day":"01","oa_version":"Published Version","file":[{"success":1,"checksum":"5492e1d18ac3eaf202633d210fa0fb75","date_updated":"2023-07-13T13:26:33Z","date_created":"2023-07-13T13:26:33Z","file_id":"13220","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":2076977,"access_level":"open_access","file_name":"2023_PlantPhys_Chen.pdf"}],"intvolume":" 192","status":"public","title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","ddc":["575"],"_id":"13213","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","abstract":[{"lang":"eng","text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth."}],"type":"journal_article"},{"file_date_updated":"2023-07-31T07:16:34Z","article_number":"1049255","date_created":"2023-02-02T08:13:28Z","date_updated":"2023-08-02T06:25:04Z","volume":14,"author":[{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Bruneaux","first_name":"L","full_name":"Bruneaux, L"},{"first_name":"P","last_name":"Oikonomou","full_name":"Oikonomou, P"},{"full_name":"Aldana, M","first_name":"M","last_name":"Aldana"},{"first_name":"P","last_name":"Cluzel","full_name":"Cluzel, P"}],"publication_status":"published","publisher":"Frontiers","department":[{"_id":"CaGu"}],"acknowledgement":"This work was supported by NIH P50 award P50GM081892-02 to the University of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.","year":"2023","pmid":1,"month":"06","publication_identifier":{"eissn":["1664-302X"]},"language":[{"iso":"eng"}],"doi":"10.3389/fmicb.2023.1049255","quality_controlled":"1","isi":1,"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":{"pmid":["37485524"],"isi":["001030002600001"]},"abstract":[{"lang":"eng","text":"In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype."}],"type":"journal_article","file":[{"file_name":"2023_FrontiersMicrobiology_Guet.pdf","access_level":"open_access","creator":"dernst","file_size":6452841,"content_type":"application/pdf","file_id":"13322","relation":"main_file","date_updated":"2023-07-31T07:16:34Z","date_created":"2023-07-31T07:16:34Z","success":1,"checksum":"7dd322347512afaa5daf72a0154f2f07"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression","intvolume":" 14","_id":"12478","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2023-06-20T00:00:00Z","article_type":"original","publication":"Frontiers in Microbiology","citation":{"short":"C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in Microbiology 14 (2023).","mla":"Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology, vol. 14, 1049255, Frontiers, 2023, doi:10.3389/fmicb.2023.1049255.","chicago":"Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of Mar Operon Expression.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1049255.","ama":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1049255","apa":"Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., & Cluzel, P. (2023). Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1049255","ieee":"C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","ista":"Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression. Frontiers in Microbiology. 14, 1049255."}},{"type":"journal_article","abstract":[{"text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation.","lang":"eng"}],"issue":"6","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","status":"public","ddc":["570"],"intvolume":" 21","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13229","oa_version":"Published Version","file":[{"date_updated":"2023-07-18T07:59:58Z","date_created":"2023-07-18T07:59:58Z","success":1,"checksum":"8e88cb0e5a6433a2f1939a9030bed384","file_id":"13246","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4431723,"file_name":"2023_PloSBiology_Shamipour.pdf","access_level":"open_access"}],"scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"e3002146","publication":"PLoS Biology","citation":{"ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146.","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146."},"date_published":"2023-06-08T00:00:00Z","file_date_updated":"2023-07-18T07:59:58Z","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Public Library of Science","year":"2023","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","pmid":1,"date_updated":"2023-08-02T06:33:14Z","date_created":"2023-07-16T22:01:09Z","volume":21,"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"full_name":"Hofmann, Laura","last_name":"Hofmann","first_name":"Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"first_name":"Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","full_name":"Steccari, Irene"},{"last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"month":"06","publication_identifier":{"eissn":["1545-7885"]},"isi":1,"quality_controlled":"1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"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":["37289834"],"isi":["001003199100005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3002146"},{"article_number":"065601","ec_funded":1,"file_date_updated":"2023-07-07T12:49:51Z","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"publication_status":"published","acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","year":"2023","volume":7,"date_created":"2023-07-07T12:48:01Z","date_updated":"2023-08-02T06:34:47Z","author":[{"first_name":"Galien M","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X","full_name":"Grosjean, Galien M"},{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"}],"publication_identifier":{"issn":["2475-9953"]},"month":"06","project":[{"name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020","grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["2304.12861"],"isi":["001019565900002"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevmaterials.7.065601","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally."}],"intvolume":" 7","title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","ddc":["537"],"status":"public","_id":"13197","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"13198","checksum":"75584730d9cdd50eeccb4c52c509776d","success":1,"date_updated":"2023-07-07T12:49:51Z","date_created":"2023-07-07T12:49:51Z","access_level":"open_access","file_name":"Mosaic_asymmetries.pdf","content_type":"application/pdf","file_size":1127040,"creator":"ggrosjea"}],"oa_version":"Submitted Version","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"has_accepted_license":"1","article_processing_charge":"No","day":"13","article_type":"original","citation":{"short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601.","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601.","ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601."},"publication":"Physical Review Materials","date_published":"2023-06-13T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08","citation":{"ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104.","short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023)."},"publication":"PLoS Computational Biology","article_type":"original","date_published":"2023-06-08T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13230","intvolume":" 19","title":"Environmental dynamics shape perceptual decision bias","ddc":["570"],"status":"public","file":[{"access_level":"open_access","file_name":"2023_PloSCompBio_Charlton.pdf","creator":"dernst","content_type":"application/pdf","file_size":2281868,"file_id":"13247","relation":"main_file","success":1,"checksum":"800761fa2c647fabd6ad034589bc526e","date_created":"2023-07-18T08:07:59Z","date_updated":"2023-07-18T08:07:59Z"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1553-7358"]},"month":"06","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":{"pmid":["37289753"],"isi":["001003410200003"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1011104","language":[{"iso":"eng"}],"article_number":"e1011104","file_date_updated":"2023-07-18T08:07:59Z","pmid":1,"acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","year":"2023","department":[{"_id":"MaJö"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"first_name":"Julie A.","last_name":"Charlton","full_name":"Charlton, Julie A."},{"full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bai, Yoon H.","first_name":"Yoon H.","last_name":"Bai"},{"last_name":"Hermundstad","first_name":"Ann M.","full_name":"Hermundstad, Ann M."},{"first_name":"Robbe L.T.","last_name":"Goris","full_name":"Goris, Robbe L.T."}],"volume":19,"date_created":"2023-07-16T22:01:09Z","date_updated":"2023-08-02T06:33:50Z"},{"abstract":[{"lang":"eng","text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study."}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"13244","date_updated":"2023-07-18T07:25:43Z","date_created":"2023-07-18T07:25:43Z","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","success":1,"file_name":"2023_Vaccines_Dormeshkin.pdf","access_level":"open_access","file_size":2339746,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","status":"public","ddc":["570"],"intvolume":" 11","_id":"13232","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-06-01T00:00:00Z","article_type":"original","publication":"Vaccines","citation":{"chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014"},"file_date_updated":"2023-07-18T07:25:43Z","article_number":"1014","date_updated":"2023-08-02T06:31:19Z","date_created":"2023-07-16T22:01:10Z","volume":11,"author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"first_name":"Mikalai","last_name":"Katsin","full_name":"Katsin, Mikalai"},{"full_name":"Stegantseva, Maria","first_name":"Maria","last_name":"Stegantseva"},{"full_name":"Golenchenko, Sergey","last_name":"Golenchenko","first_name":"Sergey"},{"full_name":"Shapira, Michail","first_name":"Michail","last_name":"Shapira"},{"last_name":"Dubovik","first_name":"Simon","full_name":"Dubovik, Simon"},{"full_name":"Lutskovich, Dzmitry","last_name":"Lutskovich","first_name":"Dzmitry"},{"last_name":"Kavaleuski","first_name":"Anton","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton"},{"full_name":"Meleshko, Alexander","first_name":"Alexander","last_name":"Meleshko"}],"publication_status":"published","publisher":"MDPI","department":[{"_id":"LeSa"}],"year":"2023","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","month":"06","publication_identifier":{"eissn":["2076-393X"]},"language":[{"iso":"eng"}],"doi":"10.3390/vaccines11061014","quality_controlled":"1","isi":1,"external_id":{"isi":["001017740000001"]},"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","article_processing_charge":"No","day":"14","article_type":"original","citation":{"ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207","ieee":"M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023.","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207."},"publication":"Physical Review E","date_published":"2023-06-14T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles."}],"intvolume":" 107","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13231","oa_version":"Preprint","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"month":"06","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"external_id":{"isi":["001020265000002"],"arxiv":["2301.01545"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.065207","article_number":"065207","publisher":"American Physical Society","department":[{"_id":"BiCh"}],"publication_status":"published","year":"2023","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","volume":107,"date_updated":"2023-08-02T06:30:46Z","date_created":"2023-07-16T22:01:10Z","author":[{"last_name":"Schörner","first_name":"Maximilian","full_name":"Schörner, Maximilian"},{"full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen","first_name":"Mandy","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"},{"first_name":"Tilo","last_name":"Döppner","full_name":"Döppner, Tilo"},{"first_name":"Dominik","last_name":"Kraus","full_name":"Kraus, Dominik"},{"last_name":"Fletcher","first_name":"Luke B.","full_name":"Fletcher, Luke B."},{"full_name":"Glenzer, Siegfried H.","first_name":"Siegfried H.","last_name":"Glenzer"},{"first_name":"Ronald","last_name":"Redmer","full_name":"Redmer, Ronald"}]},{"date_published":"2023-06-20T00:00:00Z","article_type":"letter_note","publication":"Physical Review A","citation":{"chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304"},"day":"20","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Finite-range bias in fitting three-body loss to the zero-range model","status":"public","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13233","abstract":[{"text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters.","lang":"eng"}],"issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.L061304","quality_controlled":"1","isi":1,"project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["001019748000005"],"arxiv":["2302.01022"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2302.01022"}],"month":"06","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"date_updated":"2023-08-02T06:31:52Z","date_created":"2023-07-16T22:01:10Z","volume":107,"author":[{"id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","last_name":"Agafonova","first_name":"Sofya","full_name":"Agafonova, Sofya"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"year":"2023","acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","ec_funded":1,"article_number":"L061304"},{"date_created":"2023-07-23T22:01:10Z","date_updated":"2023-08-02T06:38:07Z","volume":6,"author":[{"full_name":"Goswami, Bidyut B","first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b"},{"last_name":"An","first_name":"Soon Il","full_name":"An, Soon Il"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaMu"}],"acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","year":"2023","file_date_updated":"2023-07-31T08:00:01Z","article_number":"82","language":[{"iso":"eng"}],"doi":"10.1038/s41612-023-00411-5","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":["001024920300002"]},"month":"07","publication_identifier":{"eissn":["2397-3722"]},"file":[{"file_id":"13326","relation":"main_file","success":1,"checksum":"e9967d436a83b8ffcc6f58782e1f7500","date_created":"2023-07-31T08:00:01Z","date_updated":"2023-07-31T08:00:01Z","access_level":"open_access","file_name":"2023_npjclimate_Goswami.pdf","creator":"dernst","file_size":1750712,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["550"],"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","status":"public","intvolume":" 6","_id":"13256","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate."}],"type":"journal_article","date_published":"2023-07-08T00:00:00Z","article_type":"original","publication":"npj Climate and Atmospheric Science","citation":{"ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5."},"day":"08","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1"},{"status":"public","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","ddc":["570"],"intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13260","file":[{"date_updated":"2023-08-01T06:58:34Z","date_created":"2023-08-01T06:58:34Z","checksum":"70de3c4878de6efe00dc56de2df8812f","success":1,"relation":"main_file","file_id":"13339","file_size":2382587,"content_type":"application/pdf","creator":"dernst","file_name":"2023_GBE_Barata.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"issue":"7","article_type":"original","publication":"Genome biology and evolution","citation":{"ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023.","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113."},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"BeVi"}],"year":"2023","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","pmid":1,"date_created":"2023-07-23T22:01:11Z","date_updated":"2023-08-02T06:42:35Z","volume":15,"author":[{"id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata","first_name":"Carolina","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"full_name":"Snook, Rhonda R.","last_name":"Snook","first_name":"Rhonda R."},{"full_name":"Ritchie, Michael G.","first_name":"Michael G.","last_name":"Ritchie"},{"last_name":"Kosiol","first_name":"Carolin","full_name":"Kosiol, Carolin"}],"related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"article_number":"evad113","file_date_updated":"2023-08-01T06:58:34Z","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"},"external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evad113","month":"07","publication_identifier":{"eissn":["1759-6653"]}},{"language":[{"iso":"eng"}],"date_published":"2023-07-06T00:00:00Z","doi":"10.48550/arXiv.2307.03237","publication":"arXiv","external_id":{"arxiv":["2307.03237"]},"oa":1,"citation":{"ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237","ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.","short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.).","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.","chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.03237"}],"month":"07","day":"06","article_processing_charge":"No","date_updated":"2023-08-02T07:36:00Z","date_created":"2023-08-02T07:30:43Z","oa_version":"Preprint","author":[{"last_name":"Huber","first_name":"Daniel","full_name":"Huber, Daniel"},{"first_name":"Marc","last_name":"Pinsonneault","full_name":"Pinsonneault, Marc"},{"full_name":"Beck, Paul","first_name":"Paul","last_name":"Beck"},{"full_name":"Bedding, Timothy R.","first_name":"Timothy R.","last_name":"Bedding"},{"full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn","first_name":"Joss Bland-Hawthorn","last_name":"Joss Bland-Hawthorn"},{"full_name":"Breton, Sylvain N.","last_name":"Breton","first_name":"Sylvain N."},{"first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000","full_name":"Bugnet, Lisa Annabelle"},{"full_name":"Chaplin, William J.","last_name":"Chaplin","first_name":"William J."},{"full_name":"Garcia, Rafael A.","first_name":"Rafael A.","last_name":"Garcia"},{"full_name":"Grunblatt, Samuel K.","last_name":"Grunblatt","first_name":"Samuel K."},{"full_name":"Guzik, Joyce A.","first_name":"Joyce A.","last_name":"Guzik"},{"first_name":"Saskia","last_name":"Hekker","full_name":"Hekker, Saskia"},{"full_name":"Kawaler, Steven D.","first_name":"Steven D.","last_name":"Kawaler"},{"full_name":"Mathis, Stephane","first_name":"Stephane","last_name":"Mathis"},{"last_name":"Mathur","first_name":"Savita","full_name":"Mathur, Savita"},{"first_name":"Travis","last_name":"Metcalfe","full_name":"Metcalfe, Travis"},{"last_name":"Mosser","first_name":"Benoit","full_name":"Mosser, Benoit"},{"full_name":"Ness, Melissa K.","first_name":"Melissa K.","last_name":"Ness"},{"first_name":"Anthony L.","last_name":"Piro","full_name":"Piro, Anthony L."},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"full_name":"Sharma, Sanjib","last_name":"Sharma","first_name":"Sanjib"},{"first_name":"David R.","last_name":"Soderblom","full_name":"Soderblom, David R."},{"full_name":"Stassun, Keivan G.","first_name":"Keivan G.","last_name":"Stassun"},{"full_name":"Stello, Dennis","last_name":"Stello","first_name":"Dennis"},{"last_name":"Tayar","first_name":"Jamie","full_name":"Tayar, Jamie"},{"full_name":"Belle, Gerard T. van","last_name":"Belle","first_name":"Gerard T. van"},{"full_name":"Zinn, Joel C.","last_name":"Zinn","first_name":"Joel C."}],"publication_status":"submitted","title":"Asteroseismology with the Roman galactic bulge time-domain survey","status":"public","department":[{"_id":"LiBu"}],"_id":"13447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","abstract":[{"text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing.","lang":"eng"}],"article_number":"2307.03237","type":"preprint"},{"year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"published","related_material":{"record":[{"id":"11458","relation":"part_of_dissertation","status":"public"},{"id":"13053","relation":"part_of_dissertation","status":"public"},{"id":"12299","relation":"part_of_dissertation","status":"public"}]},"author":[{"last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"}],"date_created":"2023-05-23T17:07:53Z","date_updated":"2023-08-04T10:33:27Z","ec_funded":1,"file_date_updated":"2023-05-24T16:12:59Z","oa":1,"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"doi":"10.15479/at:ista:13074","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"05","_id":"13074","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Efficiency and generalization of sparse neural networks","ddc":["000"],"oa_version":"Published Version","file":[{"date_created":"2023-05-24T16:11:16Z","date_updated":"2023-05-24T16:11:16Z","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"relation":"main_file","file_id":"13087","content_type":"application/pdf","file_size":2152072,"creator":"epeste","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","access_level":"open_access"},{"relation":"source_file","file_id":"13088","checksum":"8d0df94bbcf4db72c991f22503b3fd60","date_updated":"2023-05-24T16:12:59Z","date_created":"2023-05-24T16:12:59Z","access_level":"closed","file_name":"PhD_Thesis_APeste.zip","content_type":"application/zip","file_size":1658293,"creator":"epeste"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"citation":{"ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074."},"page":"147","date_published":"2023-05-23T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"23"}]