[{"_id":"12856","month":"04","scopus_import":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-04-20T08:29:42Z","conference":{"start_date":"2023-04-22","name":"FASE: Fundamental Approaches to Software Engineering","location":"Paris, France","end_date":"2023-04-27"},"external_id":{"isi":["001284136600015"]},"alternative_title":["LNCS"],"volume":13991,"department":[{"_id":"ToHe"}],"corr_author":"1","publisher":"Springer Nature","type":"conference","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"citation":{"mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In <i>Fundamental Approaches to Software Engineering</i>, 13991:260–81. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13991. Springer Nature; 2023:260-281. doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in <i>Fundamental Approaches to Software Engineering</i>, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281."},"quality_controlled":"1","author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"full_name":"Mühlböck, Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian"},{"first_name":"Stefanie","last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"title":"Vamos: Middleware for best-effort third-party monitoring","date_updated":"2025-09-09T12:25:29Z","related_material":{"record":[{"relation":"later_version","id":"18169","status":"public"},{"id":"12407","relation":"earlier_version","status":"public"}]},"page":"260-281","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2023-04-25T07:16:36Z","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","publication":"Fundamental Approaches to Software Engineering","isi":1,"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"day":"20","doi":"10.1007/978-3-031-30826-0_15","file":[{"file_id":"12865","date_updated":"2023-04-25T07:16:36Z","relation":"main_file","checksum":"17a7c8e08be609cf2408d37ea55e322c","content_type":"application/pdf","date_created":"2023-04-25T07:16:36Z","success":1,"file_name":"2023_LNCS_ChalupaM.pdf","file_size":580828,"creator":"dernst","access_level":"open_access"}],"oa":1,"intvolume":"     13991","date_published":"2023-04-20T00:00:00Z","ec_funded":1,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308253"],"eissn":["1611-3349"],"eisbn":["9783031308260"]},"year":"2023"},{"publication":"Proceedings of the 40th International Conference on Machine Learning","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"day":"27","oa":1,"intvolume":"       202","date_published":"2023-10-27T00:00:00Z","year":"2023","acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone","last_name":"Bombari","first_name":"Simone"},{"id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","full_name":"Kiyani, Shayan","last_name":"Kiyani","first_name":"Shayan"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco"}],"title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","date_updated":"2025-04-15T07:50:16Z","related_material":{"link":[{"url":"https://github.com/simone-bombari/beyond-universal-robustness","relation":"software"}]},"page":"2738-2776","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Preprint","volume":202,"department":[{"_id":"GradSch"},{"_id":"MaMo"}],"corr_author":"1","publisher":"ML Research Press","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"type":"conference","abstract":[{"text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).","lang":"eng"}],"citation":{"short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:2738–76. ML Research Press, 2023.","ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 2738–76.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:2738-2776.","apa":"Bombari, S., Kiyani, S., &#38; Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776."},"quality_controlled":"1","_id":"12859","month":"10","publication_status":"published","date_created":"2023-04-23T16:11:03Z","conference":{"location":"Honolulu, HI, United States","name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23","end_date":"2023-07-29"},"external_id":{"arxiv":["2302.01629"]},"alternative_title":["PMLR"]},{"publisher":"Springer Nature","department":[{"_id":"KrCh"}],"volume":14,"quality_controlled":"1","citation":{"short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","apa":"Schmid, L., Ekbatani, F., Hilbe, C., &#38; Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>, vol. 14, 2086, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>.","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>."},"pmid":1,"type":"journal_article","abstract":[{"text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations.","lang":"eng"}],"scopus_import":"1","month":"04","_id":"12861","external_id":{"pmid":["37045828"],"isi":["001003644100020"]},"date_created":"2023-04-23T22:01:03Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"publication":"Nature Communications","year":"2023","article_type":"original","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"article_number":"2086","date_published":"2023-04-12T00:00:00Z","intvolume":"        14","file":[{"creator":"dernst","file_size":1786475,"file_name":"2023_NatureComm_Schmid.pdf","date_created":"2023-04-25T09:13:53Z","success":1,"access_level":"open_access","date_updated":"2023-04-25T09:13:53Z","file_id":"12868","content_type":"application/pdf","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","relation":"main_file"}],"oa":1,"day":"12","doi":"10.1038/s41467-023-37817-x","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-04-25T09:13:53Z","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-15T06:26:15Z","author":[{"orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Farbod","last_name":"Ekbatani","full_name":"Ekbatani, Farbod"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"}],"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","oa_version":"Published Version"},{"publisher":"Public Library of Science","volume":19,"department":[{"_id":"JoCs"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"pmid":1,"citation":{"apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., &#38; Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” <i>PLoS Computational Biology</i>, vol. 19, no. 4. Public Library of Science, 2023.","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. 2023;19(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>.","chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>.","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023)."},"quality_controlled":"1","month":"04","issue":"4","scopus_import":"1","_id":"12862","external_id":{"pmid":["37011110"],"isi":["000962668700002"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-04-23T22:01:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"publication":"PLoS Computational Biology","isi":1,"article_number":"e1010983","year":"2023","publication_identifier":{"eissn":["1553-7358"]},"article_type":"original","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","day":"01","doi":"10.1371/journal.pcbi.1010983","file":[{"access_level":"open_access","file_size":4737671,"creator":"dernst","file_name":"2023_PLoSCompBio_Safavi.pdf","date_created":"2023-04-25T08:59:18Z","success":1,"relation":"main_file","content_type":"application/pdf","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","file_id":"12867","date_updated":"2023-04-25T08:59:18Z"}],"oa":1,"intvolume":"        19","date_published":"2023-04-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","file_date_updated":"2023-04-25T08:59:18Z","has_accepted_license":"1","article_processing_charge":"No","author":[{"first_name":"Shervin","last_name":"Safavi","full_name":"Safavi, Shervin"},{"full_name":"Panagiotaropoulos, Theofanis I.","last_name":"Panagiotaropoulos","first_name":"Theofanis I."},{"first_name":"Vishal","full_name":"Kapoor, Vishal","last_name":"Kapoor"},{"first_name":"Juan F","full_name":"Ramirez Villegas, Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nikos K.","last_name":"Logothetis","full_name":"Logothetis, Nikos K."},{"last_name":"Besserve","full_name":"Besserve, Michel","first_name":"Michel"}],"title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","date_updated":"2025-04-23T08:54:49Z","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"oa_version":"Published Version"},{"acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","article_type":"original","year":"2023","publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"doi":"10.1007/s11356-023-26844-2","day":"01","date_published":"2023-05-01T00:00:00Z","intvolume":"        30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publication":"Environmental Science and Pollution Research","oa_version":"None","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","author":[{"first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić"},{"first_name":"Nesrete","last_name":"Krasnici","full_name":"Krasnici, Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"full_name":"Valić, Damir","last_name":"Valić","first_name":"Damir"},{"first_name":"Damir","last_name":"Kapetanović","full_name":"Kapetanović, Damir"},{"last_name":"Vardić Smrzlić","full_name":"Vardić Smrzlić, Irena","first_name":"Irena"},{"first_name":"Maja","last_name":"Jordanova","full_name":"Jordanova, Maja"},{"last_name":"Rebok","full_name":"Rebok, Katerina","first_name":"Katerina"},{"first_name":"Sheriban","last_name":"Ramani","full_name":"Ramani, Sheriban"},{"full_name":"Kostov, Vasil","last_name":"Kostov","first_name":"Vasil"},{"last_name":"Nastova","full_name":"Nastova, Rodne","first_name":"Rodne"},{"full_name":"Dragun, Zrinka","last_name":"Dragun","first_name":"Zrinka"}],"date_updated":"2023-10-04T11:23:10Z","page":"63510-63521","citation":{"chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521.","mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>.","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521."},"pmid":1,"abstract":[{"text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer Nature","volume":30,"department":[{"_id":"LifeSc"}],"external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"publication_status":"published","date_created":"2023-04-23T22:01:03Z","month":"05","scopus_import":"1","_id":"12863"},{"article_processing_charge":"No","scopus_import":"1","month":"02","language":[{"iso":"eng"}],"status":"public","_id":"12866","date_updated":"2024-10-21T06:01:23Z","page":"86-98","title":"Altered childhood brain development in autism and epilepsy","author":[{"first_name":"Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","full_name":"Currin, Christopher","last_name":"Currin","orcid":"0000-0002-4809-5059"},{"first_name":"Chad","full_name":"Beyer, Chad","last_name":"Beyer"}],"alternative_title":["Vol. 1: Biological Development and Physical Health"],"edition":"1","oa_version":"None","date_created":"2023-04-25T07:52:43Z","editor":[{"first_name":"Bonnie","full_name":"Halpern-Felsher, Bonnie","last_name":"Halpern-Felsher"}],"publication_status":"published","corr_author":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiVo"}],"publication":"Encyclopedia of Child and Adolescent Health","year":"2023","publication_identifier":{"isbn":["9780128188736"]},"date_published":"2023-02-01T00:00:00Z","quality_controlled":"1","citation":{"mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>.","ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.","apa":"Currin, C., &#38; Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), <i>Encyclopedia of Child and Adolescent Health</i> (1st ed., pp. 86–98). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in <i>Encyclopedia of Child and Adolescent Health</i>, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. <i>Encyclopedia of Child and Adolescent Health</i>. 1st ed. Elsevier; 2023:86-98. doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98."},"day":"01","doi":"10.1016/b978-0-12-818872-9.00129-1","abstract":[{"lang":"eng","text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain."}],"type":"book_chapter"},{"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"ddc":["000"],"publisher":"Institute of Science and Technology Austria","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-04-26T00:00:00Z","file":[{"date_updated":"2023-04-26T12:30:06Z","file_id":"12870","content_type":"application/octet-stream","checksum":"85ede12d38bb8d944022a8cba4d719f5","relation":"main_file","date_created":"2023-04-26T12:30:06Z","success":1,"file_name":"README.md","creator":"alaurits","file_size":4567,"access_level":"open_access"},{"file_id":"12871","date_updated":"2023-04-26T12:27:34Z","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"25bf79452ae895f9c8a20571a096b4c3","date_created":"2023-04-26T12:27:34Z","file_name":"simulations_era=10_flux_varied_europe.zip","success":1,"file_size":732586731,"creator":"alaurits","access_level":"open_access"},{"access_level":"open_access","file_size":1743893150,"creator":"alaurits","success":1,"date_created":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"bca48d80ece73eb169aee7211a4a751a","file_id":"12872","date_updated":"2023-04-26T12:29:53Z"},{"success":1,"file_name":"simulations_era=10_R_varied_torus.zip","date_created":"2023-04-26T12:29:19Z","creator":"alaurits","file_size":878391851,"access_level":"open_access","date_updated":"2023-04-26T12:29:19Z","file_id":"12873","checksum":"e77a655db15486a387a36362fbf0b665","content_type":"application/x-zip-compressed","relation":"main_file"},{"file_size":201652478,"creator":"alaurits","success":1,"date_created":"2023-04-26T12:30:05Z","file_name":"simulations_era=100.zip","access_level":"open_access","file_id":"12874","date_updated":"2023-04-26T12:30:05Z","relation":"main_file","checksum":"8556406513adc4aa2e0417f46680f627","content_type":"application/x-zip-compressed"}],"oa":1,"citation":{"short":"F.R. Klausen, A.B. Lauritsen, (2023).","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. <i>Research Data for: A Stochastic Cellular Automaton Model of Culture Formation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>"},"type":"research_data","doi":"10.15479/AT:ISTA:12869","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage.  We first analyse the model  with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ","lang":"eng"}],"day":"26","acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","year":"2023","date_updated":"2025-09-09T12:26:01Z","_id":"12869","related_material":{"record":[{"status":"deleted","relation":"used_in_publication","id":"14505"},{"status":"public","relation":"used_in_publication","id":"12890"}]},"author":[{"first_name":"Frederik Ravn","full_name":"Klausen, Frederik Ravn","last_name":"Klausen"},{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard"}],"title":"Research data for: A stochastic cellular automaton model of culture formation","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2023-04-26T12:30:06Z","month":"04","status":"public","oa_version":"Published Version","date_created":"2023-04-26T12:34:49Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"publisher":"Oxford University Press","department":[{"_id":"ToHe"}],"volume":39,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data."}],"type":"journal_article","pmid":1,"citation":{"short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>, vol. 39, no. 4, btad158, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” <i>Bioinformatics</i>, vol. 39, no. 4. Oxford University Press, 2023.","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. 2023;39(4). doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>"},"issue":"4","scopus_import":"1","month":"04","_id":"12876","external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"date_created":"2023-04-30T22:01:05Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["000"],"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Bioinformatics","isi":1,"ec_funded":1,"article_type":"original","publication_identifier":{"eissn":["1367-4811"]},"acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","year":"2023","article_number":"btad158","intvolume":"        39","date_published":"2023-04-03T00:00:00Z","day":"03","doi":"10.1093/bioinformatics/btad158","oa":1,"file":[{"access_level":"open_access","success":1,"date_created":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","file_size":478740,"creator":"dernst","relation":"main_file","checksum":"2cb90ddf781baefddf47eac4b54e2a03","content_type":"application/pdf","file_id":"12886","date_updated":"2023-05-02T07:39:04Z"}],"file_date_updated":"2023-05-02T07:39:04Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-05-14T11:06:50Z","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.7688740"}]},"title":"Boolean network sketches: A unifying framework for logical model inference","author":[{"first_name":"Nikola","last_name":"Beneš","full_name":"Beneš, Nikola"},{"full_name":"Brim, Luboš","last_name":"Brim","first_name":"Luboš"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"first_name":"Samuel","last_name":"Pastva","full_name":"Pastva, Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331"},{"last_name":"Šafránek","full_name":"Šafránek, David","first_name":"David"}],"oa_version":"Published Version"},{"_id":"12877","scopus_import":"1","month":"08","date_created":"2023-04-30T22:01:05Z","publication_status":"published","external_id":{"arxiv":["1905.00890"],"isi":["000978887600001"]},"department":[{"_id":"VaKa"}],"volume":233,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.00890","open_access":"1"}],"publisher":"Springer Nature","quality_controlled":"1","citation":{"short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 829–901.","ista":"De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 233, 829–901.","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>.","mla":"De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>, vol. 233, Springer Nature, 2023, pp. 829–901, doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>.","ieee":"J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination of analytic chaotic billiards with axial symmetries,” <i>Inventiones Mathematicae</i>, vol. 233. Springer Nature, pp. 829–901, 2023.","ama":"De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. 2023;233:829-901. doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>","apa":"De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2023). Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>"},"type":"journal_article","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table."}],"page":"829-901","date_updated":"2025-04-14T07:53:46Z","author":[{"first_name":"Jacopo","last_name":"De Simoi","full_name":"De Simoi, Jacopo"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim"},{"last_name":"Leguil","full_name":"Leguil, Martin","first_name":"Martin"}],"title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Preprint","isi":1,"publication":"Inventiones Mathematicae","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707","call_identifier":"H2020"}],"date_published":"2023-08-01T00:00:00Z","intvolume":"       233","oa":1,"day":"01","doi":"10.1007/s00222-023-01191-8","acknowledgement":"J.D.S. and M.L. have been partially supported by the NSERC Discovery grant, reference number 502617-2017. M.L. was also supported by the ERC project 692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012). V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"year":"2023","article_type":"original","ec_funded":1},{"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","author":[{"last_name":"Jiang","full_name":"Jiang, Lihui","first_name":"Lihui"},{"last_name":"Yao","full_name":"Yao, Baolin","first_name":"Baolin"},{"last_name":"Zhang","full_name":"Zhang, Xiaoyan","first_name":"Xiaoyan"},{"full_name":"Wu, Lixia","last_name":"Wu","first_name":"Lixia"},{"first_name":"Qijing","last_name":"Fu","full_name":"Fu, Qijing"},{"first_name":"Yiting","full_name":"Zhao, Yiting","last_name":"Zhao"},{"last_name":"Cao","full_name":"Cao, Yuxin","first_name":"Yuxin"},{"first_name":"Ruomeng","last_name":"Zhu","full_name":"Zhu, Ruomeng"},{"last_name":"Lu","full_name":"Lu, Xinqi","first_name":"Xinqi"},{"first_name":"Wuying","full_name":"Huang, Wuying","last_name":"Huang"},{"full_name":"Zhao, Jianping","last_name":"Zhao","first_name":"Jianping"},{"last_name":"Li","full_name":"Li, Kuixiu","first_name":"Kuixiu"},{"first_name":"Shuanglu","last_name":"Zhao","full_name":"Zhao, Shuanglu"},{"full_name":"Han, Li","last_name":"Han","first_name":"Li"},{"first_name":"Xuan","last_name":"Zhou","full_name":"Zhou, Xuan"},{"full_name":"Luo, Chongyu","last_name":"Luo","first_name":"Chongyu"},{"first_name":"Haiyan","full_name":"Zhu, Haiyan","last_name":"Zhu"},{"last_name":"Yang","full_name":"Yang, Jing","first_name":"Jing"},{"full_name":"Huang, Huichuan","last_name":"Huang","first_name":"Huichuan"},{"full_name":"Zhu, Zhengge","last_name":"Zhu","first_name":"Zhengge"},{"first_name":"Xiahong","full_name":"He, Xiahong","last_name":"He"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Zhang","full_name":"Zhang, Zhongkai","first_name":"Zhongkai"},{"first_name":"Changning","full_name":"Liu, Changning","last_name":"Liu"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"}],"date_updated":"2025-06-25T08:50:43Z","page":"155-174","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication":"Plant Journal","isi":1,"acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","year":"2023","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"article_type":"original","doi":"10.1111/tpj.16218","day":"01","oa":1,"intvolume":"       115","date_published":"2023-07-01T00:00:00Z","month":"07","scopus_import":"1","issue":"1","_id":"12878","external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"publication_status":"published","date_created":"2023-04-30T22:01:06Z","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/tpj.16218"}],"volume":115,"OA_type":"free access","department":[{"_id":"JiFr"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"pmid":1,"citation":{"short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>.","ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>.","ieee":"L. Jiang <i>et al.</i>, “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” <i>Plant Journal</i>, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. 2023;115(1):155-174. doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>"},"quality_controlled":"1"},{"oa_version":"Published Version","date_updated":"2023-08-01T14:18:10Z","author":[{"first_name":"Ke","last_name":"Chen","full_name":"Chen, Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d"},{"last_name":"Kunkel","full_name":"Kunkel, Christian","first_name":"Christian"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Reuter, Karsten","last_name":"Reuter","first_name":"Karsten"},{"last_name":"Margraf","full_name":"Margraf, Johannes T.","first_name":"Johannes T."}],"title":"Physics-inspired machine learning of localized intensive properties","has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2023-05-02T07:17:05Z","status":"public","language":[{"iso":"eng"}],"date_published":"2023-04-10T00:00:00Z","oa":1,"file":[{"file_name":"2023_ChemialScience_Chen.pdf","date_created":"2023-05-02T07:17:05Z","success":1,"creator":"dernst","file_size":1515446,"access_level":"open_access","date_updated":"2023-05-02T07:17:05Z","file_id":"12883","checksum":"5eeec69a51e192dcd94b955d84423836","content_type":"application/pdf","relation":"main_file"}],"day":"10","doi":"10.1039/d3sc00841j","year":"2023","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","article_type":"original","isi":1,"publication":"Chemical Science","ddc":["000","540"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-04-30T22:01:06Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"publication_status":"published","external_id":{"isi":["000971508100001"]},"_id":"12879","scopus_import":"1","month":"04","quality_controlled":"1","citation":{"ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. 2023. doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” <i>Chemical Science</i>. Royal Society of Chemistry, 2023.","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., &#38; Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>.","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>, Royal Society of Chemistry, 2023, doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023)."},"type":"journal_article","abstract":[{"lang":"eng","text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations."}],"department":[{"_id":"BiCh"}],"publisher":"Royal Society of Chemistry"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"publication":"Nucleus","isi":1,"article_number":"2202548","year":"2023","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"article_type":"original","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","doi":"10.1080/19491034.2023.2202548","day":"18","file":[{"file_id":"12884","date_updated":"2023-05-02T07:24:55Z","relation":"main_file","content_type":"application/pdf","checksum":"8e707eda84f64dbad7f03545ae0a83ef","success":1,"date_created":"2023-05-02T07:24:55Z","file_name":"2023_Nucleus_Kaneshiro.pdf","file_size":3811113,"creator":"dernst","access_level":"open_access"}],"oa":1,"intvolume":"        14","date_published":"2023-04-18T00:00:00Z","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2023-05-02T07:24:55Z","has_accepted_license":"1","article_processing_charge":"No","title":"Lamin B1 overexpression alters chromatin organization and gene expression","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"first_name":"Juliana S.","full_name":"Capitanio, Juliana S.","last_name":"Capitanio"},{"first_name":"Martin W","full_name":"Hetzer, Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"date_updated":"2024-10-09T21:05:01Z","oa_version":"Published Version","corr_author":"1","publisher":"Taylor & Francis","volume":14,"department":[{"_id":"MaHe"}],"abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"type":"journal_article","pmid":1,"citation":{"apa":"Kaneshiro, J. M., Capitanio, J. S., &#38; Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” <i>Nucleus</i>, vol. 14, no. 1. Taylor &#38; Francis, 2023.","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>.","mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>, vol. 14, no. 1, 2202548, Taylor &#38; Francis, 2023, doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023)."},"quality_controlled":"1","month":"04","issue":"1","scopus_import":"1","_id":"12880","external_id":{"isi":["000971629400001"],"pmid":["37071033"]},"publication_status":"published","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"date_created":"2023-04-30T22:01:06Z"},{"issue":"5","scopus_import":"1","month":"11","_id":"12890","external_id":{"pmid":["38115445"],"arxiv":["2305.02153"],"isi":["001106396300005"]},"date_created":"2023-05-04T08:35:01Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.02153"}],"publisher":"American Physical Society","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"volume":108,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders."}],"pmid":1,"type":"journal_article","citation":{"apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023)."},"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-09-09T12:26:01Z","related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"relation":"research_data","id":"12869","status":"public"}]},"author":[{"last_name":"Klausen","full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard"}],"title":"Stochastic cellular automaton model of culture formation","oa_version":"Preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"Physical Review E","isi":1,"article_type":"original","year":"2023","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","article_number":"054307","intvolume":"       108","date_published":"2023-11-08T00:00:00Z","day":"08","doi":"10.1103/PhysRevE.108.054307","oa":1},{"external_id":{"isi":["000990804300001"],"arxiv":["2106.11217"]},"publication_status":"published","date_created":"2023-05-07T22:01:02Z","month":"08","scopus_import":"1","issue":"4","_id":"12911","citation":{"short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>Journal of Functional Analysis</i>, vol. 285, no. 4. Elsevier, 2023.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. 2023;285(4). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>, vol. 285, no. 4, 109963, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>.","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>.","ista":"Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963."},"abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"volume":285,"department":[{"_id":"RoSe"},{"_id":"JaMa"}],"oa_version":"Preprint","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","author":[{"first_name":"Dario","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530"},{"first_name":"Augusto","last_name":"Gerolin","full_name":"Gerolin, Augusto"},{"full_name":"Portinale, Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"}],"date_updated":"2025-04-15T08:31:52Z","related_material":{"record":[{"id":"9792","relation":"earlier_version","status":"public"}]},"article_number":"109963","year":"2023","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813.","article_type":"original","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"ec_funded":1,"oa":1,"day":"15","doi":"10.1016/j.jfa.2023.109963","date_published":"2023-08-15T00:00:00Z","intvolume":"       285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":"F06504"}],"isi":1,"publication":"Journal of Functional Analysis","arxiv":1},{"_id":"12912","month":"04","issue":"16","scopus_import":"1","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2023-05-07T22:01:03Z","external_id":{"pmid":["37093149"],"arxiv":["2302.01297"],"isi":["001010676000010"]},"volume":158,"department":[{"_id":"BiCh"}],"corr_author":"1","publisher":"AIP Publishing","type":"journal_article","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"pmid":1,"citation":{"ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. 2023;158(16). doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16. AIP Publishing, 2023.","apa":"Schmid, R., &#38; Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>","mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>.","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023)."},"quality_controlled":"1","title":"Computing chemical potentials of adsorbed or confined fluids","author":[{"full_name":"Schmid, Rochus","last_name":"Schmid","first_name":"Rochus"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"}],"date_updated":"2024-10-09T21:05:04Z","related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"language":[{"iso":"eng"}],"status":"public","file_date_updated":"2023-05-08T07:44:49Z","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","arxiv":1,"publication":"The Journal of Chemical Physics","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["540"],"doi":"10.1063/5.0146711","day":"24","oa":1,"file":[{"access_level":"open_access","date_created":"2023-05-08T07:44:49Z","success":1,"file_name":"2023_JourChemicalPhysics_Schmid.pdf","file_size":6499468,"creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"4ab8c965f2fa4e17920bfa846847f137","file_id":"12918","date_updated":"2023-05-08T07:44:49Z"}],"intvolume":"       158","date_published":"2023-04-24T00:00:00Z","article_number":"161101 ","article_type":"original","acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.","year":"2023","publication_identifier":{"eissn":["1089-7690"]}},{"publisher":"Springer Nature","department":[{"_id":"AnHi"}],"volume":14,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices."}],"pmid":1,"type":"journal_article","citation":{"ieee":"J. Díez-Mérida <i>et al.</i>, “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>","mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>, vol. 14, 2396, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>.","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>.","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023)."},"scopus_import":"1","month":"04","_id":"12913","external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"date_created":"2023-05-07T22:01:03Z","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature Communications","isi":1,"article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","year":"2023","article_number":"2396","intvolume":"        14","date_published":"2023-04-26T00:00:00Z","doi":"10.1038/s41467-023-38005-7","day":"26","file":[{"file_size":1405588,"creator":"dernst","success":1,"file_name":"2023_NatureComm_DiezMerida.pdf","date_created":"2023-05-08T07:26:40Z","access_level":"open_access","file_id":"12917","date_updated":"2023-05-08T07:26:40Z","relation":"main_file","checksum":"a778105665c10beb2354c92d2b295115","content_type":"application/pdf"}],"oa":1,"file_date_updated":"2023-05-08T07:26:40Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","date_updated":"2023-08-01T14:34:00Z","author":[{"first_name":"J.","full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida"},{"first_name":"A.","full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón"},{"first_name":"S. Y.","last_name":"Yang","full_name":"Yang, S. Y."},{"last_name":"Xie","full_name":"Xie, Y. M.","first_name":"Y. M."},{"full_name":"Gao, X. J.","last_name":"Gao","first_name":"X. J."},{"last_name":"Senior","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"X.","last_name":"Lu","full_name":"Lu, X."},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","first_name":"Andrew P"},{"last_name":"Law","full_name":"Law, K. T.","first_name":"K. T."},{"first_name":"Dmitri K.","full_name":"Efetov, Dmitri K.","last_name":"Efetov"}],"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","oa_version":"Published Version"},{"date_updated":"2025-04-14T07:44:01Z","author":[{"id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","last_name":"Suzuki","full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970","first_name":"Fumika"},{"first_name":"William G.","full_name":"Unruh, William G.","last_name":"Unruh"}],"title":"Numerical quantum clock simulations for measuring tunneling times","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Preprint","isi":1,"publication":"Physical Review A","arxiv":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2023-04-20T00:00:00Z","intvolume":"       107","oa":1,"day":"20","doi":"10.1103/PhysRevA.107.042216","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"year":"2023","article_type":"original","acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","ec_funded":1,"article_number":"042216","_id":"12914","issue":"4","scopus_import":"1","month":"04","date_created":"2023-05-07T22:01:03Z","publication_status":"published","external_id":{"isi":["000975799300006"],"arxiv":["2207.13130"]},"department":[{"_id":"MiLe"}],"volume":107,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.13130"}],"corr_author":"1","publisher":"American Physical Society","quality_controlled":"1","citation":{"short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” <i>Physical Review A</i>, vol. 107, no. 4. American Physical Society, 2023.","apa":"Suzuki, F., &#38; Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">https://doi.org/10.1103/PhysRevA.107.042216</a>","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. <i>Physical Review A</i>. 2023;107(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">10.1103/PhysRevA.107.042216</a>","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” <i>Physical Review A</i>, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">10.1103/PhysRevA.107.042216</a>.","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">https://doi.org/10.1103/PhysRevA.107.042216</a>."},"abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"type":"journal_article"},{"article_type":"original","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"acknowledgement":"The authors acknowledge support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/and by “ERDF A way of making Europe”, and by the “European Union”. K.X. and B.N. thank the China Scholarship Council (CSC) for scholarship support. The authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246. ICN2 is supported by the Severo Ochoa program from the Spanish MCIN/AEI (Grant No.: CEX2021-001214-S). IREC and ICN2 are funded by the CERCA Programme/Generalitat de Catalunya. J.L. acknowledges support from the Natural Science Foundation of Sichuan province (2022NSFSC1229). Part of the present work was performed in the frameworks of Universitat de Barcelona Nanoscience Ph.D. program and Universitat Autònoma de Barcelona Materials Science Ph.D. program. Y.L. acknowledges funding from the National Natural Science Foundation of China (Grant No. 22209034) and the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grants No. 2022LCX002). K.H.L. acknowledges the financial support of the National Natural Science Foundation of China (Grant No. 22208293).","year":"2023","oa":1,"day":"09","doi":"10.1021/acsnano.3c00495","date_published":"2023-05-09T00:00:00Z","intvolume":"        17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","isi":1,"publication":"ACS Nano","oa_version":"Submitted Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites","author":[{"first_name":"Congcong","full_name":"Xing, Congcong","last_name":"Xing"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Ke","last_name":"Xiao","full_name":"Xiao, Ke"},{"first_name":"Xu","full_name":"Han, Xu","last_name":"Han"},{"first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"last_name":"Nan","full_name":"Nan, Bingfei","first_name":"Bingfei"},{"first_name":"Maria Garcia","last_name":"Ramon","full_name":"Ramon, Maria Garcia","id":"1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Poudel","full_name":"Poudel, Bed","first_name":"Bed"},{"first_name":"Amin","full_name":"Nozariasbmarz, Amin","last_name":"Nozariasbmarz"},{"first_name":"Wenjie","last_name":"Li","full_name":"Li, Wenjie"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"page":"8442-8452","date_updated":"2025-06-25T06:01:54Z","citation":{"short":"C. Xing, Y. Zhang, K. Xiao, X. Han, Y. Liu, B. Nan, M.G. Ramon, K.H. Lim, J. Li, J. Arbiol, B. Poudel, A. Nozariasbmarz, W. Li, M. Ibáñez, A. Cabot, ACS Nano 17 (2023) 8442–8452.","ieee":"C. Xing <i>et al.</i>, “Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites,” <i>ACS Nano</i>, vol. 17, no. 9. American Chemical Society, pp. 8442–8452, 2023.","ama":"Xing C, Zhang Y, Xiao K, et al. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. <i>ACS Nano</i>. 2023;17(9):8442-8452. doi:<a href=\"https://doi.org/10.1021/acsnano.3c00495\">10.1021/acsnano.3c00495</a>","apa":"Xing, C., Zhang, Y., Xiao, K., Han, X., Liu, Y., Nan, B., … Cabot, A. (2023). Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c00495\">https://doi.org/10.1021/acsnano.3c00495</a>","ista":"Xing C, Zhang Y, Xiao K, Han X, Liu Y, Nan B, Ramon MG, Lim KH, Li J, Arbiol J, Poudel B, Nozariasbmarz A, Li W, Ibáñez M, Cabot A. 2023. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 17(9), 8442–8452.","chicago":"Xing, Congcong, Yu Zhang, Ke Xiao, Xu Han, Yu Liu, Bingfei Nan, Maria Garcia Ramon, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.3c00495\">https://doi.org/10.1021/acsnano.3c00495</a>.","mla":"Xing, Congcong, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” <i>ACS Nano</i>, vol. 17, no. 9, American Chemical Society, 2023, pp. 8442–52, doi:<a href=\"https://doi.org/10.1021/acsnano.3c00495\">10.1021/acsnano.3c00495</a>."},"abstract":[{"text":"Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K.","lang":"eng"}],"type":"journal_article","pmid":1,"quality_controlled":"1","corr_author":"1","publisher":"American Chemical Society","main_file_link":[{"url":"https://ddd.uab.cat/pub/artpub/2023/zlnqprw07rek/acsnan_a2023_Pre.pdf","open_access":"1"}],"volume":17,"OA_type":"green","department":[{"_id":"MaIb"}],"external_id":{"isi":["000976063200001"],"pmid":["37071412"]},"publication_status":"published","date_created":"2023-05-07T22:01:04Z","month":"05","issue":"9","scopus_import":"1","_id":"12915"},{"external_id":{"arxiv":["2007.14182"]},"publication_status":"published","date_created":"2023-05-07T22:01:04Z","month":"02","scopus_import":"1","issue":"1","_id":"12916","abstract":[{"text":"We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.\r\n","lang":"eng"}],"type":"journal_article","citation":{"short":"D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204.","ama":"Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic fibrations. <i>Annali della Scuola Normale Superiore di Pisa - Classe di Scienze</i>. 2023;24(1):173-204. doi:<a href=\"https://doi.org/10.2422/2036-2145.202010_018\">10.2422/2036-2145.202010_018</a>","ieee":"D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic fibrations,” <i>Annali della Scuola Normale Superiore di Pisa - Classe di Scienze</i>, vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204, 2023.","apa":"Bonolis, D., &#38; Browning, T. D. (2023). Uniform bounds for rational points on hyperelliptic fibrations. <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale. <a href=\"https://doi.org/10.2422/2036-2145.202010_018\">https://doi.org/10.2422/2036-2145.202010_018</a>","chicago":"Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale, 2023. <a href=\"https://doi.org/10.2422/2036-2145.202010_018\">https://doi.org/10.2422/2036-2145.202010_018</a>.","ista":"Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 24(1), 173–204.","mla":"Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della Normale, 2023, pp. 173–204, doi:<a href=\"https://doi.org/10.2422/2036-2145.202010_018\">10.2422/2036-2145.202010_018</a>."},"quality_controlled":"1","publisher":"Scuola Normale Superiore - Edizioni della Normale","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2007.14182","open_access":"1"}],"volume":24,"department":[{"_id":"TiBr"}],"oa_version":"Preprint","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Dante","id":"6A459894-5FDD-11E9-AF35-BB24E6697425","full_name":"Bonolis, Dante","last_name":"Bonolis"},{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D"}],"title":"Uniform bounds for rational points on hyperelliptic fibrations","page":"173-204","date_updated":"2024-10-09T21:05:05Z","year":"2023","article_type":"original","publication_identifier":{"issn":["0391-173X"],"eissn":["2036-2145"]},"day":"16","doi":"10.2422/2036-2145.202010_018","oa":1,"intvolume":"        24","date_published":"2023-02-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Annali della Scuola Normale Superiore di Pisa - Classe di Scienze","arxiv":1},{"volume":55,"publisher":"Georg Thieme Verlag","quality_controlled":"1","citation":{"short":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, B. Pieber, Synthesis 55 (2023) 1367–1374.","chicago":"Murakami, Sho, Cosima Brudy, Moritz Bachmann, Yoshiji Takemoto, and Bartholomäus Pieber. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” <i>Synthesis</i>. Georg Thieme Verlag, 2023. <a href=\"https://doi.org/10.1055/a-1979-5933\">https://doi.org/10.1055/a-1979-5933</a>.","ista":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. 2023. Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. 55(09), 1367–1374.","mla":"Murakami, Sho, et al. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” <i>Synthesis</i>, vol. 55, no. 09, Georg Thieme Verlag, 2023, pp. 1367–74, doi:<a href=\"https://doi.org/10.1055/a-1979-5933\">10.1055/a-1979-5933</a>.","ama":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. Photocatalytic cleavage of trityl protected thiols and alcohols. <i>Synthesis</i>. 2023;55(09):1367-1374. doi:<a href=\"https://doi.org/10.1055/a-1979-5933\">10.1055/a-1979-5933</a>","apa":"Murakami, S., Brudy, C., Bachmann, M., Takemoto, Y., &#38; Pieber, B. (2023). Photocatalytic cleavage of trityl protected thiols and alcohols. <i>Synthesis</i>. Georg Thieme Verlag. <a href=\"https://doi.org/10.1055/a-1979-5933\">https://doi.org/10.1055/a-1979-5933</a>","ieee":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, and B. Pieber, “Photocatalytic cleavage of trityl protected thiols and alcohols,” <i>Synthesis</i>, vol. 55, no. 09. Georg Thieme Verlag, pp. 1367–1374, 2023."},"abstract":[{"text":"We report the visible light photocatalytic cleavage of trityl thioethers or ethers under pH-neutral conditions. The method results in the formation of the respective symmetrical disulfides and alcohols in moderate to excellent yield. The protocol only requires the addition of a suitable photocatalyst and light rendering it orthogonal to several functionalities, including acid labile protective groups. The same conditions can be used to directly convert trityl-protected thiols into unsymmetrical disulfides or selenosulfides, and to cleave trityl resins in solid phase organic synthesis.","lang":"eng"}],"extern":"1","type":"journal_article","_id":"12919","issue":"09","scopus_import":"1","month":"05","date_created":"2023-05-08T08:25:08Z","publication_status":"published","publication":"Synthesis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-05-01T00:00:00Z","intvolume":"        55","doi":"10.1055/a-1979-5933","day":"01","article_type":"original","year":"2023","publication_identifier":{"eissn":["1437-210X"],"issn":["0039-7881"]},"date_updated":"2024-10-14T12:08:22Z","page":"1367-1374","author":[{"full_name":"Murakami, Sho","last_name":"Murakami","first_name":"Sho"},{"last_name":"Brudy","full_name":"Brudy, Cosima","first_name":"Cosima"},{"first_name":"Moritz","full_name":"Bachmann, Moritz","last_name":"Bachmann"},{"full_name":"Takemoto, Yoshiji","last_name":"Takemoto","first_name":"Yoshiji"},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X"}],"title":"Photocatalytic cleavage of trityl protected thiols and alcohols","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"None","keyword":["Organic Chemistry","Catalysis"]}]