[{"intvolume":" 39","month":"04","scopus_import":"1","oa_version":"Published Version","pmid":1,"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."}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"issue":"4","volume":39,"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-02T07:39:04Z","file_size":478740,"date_created":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2cb90ddf781baefddf47eac4b54e2a03","file_id":"12886","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1367-4811"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"12876","file_date_updated":"2023-05-02T07:39:04Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-01T14:27:28Z","oa":1,"publisher":"Oxford Academic","quality_controlled":"1","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.].","date_created":"2023-04-30T22:01:05Z","date_published":"2023-04-03T00:00:00Z","doi":"10.1093/bioinformatics/btad158","publication":"Bioinformatics","day":"03","year":"2023","isi":1,"has_accepted_license":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_number":"btad158","title":"Boolean network sketches: A unifying framework for logical model inference","article_processing_charge":"No","external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"first_name":"Luboš","full_name":"Brim, Luboš","last_name":"Brim"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","full_name":"Pastva, Samuel"},{"last_name":"Šafránek","full_name":"Šafránek, David","first_name":"David"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","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.","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.","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."}},{"department":[{"_id":"MaHe"}],"file_date_updated":"2023-05-02T07:24:55Z","date_updated":"2023-08-01T14:18:46Z","ddc":["570"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","_id":"12880","volume":14,"issue":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"publication_status":"published","file":[{"file_id":"12884","checksum":"8e707eda84f64dbad7f03545ae0a83ef","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-02T07:24:55Z","file_name":"2023_Nucleus_Kaneshiro.pdf","date_updated":"2023-05-02T07:24:55Z","file_size":3811113,"creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 14","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."}],"oa_version":"Published Version","pmid":1,"author":[{"first_name":"Jeanae M.","last_name":"Kaneshiro","full_name":"Kaneshiro, Jeanae M."},{"first_name":"Juliana S.","last_name":"Capitanio","full_name":"Capitanio, Juliana S."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X","last_name":"Hetzer"}],"external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"article_processing_charge":"No","title":"Lamin B1 overexpression alters chromatin organization and gene expression","citation":{"mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","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","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","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.","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"2202548","date_published":"2023-04-18T00:00:00Z","doi":"10.1080/19491034.2023.2202548","date_created":"2023-04-30T22:01:06Z","isi":1,"has_accepted_license":"1","year":"2023","day":"18","publication":"Nucleus","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"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."},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"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.","doi":"10.1103/PhysRevA.107.042216","date_published":"2023-04-20T00:00:00Z","date_created":"2023-05-07T22:01:03Z","isi":1,"year":"2023","day":"20","publication":"Physical Review A","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"042216","author":[{"id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","first_name":"Fumika","full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970","last_name":"Suzuki"},{"full_name":"Unruh, William G.","last_name":"Unruh","first_name":"William G."}],"article_processing_charge":"No","external_id":{"arxiv":["2207.13130"],"isi":["000975799300006"]},"title":"Numerical quantum clock simulations for measuring tunneling times","citation":{"chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216.","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 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.","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.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.13130"}],"month":"04","intvolume":" 107","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","volume":107,"issue":"4","ec_funded":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"12914","department":[{"_id":"MiLe"}],"date_updated":"2023-08-01T14:33:21Z"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12913","department":[{"_id":"AnHi"}],"file_date_updated":"2023-05-08T07:26:40Z","ddc":["530"],"date_updated":"2023-08-01T14:34:00Z","intvolume":" 14","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","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."}],"volume":14,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-08T07:26:40Z","file_size":1405588,"date_created":"2023-05-08T07:26:40Z","file_name":"2023_NatureComm_DiezMerida.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a778105665c10beb2354c92d2b295115","file_id":"12917","success":1}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"article_number":"2396","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","article_processing_charge":"No","external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"author":[{"first_name":"J.","full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida"},{"first_name":"A.","full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón"},{"first_name":"S. Y.","full_name":"Yang, S. Y.","last_name":"Yang"},{"first_name":"Y. M.","full_name":"Xie, Y. M.","last_name":"Xie"},{"full_name":"Gao, X. J.","last_name":"Gao","first_name":"X. J."},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","full_name":"Senior, Jorden L"},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"last_name":"Lu","full_name":"Lu, X.","first_name":"X."},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"full_name":"Law, K. T.","last_name":"Law","first_name":"K. T."},{"first_name":"Dmitri K.","full_name":"Efetov, Dmitri K.","last_name":"Efetov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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.","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.","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.","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."},"oa":1,"quality_controlled":"1","publisher":"Springer Nature","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.","date_created":"2023-05-07T22:01:03Z","date_published":"2023-04-26T00:00:00Z","doi":"10.1038/s41467-023-38005-7","publication":"Nature Communications","day":"26","year":"2023","isi":1,"has_accepted_license":"1"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10550","file_date_updated":"2023-06-19T07:33:53Z","department":[{"_id":"JuFi"}],"date_updated":"2023-08-01T14:40:33Z","ddc":["510"],"scopus_import":"1","month":"06","intvolume":" 33","abstract":[{"text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.","lang":"eng"}],"oa_version":"Published Version","volume":33,"publication_identifier":{"eissn":["1432-1467"],"issn":["0938-8974"]},"publication_status":"published","file":[{"file_name":"2023_JourNonlinearScience_Fellner.pdf","date_created":"2023-06-19T07:33:53Z","creator":"dernst","file_size":742315,"date_updated":"2023-06-19T07:33:53Z","success":1,"checksum":"f3f0f0886098e31c81116cff8183750b","file_id":"13149","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"article_number":"66","author":[{"last_name":"Fellner","full_name":"Fellner, Klemens","first_name":"Klemens"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael","last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"},{"last_name":"Tang","full_name":"Tang, Bao Quoc","first_name":"Bao Quoc"}],"article_processing_charge":"No","external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","citation":{"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.","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.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Springer Nature","oa":1,"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.","date_published":"2023-06-07T00:00:00Z","doi":"10.1007/s00332-023-09926-w","date_created":"2021-12-16T12:15:35Z","isi":1,"has_accepted_license":"1","year":"2023","day":"07","publication":"Journal of Nonlinear Science"},{"publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"publication_status":"published","file":[{"date_created":"2023-05-22T07:24:13Z","file_name":"2023_Interfaces_Hensel.pdf","creator":"dernst","date_updated":"2023-05-22T07:24:13Z","file_size":867876,"file_id":"13045","checksum":"622422484810441e48f613e968c7e7a4","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"10013","relation":"earlier_version"}]},"volume":25,"issue":"1","ec_funded":1,"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"}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 25","date_updated":"2023-08-01T14:43:29Z","ddc":["510"],"department":[{"_id":"JuFi"}],"file_date_updated":"2023-05-22T07:24:13Z","_id":"13043","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","isi":1,"year":"2023","day":"20","publication":"Interfaces and Free Boundaries","page":"37-107","date_published":"2023-04-20T00:00:00Z","doi":"10.4171/IFB/484","date_created":"2023-05-21T22:01:06Z","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.","publisher":"EMS Press","quality_controlled":"1","oa":1,"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","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","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"external_id":{"arxiv":["2108.01733"],"isi":["000975817300002"]},"article_processing_charge":"No","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}]},{"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.","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","publication":"The Journal of Chemical Physics","day":"24","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-05-07T22:01:03Z","date_published":"2023-04-24T00:00:00Z","doi":"10.1063/5.0146711","article_number":"161101 ","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","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.","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.","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","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."},"title":"Computing chemical potentials of adsorbed or confined fluids","external_id":{"pmid":["37093149"],"isi":["001010676000010"],"arxiv":["2302.01297"]},"article_processing_charge":"No","author":[{"first_name":"Rochus","last_name":"Schmid","full_name":"Schmid, Rochus"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"pmid":1,"oa_version":"Published Version","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"}],"intvolume":" 158","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"4ab8c965f2fa4e17920bfa846847f137","file_id":"12918","creator":"dernst","file_size":6499468,"date_updated":"2023-05-08T07:44:49Z","file_name":"2023_JourChemicalPhysics_Schmid.pdf","date_created":"2023-05-08T07:44:49Z"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"]},"related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"issue":"16","volume":158,"_id":"12912","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["540"],"date_updated":"2023-08-01T14:34:49Z","department":[{"_id":"BiCh"}],"file_date_updated":"2023-05-08T07:44:49Z"},{"citation":{"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 ","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 ","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409.","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.","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 .","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.","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 ."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["001000062600033"]},"article_processing_charge":"No","author":[{"first_name":"Zhenyuan","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","last_name":"Liu","orcid":"0000-0001-9200-5690","full_name":"Liu, Zhenyuan"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","full_name":"Hafner, Christian"},{"first_name":"Raphael","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1","last_name":"Charrondiere","full_name":"Charrondiere, Raphael"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"title":"Directionality-aware design of embroidery patterns","project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"year":"2023","isi":1,"has_accepted_license":"1","publication":"Computer Graphics Forum","day":"08","page":"397-409","date_created":"2023-05-16T08:47:25Z","doi":"10.1111/cgf.14770 ","date_published":"2023-05-08T00:00:00Z","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.","oa":1,"publisher":"Wiley","quality_controlled":"1","date_updated":"2023-08-01T14:47:05Z","ddc":["004"],"department":[{"_id":"BeBi"}],"file_date_updated":"2023-05-16T08:28:37Z","_id":"12972","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"conference":{"name":"EG: Eurographics","end_date":"2023-05-12","location":"Saarbrucken, Germany","start_date":"2023-05-08"},"type":"journal_article","article_type":"original","keyword":["embroidery","design","directionality","density","image"],"status":"public","publication_status":"published","publication_identifier":{"issn":["1467-8659"]},"language":[{"iso":"eng"}],"file":[{"creator":"mpiovarc","date_updated":"2023-05-16T08:28:37Z","file_size":24003702,"date_created":"2023-05-16T08:28:37Z","file_name":"Zhenyuan2023.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4c188c2be4745467a8790bbf5d6491aa","file_id":"12974","success":1}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"volume":42,"issue":"2","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","intvolume":" 42","month":"05"},{"volume":13,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"issue":"1","publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","file":[{"file_size":3055077,"date_updated":"2023-05-22T07:57:37Z","creator":"dernst","file_name":"2023_ScientificReports_Zavadakova.pdf","date_created":"2023-05-22T07:57:37Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13047","checksum":"8c1b769693ff4288df8376e59ad1176d"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 13","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","department":[{"_id":"Bio"}],"file_date_updated":"2023-05-22T07:57:37Z","date_updated":"2023-08-01T14:46:06Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Multidisciplinary"],"_id":"13033","doi":"10.1038/s41598-023-35162-z","date_published":"2023-05-17T00:00:00Z","date_created":"2023-05-19T11:12:25Z","isi":1,"has_accepted_license":"1","year":"2023","day":"17","publication":"Scientific Reports","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","author":[{"last_name":"Zavadakova","full_name":"Zavadakova, Anna","first_name":"Anna"},{"first_name":"Lucie","last_name":"Vistejnova","full_name":"Vistejnova, Lucie"},{"id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","first_name":"Tereza","full_name":"Belinova, Tereza","last_name":"Belinova"},{"first_name":"Filip","full_name":"Tichanek, Filip","last_name":"Tichanek"},{"full_name":"Bilikova, Dagmar","last_name":"Bilikova","first_name":"Dagmar"},{"first_name":"Peter R.","last_name":"Mouton","full_name":"Mouton, Peter R."}],"external_id":{"isi":["000995271600104"]},"article_processing_charge":"No","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","citation":{"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","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","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.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"7959"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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","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.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711."},"title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","article_processing_charge":"No","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"author":[{"full_name":"Troussicot, Laura","last_name":"Troussicot","first_name":"Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3"},{"first_name":"Alicia","full_name":"Vallet, Alicia","last_name":"Vallet"},{"last_name":"Molin","full_name":"Molin, Mikael","first_name":"Mikael"},{"first_name":"Björn M.","last_name":"Burmann","full_name":"Burmann, Björn M."},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"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. ","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","publication":"Journal of the American Chemical Society","day":"04","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-05-28T22:01:04Z","date_published":"2023-05-04T00:00:00Z","doi":"10.1021/jacs.3c01200","page":"10700–10711","_id":"13095","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["540"],"date_updated":"2023-08-01T14:48:09Z","department":[{"_id":"PaSc"}],"file_date_updated":"2023-05-30T07:05:28Z","pmid":1,"oa_version":"Published Version","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."}],"intvolume":" 145","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"0758a930ef21c62fc91b14e657479f83","file_id":"13098","success":1,"creator":"dernst","date_updated":"2023-05-30T07:05:28Z","file_size":6719299,"date_created":"2023-05-30T07:05:28Z","file_name":"2023_JACS_Troussicot.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"related_material":{"record":[{"relation":"research_data","status":"public","id":"12820"}]},"volume":145,"issue":"19"},{"scopus_import":"1","intvolume":" 30","month":"05","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"}],"oa_version":"Published Version","issue":"2","volume":30,"publication_status":"published","publication_identifier":{"eissn":["1077-8926"]},"language":[{"iso":"eng"}],"file":[{"checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","file_id":"13046","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-22T07:43:19Z","file_name":"2023_JourCombinatorics_Anastos.pdf","creator":"dernst","date_updated":"2023-05-22T07:43:19Z","file_size":448736}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13042","file_date_updated":"2023-05-22T07:43:19Z","department":[{"_id":"MaKw"}],"date_updated":"2023-08-01T14:44:52Z","ddc":["510"],"oa":1,"publisher":"Electronic Journal of Combinatorics","quality_controlled":"1","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","date_created":"2023-05-21T22:01:05Z","doi":"10.37236/11471","date_published":"2023-05-05T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Electronic Journal of Combinatorics","day":"05","article_number":"P2.21","external_id":{"arxiv":["2105.13828"],"isi":["000988285500001"]},"article_processing_charge":"No","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"}],"title":"A note on long cycles in sparse random graphs","citation":{"ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21.","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.","short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","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","ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"year":"2023","has_accepted_license":"1","day":"18","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"54a619605e44c871214fb0e07b05c6bf","file_id":"12823","success":1,"date_updated":"2023-04-14T09:39:33Z","file_size":54184807,"creator":"pschanda","date_created":"2023-04-14T09:39:33Z","file_name":"data_deposition.zip"},{"content_type":"application/octet-stream","relation":"main_file","access_level":"open_access","success":1,"checksum":"8dede9fc78399d13144eb05c62bf5750","file_id":"12824","file_size":4978,"date_updated":"2023-04-14T09:39:58Z","creator":"pschanda","file_name":"README","date_created":"2023-04-14T09:39:58Z"}],"date_created":"2023-04-10T05:55:56Z","contributor":[{"last_name":"Troussicot","first_name":"Laura","contributor_type":"researcher"},{"last_name":"Burmann","contributor_type":"researcher","first_name":"Björn M."}],"date_published":"2023-04-18T00:00:00Z","doi":"10.15479/AT:ISTA:12820","related_material":{"record":[{"relation":"used_in_publication","id":"13095","status":"public"}]},"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"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"04","date_updated":"2023-08-01T14:48:08Z","citation":{"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).","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.","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","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.","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."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"file_date_updated":"2023-04-14T09:39:58Z","department":[{"_id":"PaSc"}],"title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","_id":"12820","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"research_data","status":"public"},{"date_updated":"2023-08-01T14:45:25Z","department":[{"_id":"BiCh"}],"_id":"13039","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":107,"issue":"13","abstract":[{"lang":"eng","text":"We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression."}],"oa_version":"None","scopus_import":"1","month":"04","intvolume":" 107","citation":{"chicago":"French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.134109.","ista":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 107(13), 134109.","mla":"French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109, American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109.","ama":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 2023;107(13). doi:10.1103/PhysRevB.107.134109","apa":"French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109","short":"M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B 107 (2023).","ieee":"M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation of the reflectivity of molecular fluids under shock compression,” Physical Review B, vol. 107, no. 13. American Physical Society, 2023."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Martin","full_name":"French, Martin","last_name":"French"},{"first_name":"Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"},{"first_name":"Alessandra","last_name":"Ravasio","full_name":"Ravasio, Alessandra"},{"last_name":"Hernandez","full_name":"Hernandez, Jean Alexis","first_name":"Jean Alexis"}],"article_processing_charge":"No","external_id":{"isi":["000974672600001"]},"title":"Ab initio calculation of the reflectivity of molecular fluids under shock compression","article_number":"134109","isi":1,"year":"2023","day":"01","publication":"Physical Review B","doi":"10.1103/PhysRevB.107.134109","date_published":"2023-04-01T00:00:00Z","date_created":"2023-05-21T22:01:04Z","acknowledgement":"We thank R. Redmer for helpful discussions. M.F. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge support form the French National Research Agency (ANR) through the projects POMPEI (Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The ab initio calculations were performed at the NorthGerman Supercomputing Alliance (HLRN) facilities. ","publisher":"American Physical Society","quality_controlled":"1"},{"has_accepted_license":"1","isi":1,"year":"2023","day":"04","publication":"ACS Applied Materials and Interfaces","page":"23380–23389","doi":"10.1021/acsami.3c00625","date_published":"2023-05-04T00:00:00Z","date_created":"2023-05-28T22:01:03Z","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.","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"citation":{"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","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","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.","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Bingfei","full_name":"Nan, Bingfei","last_name":"Nan"},{"full_name":"Song, Xuan","last_name":"Song","first_name":"Xuan"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"last_name":"Xiao","full_name":"Xiao, Ke","first_name":"Ke"},{"first_name":"Yu","full_name":"Zhang, Yu","last_name":"Zhang"},{"first_name":"Linlin","full_name":"Yang, Linlin","last_name":"Yang"},{"full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"article_processing_charge":"No","external_id":{"isi":["000985497900001"],"pmid":["37141543"]},"title":"Bottom-up synthesis of SnTe-based thermoelectric composites","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889"}],"publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"publication_status":"published","file":[{"success":1,"file_id":"13099","checksum":"23893be46763c4c78daacddd019de821","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_ACSAppliedMaterials_Nan.pdf","date_created":"2023-05-30T07:38:44Z","file_size":5640829,"date_updated":"2023-05-30T07:38:44Z","creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"19","volume":15,"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 15","date_updated":"2023-08-01T14:50:09Z","ddc":["540"],"department":[{"_id":"MaIb"}],"file_date_updated":"2023-05-30T07:38:44Z","_id":"13092","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"letter_note","type":"journal_article","_id":"13094","department":[{"_id":"AnSa"}],"file_date_updated":"2023-05-30T07:55:31Z","ddc":["540"],"date_updated":"2023-08-01T14:51:25Z","intvolume":" 23","month":"05","scopus_import":"1","oa_version":"Published Version","pmid":1,"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."}],"ec_funded":1,"volume":23,"issue":"10","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13100","checksum":"9734d4c617bab3578ef62916b764547a","success":1,"date_updated":"2023-05-30T07:55:31Z","file_size":3654910,"creator":"dernst","date_created":"2023-05-30T07:55:31Z","file_name":"2023_NanoLetters_Azadbakht.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"article_processing_charge":"No","author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"first_name":"Thijs","full_name":"Varkevisser, Thijs","last_name":"Varkevisser"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","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."},"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","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).","date_created":"2023-05-28T22:01:03Z","doi":"10.1021/acs.nanolett.3c00375","date_published":"2023-05-04T00:00:00Z","page":"4267–4273","publication":"Nano Letters","day":"04","year":"2023","has_accepted_license":"1","isi":1},{"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."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1021/acsaelm.3c00055","open_access":"1"}],"month":"05","publication_identifier":{"eissn":["2637-6113"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"_id":"13093","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-01T14:50:48Z","department":[{"_id":"MaIb"}],"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.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"isi":1,"year":"2023","day":"05","publication":"ACS Applied Electronic Materials","doi":"10.1021/acsaelm.3c00055","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-28T22:01:03Z","project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"citation":{"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.","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.","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.","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","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.","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Bingfei","full_name":"Nan, Bingfei","last_name":"Nan"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Ke","full_name":"Xiao, Ke","last_name":"Xiao"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"first_name":"Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang"},{"full_name":"Han, Xu","last_name":"Han","first_name":"Xu"},{"full_name":"Zuo, Yong","last_name":"Zuo","first_name":"Yong"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"article_processing_charge":"No","external_id":{"isi":["000986859000001"]},"title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature"},{"oa_version":"Published Version","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."}],"intvolume":" 17","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"5d5d67b235905650e33cf7065d7583b4","file_id":"13101","creator":"dernst","file_size":1430719,"date_updated":"2023-05-30T08:05:22Z","file_name":"2023_AlgebraNumberTheory_Browning.pdf","date_created":"2023-05-30T08:05:22Z"}],"publication_status":"published","publication_identifier":{"issn":["1937-0652"],"eissn":["1944-7833"]},"issue":"3","volume":17,"_id":"13091","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-08-01T14:51:57Z","department":[{"_id":"TiBr"}],"file_date_updated":"2023-05-30T08:05:22Z","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.","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","publication":"Algebra and Number Theory","day":"12","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-05-28T22:01:02Z","date_published":"2023-04-12T00:00:00Z","doi":"10.2140/ant.2023.17.719","page":"719-748","project":[{"_id":"26A8D266-B435-11E9-9278-68D0E5697425","name":"Between rational and integral points","grant_number":"EP-P026710-2"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","short":"T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.","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","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"},"title":"Free rational curves on low degree hypersurfaces and the circle method","article_processing_charge":"No","external_id":{"isi":["000996014700004"],"arxiv":["1810.06882"]},"author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}]},{"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"success":1,"file_id":"13123","checksum":"a857df40f0882859c48a1ff1e2001ec2","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NaturePhysics_Redchenko.pdf","date_created":"2023-06-06T07:31:20Z","creator":"dernst","file_size":1654389,"date_updated":"2023-06-06T07:31:20Z"}],"language":[{"iso":"eng"}],"volume":14,"related_material":{"record":[{"relation":"research_data","status":"public","id":"13124"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 14","date_updated":"2023-08-02T06:10:26Z","ddc":["530"],"file_date_updated":"2023-06-06T07:31:20Z","department":[{"_id":"JoFi"}],"_id":"13117","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","isi":1,"year":"2023","day":"24","publication":"Nature Communications","doi":"10.1038/s41467-023-38761-6","date_published":"2023-05-24T00:00:00Z","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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"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.","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","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","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"first_name":"Alexander V.","last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander V."},{"first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","full_name":"Sett, Riya"},{"first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"}],"article_processing_charge":"No","external_id":{"isi":["001001099700002"],"arxiv":["2205.03293"]},"title":"Tunable directional photon scattering from a pair of superconducting qubits","article_number":"2998","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}]},{"title":"Entangling microwaves with light","external_id":{"arxiv":["2301.03315"],"isi":["000996515200004"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","full_name":"Hease, William J","last_name":"Hease"},{"first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","last_name":"Arnold"},{"last_name":"Minoguchi","full_name":"Minoguchi, Y.","first_name":"Y."},{"first_name":"P.","full_name":"Rabl, P.","last_name":"Rabl"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","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."},"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","grant_number":"F07105"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"date_created":"2023-05-31T11:39:24Z","doi":"10.1126/science.adg3812","date_published":"2023-05-18T00:00:00Z","page":"718-721","publication":"Science","day":"18","year":"2023","isi":1,"oa":1,"quality_controlled":"1","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).","department":[{"_id":"JoFi"}],"date_updated":"2023-08-02T06:08:57Z","keyword":["Multidisciplinary"],"status":"public","article_type":"original","type":"journal_article","_id":"13106","ec_funded":1,"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":[{"id":"13122","status":"public","relation":"research_data"}]},"issue":"6646","volume":380,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"intvolume":" 380","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"oa_version":"Preprint","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."}]},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13129","department":[{"_id":"JuFi"}],"date_updated":"2023-08-02T06:12:39Z","ddc":["510"],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10208-023-09613-y","open_access":"1"}],"month":"05","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"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"author":[{"last_name":"Clozeau","full_name":"Clozeau, Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas"},{"first_name":"Marc","last_name":"Josien","full_name":"Josien, Marc"},{"full_name":"Otto, Felix","last_name":"Otto","first_name":"Felix"},{"first_name":"Qiang","full_name":"Xu, Qiang","last_name":"Xu"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000999623100001"]},"title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","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.","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.","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","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","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","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","date_published":"2023-05-30T00:00:00Z","doi":"10.1007/s10208-023-09613-y","date_created":"2023-06-11T22:00:40Z","has_accepted_license":"1","isi":1,"year":"2023","day":"30","publication":"Foundations of Computational Mathematics"}]