[{"day":"20","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13991,"title":"Vamos: Middleware for best-effort third-party monitoring","status":"public","oa_version":"Published Version","date_created":"2023-04-20T08:29:42Z","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"publication":"Fundamental Approaches to Software Engineering","file_date_updated":"2023-04-25T07:16:36Z","type":"conference","_id":"12856","article_processing_charge":"No","author":[{"last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","full_name":"Chalupa, Marek"},{"first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"}],"department":[{"_id":"ToHe"}],"month":"04","date_published":"2023-04-20T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-04-25T07:19:07Z","publisher":"Springer Nature","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308253"],"eisbn":["9783031308260"],"issn":["0302-9743"]},"has_accepted_license":"1","intvolume":"     13991","ec_funded":1,"quality_controlled":"1","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.","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.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 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>.","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>","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>"},"doi":"10.1007/978-3-031-30826-0_15","related_material":{"record":[{"status":"public","id":"12407","relation":"earlier_version"}]},"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.","conference":{"start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France","name":"FASE: Fundamental Approaches to Software Engineering"},"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."}],"ddc":["000"],"oa":1,"file":[{"creator":"dernst","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_size":580828,"date_updated":"2023-04-25T07:16:36Z","access_level":"open_access","date_created":"2023-04-25T07:16:36Z","file_id":"12865","relation":"main_file","file_name":"2023_LNCS_ChalupaM.pdf","content_type":"application/pdf","success":1}],"page":"260-281","alternative_title":["LNCS"]},{"date_created":"2023-04-23T16:11:03Z","oa_version":"Preprint","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"publication":"Proceedings of the 40th International Conference on Machine Learning","_id":"12859","type":"conference","article_processing_charge":"No","author":[{"last_name":"Bombari","first_name":"Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone"},{"full_name":"Kiyani, Shayan","first_name":"Shayan","id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","last_name":"Kiyani"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"department":[{"_id":"GradSch"},{"_id":"MaMo"}],"day":"27","volume":202,"title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"month":"10","date_published":"2023-10-27T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-09-10T13:03:19Z","publisher":"ML Research Press","quality_controlled":"1","citation":{"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.","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.","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.","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.","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.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","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."},"related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}]},"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","conference":{"location":"Honolulu, HI, United States","end_date":"2023-07-29","start_date":"2023-07-23","name":"ICML: International Conference on Machine Learning"},"year":"2023","language":[{"iso":"eng"}],"arxiv":1,"intvolume":"       202","page":"2738-2776","alternative_title":["PMLR"],"external_id":{"arxiv":["2302.01629"]},"abstract":[{"lang":"eng","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)."}],"oa":1},{"month":"04","date_published":"2023-04-12T00:00:00Z","article_type":"original","publisher":"Springer Nature","date_updated":"2025-07-14T09:09:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","scopus_import":"1","day":"12","article_number":"2086","status":"public","volume":14,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","article_processing_charge":"No","_id":"12861","type":"journal_article","publication":"Nature Communications","file_date_updated":"2023-04-25T09:13:53Z","project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"oa_version":"Published Version","date_created":"2023-04-23T22:01:03Z","department":[{"_id":"KrCh"}],"author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura"},{"last_name":"Ekbatani","first_name":"Farbod","full_name":"Ekbatani, Farbod"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"}],"file":[{"relation":"main_file","file_name":"2023_NatureComm_Schmid.pdf","content_type":"application/pdf","success":1,"date_created":"2023-04-25T09:13:53Z","access_level":"open_access","file_id":"12868","date_updated":"2023-04-25T09:13:53Z","creator":"dernst","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","file_size":1786475}],"ddc":["000"],"oa":1,"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"}],"external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"isi":1,"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"year":"2023","pmid":1,"intvolume":"        14","has_accepted_license":"1","citation":{"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>","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.","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","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>.","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>","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>.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023)."},"doi":"10.1038/s41467-023-37817-x","quality_controlled":"1","ec_funded":1,"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."},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"year":"2023","intvolume":"        19","has_accepted_license":"1","quality_controlled":"1","citation":{"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>","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>","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>.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","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.","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.","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>."},"doi":"10.1371/journal.pcbi.1010983","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. ","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"file":[{"file_name":"2023_PLoSCompBio_Safavi.pdf","relation":"main_file","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2023-04-25T08:59:18Z","file_id":"12867","date_updated":"2023-04-25T08:59:18Z","creator":"dernst","file_size":4737671,"checksum":"edeb9d09f3e41ba7c0251308b9e372e7"}],"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."}],"ddc":["570"],"oa":1,"external_id":{"isi":["000962668700002"]},"isi":1,"day":"01","status":"public","article_number":"e1010983","volume":19,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","file_date_updated":"2023-04-25T08:59:18Z","publication":"PLoS Computational Biology","issue":"4","_id":"12862","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2023-04-23T22:01:03Z","department":[{"_id":"JoCs"}],"author":[{"last_name":"Safavi","first_name":"Shervin","full_name":"Safavi, Shervin"},{"first_name":"Theofanis I.","last_name":"Panagiotaropoulos","full_name":"Panagiotaropoulos, Theofanis I."},{"first_name":"Vishal","last_name":"Kapoor","full_name":"Kapoor, Vishal"},{"full_name":"Ramirez Villegas, Juan F","first_name":"Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas"},{"full_name":"Logothetis, Nikos K.","last_name":"Logothetis","first_name":"Nikos K."},{"last_name":"Besserve","first_name":"Michel","full_name":"Besserve, Michel"}],"article_type":"original","date_published":"2023-04-01T00:00:00Z","month":"04","date_updated":"2023-08-01T14:15:16Z","publisher":"Public Library of Science","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1"},{"month":"04","date_published":"2023-04-26T00:00:00Z","file":[{"checksum":"85ede12d38bb8d944022a8cba4d719f5","file_size":4567,"creator":"alaurits","date_updated":"2023-04-26T12:30:06Z","file_id":"12870","access_level":"open_access","date_created":"2023-04-26T12:30:06Z","content_type":"application/octet-stream","success":1,"relation":"main_file","file_name":"README.md"},{"content_type":"application/x-zip-compressed","success":1,"file_name":"simulations_era=10_flux_varied_europe.zip","relation":"main_file","file_id":"12871","access_level":"open_access","date_created":"2023-04-26T12:27:34Z","date_updated":"2023-04-26T12:27:34Z","checksum":"25bf79452ae895f9c8a20571a096b4c3","file_size":732586731,"creator":"alaurits"},{"file_id":"12872","access_level":"open_access","date_created":"2023-04-26T12:29:53Z","content_type":"application/x-zip-compressed","success":1,"relation":"main_file","file_name":"simulations_era=10_flux_varied_torus.zip","checksum":"bca48d80ece73eb169aee7211a4a751a","file_size":1743893150,"creator":"alaurits","date_updated":"2023-04-26T12:29:53Z"},{"checksum":"e77a655db15486a387a36362fbf0b665","file_size":878391851,"creator":"alaurits","date_updated":"2023-04-26T12:29:19Z","file_id":"12873","access_level":"open_access","date_created":"2023-04-26T12:29:19Z","content_type":"application/x-zip-compressed","success":1,"relation":"main_file","file_name":"simulations_era=10_R_varied_torus.zip"},{"access_level":"open_access","date_created":"2023-04-26T12:30:05Z","file_id":"12874","file_name":"simulations_era=100.zip","relation":"main_file","success":1,"content_type":"application/x-zip-compressed","creator":"alaurits","checksum":"8556406513adc4aa2e0417f46680f627","file_size":201652478,"date_updated":"2023-04-26T12:30:05Z"}],"oa":1,"ddc":["000"],"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"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2023-11-13T07:47:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12869","article_processing_charge":"No","type":"research_data","file_date_updated":"2023-04-26T12:30:06Z","citation":{"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>","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>.","short":"F.R. Klausen, A.B. Lauritsen, (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>","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>.","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>.","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."},"doi":"10.15479/AT:ISTA:12869","oa_version":"Published Version","date_created":"2023-04-26T12:34:49Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"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. ","related_material":{"record":[{"status":"for_moderation","id":"14505","relation":"used_in_publication"},{"status":"public","id":"12890","relation":"used_in_publication"}]},"author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288"}],"year":"2023","day":"26","status":"public","title":"Research data for: A stochastic cellular automaton model of culture formation","tmp":{"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)","short":"CC0 (1.0)"},"has_accepted_license":"1"},{"scopus_import":"1","article_type":"original","month":"04","date_published":"2023-04-03T00:00:00Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T14:27:28Z","publisher":"Oxford Academic","oa_version":"Published Version","date_created":"2023-04-30T22:01:05Z","project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"file_date_updated":"2023-05-02T07:39:04Z","publication":"Bioinformatics","type":"journal_article","_id":"12876","issue":"4","article_processing_charge":"No","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"full_name":"Brim, Luboš","first_name":"Luboš","last_name":"Brim"},{"last_name":"Huvar","first_name":"Ondřej","full_name":"Huvar, Ondřej"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","last_name":"Pastva","full_name":"Pastva, Samuel"},{"first_name":"David","last_name":"Šafránek","full_name":"Šafránek, David"}],"department":[{"_id":"ToHe"}],"day":"03","volume":39,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Boolean network sketches: A unifying framework for logical model inference","status":"public","article_number":"btad158","isi":1,"external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"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."}],"ddc":["000"],"oa":1,"file":[{"date_updated":"2023-05-02T07:39:04Z","creator":"dernst","checksum":"2cb90ddf781baefddf47eac4b54e2a03","file_size":478740,"file_name":"2023_Bioinformatics_Benes.pdf","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2023-05-02T07:39:04Z","file_id":"12886"}],"quality_controlled":"1","ec_funded":1,"doi":"10.1093/bioinformatics/btad158","citation":{"mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>, vol. 39, no. 4, btad158, Oxford Academic, 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 Academic, 2023.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","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 Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>.","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 Academic. <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>"},"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"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","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1367-4811"]},"has_accepted_license":"1","intvolume":"        39","pmid":1},{"arxiv":1,"intvolume":"       233","publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"language":[{"iso":"eng"}],"year":"2023","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.","citation":{"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>","short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 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>.","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.","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.","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>.","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>"},"doi":"10.1007/s00222-023-01191-8","ec_funded":1,"quality_controlled":"1","oa":1,"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."}],"external_id":{"isi":["000978887600001"],"arxiv":["1905.00890"]},"isi":1,"page":"829-901","status":"public","title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","volume":233,"day":"01","department":[{"_id":"VaKa"}],"author":[{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Martin","last_name":"Leguil","full_name":"Leguil, Martin"}],"article_processing_charge":"No","_id":"12877","type":"journal_article","publication":"Inventiones Mathematicae","project":[{"grant_number":"885707","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"date_created":"2023-04-30T22:01:05Z","oa_version":"Preprint","publisher":"Springer Nature","date_updated":"2023-10-04T11:25:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2023-08-01T00:00:00Z","month":"08","article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.00890","open_access":"1"}]},{"isi":1,"external_id":{"isi":["000971508100001"]},"abstract":[{"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.","lang":"eng"}],"ddc":["000","540"],"oa":1,"file":[{"creator":"dernst","checksum":"5eeec69a51e192dcd94b955d84423836","file_size":1515446,"date_updated":"2023-05-02T07:17:05Z","date_created":"2023-05-02T07:17:05Z","access_level":"open_access","file_id":"12883","file_name":"2023_ChemialScience_Chen.pdf","relation":"main_file","success":1,"content_type":"application/pdf"}],"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.","quality_controlled":"1","doi":"10.1039/d3sc00841j","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.","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","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>.","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>","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>.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023)."},"has_accepted_license":"1","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"scopus_import":"1","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T14:18:10Z","publisher":"Royal Society of Chemistry","article_type":"original","date_published":"2023-04-10T00:00:00Z","month":"04","author":[{"full_name":"Chen, Ke","first_name":"Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","last_name":"Chen"},{"full_name":"Kunkel, Christian","first_name":"Christian","last_name":"Kunkel"},{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"full_name":"Reuter, Karsten","first_name":"Karsten","last_name":"Reuter"},{"full_name":"Margraf, Johannes T.","last_name":"Margraf","first_name":"Johannes T."}],"department":[{"_id":"BiCh"}],"oa_version":"Published Version","date_created":"2023-04-30T22:01:06Z","publication":"Chemical Science","file_date_updated":"2023-05-02T07:17:05Z","type":"journal_article","_id":"12879","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"title":"Physics-inspired machine learning of localized intensive properties","status":"public","day":"10"},{"year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1949-1042"],"issn":["1949-1034"]},"has_accepted_license":"1","pmid":1,"intvolume":"        14","doi":"10.1080/19491034.2023.2202548","citation":{"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>","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>.","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.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","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>.","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>"},"quality_controlled":"1","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","ddc":["570"],"oa":1,"abstract":[{"lang":"eng","text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1."}],"file":[{"creator":"dernst","file_size":3811113,"checksum":"8e707eda84f64dbad7f03545ae0a83ef","date_updated":"2023-05-02T07:24:55Z","access_level":"open_access","date_created":"2023-05-02T07:24:55Z","file_id":"12884","file_name":"2023_Nucleus_Kaneshiro.pdf","relation":"main_file","success":1,"content_type":"application/pdf"}],"isi":1,"external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"day":"18","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Lamin B1 overexpression alters chromatin organization and gene expression","volume":14,"article_number":"2202548","status":"public","date_created":"2023-04-30T22:01:06Z","oa_version":"Published Version","_id":"12880","type":"journal_article","issue":"1","article_processing_charge":"No","file_date_updated":"2023-05-02T07:24:55Z","publication":"Nucleus","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"last_name":"Capitanio","first_name":"Juliana S.","full_name":"Capitanio, Juliana S."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"Hetzer","orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W"}],"department":[{"_id":"MaHe"}],"month":"04","date_published":"2023-04-18T00:00:00Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Taylor & Francis","date_updated":"2023-08-01T14:18:46Z","scopus_import":"1"},{"ec_funded":1,"doi":"10.15479/at:ista:12885","citation":{"mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>"},"related_material":{"record":[{"id":"10806","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"status":"public","id":"12237","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"9118"},{"id":"10123","status":"public","relation":"part_of_dissertation"}]},"year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"has_accepted_license":"1","supervisor":[{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"alternative_title":["ISTA Thesis"],"page":"82","abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"degree_awarded":"PhD","ddc":["546","541"],"oa":1,"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Calcabrini.docx","file_id":"12887","access_level":"closed","date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z","file_size":99627036,"checksum":"9347b0e09425f56fdcede5d3528404dc","creator":"mcalcabr"},{"date_created":"2023-05-02T07:42:45Z","access_level":"open_access","file_id":"12888","relation":"main_file","file_name":"Thesis_Calcabrini_pdfa.pdf","content_type":"application/pdf","success":1,"creator":"mcalcabr","checksum":"2d188b76621086cd384f0b9264b0a576","file_size":8742220,"date_updated":"2023-05-02T07:42:45Z"}],"oa_version":"Published Version","date_created":"2023-05-02T07:58:57Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020"}],"file_date_updated":"2023-05-02T07:43:18Z","type":"dissertation","_id":"12885","article_processing_charge":"No","author":[{"full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877","last_name":"Calcabrini","first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"day":"28","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","status":"public","month":"04","date_published":"2023-04-28T00:00:00Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-08-14T07:25:26Z","publisher":"Institute of Science and Technology Austria"},{"author":[{"full_name":"Klausen, Frederik Ravn","last_name":"Klausen","first_name":"Frederik Ravn"},{"full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard"}],"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_created":"2023-05-04T08:35:01Z","oa_version":"Preprint","type":"journal_article","_id":"12890","issue":"5","article_processing_charge":"No","publication":"Physical Review E","title":"Stochastic cellular automaton model of culture formation","volume":108,"article_number":"054307","status":"public","day":"08","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"American Physical Society","date_updated":"2023-11-13T07:47:30Z","month":"11","date_published":"2023-11-08T00:00:00Z","article_type":"original","related_material":{"record":[{"relation":"research_data","id":"12869","status":"public"}],"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}]},"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.","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>","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).","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.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","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>.","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>"},"doi":"10.1103/PhysRevE.108.054307","quality_controlled":"1","arxiv":1,"intvolume":"       108","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"external_id":{"arxiv":["2305.02153"]},"oa":1,"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 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.","lang":"eng"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"year":"2023","has_accepted_license":"1","ec_funded":1,"doi":"10.15479/at:ista:12897","citation":{"mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>"},"related_material":{"record":[{"status":"public","id":"9817","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7117"},{"id":"13188","status":"public","relation":"dissertation_contains"}]},"file":[{"embargo":"2023-12-07","file_size":50714445,"checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","creator":"chafner","date_updated":"2023-12-08T23:30:04Z","file_id":"12942","access_level":"open_access","date_created":"2023-05-11T10:43:20Z","content_type":"application/pdf","relation":"main_file","file_name":"thesis-hafner-2023may11-a2b.pdf"},{"content_type":"application/pdf","relation":"source_file","file_name":"thesis-release-form.pdf","file_id":"12943","embargo_to":"open_access","date_created":"2023-05-11T10:43:44Z","access_level":"closed","date_updated":"2023-12-08T23:30:04Z","checksum":"a6b51334be2b81672357b1549afab40c","file_size":265319,"creator":"chafner"}],"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"ddc":["516","004","518","531"],"oa":1,"supervisor":[{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"page":"180","alternative_title":["ISTA Thesis"],"day":"05","status":"public","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","file_date_updated":"2023-12-08T23:30:04Z","type":"dissertation","_id":"12897","article_processing_charge":"No","oa_version":"Published Version","date_created":"2023-05-05T10:40:14Z","project":[{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"department":[{"_id":"GradSch"},{"_id":"BeBi"}],"author":[{"full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"date_published":"2023-05-05T00:00:00Z","month":"05","date_updated":"2024-01-29T10:47:51Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"scopus_import":"1","month":"08","date_published":"2023-08-15T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Elsevier","date_updated":"2023-11-14T13:21:01Z","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117"},{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","grant_number":" F06504"}],"date_created":"2023-05-07T22:01:02Z","oa_version":"Preprint","issue":"4","_id":"12911","article_processing_charge":"No","type":"journal_article","publication":"Journal of Functional Analysis","author":[{"last_name":"Feliciangeli","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530"},{"last_name":"Gerolin","first_name":"Augusto","full_name":"Gerolin, Augusto"},{"last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"department":[{"_id":"RoSe"},{"_id":"JaMa"}],"day":"15","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","volume":285,"article_number":"109963","status":"public","isi":1,"external_id":{"arxiv":["2106.11217"],"isi":["000990804300001"]},"oa":1,"abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.jfa.2023.109963","citation":{"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.","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.","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>.","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>","short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","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>.","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>"},"ec_funded":1,"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"9792","relation":"earlier_version"}]},"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.","year":"2023","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"language":[{"iso":"eng"}],"arxiv":1,"intvolume":"       285"},{"department":[{"_id":"BiCh"}],"author":[{"full_name":"Schmid, Rochus","first_name":"Rochus","last_name":"Schmid"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng"}],"publication":"The Journal of Chemical Physics","file_date_updated":"2023-05-08T07:44:49Z","_id":"12912","type":"journal_article","issue":"16","article_processing_charge":"No","oa_version":"Published Version","date_created":"2023-05-07T22:01:03Z","status":"public","article_number":"161101 ","volume":158,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Computing chemical potentials of adsorbed or confined fluids","day":"24","scopus_import":"1","date_updated":"2023-08-01T14:34:49Z","publisher":"AIP Publishing","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","month":"04","date_published":"2023-04-24T00:00:00Z","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.","related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"quality_controlled":"1","doi":"10.1063/5.0146711","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.","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","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>.","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>","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <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>."},"arxiv":1,"intvolume":"       158","pmid":1,"has_accepted_license":"1","publication_identifier":{"eissn":["1089-7690"]},"language":[{"iso":"eng"}],"year":"2023","external_id":{"arxiv":["2302.01297"],"pmid":["37093149"],"isi":["001010676000010"]},"isi":1,"file":[{"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2023_JourChemicalPhysics_Schmid.pdf","file_id":"12918","access_level":"open_access","date_created":"2023-05-08T07:44:49Z","date_updated":"2023-05-08T07:44:49Z","checksum":"4ab8c965f2fa4e17920bfa846847f137","file_size":6499468,"creator":"dernst"}],"abstract":[{"lang":"eng","text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes."}],"ddc":["540"],"oa":1},{"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"year":"2023","intvolume":"        14","pmid":1,"has_accepted_license":"1","quality_controlled":"1","doi":"10.1038/s41467-023-38005-7","citation":{"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>.","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.","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.","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>.","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).","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>"},"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.","file":[{"success":1,"content_type":"application/pdf","file_name":"2023_NatureComm_DiezMerida.pdf","relation":"main_file","file_id":"12917","date_created":"2023-05-08T07:26:40Z","access_level":"open_access","date_updated":"2023-05-08T07:26:40Z","checksum":"a778105665c10beb2354c92d2b295115","file_size":1405588,"creator":"dernst"}],"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."}],"oa":1,"ddc":["530"],"external_id":{"pmid":["37100775"],"isi":["000979744000004"]},"isi":1,"day":"26","status":"public","article_number":"2396","volume":14,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","publication":"Nature Communications","file_date_updated":"2023-05-08T07:26:40Z","article_processing_charge":"No","_id":"12913","type":"journal_article","oa_version":"Published Version","date_created":"2023-05-07T22:01:03Z","department":[{"_id":"AnHi"}],"author":[{"full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida","first_name":"J."},{"last_name":"Díez-Carlón","first_name":"A.","full_name":"Díez-Carlón, A."},{"full_name":"Yang, S. Y.","first_name":"S. Y.","last_name":"Yang"},{"first_name":"Y. M.","last_name":"Xie","full_name":"Xie, Y. M."},{"last_name":"Gao","first_name":"X. J.","full_name":"Gao, X. J."},{"first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","full_name":"Senior, Jorden L"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"full_name":"Lu, X.","last_name":"Lu","first_name":"X."},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"full_name":"Law, K. T.","first_name":"K. T.","last_name":"Law"},{"last_name":"Efetov","first_name":"Dmitri K.","full_name":"Efetov, Dmitri K."}],"article_type":"original","month":"04","date_published":"2023-04-26T00:00:00Z","date_updated":"2023-08-01T14:34:00Z","publisher":"Springer Nature","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1"},{"arxiv":1,"intvolume":"       107","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"year":"2023","acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","doi":"10.1103/PhysRevA.107.042216","citation":{"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>.","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.","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>.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (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>"},"ec_funded":1,"quality_controlled":"1","oa":1,"abstract":[{"text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier.","lang":"eng"}],"external_id":{"isi":["000975799300006"],"arxiv":["2207.13130"]},"isi":1,"article_number":"042216","status":"public","title":"Numerical quantum clock simulations for measuring tunneling times","volume":107,"day":"20","department":[{"_id":"MiLe"}],"author":[{"full_name":"Suzuki, Fumika","orcid":"0000-0003-4982-5970","last_name":"Suzuki","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","first_name":"Fumika"},{"full_name":"Unruh, William G.","last_name":"Unruh","first_name":"William G."}],"_id":"12914","issue":"4","article_processing_charge":"No","type":"journal_article","publication":"Physical Review A","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"oa_version":"Preprint","date_created":"2023-05-07T22:01:03Z","publisher":"American Physical Society","date_updated":"2023-08-01T14:33:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_published":"2023-04-20T00:00:00Z","month":"04","article_type":"original","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}]},{"publisher":"Scuola Normale Superiore - Edizioni della Normale","date_updated":"2023-10-18T06:54:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"02","date_published":"2023-02-16T00:00:00Z","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.14182"}],"status":"public","title":"Uniform bounds for rational points on hyperelliptic fibrations","volume":24,"day":"16","department":[{"_id":"TiBr"}],"author":[{"last_name":"Bonolis","id":"6A459894-5FDD-11E9-AF35-BB24E6697425","first_name":"Dante","full_name":"Bonolis, Dante"},{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"}],"_id":"12916","issue":"1","article_processing_charge":"No","type":"journal_article","publication":"Annali della Scuola Normale Superiore di Pisa - Classe di Scienze","date_created":"2023-05-07T22:01:04Z","oa_version":"Preprint","oa":1,"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"}],"external_id":{"arxiv":["2007.14182"]},"page":"173-204","intvolume":"        24","arxiv":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0391-173X"],"eissn":["2036-2145"]},"year":"2023","doi":"10.2422/2036-2145.202010_018","citation":{"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>.","short":"D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204.","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>","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>.","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.","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.","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>"},"quality_controlled":"1"},{"article_number":"e202202967","status":"public","title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","volume":29,"day":"18","author":[{"full_name":"Traxler, Michael","last_name":"Traxler","first_name":"Michael"},{"first_name":"Susanne","last_name":"Reischauer","full_name":"Reischauer, Susanne"},{"first_name":"Sarah","last_name":"Vogl","full_name":"Vogl, Sarah"},{"full_name":"Roeser, Jérôme","last_name":"Roeser","first_name":"Jérôme"},{"first_name":"Jabor","last_name":"Rabeah","full_name":"Rabeah, Jabor"},{"full_name":"Penschke, Christopher","last_name":"Penschke","first_name":"Christopher"},{"full_name":"Saalfrank, Peter","last_name":"Saalfrank","first_name":"Peter"},{"orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber"},{"first_name":"Arne","last_name":"Thomas","full_name":"Thomas, Arne"}],"_id":"12920","issue":"4","article_processing_charge":"No","type":"journal_article","publication":"Chemistry – A European Journal","oa_version":"Published Version","date_created":"2023-05-08T08:25:34Z","publisher":"Wiley","date_updated":"2023-05-15T08:39:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2023-01-18T00:00:00Z","month":"01","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/chem.202202967"}],"intvolume":"        29","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"year":"2023","extern":"1","doi":"10.1002/chem.202202967","citation":{"ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. <i>Chemistry – A European Journal</i>. 2023;29(4). doi:<a href=\"https://doi.org/10.1002/chem.202202967\">10.1002/chem.202202967</a>","apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. <i>Chemistry – A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.202202967\">https://doi.org/10.1002/chem.202202967</a>","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).","chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” <i>Chemistry – A European Journal</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/chem.202202967\">https://doi.org/10.1002/chem.202202967</a>.","ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967.","ieee":"M. Traxler <i>et al.</i>, “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” <i>Chemistry – A European Journal</i>, vol. 29, no. 4. Wiley, 2023.","mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” <i>Chemistry – A European Journal</i>, vol. 29, no. 4, e202202967, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/chem.202202967\">10.1002/chem.202202967</a>."},"quality_controlled":"1","oa":1,"abstract":[{"lang":"eng","text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation."}],"keyword":["General Chemistry","Catalysis","Organic Chemistry"]},{"quality_controlled":"1","citation":{"mla":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” <i>ChemCatChem</i>, vol. 15, no. 7, e202201583, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/cctc.202201583\">10.1002/cctc.202201583</a>.","ieee":"A. Madani and B. Pieber, “In situ reaction monitoring in photocatalytic organic synthesis,” <i>ChemCatChem</i>, vol. 15, no. 7. Wiley, 2023.","ista":"Madani A, Pieber B. 2023. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 15(7), e202201583.","short":"A. Madani, B. Pieber, ChemCatChem 15 (2023).","chicago":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” <i>ChemCatChem</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/cctc.202201583\">https://doi.org/10.1002/cctc.202201583</a>.","apa":"Madani, A., &#38; Pieber, B. (2023). In situ reaction monitoring in photocatalytic organic synthesis. <i>ChemCatChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cctc.202201583\">https://doi.org/10.1002/cctc.202201583</a>","ama":"Madani A, Pieber B. In situ reaction monitoring in photocatalytic organic synthesis. <i>ChemCatChem</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1002/cctc.202201583\">10.1002/cctc.202201583</a>"},"doi":"10.1002/cctc.202201583","extern":"1","intvolume":"        15","year":"2023","publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions."}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Catalysis"],"oa":1,"author":[{"last_name":"Madani","first_name":"Amiera","full_name":"Madani, Amiera"},{"full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","last_name":"Pieber","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"}],"oa_version":"Published Version","date_created":"2023-05-08T08:25:55Z","publication":"ChemCatChem","article_processing_charge":"No","_id":"12921","type":"journal_article","issue":"7","volume":15,"title":"In situ reaction monitoring in photocatalytic organic synthesis","status":"public","article_number":"e202201583","day":"06","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1002/cctc.202201583","open_access":"1"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-05-15T08:35:48Z","publisher":"Wiley","article_type":"original","date_published":"2023-04-06T00:00:00Z","month":"04"},{"keyword":["General Chemistry","Catalysis"],"abstract":[{"text":"The influence of structural modifications on the catalytic activity of carbon materials is poorly understood. A collection of carbonaceous materials with different pore networks and high nitrogen content was characterized and used to catalyze four reactions to deduce structure–activity relationships. The CO2 cycloaddition and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species). The absence of large conjugated carbon domains resulting from the introduction of large amounts of nitrogen in the carbon network is responsible for poor redox activity, as observed through the catalytic reduction of nitrobenzene with hydrazine and the catalytic oxidation of 3,3′,5,5′-tetramethylbenzidine using hydroperoxide. The material with the highest activity towards Lewis acid catalysis (in the hydrolysis of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule activation and presents the highest concentration of electron-poor nitrogen species.","lang":"eng"}],"oa":1,"extern":"1","quality_controlled":"1","citation":{"ama":"Lepre E, Rat S, Cavedon C, et al. Catalytic properties of high nitrogen content carbonaceous materials. <i>Angewandte Chemie International Edition</i>. 2023;62(2). doi:<a href=\"https://doi.org/10.1002/anie.202211663\">10.1002/anie.202211663</a>","ista":"Lepre E, Rat S, Cavedon C, Seeberger PH, Pieber B, Antonietti M, López‐Salas N. 2023. Catalytic properties of high nitrogen content carbonaceous materials. Angewandte Chemie International Edition. 62(2), e202211663.","ieee":"E. Lepre <i>et al.</i>, “Catalytic properties of high nitrogen content carbonaceous materials,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 2. Wiley, 2023.","mla":"Lepre, Enrico, et al. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 2, e202211663, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202211663\">10.1002/anie.202211663</a>.","apa":"Lepre, E., Rat, S., Cavedon, C., Seeberger, P. H., Pieber, B., Antonietti, M., &#38; López‐Salas, N. (2023). Catalytic properties of high nitrogen content carbonaceous materials. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202211663\">https://doi.org/10.1002/anie.202211663</a>","chicago":"Lepre, Enrico, Sylvain Rat, Cristian Cavedon, Peter H. Seeberger, Bartholomäus Pieber, Markus Antonietti, and Nieves López‐Salas. “Catalytic Properties of High Nitrogen Content Carbonaceous Materials.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202211663\">https://doi.org/10.1002/anie.202211663</a>.","short":"E. Lepre, S. Rat, C. Cavedon, P.H. Seeberger, B. Pieber, M. Antonietti, N. López‐Salas, Angewandte Chemie International Edition 62 (2023)."},"doi":"10.1002/anie.202211663","intvolume":"        62","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"language":[{"iso":"eng"}],"year":"2023","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202211663"}],"date_updated":"2023-08-21T09:18:12Z","publisher":"Wiley","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","date_published":"2023-01-09T00:00:00Z","month":"01","author":[{"first_name":"Enrico","last_name":"Lepre","full_name":"Lepre, Enrico"},{"full_name":"Rat, Sylvain","first_name":"Sylvain","last_name":"Rat"},{"first_name":"Cristian","last_name":"Cavedon","full_name":"Cavedon, Cristian"},{"last_name":"Seeberger","first_name":"Peter H.","full_name":"Seeberger, Peter H."},{"last_name":"Pieber","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"first_name":"Markus","last_name":"Antonietti","full_name":"Antonietti, Markus"},{"full_name":"López‐Salas, Nieves","last_name":"López‐Salas","first_name":"Nieves"}],"publication":"Angewandte Chemie International Edition","issue":"2","_id":"12922","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2023-05-08T08:28:14Z","status":"public","article_number":"e202211663","title":"Catalytic properties of high nitrogen content carbonaceous materials","volume":62,"day":"09"}]