[{"article_number":"btad158","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"citation":{"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","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Beneš","full_name":"Beneš, Nikola","first_name":"Nikola"},{"full_name":"Brim, Luboš","last_name":"Brim","first_name":"Luboš"},{"first_name":"Ondřej","full_name":"Huvar, Ondřej","last_name":"Huvar"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","last_name":"Pastva","full_name":"Pastva, Samuel"},{"first_name":"David","full_name":"Šafránek, David","last_name":"Šafránek"}],"article_processing_charge":"No","external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"title":"Boolean network sketches: A unifying framework for logical model inference","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.].","quality_controlled":"1","publisher":"Oxford Academic","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"03","publication":"Bioinformatics","doi":"10.1093/bioinformatics/btad158","date_published":"2023-04-03T00:00:00Z","date_created":"2023-04-30T22:01:05Z","_id":"12876","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","date_updated":"2023-08-01T14:27:28Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2023-05-02T07:39:04Z","abstract":[{"text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 39","publication_identifier":{"eissn":["1367-4811"]},"publication_status":"published","file":[{"success":1,"file_id":"12886","checksum":"2cb90ddf781baefddf47eac4b54e2a03","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_Bioinformatics_Benes.pdf","date_created":"2023-05-02T07:39:04Z","file_size":478740,"date_updated":"2023-05-02T07:39:04Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":39,"issue":"4","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7688740"}]},"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1},{"publication_status":"published","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-02T07:24:55Z","file_size":3811113,"date_created":"2023-05-02T07:24:55Z","file_name":"2023_Nucleus_Kaneshiro.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8e707eda84f64dbad7f03545ae0a83ef","file_id":"12884","success":1}],"issue":"1","volume":14,"abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 14","month":"04","date_updated":"2023-08-01T14:18:46Z","ddc":["570"],"file_date_updated":"2023-05-02T07:24:55Z","department":[{"_id":"MaHe"}],"_id":"12880","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":"journal_article","article_type":"original","status":"public","year":"2023","isi":1,"has_accepted_license":"1","publication":"Nucleus","day":"18","date_created":"2023-04-30T22:01:06Z","doi":"10.1080/19491034.2023.2202548","date_published":"2023-04-18T00:00:00Z","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.","oa":1,"publisher":"Taylor & Francis","quality_controlled":"1","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.","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","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.","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","external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"article_processing_charge":"No","author":[{"first_name":"Jeanae M.","last_name":"Kaneshiro","full_name":"Kaneshiro, Jeanae M."},{"last_name":"Capitanio","full_name":"Capitanio, Juliana S.","first_name":"Juliana S."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"Hetzer","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W"}],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","article_number":"2202548"},{"type":"journal_article","article_type":"original","status":"public","_id":"12914","department":[{"_id":"MiLe"}],"date_updated":"2023-08-01T14:33:21Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}],"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","issue":"4","volume":107,"ec_funded":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"042216","author":[{"last_name":"Suzuki","orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika","first_name":"Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E"},{"last_name":"Unruh","full_name":"Unruh, William G.","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":{"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","apa":"Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"},{"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 14","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12917","checksum":"a778105665c10beb2354c92d2b295115","file_size":1405588,"date_updated":"2023-05-08T07:26:40Z","creator":"dernst","file_name":"2023_NatureComm_DiezMerida.pdf","date_created":"2023-05-08T07:26:40Z"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"volume":14,"_id":"12913","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":["530"],"date_updated":"2023-08-01T14:34:00Z","file_date_updated":"2023-05-08T07:26:40Z","department":[{"_id":"AnHi"}],"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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Communications","day":"26","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-05-07T22:01:03Z","doi":"10.1038/s41467-023-38005-7","date_published":"2023-04-26T00:00:00Z","article_number":"2396","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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).","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.","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."},"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","article_processing_charge":"No","external_id":{"pmid":["37100775"],"isi":["000979744000004"]},"author":[{"full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida","first_name":"J."},{"first_name":"A.","full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón"},{"full_name":"Yang, S. Y.","last_name":"Yang","first_name":"S. Y."},{"last_name":"Xie","full_name":"Xie, Y. M.","first_name":"Y. M."},{"full_name":"Gao, X. J.","last_name":"Gao","first_name":"X. J."},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","last_name":"Senior"},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"first_name":"T.","full_name":"Taniguchi, T.","last_name":"Taniguchi"},{"first_name":"X.","full_name":"Lu, X.","last_name":"Lu"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K. T.","last_name":"Law","full_name":"Law, K. T."},{"first_name":"Dmitri K.","full_name":"Efetov, Dmitri K.","last_name":"Efetov"}]},{"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.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"07","publication":"Journal of Nonlinear Science","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-06-07T00:00:00Z","doi":"10.1007/s00332-023-09926-w","date_created":"2021-12-16T12:15:35Z","article_number":"66","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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).","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","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","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."},"title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","author":[{"first_name":"Klemens","full_name":"Fellner, Klemens","last_name":"Fellner"},{"last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael","last_name":"Kniely"},{"last_name":"Tang","full_name":"Tang, Bao Quoc","first_name":"Bao Quoc"}],"external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter."}],"month":"06","intvolume":" 33","scopus_import":"1","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13149","checksum":"f3f0f0886098e31c81116cff8183750b","success":1,"creator":"dernst","date_updated":"2023-06-19T07:33:53Z","file_size":742315,"date_created":"2023-06-19T07:33:53Z","file_name":"2023_JourNonlinearScience_Fellner.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"publication_status":"published","volume":33,"_id":"10550","status":"public","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)"},"ddc":["510"],"date_updated":"2023-08-01T14:40:33Z","file_date_updated":"2023-06-19T07:33:53Z","department":[{"_id":"JuFi"}]},{"year":"2023","has_accepted_license":"1","isi":1,"publication":"Interfaces and Free Boundaries","day":"20","page":"37-107","date_created":"2023-05-21T22:01:06Z","date_published":"2023-04-20T00:00:00Z","doi":"10.4171/IFB/484","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.","oa":1,"quality_controlled":"1","publisher":"EMS Press","citation":{"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.","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","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","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000975817300002"],"arxiv":["2108.01733"]},"author":[{"first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819","name":"Bridging Scales in Random Materials"}],"publication_status":"published","publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-05-22T07:24:13Z","file_size":867876,"date_created":"2023-05-22T07:24:13Z","file_name":"2023_Interfaces_Hensel.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"622422484810441e48f613e968c7e7a4","file_id":"13045","success":1}],"ec_funded":1,"related_material":{"record":[{"id":"10013","status":"public","relation":"earlier_version"}]},"volume":25,"issue":"1","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 25","month":"04","date_updated":"2023-08-01T14:43:29Z","ddc":["510"],"file_date_updated":"2023-05-22T07:24:13Z","department":[{"_id":"JuFi"}],"_id":"13043","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","status":"public"},{"title":"Computing chemical potentials of adsorbed or confined fluids","external_id":{"arxiv":["2302.01297"],"pmid":["37093149"],"isi":["001010676000010"]},"article_processing_charge":"No","author":[{"full_name":"Schmid, Rochus","last_name":"Schmid","first_name":"Rochus"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","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","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","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."},"article_number":"161101 ","date_created":"2023-05-07T22:01:03Z","doi":"10.1063/5.0146711","date_published":"2023-04-24T00:00:00Z","publication":"The Journal of Chemical Physics","day":"24","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"AIP Publishing","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.","department":[{"_id":"BiCh"}],"file_date_updated":"2023-05-08T07:44:49Z","ddc":["540"],"date_updated":"2023-08-01T14:34:49Z","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":"12912","issue":"16","volume":158,"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/mu-adsorption"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"4ab8c965f2fa4e17920bfa846847f137","file_id":"12918","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-08T07:44:49Z","file_name":"2023_JourChemicalPhysics_Schmid.pdf","creator":"dernst","date_updated":"2023-05-08T07:44:49Z","file_size":6499468}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"]},"intvolume":" 158","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"date_created":"2023-05-16T08:47:25Z","date_published":"2023-05-08T00:00:00Z","doi":"10.1111/cgf.14770 ","page":"397-409","publication":"Computer Graphics Forum","day":"08","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Wiley","quality_controlled":"1","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.","title":"Directionality-aware design of embroidery patterns","external_id":{"isi":["001000062600033"]},"article_processing_charge":"No","author":[{"last_name":"Liu","orcid":"0000-0001-9200-5690","full_name":"Liu, Zhenyuan","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19","first_name":"Zhenyuan"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Charrondiere, Raphael","last_name":"Charrondiere","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1","first_name":"Raphael"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409.","apa":"Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ","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 ","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 ."},"project":[{"name":"Perception-Aware Appearance Fabrication","grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"issue":"2","volume":42,"language":[{"iso":"eng"}],"file":[{"file_id":"12974","checksum":"4c188c2be4745467a8790bbf5d6491aa","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-05-16T08:28:37Z","file_name":"Zhenyuan2023.pdf","date_updated":"2023-05-16T08:28:37Z","file_size":24003702,"creator":"mpiovarc"}],"publication_status":"published","publication_identifier":{"issn":["1467-8659"]},"intvolume":" 42","month":"05","oa_version":"Published Version","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."}],"file_date_updated":"2023-05-16T08:28:37Z","department":[{"_id":"BeBi"}],"ddc":["004"],"date_updated":"2023-08-01T14:47:05Z","keyword":["embroidery","design","directionality","density","image"],"status":"public","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","start_date":"2023-05-08","end_date":"2023-05-12","location":"Saarbrucken, Germany"},"type":"journal_article","article_type":"original","_id":"12972"},{"article_number":"7959","citation":{"chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z.","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.","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)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Anna","last_name":"Zavadakova","full_name":"Zavadakova, Anna"},{"first_name":"Lucie","last_name":"Vistejnova","full_name":"Vistejnova, Lucie"},{"full_name":"Belinova, Tereza","last_name":"Belinova","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","first_name":"Tereza"},{"first_name":"Filip","full_name":"Tichanek, Filip","last_name":"Tichanek"},{"first_name":"Dagmar","full_name":"Bilikova, Dagmar","last_name":"Bilikova"},{"last_name":"Mouton","full_name":"Mouton, Peter R.","first_name":"Peter R."}],"external_id":{"isi":["000995271600104"]},"article_processing_charge":"No","title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","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.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"17","publication":"Scientific Reports","date_published":"2023-05-17T00:00:00Z","doi":"10.1038/s41598-023-35162-z","date_created":"2023-05-19T11:12:25Z","_id":"13033","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","keyword":["Multidisciplinary"],"date_updated":"2023-08-01T14:46:06Z","ddc":["570"],"department":[{"_id":"Bio"}],"file_date_updated":"2023-05-22T07:57:37Z","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","scopus_import":"1","month":"05","intvolume":" 13","publication_identifier":{"issn":["2045-2322"]},"publication_status":"published","file":[{"date_created":"2023-05-22T07:57:37Z","file_name":"2023_ScientificReports_Zavadakova.pdf","creator":"dernst","date_updated":"2023-05-22T07:57:37Z","file_size":3055077,"file_id":"13047","checksum":"8c1b769693ff4288df8376e59ad1176d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41598-023-37265-z"}]},"volume":13},{"date_published":"2023-05-04T00:00:00Z","doi":"10.1021/jacs.3c01200","date_created":"2023-05-28T22:01:04Z","page":"10700–10711","day":"04","publication":"Journal of the American Chemical Society","has_accepted_license":"1","isi":1,"year":"2023","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"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. ","title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","author":[{"last_name":"Troussicot","full_name":"Troussicot, Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","first_name":"Laura"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"first_name":"Mikael","last_name":"Molin","full_name":"Molin, Mikael"},{"full_name":"Burmann, Björn M.","last_name":"Burmann","first_name":"Björn M."},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"}],"article_processing_charge":"No","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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."},"related_material":{"record":[{"relation":"research_data","id":"12820","status":"public"}]},"volume":145,"issue":"19","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"0758a930ef21c62fc91b14e657479f83","file_id":"13098","file_size":6719299,"date_updated":"2023-05-30T07:05:28Z","creator":"dernst","file_name":"2023_JACS_Troussicot.pdf","date_created":"2023-05-30T07:05:28Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","month":"05","intvolume":" 145","scopus_import":"1","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."}],"department":[{"_id":"PaSc"}],"file_date_updated":"2023-05-30T07:05:28Z","ddc":["540"],"date_updated":"2023-08-01T14:48:09Z","status":"public","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)"},"_id":"13095"}]