[{"isi":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"department":[{"_id":"BiCh"}],"intvolume":" 109","date_published":"2024-02-14T00:00:00Z","article_number":"054305","year":"2024","issue":"5","type":"journal_article","language":[{"iso":"eng"}],"publication":"Physical Review B","title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","date_created":"2024-03-04T07:41:23Z","scopus_import":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 2024;109(5). doi:10.1103/physrevb.109.054305","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305.","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/physrevb.109.054305."},"status":"public","volume":109,"article_type":"original","oa_version":"None","date_updated":"2025-09-04T12:11:58Z","month":"02","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","ec_funded":1,"_id":"15052","external_id":{"isi":["001198615900003"]},"author":[{"last_name":"Cheng","full_name":"Cheng, Ruihuan","first_name":"Ruihuan"},{"first_name":"Zezhu","full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","last_name":"Zeng"},{"last_name":"Wang","first_name":"Chen","full_name":"Wang, Chen"},{"last_name":"Ouyang","full_name":"Ouyang, Niuchang","first_name":"Niuchang"},{"last_name":"Chen","full_name":"Chen, Yue","first_name":"Yue"}],"publication_status":"published","publisher":"American Physical Society","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"day":"14","doi":"10.1103/physrevb.109.054305","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}]},{"publication_identifier":{"eissn":["2643-1564"]},"department":[{"_id":"MiLe"}],"arxiv":1,"date_published":"2024-02-13T00:00:00Z","article_number":"013158","DOAJ_listed":"1","intvolume":" 6","file":[{"file_size":4025988,"relation":"main_file","checksum":"ba2ae3e3a011f8897d3803c9366a67e2","file_name":"2024_PhysicalReviewResearch_Jin.pdf","date_updated":"2024-03-04T07:53:08Z","date_created":"2024-03-04T07:53:08Z","content_type":"application/pdf","access_level":"open_access","file_id":"15054","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication":"Physical Review Research","title":"Multipurpose platform for analog quantum simulation","issue":"1","type":"journal_article","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024."},"status":"public","volume":6,"date_created":"2024-03-04T07:42:52Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","keyword":["General Physics and Astronomy"],"file_date_updated":"2024-03-04T07:53:08Z","oa_version":"Published Version","oa":1,"article_type":"original","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","has_accepted_license":"1","date_updated":"2025-05-14T09:32:25Z","month":"02","ddc":["530"],"doi":"10.1103/physrevresearch.6.013158","article_processing_charge":"Yes","abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"external_id":{"arxiv":["2304.08433"]},"_id":"15053","publication_status":"published","author":[{"last_name":"Jin","first_name":"Shuwei","full_name":"Jin, Shuwei"},{"full_name":"Dai, Kunlun","first_name":"Kunlun","last_name":"Dai"},{"full_name":"Verstraten, Joris","first_name":"Joris","last_name":"Verstraten"},{"last_name":"Dixmerias","first_name":"Maxime","full_name":"Dixmerias, Maxime"},{"full_name":"Al Hyder, Ragheed","first_name":"Ragheed","id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder"},{"first_name":"Christophe","full_name":"Salomon, Christophe","last_name":"Salomon"},{"last_name":"Peaudecerf","first_name":"Bruno","full_name":"Peaudecerf, Bruno"},{"last_name":"de Jongh","first_name":"Tim","full_name":"de Jongh, Tim"},{"last_name":"Yefsah","first_name":"Tarik","full_name":"Yefsah, Tarik"}],"publisher":"American Physical Society","day":"13"},{"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"15108"},{"relation":"dissertation_contains","status":"public","id":"19903"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website"}]},"date_created":"2024-03-05T09:18:49Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","volume":121,"APC_amount":"3041,76 EUR","citation":{"short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. 121(10), e2315558121.","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(10). doi:10.1073/pnas.2315558121","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 10, e2315558121, National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121.","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 10. National Academy of Sciences, 2024.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"type":"journal_article","issue":"10","year":"2024","publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","file":[{"relation":"main_file","file_size":2203220,"checksum":"068520e3efd4d008bb9177e8aedb7d22","file_name":"2024_PNAS_Huebner.pdf","date_updated":"2024-03-12T13:12:22Z","date_created":"2024-03-12T13:12:22Z","content_type":"application/pdf","access_level":"open_access","file_id":"15109","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"intvolume":" 121","article_number":"e2315558121","date_published":"2024-03-05T00:00:00Z","isi":1,"department":[{"_id":"KrCh"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"OA_place":"publisher","project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"day":"05","_id":"15083","author":[{"full_name":"Hübner, Valentin","orcid":"0009-0001-5009-4987","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","last_name":"Hübner"},{"last_name":"Staab","first_name":"Manuel","full_name":"Staab, Manuel"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","first_name":"Maria"}],"publisher":"National Academy of Sciences","publication_status":"published","external_id":{"isi":["001207786500004"],"pmid":["38408249"]},"doi":"10.1073/pnas.2315558121","article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation."}],"ddc":["000"],"ec_funded":1,"month":"03","has_accepted_license":"1","date_updated":"2026-04-07T12:30:56Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","OA_type":"hybrid","oa":1,"article_type":"original","file_date_updated":"2024-03-12T13:12:22Z","oa_version":"Published Version"},{"oa_version":"Preprint","OA_place":"repository","oa":1,"department":[{"_id":"HeEd"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"arxiv":1,"article_number":"2212.03128","date_published":"2024-02-07T00:00:00Z","date_updated":"2026-04-07T12:58:47Z","month":"02","language":[{"iso":"eng"}],"title":"Chromatic alpha complexes","corr_author":"1","publication":"arXiv","type":"preprint","year":"2024","citation":{"short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv. doi:10.48550/arXiv.2212.03128","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128, doi:10.48550/arXiv.2212.03128.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv. https://doi.org/10.48550/arXiv.2212.03128","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2212.03128."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","abstract":[{"text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided.","lang":"eng"}],"status":"public","doi":"10.48550/arXiv.2212.03128","publication_status":"draft","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"15091","author":[{"first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano"},{"first_name":"Ondrej","full_name":"Draganov, Ondrej","orcid":"0000-0003-0464-3823","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"external_id":{"arxiv":["2212.03128"]},"date_created":"2024-03-08T10:13:59Z","related_material":{"record":[{"id":"20585","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"18979","status":"public"},{"relation":"dissertation_contains","id":"15094","status":"public"}]},"day":"07"},{"publication_identifier":{"eisbn":["9781611977912"]},"department":[{"_id":"HeEd"},{"_id":"MoHe"}],"page":"243 - 295","arxiv":1,"date_published":"2024-01-04T00:00:00Z","year":"2024","type":"conference","language":[{"iso":"eng"}],"corr_author":"1","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","title":"Dynamically maintaining the persistent homology of time series","date_created":"2024-03-08T10:27:39Z","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"15094","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorithms, 243–295.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11"},"status":"public","oa":1,"oa_version":"Preprint","editor":[{"full_name":"Woodruff, David P.","first_name":"David P.","last_name":"Woodruff"}],"date_updated":"2026-04-07T12:58:47Z","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","ec_funded":1,"_id":"15093","external_id":{"arxiv":["2311.01115"]},"publication_status":"published","author":[{"first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Ost","full_name":"Ost, Lara","first_name":"Lara"}],"publisher":"Society for Industrial and Applied Mathematics","project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"},{"name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"conference":{"end_date":"2024-01-10","name":"SODA: Symposium on Discrete Algorithms","start_date":"2024-01-07","location":"Alexandria, VA, USA"},"day":"04","doi":"10.1137/1.9781611977912.11","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"article_processing_charge":"No"},{"date_published":"2024-03-08T00:00:00Z","alternative_title":["ISTA Thesis"],"page":"108","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024."},"related_material":{"record":[{"id":"15091","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11660","status":"public"},{"status":"public","id":"15090","relation":"part_of_dissertation"},{"status":"public","id":"15093","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13182","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11658"}]},"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"date_created":"2024-03-08T15:28:10Z","title":"Persistence and Morse theory for discrete geometric structures","corr_author":"1","language":[{"iso":"eng"}],"file":[{"creator":"scultrer","success":1,"file_id":"15112","access_level":"open_access","content_type":"application/pdf","date_created":"2024-03-14T08:55:07Z","date_updated":"2024-03-14T08:55:07Z","file_name":"Thesis Sebastiano.pdf","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_size":4106872,"relation":"main_file"},{"creator":"scultrer","file_id":"15113","access_level":"closed","content_type":"application/zip","date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z","file_name":"Thesis (1).zip","checksum":"bcbd213490f5a7e68855a092bbce93f1","relation":"source_file","file_size":4746234}],"type":"dissertation","year":"2024","month":"03","date_updated":"2026-04-07T12:58:48Z","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2024-03-14T14:14:35Z","oa":1,"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"article_processing_charge":"No","doi":"10.15479/at:ista:15094","day":"08","project":[{"grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","call_identifier":"FWF","grant_number":"Z00342"},{"grant_number":"I4887","name":"Persistent Homology, Algorithms and Stochastic Geometry","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"_id":"15094","publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano"}],"ec_funded":1,"ddc":["514","500","516"]},{"oa_version":"Published Version","file_date_updated":"2024-03-13T08:59:21Z","article_type":"original","oa":1,"acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","has_accepted_license":"1","date_updated":"2025-09-04T12:17:17Z","month":"02","ddc":["550"],"doi":"10.5194/gmd-17-1563-2024","abstract":[{"lang":"eng","text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study."}],"article_processing_charge":"Yes (via OA deal)","_id":"15097","publication_status":"published","external_id":{"isi":["001190535000001"]},"publisher":"European Geosciences Union","author":[{"first_name":"Hauke","full_name":"Schmidt, Hauke","last_name":"Schmidt"},{"last_name":"Rast","full_name":"Rast, Sebastian","first_name":"Sebastian"},{"full_name":"Bao, Jiawei","first_name":"Jiawei","last_name":"Bao","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"last_name":"Cassim","full_name":"Cassim, Amrit","first_name":"Amrit"},{"first_name":"Shih Wei","full_name":"Fang, Shih Wei","last_name":"Fang"},{"first_name":"Diego","full_name":"Jimenez-De La Cuesta, Diego","last_name":"Jimenez-De La Cuesta"},{"last_name":"Keil","full_name":"Keil, Paul","first_name":"Paul"},{"first_name":"Lukas","full_name":"Kluft, Lukas","last_name":"Kluft"},{"last_name":"Kroll","full_name":"Kroll, Clarissa","first_name":"Clarissa"},{"first_name":"Theresa","full_name":"Lang, Theresa","last_name":"Lang"},{"first_name":"Ulrike","full_name":"Niemeier, Ulrike","last_name":"Niemeier"},{"full_name":"Schneidereit, Andrea","first_name":"Andrea","last_name":"Schneidereit"},{"last_name":"Williams","full_name":"Williams, Andrew I.L.","first_name":"Andrew I.L."},{"full_name":"Stevens, Bjorn","first_name":"Bjorn","last_name":"Stevens"}],"day":"22","isi":1,"department":[{"_id":"CaMu"}],"publication_identifier":{"issn":["1991-959X"],"eissn":["1991-9603"]},"page":"1563-1584","date_published":"2024-02-22T00:00:00Z","intvolume":" 17","file":[{"content_type":"application/pdf","date_created":"2024-03-13T08:59:21Z","date_updated":"2024-03-13T08:59:21Z","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","checksum":"270d2340402729b0532f7072ea914cae","file_size":13364601,"relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_id":"15111"}],"language":[{"iso":"eng"}],"publication":"Geoscientific Model Development","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","type":"journal_article","issue":"4","year":"2024","citation":{"apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024.","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":17,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-03-10T23:00:53Z","quality_controlled":"1","scopus_import":"1"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_updated":"2025-01-09T08:23:36Z","date_created":"2025-01-09T08:23:36Z","checksum":"d55cac8bddea09a97f06612825c4f229","file_name":"2024_MathAnnalen_Agresti.pdf","relation":"main_file","file_size":661557,"creator":"dernst","success":1,"file_id":"18790","access_level":"open_access"}],"title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","publication":"Mathematische Annalen","type":"journal_article","year":"2024","pmid":1,"citation":{"ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024;390:2727-2766. doi:10.1007/s00208-024-02812-0","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, vol. 390, Springer Nature, 2024, pp. 2727–66, doi:10.1007/s00208-024-02812-0.","short":"A. Agresti, E. Luongo, Mathematische Annalen 390 (2024) 2727–2766.","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 390, 2727–2766.","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0.","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen, vol. 390. Springer Nature, pp. 2727–2766, 2024.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":390,"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-03-10T23:00:54Z","quality_controlled":"1","scopus_import":"1","OA_place":"publisher","department":[{"_id":"JuFi"}],"publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"isi":1,"arxiv":1,"page":"2727-2766","date_published":"2024-10-01T00:00:00Z","intvolume":" 390","ec_funded":1,"ddc":["510"],"abstract":[{"lang":"eng","text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force."}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00208-024-02812-0","external_id":{"arxiv":["2306.11081"],"isi":["001172711400002"],"pmid":["39351582"]},"_id":"15098","publication_status":"published","publisher":"Springer Nature","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","last_name":"Agresti","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","first_name":"Antonio"},{"full_name":"Luongo, Eliseo","first_name":"Eliseo","last_name":"Luongo"}],"day":"01","project":[{"call_identifier":"H2020","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials"}],"file_date_updated":"2025-01-09T08:23:36Z","oa_version":"Published Version","oa":1,"article_type":"original","OA_type":"hybrid","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","date_updated":"2025-09-04T12:19:59Z","has_accepted_license":"1","month":"10"},{"doi":"10.1016/j.tig.2024.01.002","abstract":[{"text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","day":"01","_id":"15099","external_id":{"pmid":["38395682"],"isi":["001224671300001"]},"author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"}],"publication_status":"published","publisher":"Elsevier","ddc":["570"],"acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","month":"04","has_accepted_license":"1","date_updated":"2025-09-04T12:18:08Z","oa_version":"Published Version","file_date_updated":"2024-07-22T12:05:58Z","article_type":"review","oa":1,"status":"public","volume":40,"citation":{"chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Elsevier, 2024. https://doi.org/10.1016/j.tig.2024.01.002.","apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2024.01.002","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics, vol. 40, no. 4. Elsevier, pp. 337–351, 2024.","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, vol. 40, no. 4, Elsevier, 2024, pp. 337–51, doi:10.1016/j.tig.2024.01.002.","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024;40(4):337-351. doi:10.1016/j.tig.2024.01.002","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics 40 (2024) 337–351.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 40(4), 337–351."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-03-10T23:00:54Z","publication":"Trends in Genetics","title":"Diverse pathways to speciation revealed by marine snails","file":[{"creator":"dernst","success":1,"access_level":"open_access","file_id":"17313","content_type":"application/pdf","date_created":"2024-07-22T12:05:58Z","date_updated":"2024-07-22T12:05:58Z","file_name":"2024_TrendsGenetics_Johannesson.pdf","checksum":"3077ea808c4cdc24d02dc58aced7eb35","relation":"main_file","file_size":2288340}],"language":[{"iso":"eng"}],"pmid":1,"year":"2024","type":"journal_article","issue":"4","date_published":"2024-04-01T00:00:00Z","page":"337-351","intvolume":" 40","isi":1,"department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]}},{"citation":{"chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167.","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","short":"V. Hübner, M. Kleshnina, (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below.","lang":"eng"}],"doi":"10.5281/ZENODO.10639167","status":"public","publisher":"Zenodo","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"15108","date_created":"2024-03-12T13:02:58Z","author":[{"first_name":"Valentin","orcid":"0009-0001-5009-4987","full_name":"Hübner, Valentin","last_name":"Hübner","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","first_name":"Maria"}],"day":"09","related_material":{"record":[{"status":"public","id":"15083","relation":"used_in_publication"}]},"title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","corr_author":"1","type":"research_data_reference","ddc":["000"],"year":"2024","main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"date_published":"2024-02-09T00:00:00Z","date_updated":"2025-09-04T12:14:54Z","has_accepted_license":"1","month":"02","oa_version":"Published Version","department":[{"_id":"KrCh"}],"oa":1},{"date_updated":"2025-09-04T13:02:40Z","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ces.2024.119959"}],"OA_type":"free access","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","oa":1,"article_type":"original","oa_version":"None","_id":"15114","publication_status":"published","author":[{"last_name":"Yao","first_name":"Zihao","full_name":"Yao, Zihao"},{"last_name":"Liu","full_name":"Liu, Xu","first_name":"Xu"},{"last_name":"Bunting","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","first_name":"Rhys","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys"},{"full_name":"Wang, Jianguo","first_name":"Jianguo","last_name":"Wang"}],"external_id":{"isi":["001203872000001"]},"publisher":"Elsevier","day":"05","article_processing_charge":"No","abstract":[{"text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.","lang":"eng"}],"doi":"10.1016/j.ces.2024.119959","intvolume":" 291","date_published":"2024-06-05T00:00:00Z","article_number":"119959","department":[{"_id":"MaIb"}],"publication_identifier":{"issn":["0009-2509"]},"isi":1,"date_created":"2024-03-17T23:00:57Z","scopus_import":"1","quality_controlled":"1","citation":{"apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.","chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.","ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.","ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":291,"status":"public","year":"2024","type":"journal_article","language":[{"iso":"eng"}],"title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","publication":"Chemical Engineering Science"},{"doi":"10.1073/pnas.2313162121","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"day":"12","publication_status":"published","_id":"15116","publisher":"National Academy of Sciences","author":[{"full_name":"Giubertoni, Giulia","first_name":"Giulia","last_name":"Giubertoni"},{"full_name":"Feng, Liru","first_name":"Liru","last_name":"Feng"},{"full_name":"Klein, Kevin","first_name":"Kevin","last_name":"Klein"},{"last_name":"Giannetti","full_name":"Giannetti, Guido","first_name":"Guido"},{"last_name":"Rutten","full_name":"Rutten, Luco","first_name":"Luco"},{"full_name":"Choi, Yeji","first_name":"Yeji","last_name":"Choi"},{"last_name":"Van Der Net","first_name":"Anouk","full_name":"Van Der Net, Anouk"},{"last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard","first_name":"Gerard"},{"last_name":"Caporaletti","first_name":"Federico","full_name":"Caporaletti, Federico"},{"last_name":"Micha","full_name":"Micha, Dimitra","first_name":"Dimitra"},{"last_name":"Hunger","full_name":"Hunger, Johannes","first_name":"Johannes"},{"last_name":"Deblais","first_name":"Antoine","full_name":"Deblais, Antoine"},{"first_name":"Daniel","full_name":"Bonn, Daniel","last_name":"Bonn"},{"last_name":"Sommerdijk","full_name":"Sommerdijk, Nico","first_name":"Nico"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"},{"last_name":"Ilie","full_name":"Ilie, Ioana M.","first_name":"Ioana M."},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"last_name":"Woutersen","first_name":"Sander","full_name":"Woutersen, Sander"}],"external_id":{"pmid":["38451946"],"isi":["001206387400001"]},"ddc":["550"],"acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","month":"03","has_accepted_license":"1","date_updated":"2025-09-04T13:03:56Z","file_date_updated":"2024-03-19T10:22:42Z","oa_version":"Published Version","oa":1,"article_type":"original","status":"public","volume":121,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. National Academy of Sciences, 2024.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121."},"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"15126","relation":"research_data"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-03-17T23:00:57Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","file":[{"success":1,"access_level":"open_access","file_id":"15125","creator":"dernst","file_name":"2024_PNAS_Giubertoni.pdf","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","relation":"main_file","file_size":12952586,"content_type":"application/pdf","date_created":"2024-03-19T10:22:42Z","date_updated":"2024-03-19T10:22:42Z"}],"language":[{"iso":"eng"}],"pmid":1,"type":"journal_article","year":"2024","issue":"11","article_number":"e2313162121","date_published":"2024-03-12T00:00:00Z","intvolume":" 121","isi":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"department":[{"_id":"AnSa"}]},{"citation":{"ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":383,"date_created":"2024-03-17T23:00:57Z","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"corr_author":"1","publication":"Science","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","type":"journal_article","year":"2024","issue":"6687","pmid":1,"page":"eadg6757","date_published":"2024-03-08T00:00:00Z","intvolume":" 383","isi":1,"publication_identifier":{"eissn":["1095-9203"]},"department":[{"_id":"PeJo"}],"doi":"10.1126/science.adg6757","article_processing_charge":"No","abstract":[{"text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations.","lang":"eng"}],"_id":"15117","publisher":"AAAS","publication_status":"published","author":[{"last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"external_id":{"isi":["001216996700015"],"pmid":["38452088"]},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"}],"day":"08","ec_funded":1,"acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","date_updated":"2025-09-04T13:04:34Z","month":"03","oa_version":"None","article_type":"review"},{"abstract":[{"lang":"eng","text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea."}],"article_processing_charge":"No","doi":"10.1038/s41564-024-01600-5","day":"04","project":[{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division"}],"publisher":"Springer Nature","_id":"15118","publication_status":"published","external_id":{"pmid":["38443575"],"isi":["001183270800021"]},"author":[{"last_name":"Nußbaum","full_name":"Nußbaum, Phillip","first_name":"Phillip"},{"last_name":"Kureisaite-Ciziene","first_name":"Danguole","full_name":"Kureisaite-Ciziene, Danguole"},{"last_name":"Bellini","first_name":"Dom","full_name":"Bellini, Dom"},{"full_name":"Van Der Does, Chris","first_name":"Chris","last_name":"Van Der Does"},{"id":"73e7ecd4-dc85-11ea-9058-88a16394b160","last_name":"Kojic","full_name":"Kojic, Marko","orcid":"0000-0001-7244-8128","first_name":"Marko"},{"last_name":"Taib","full_name":"Taib, Najwa","first_name":"Najwa"},{"full_name":"Yeates, Anna","first_name":"Anna","last_name":"Yeates"},{"last_name":"Tourte","full_name":"Tourte, Maxime","first_name":"Maxime"},{"last_name":"Gribaldo","first_name":"Simonetta","full_name":"Gribaldo, Simonetta"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"first_name":"Jan","full_name":"Löwe, Jan","last_name":"Löwe"},{"last_name":"Albers","first_name":"Sonja Verena","full_name":"Albers, Sonja Verena"}],"oa_version":"None","article_type":"original","acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","month":"03","date_updated":"2026-04-07T12:27:57Z","title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","publication":"Nature Microbiology","language":[{"iso":"eng"}],"pmid":1,"type":"journal_article","issue":"3","year":"2024","volume":9,"status":"public","citation":{"chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5","ieee":"P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024.","mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","id":"20741","relation":"dissertation_contains"}]},"scopus_import":"1","quality_controlled":"1","date_created":"2024-03-17T23:00:58Z","department":[{"_id":"MaLo"}],"publication_identifier":{"eissn":["2058-5276"]},"isi":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"date_published":"2024-03-04T00:00:00Z","page":"698-711","intvolume":" 9"},{"date_updated":"2024-10-09T21:08:30Z","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","article_type":"original","oa":1,"oa_version":"Preprint","external_id":{"arxiv":["2106.01274"]},"_id":"15119","publication_status":"published","author":[{"last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","first_name":"Antonio"},{"first_name":"Mark","full_name":"Veraar, Mark","last_name":"Veraar"}],"publisher":"Institute of Mathematical Statistics","day":"01","doi":"10.1214/22-AIHP1333","article_processing_charge":"No","abstract":[{"lang":"eng","text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness."}],"intvolume":" 60","arxiv":1,"page":"413-430","date_published":"2024-02-01T00:00:00Z","department":[{"_id":"JuFi"}],"publication_identifier":{"issn":["0246-0203"]},"date_created":"2024-03-17T23:00:58Z","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430.","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333","mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":60,"year":"2024","type":"journal_article","issue":"1","language":[{"iso":"eng"}],"corr_author":"1","publication":"Annales de l'institut Henri Poincare Probability and Statistics","title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions"},{"file_date_updated":"2024-03-19T07:16:38Z","oa_version":"Published Version","article_type":"original","oa":1,"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","month":"03","date_updated":"2025-05-14T09:32:15Z","has_accepted_license":"1","ddc":["530"],"abstract":[{"text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA.","lang":"eng"}],"article_processing_charge":"Yes","doi":"10.1103/PhysRevResearch.6.013223","day":"01","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IMB PhD Nomination Fellowship - Stefan Sack"}],"_id":"15122","author":[{"full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack"},{"full_name":"Egger, Daniel J.","first_name":"Daniel J.","last_name":"Egger"}],"external_id":{"arxiv":["2307.14427"]},"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["2643-1564"]},"article_number":"013223","date_published":"2024-03-01T00:00:00Z","arxiv":1,"intvolume":" 6","DOAJ_listed":"1","title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","publication":"Physical Review Research","corr_author":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"15123","success":1,"creator":"dernst","relation":"main_file","file_size":2777593,"checksum":"274c9f1b15b3547a10a03f39e4ccc582","file_name":"2024_PhysicalReviewResearch_Sack.pdf","date_updated":"2024-03-19T07:16:38Z","date_created":"2024-03-19T07:16:38Z","content_type":"application/pdf"}],"type":"journal_article","year":"2024","issue":"1","volume":6,"status":"public","citation":{"chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.","apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","date_created":"2024-03-17T23:00:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"title":"Dataset Collagen Self Assembly in H2O and D2O","ddc":["550"],"year":"2024","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, 10.21942/UVA.24829896.","short":"G. Giubertoni, S. Woutersen, (2024).","ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:10.21942/UVA.24829896","mla":"Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O and D2O. Figshare, 2024, doi:10.21942/UVA.24829896.","ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","apa":"Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896","chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896."},"abstract":[{"text":"This zip file contains data, and analysis for the paper \"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration\".","lang":"eng"}],"article_processing_charge":"No","status":"public","doi":"10.21942/UVA.24829896","extern":"1","date_created":"2024-03-19T10:47:16Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"15126","publisher":"Figshare","author":[{"first_name":"G.","full_name":"Giubertoni, G.","last_name":"Giubertoni"},{"full_name":"Woutersen, S.","first_name":"S.","last_name":"Woutersen"}],"day":"14","related_material":{"record":[{"relation":"used_in_publication","id":"15116","status":"public"}]},"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21942/UVA.24829896"}],"date_published":"2024-02-14T00:00:00Z","date_updated":"2025-09-04T13:03:56Z","has_accepted_license":"1","month":"02"},{"scopus_import":"1","quality_controlled":"1","date_created":"2024-03-21T06:45:51Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","volume":223,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125."},"pmid":1,"issue":"6","type":"journal_article","year":"2024","publication":"Journal of Cell Biology","corr_author":"1","title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","file":[{"file_size":11907016,"relation":"main_file","checksum":"90d1984a93660735e506c2a304bc3f73","file_name":"2024_JCB_Zens.pdf","date_updated":"2024-03-25T12:52:04Z","date_created":"2024-03-25T12:52:04Z","content_type":"application/pdf","file_id":"15188","access_level":"open_access","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"intvolume":" 223","article_number":"e202309125","date_published":"2024-03-20T00:00:00Z","isi":1,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"grant_number":"E435","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy","_id":"7bd318a1-9f16-11ee-852c-cc9217763180"},{"grant_number":"724373","call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"},{"grant_number":"21317","_id":"2615199A-B435-11E9-9278-68D0E5697425","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"name":"CryoMinflux-guided in-situ visual proteomics and structure determination","_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01"}],"day":"20","_id":"15146","publication_status":"published","author":[{"first_name":"Bettina","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler"},{"orcid":"0000-0001-7967-2085","full_name":"Hansen, Jesse","first_name":"Jesse","last_name":"Hansen","id":"1063c618-6f9b-11ec-9123-f912fccded63"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","full_name":"Datler, Julia","first_name":"Julia"},{"first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa"},{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alanko","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","first_name":"Jonna H"},{"first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur"}],"publisher":"Rockefeller University Press","external_id":{"pmid":["38506714"],"isi":["001264190100001"]},"doi":"10.1083/jcb.202309125","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly."}],"ddc":["570"],"ec_funded":1,"month":"03","has_accepted_license":"1","date_updated":"2025-09-04T13:17:16Z","acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","article_type":"original","oa":1,"file_date_updated":"2024-03-25T12:52:04Z","oa_version":"Published Version"},{"issue":"6","year":"2024","type":"journal_article","title":"Decompositions into two linear forests of bounded lengths","corr_author":"1","publication":"Discrete Mathematics","language":[{"iso":"eng"}],"scopus_import":"1","quality_controlled":"1","date_created":"2024-03-24T23:00:58Z","volume":347,"status":"public","citation":{"short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962.","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962","mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962.","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0012-365X"]},"department":[{"_id":"MaKw"}],"isi":1,"intvolume":" 347","article_number":"113962","date_published":"2024-06-01T00:00:00Z","arxiv":1,"day":"01","_id":"15163","publication_status":"published","author":[{"first_name":"Rutger","full_name":"Campbell, Rutger","last_name":"Campbell"},{"last_name":"Hörsch","first_name":"Florian","full_name":"Hörsch, Florian"},{"first_name":"Benjamin","full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","last_name":"Moore"}],"publisher":"Elsevier","external_id":{"isi":["001226893800001"],"arxiv":["2301.11615"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs."}],"doi":"10.1016/j.disc.2024.113962","article_type":"original","oa":1,"oa_version":"Preprint","month":"06","date_updated":"2025-09-04T13:10:26Z","acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.11615","open_access":"1"}]},{"article_number":"104143","date_published":"2024-04-01T00:00:00Z","intvolume":" 126","isi":1,"department":[{"_id":"PreCl"}],"publication_identifier":{"issn":["1350-4533"],"eissn":["1873-4030"]},"citation":{"chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024.","mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024)."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":126,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2024-03-24T23:00:58Z","quality_controlled":"1","scopus_import":"1","file":[{"content_type":"application/pdf","date_created":"2024-03-25T08:29:52Z","date_updated":"2024-03-25T08:29:52Z","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","checksum":"974acbf2731e7382dcf5920ac762e551","file_size":10039402,"relation":"main_file","creator":"dernst","success":1,"access_level":"open_access","file_id":"15177"}],"language":[{"iso":"eng"}],"publication":"Medical Engineering and Physics","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","year":"2024","type":"journal_article","pmid":1,"acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","has_accepted_license":"1","date_updated":"2025-09-04T13:11:03Z","month":"04","file_date_updated":"2024-03-25T08:29:52Z","oa_version":"Published Version","article_type":"original","oa":1,"doi":"10.1016/j.medengphy.2024.104143","article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction."}],"external_id":{"pmid":["38621845"],"isi":["001219145400001"]},"_id":"15164","publication_status":"published","author":[{"full_name":"Silva-Henao, Juan D.","first_name":"Juan D.","last_name":"Silva-Henao"},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","last_name":"Schober","full_name":"Schober, Sophie","first_name":"Sophie"},{"last_name":"Pahr","first_name":"Dieter H.","full_name":"Pahr, Dieter H."},{"last_name":"Reisinger","full_name":"Reisinger, Andreas G.","first_name":"Andreas G."}],"publisher":"Elsevier","day":"01","ddc":["610"]}]