[{"author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-05-24T11:56:02Z","page":"125","file":[{"checksum":"4f0abe64114cfed264f9d36e8d1197e3","access_level":"open_access","date_created":"2021-05-24T11:22:29Z","file_id":"9419","content_type":"application/pdf","relation":"main_file","file_name":"mph-thesis-v519-pdfimages.pdf","date_updated":"2021-05-24T11:22:29Z","creator":"bphuong","success":1,"file_size":2673905},{"date_updated":"2021-05-24T11:56:02Z","creator":"bphuong","file_size":92995100,"access_level":"closed","checksum":"f5699e876bc770a9b0df8345a77720a2","file_id":"9420","content_type":"application/zip","date_created":"2021-05-24T11:56:02Z","relation":"source_file","file_name":"thesis.zip"}],"date_created":"2021-05-24T13:06:23Z","degree_awarded":"PhD","date_updated":"2026-04-08T07:01:17Z","month":"05","citation":{"apa":"Phuong, M. (2021). <i>Underspecification in deep learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>","chicago":"Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9418\">https://doi.org/10.15479/AT:ISTA:9418</a>.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","mla":"Phuong, Mary. <i>Underspecification in Deep Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>.","ama":"Phuong M. Underspecification in deep learning. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9418\">10.15479/AT:ISTA:9418</a>","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021."},"related_material":{"record":[{"id":"7435","status":"deleted","relation":"part_of_dissertation"},{"status":"public","id":"7481","relation":"part_of_dissertation"},{"status":"public","id":"9416","relation":"part_of_dissertation"},{"status":"public","id":"7479","relation":"part_of_dissertation"}]},"year":"2021","language":[{"iso":"eng"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","corr_author":"1","abstract":[{"lang":"eng","text":"Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"doi":"10.15479/AT:ISTA:9418","has_accepted_license":"1","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","OA_place":"publisher","oa":1,"article_processing_charge":"No","status":"public","alternative_title":["ISTA Thesis"],"date_published":"2021-05-30T00:00:00Z","type":"dissertation","ddc":["000"],"_id":"9418","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"publication_identifier":{"issn":["2663-337X"]},"day":"30","title":"Underspecification in deep learning"},{"place":"Klosterneuburg","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"187","status":"public","relation":"part_of_dissertation"},{"id":"8703","status":"public","relation":"part_of_dissertation"}]},"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Osang, G. F. (2021). <i>Multi-cover persistence and Delaunay mosaics</i>. Institute of Science and Technology Austria, Klosterneuburg. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>","short":"G.F. Osang, Multi-Cover Persistence and Delaunay Mosaics, Institute of Science and Technology Austria, 2021.","chicago":"Osang, Georg F. “Multi-Cover Persistence and Delaunay Mosaics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9056\">https://doi.org/10.15479/AT:ISTA:9056</a>.","mla":"Osang, Georg F. <i>Multi-Cover Persistence and Delaunay Mosaics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>.","ista":"Osang GF. 2021. Multi-cover persistence and Delaunay mosaics. Klosterneuburg: Institute of Science and Technology Austria.","ieee":"G. F. Osang, “Multi-cover persistence and Delaunay mosaics,” Institute of Science and Technology Austria, Klosterneuburg, 2021.","ama":"Osang GF. Multi-cover persistence and Delaunay mosaics. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9056\">10.15479/AT:ISTA:9056</a>"},"month":"02","date_updated":"2026-04-08T07:01:30Z","date_created":"2021-02-02T14:11:06Z","degree_awarded":"PhD","file":[{"creator":"patrickd","date_updated":"2021-02-03T10:37:28Z","file_size":13446994,"date_created":"2021-02-02T14:09:25Z","content_type":"application/zip","file_id":"9063","checksum":"bcf27986147cab0533b6abadd74e7629","access_level":"closed","file_name":"thesis_source.zip","relation":"source_file"},{"file_name":"thesis_pdfA2b.pdf","relation":"main_file","file_id":"9064","content_type":"application/pdf","date_created":"2021-02-02T14:09:18Z","access_level":"open_access","checksum":"9cc8af266579a464385bbe2aff6af606","file_size":5210329,"success":1,"creator":"patrickd","date_updated":"2021-02-02T14:09:18Z"}],"author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang"}],"page":"134","file_date_updated":"2021-02-03T10:37:28Z","title":"Multi-cover persistence and Delaunay mosaics","day":"01","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"_id":"9056","ddc":["006","514","516"],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-02-01T00:00:00Z","article_processing_charge":"No","status":"public","oa":1,"OA_place":"publisher","doi":"10.15479/AT:ISTA:9056","has_accepted_license":"1","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,\r\nand thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration\r\nfunction on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","publisher":"Institute of Science and Technology Austria"},{"file_date_updated":"2021-05-24T11:15:57Z","author":[{"full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"date_created":"2021-05-24T11:16:46Z","file":[{"creator":"bphuong","date_updated":"2021-05-24T11:15:57Z","file_size":502356,"file_id":"9417","content_type":"application/pdf","date_created":"2021-05-24T11:15:57Z","access_level":"open_access","checksum":"f34ff17017527db5ba6927f817bdd125","file_name":"iclr2021_conference.pdf","relation":"main_file"}],"scopus_import":"1","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Virtual","end_date":"2021-05-07","start_date":"2021-05-03"},"month":"05","date_updated":"2026-04-08T07:01:16Z","citation":{"ieee":"M. Phuong and C. Lampert, “The inductive bias of ReLU networks on orthogonally separable data,” in <i>9th International Conference on Learning Representations</i>, Virtual, 2021.","ista":"Phuong M, Lampert C. 2021. The inductive bias of ReLU networks on orthogonally separable data. 9th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Phuong M, Lampert C. The inductive bias of ReLU networks on orthogonally separable data. In: <i>9th International Conference on Learning Representations</i>. ; 2021.","mla":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” <i>9th International Conference on Learning Representations</i>, 2021.","chicago":"Phuong, Mary, and Christoph Lampert. “The Inductive Bias of ReLU Networks on Orthogonally Separable Data.” In <i>9th International Conference on Learning Representations</i>, 2021.","short":"M. Phuong, C. Lampert, in:, 9th International Conference on Learning Representations, 2021.","apa":"Phuong, M., &#38; Lampert, C. (2021). The inductive bias of ReLU networks on orthogonally separable data. In <i>9th International Conference on Learning Representations</i>. Virtual."},"year":"2021","related_material":{"record":[{"status":"public","id":"9418","relation":"dissertation_contains"}]},"publication":"9th International Conference on Learning Representations","language":[{"iso":"eng"}],"publication_status":"published","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","abstract":[{"lang":"eng","text":"We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time  onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks."}],"main_file_link":[{"url":"https://openreview.net/pdf?id=krz7T0xU9Z_","open_access":"1"}],"oa_version":"Published Version","has_accepted_license":"1","oa":1,"status":"public","article_processing_charge":"No","type":"conference","date_published":"2021-05-01T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"_id":"9416","ddc":["000"],"title":"The inductive bias of ReLU networks on orthogonally separable data","day":"01"},{"ec_funded":1,"day":"23","title":"On the adaptive security of graph-based games","ddc":["519"],"_id":"10035","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"I want to acknowledge the funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).\r\n","alternative_title":["ISTA Thesis"],"date_published":"2021-09-23T00:00:00Z","type":"dissertation","article_processing_charge":"No","status":"public","OA_place":"publisher","oa":1,"doi":"10.15479/at:ista:10035","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"Many security definitions come in two flavors: a stronger “adaptive” flavor, where the adversary can arbitrarily make various choices during the course of the attack, and a weaker “selective” flavor where the adversary must commit to some or all of their choices a-priori. For example, in the context of identity-based encryption, selective security requires the adversary to decide on the identity of the attacked party at the very beginning of the game whereas adaptive security allows the attacker to first see the master public key and some secret keys before making this choice. Often, it appears to be much easier to achieve selective security than it is to achieve adaptive security. A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework (published at Crypto ’17 [JKK+17a]) that connects all of these works and allows us to present them in a unified and simplified fashion. Having the framework in place, we show how to achieve adaptive security for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the first adaptive security proofs for continuous group key agreement protocols (published at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that currently used proof techniques cannot lead to significantly better security guarantees for \"graph-building\" games (published at TCC ’21 [KKPW21a]). These games cover generalized selective decryption, as well as the security of prominent constructions for constrained PRFs, continuous group key agreement, and proxy re-encryption. Finally, we revisit the adaptive security of Yao’s garbled circuits and extend the analysis of Jafargholi and Wichs in two directions: While they prove adaptive security only for a modified construction with increased online complexity, we provide the first positive results for the original construction by Yao (published at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi and Wichs are essentially optimal by showing that no black-box reduction can provide a significantly better security bound (published at Crypto ’21 [KKPW21c]).","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","publisher":"Institute of Science and Technology Austria","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10044","status":"public"},{"id":"10048","status":"public","relation":"part_of_dissertation"},{"id":"10041","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10049"},{"relation":"part_of_dissertation","status":"public","id":"6430"},{"status":"public","id":"637","relation":"part_of_dissertation"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","citation":{"ista":"Klein K. 2021. On the adaptive security of graph-based games. Institute of Science and Technology Austria.","ama":"Klein K. On the adaptive security of graph-based games. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10035\">10.15479/at:ista:10035</a>","ieee":"K. Klein, “On the adaptive security of graph-based games,” Institute of Science and Technology Austria, 2021.","mla":"Klein, Karen. <i>On the Adaptive Security of Graph-Based Games</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10035\">10.15479/at:ista:10035</a>.","chicago":"Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10035\">https://doi.org/10.15479/at:ista:10035</a>.","short":"K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science and Technology Austria, 2021.","apa":"Klein, K. (2021). <i>On the adaptive security of graph-based games</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10035\">https://doi.org/10.15479/at:ista:10035</a>"},"date_updated":"2026-04-08T07:01:44Z","month":"09","file":[{"success":1,"creator":"cchlebak","date_updated":"2021-10-04T12:22:33Z","file_size":2104726,"file_id":"10082","content_type":"application/pdf","date_created":"2021-10-04T12:22:33Z","access_level":"open_access","checksum":"73a44345c683e81f3e765efbf86fdcc5","file_name":"thesis_pdfa.pdf","relation":"main_file"},{"creator":"cchlebak","date_updated":"2022-03-10T12:15:18Z","file_size":9538359,"content_type":"application/x-zip-compressed","file_id":"10085","date_created":"2021-10-05T07:04:37Z","access_level":"closed","checksum":"7b80df30a0e686c3ef6a56d4e1c59e29","file_name":"thesis_final (1).zip","relation":"source_file"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"degree_awarded":"PhD","date_created":"2021-09-23T07:31:44Z","author":[{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"}],"page":"276","file_date_updated":"2022-03-10T12:15:18Z"},{"ec_funded":1,"intvolume":"     12826","title":"Limits on the Adaptive Security of Yao’s Garbling","day":"11","department":[{"_id":"KrPi"}],"_id":"10041","acknowledgement":"We would like to thank the anonymous reviewers of Crypto’21 whose detailed comments helped us considerably improve the presentation of the paper.","publication_identifier":{"eisbn":["978-3-030-84245-1"],"isbn":["978-3-030-84244-4"],"issn":["0302-9743"],"eissn":["1611-3349"]},"type":"conference","date_published":"2021-08-11T00:00:00Z","alternative_title":["LCNS"],"article_processing_charge":"No","status":"public","oa":1,"doi":"10.1007/978-3-030-84245-1_17","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2021/945","open_access":"1"}],"abstract":[{"text":"Yao’s garbling scheme is one of the most fundamental cryptographic constructions. Lindell and Pinkas (Journal of Cryptograhy 2009) gave a formal proof of security in the selective setting where the adversary chooses the challenge inputs before seeing the garbled circuit assuming secure symmetric-key encryption (and hence one-way functions). This was followed by results, both positive and negative, concerning its security in the, stronger, adaptive setting. Applebaum et al. (Crypto 2013) showed that it cannot satisfy adaptive security as is, due to a simple incompressibility argument. Jafargholi and Wichs (TCC 2017) considered a natural adaptation of Yao’s scheme (where the output mapping is sent in the online phase, together with the garbled input) that circumvents this negative result, and proved that it is adaptively secure, at least for shallow circuits. In particular, they showed that for the class of circuits of depth   δ , the loss in security is at most exponential in   δ . The above results all concern the simulation-based notion of security. In this work, we show that the upper bound of Jafargholi and Wichs is basically optimal in a strong sense. As our main result, we show that there exists a family of Boolean circuits, one for each depth  δ∈N , such that any black-box reduction proving the adaptive indistinguishability of the natural adaptation of Yao’s scheme from any symmetric-key encryption has to lose a factor that is exponential in   δ√ . Since indistinguishability is a weaker notion than simulation, our bound also applies to adaptive simulation. To establish our results, we build on the recent approach of Kamath et al. (Eprint 2021), which uses pebbling lower bounds in conjunction with oracle separations to prove fine-grained lower bounds on loss in cryptographic security.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publisher":"Springer Nature","place":"Cham","external_id":{"isi":["000696697800017"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"10035","relation":"dissertation_contains"}]},"publication":"41st Annual International Cryptology Conference, Part II ","year":"2021","citation":{"mla":"Kamath Hosdurg, Chethan, et al. “Limits on the Adaptive Security of Yao’s Garbling.” <i>41st Annual International Cryptology Conference, Part II </i>, vol. 12826, Springer Nature, 2021, pp. 486–515, doi:<a href=\"https://doi.org/10.1007/978-3-030-84245-1_17\">10.1007/978-3-030-84245-1_17</a>.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and D. Wichs, “Limits on the Adaptive Security of Yao’s Garbling,” in <i>41st Annual International Cryptology Conference, Part II </i>, Virtual, 2021, vol. 12826, pp. 486–515.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. Limits on the Adaptive Security of Yao’s Garbling. In: <i>41st Annual International Cryptology Conference, Part II </i>. Vol 12826. Cham: Springer Nature; 2021:486-515. doi:<a href=\"https://doi.org/10.1007/978-3-030-84245-1_17\">10.1007/978-3-030-84245-1_17</a>","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Wichs D. 2021. Limits on the Adaptive Security of Yao’s Garbling. 41st Annual International Cryptology Conference, Part II . CRYPTO: Annual International Cryptology Conference, LCNS, vol. 12826, 486–515.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Daniel Wichs. “Limits on the Adaptive Security of Yao’s Garbling.” In <i>41st Annual International Cryptology Conference, Part II </i>, 12826:486–515. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-84245-1_17\">https://doi.org/10.1007/978-3-030-84245-1_17</a>.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, D. Wichs, in:, 41st Annual International Cryptology Conference, Part II , Springer Nature, Cham, 2021, pp. 486–515.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Wichs, D. (2021). Limits on the Adaptive Security of Yao’s Garbling. In <i>41st Annual International Cryptology Conference, Part II </i> (Vol. 12826, pp. 486–515). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-84245-1_17\">https://doi.org/10.1007/978-3-030-84245-1_17</a>"},"month":"08","isi":1,"date_updated":"2026-04-08T07:01:43Z","conference":{"name":"CRYPTO: Annual International Cryptology Conference","end_date":"2021-08-20","start_date":"2021-08-16","location":"Virtual"},"volume":12826,"date_created":"2021-09-23T14:06:15Z","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"scopus_import":"1","author":[{"last_name":"Kamath Hosdurg","first_name":"Chethan","orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Wichs","first_name":"Daniel","full_name":"Wichs, Daniel"}],"page":"486-515"},{"conference":{"location":"San Francisco, CA, United States","end_date":"2021-05-27","start_date":"2021-05-24","name":"SP: Symposium on Security and Privacy"},"month":"08","isi":1,"date_updated":"2026-04-08T07:01:44Z","page":"268-284","author":[{"last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo"},{"full_name":"Walter, Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0006-6812-7317","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Capretto, Margarita","last_name":"Capretto","first_name":"Margarita"},{"first_name":"Miguel","orcid":"0000-0002-2505-4246","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel"},{"last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","first_name":"Ilia","full_name":"Markov, Ilia"},{"full_name":"Yeo, Michelle X","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0001-3676-4809","last_name":"Yeo"},{"full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2021-09-27T13:46:27Z","scopus_import":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["001316065000016"]},"citation":{"short":"K. Klein, G. Pascual Perez, M. Walter, C. Kamath Hosdurg, M. Capretto, M. Cueto Noval, I. Markov, M.X. Yeo, J.F. Alwen, K.Z. Pietrzak, in:, 2021 IEEE Symposium on Security and Privacy , IEEE, 2021, pp. 268–284.","chicago":"Klein, Karen, Guillermo Pascual Perez, Michael Walter, Chethan Kamath Hosdurg, Margarita Capretto, Miguel Cueto Noval, Ilia Markov, Michelle X Yeo, Joel F Alwen, and Krzysztof Z Pietrzak. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” In <i>2021 IEEE Symposium on Security and Privacy </i>, 268–84. IEEE, 2021. <a href=\"https://doi.org/10.1109/sp40001.2021.00035\">https://doi.org/10.1109/sp40001.2021.00035</a>.","ista":"Klein K, Pascual Perez G, Walter M, Kamath Hosdurg C, Capretto M, Cueto Noval M, Markov I, Yeo MX, Alwen JF, Pietrzak KZ. 2021. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. 2021 IEEE Symposium on Security and Privacy . SP: Symposium on Security and Privacy, 268–284.","ama":"Klein K, Pascual Perez G, Walter M, et al. Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In: <i>2021 IEEE Symposium on Security and Privacy </i>. IEEE; 2021:268-284. doi:<a href=\"https://doi.org/10.1109/sp40001.2021.00035\">10.1109/sp40001.2021.00035</a>","ieee":"K. Klein <i>et al.</i>, “Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement,” in <i>2021 IEEE Symposium on Security and Privacy </i>, San Francisco, CA, United States, 2021, pp. 268–284.","mla":"Klein, Karen, et al. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively Secure Continuous Group Key Agreement.” <i>2021 IEEE Symposium on Security and Privacy </i>, IEEE, 2021, pp. 268–84, doi:<a href=\"https://doi.org/10.1109/sp40001.2021.00035\">10.1109/sp40001.2021.00035</a>.","apa":"Klein, K., Pascual Perez, G., Walter, M., Kamath Hosdurg, C., Capretto, M., Cueto Noval, M., … Pietrzak, K. Z. (2021). Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement. In <i>2021 IEEE Symposium on Security and Privacy </i> (pp. 268–284). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp40001.2021.00035\">https://doi.org/10.1109/sp40001.2021.00035</a>"},"year":"2021","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"18088"},{"status":"public","id":"10035","relation":"dissertation_contains"}]},"publication":"2021 IEEE Symposium on Security and Privacy ","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2019/1489","open_access":"1"}],"doi":"10.1109/sp40001.2021.00035","oa":1,"corr_author":"1","publisher":"IEEE","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","abstract":[{"lang":"eng","text":"While messaging systems with strong security guarantees are widely used in practice, designing a protocol that scales efficiently to large groups and enjoys similar security guarantees remains largely open. The two existing proposals to date are ART (Cohn-Gordon et al., CCS18) and TreeKEM (IETF, The Messaging Layer Security Protocol, draft). TreeKEM is the currently considered candidate by the IETF MLS working group, but dynamic group operations (i.e. adding and removing users) can cause efficiency issues. In this paper we formalize and analyze a variant of TreeKEM which we term Tainted TreeKEM (TTKEM for short). The basic idea underlying TTKEM was suggested by Millican (MLS mailing list, February 2018). This version is more efficient than TreeKEM for some natural distributions of group operations, we quantify this through simulations.Our second contribution is two security proofs for TTKEM which establish post compromise and forward secrecy even against adaptive attackers. The security loss (to the underlying PKE) in the Random Oracle Model is a polynomial factor, and a quasipolynomial one in the Standard Model. Our proofs can be adapted to TreeKEM as well. Before our work no security proof for any TreeKEM-like protocol establishing tight security against an adversary who can adaptively choose the sequence of operations was known. We also are the first to prove (or even formalize) active security where the server can arbitrarily deviate from the protocol specification. Proving fully active security – where also the users can arbitrarily deviate – remains open."}],"acknowledgement":"The first three authors contributed equally to this work. Funded by the European Research Council (ERC) under the European Union’s Horizon2020 research and innovation programme (682815-TOCNeT). Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No.665385.","department":[{"_id":"KrPi"},{"_id":"DaAl"}],"_id":"10049","title":"Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous group key agreement","day":"26","ec_funded":1,"status":"public","article_processing_charge":"No","type":"conference","date_published":"2021-08-26T00:00:00Z"},{"conference":{"location":"Raleigh, NC, United States","start_date":"2021-11-08","end_date":"2021-11-11","name":"TCC: Theory of Cryptography Conference"},"date_updated":"2026-04-08T07:01:43Z","month":"07","oa":1,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://ia.cr/2021/059"}],"date_created":"2021-09-27T12:52:05Z","abstract":[{"text":"The security of cryptographic primitives and protocols against adversaries that are allowed to make adaptive choices (e.g., which parties to corrupt or which queries to make) is notoriously difficult to establish. A broad theoretical\r\nframework was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper we initiate the study of lower bounds on loss in adaptive security for certain cryptographic protocols considered in the framework. We prove lower\r\nbounds that almost match the upper bounds (proven using the framework) for proxy re-encryption, prefix-constrained PRFs and generalized selective decryption, a security game that captures the security of certain group messaging and\r\nbroadcast encryption schemes. Those primitives have in common that their security game involves an underlying graph that can be adaptively built by the adversary. Some of our lower bounds only apply to a restricted class of black-box reductions which we term “oblivious” (the existing upper bounds are of this restricted type), some apply to the broader but still restricted class of non-rewinding reductions, while our lower bound for proxy re-encryption applies to all black-box reductions. The fact that some of our lower bounds seem to crucially rely on obliviousness or at least a non-rewinding reduction hints to the exciting possibility that the existing upper bounds can be improved by using more sophisticated reductions. Our main conceptual contribution is a two-player multi-stage game called the Builder-Pebbler Game. We can translate bounds on the winning probabilities for various instantiations of this game into cryptographic lower bounds for the above-mentioned primitives using oracle separation techniques.\r\n","lang":"eng"}],"publisher":"International Association for Cryptologic Research","quality_controlled":"1","author":[{"orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Walter, Michael","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","publication_status":"published","title":"The cost of adaptivity in security games on graphs","language":[{"iso":"eng"}],"_id":"10048","department":[{"_id":"KrPi"}],"year":"2021","date_published":"2021-07-08T00:00:00Z","related_material":{"record":[{"status":"public","id":"10410","relation":"later_version"},{"relation":"dissertation_contains","id":"10035","status":"public"}]},"type":"conference","publication":"19th Theory of Cryptography Conference 2021","status":"public","article_processing_charge":"No","citation":{"chicago":"Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “The Cost of Adaptivity in Security Games on Graphs.” In <i>19th Theory of Cryptography Conference 2021</i>. International Association for Cryptologic Research, 2021.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","mla":"Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on Graphs.” <i>19th Theory of Cryptography Conference 2021</i>, International Association for Cryptologic Research, 2021.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity in security games on graphs. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference.","ieee":"C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity in security games on graphs,” in <i>19th Theory of Cryptography Conference 2021</i>, Raleigh, NC, United States, 2021.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in security games on graphs. In: <i>19th Theory of Cryptography Conference 2021</i>. International Association for Cryptologic Research; 2021.","apa":"Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2021). The cost of adaptivity in security games on graphs. In <i>19th Theory of Cryptography Conference 2021</i>. Raleigh, NC, United States: International Association for Cryptologic Research."}},{"article_processing_charge":"No","citation":{"apa":"Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In <i>19th Theory of Cryptography Conference 2021</i>. Raleigh, NC, United States: International Association for Cryptologic Research.","ista":"Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th Theory of Cryptography Conference 2021. TCC: Theory of Cryptography Conference, 2021/926.","ieee":"C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in <i>19th Theory of Cryptography Conference 2021</i>, Raleigh, NC, United States, 2021.","ama":"Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: <i>19th Theory of Cryptography Conference 2021</i>. International Association for Cryptologic Research; 2021.","mla":"Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” <i>19th Theory of Cryptography Conference 2021</i>, 2021/926, International Association for Cryptologic Research, 2021.","short":"C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th Theory of Cryptography Conference 2021, International Association for Cryptologic Research, 2021.","chicago":"Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In <i>19th Theory of Cryptography Conference 2021</i>. International Association for Cryptologic Research, 2021."},"status":"public","date_published":"2021-07-08T00:00:00Z","type":"conference","related_material":{"record":[{"relation":"later_version","id":"10409","status":"public"},{"relation":"dissertation_contains","id":"10035","status":"public"}]},"publication":"19th Theory of Cryptography Conference 2021","year":"2021","_id":"10044","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"acknowledgement":"We would like to thank Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling.  ","ec_funded":1,"day":"08","title":"On treewidth, separators and Yao's garbling","publication_status":"published","quality_controlled":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Kamath Hosdurg, Chethan","orcid":"0009-0006-6812-7317","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"publisher":"International Association for Cryptologic Research","abstract":[{"text":"We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a S^O(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(d w log(S)), d being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity.","lang":"eng"}],"project":[{"grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"date_created":"2021-09-24T12:01:34Z","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2021/926","open_access":"1"}],"date_updated":"2026-04-08T07:01:43Z","oa":1,"month":"07","conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2021-11-11","start_date":"2021-11-08","location":"Raleigh, NC, United States"},"article_number":"2021/926"},{"doi":"10.1103/PRXQuantum.2.040341","oa_version":"Published Version","has_accepted_license":"1","oa":1,"keyword":["quantum physics","mesoscale and nanoscale physics"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","arxiv":1,"quality_controlled":"1","corr_author":"1","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one, the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wave function. In the other, the junction is added in parallel, which gives rise to an extended phase variable, continuous wave functions, and a rich energy-level structure due to the loop topology. While the corresponding rf superconducting quantum interference device Hamiltonian was introduced as a quadratic quasi-one-dimensional potential approximation to describe the fluxonium qubit implemented with long Josephson-junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits, all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasicharge qubit with strongly enhanced zero-point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high reproducibility of the inductive energy as guaranteed by top-down lithography—a key ingredient for intrinsically protected superconducting qubits."}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"department":[{"_id":"JoFi"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["530"],"_id":"9928","acknowledgement":"We thank W. Hughes for analytic and numerical modeling during the early stages of this work, J. Koch for discussions and support with the scqubits package, R. Sett, P. Zielinski, and L. Drmic for software development, and G. Katsaros for equipment support, as well as the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility. We thank I. Pop, S. Deleglise, and E. Flurin for discussions. This work was supported by a NOMIS Foundation research grant, the Austrian Science Fund (FWF) through BeyondC (F7105), and IST Austria. M.P. is the recipient of a Pöttinger scholarship at IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","publication_identifier":{"eissn":["2691-3399"]},"ec_funded":1,"intvolume":"         2","title":"Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction","day":"24","article_processing_charge":"No","status":"public","type":"journal_article","date_published":"2021-11-24T00:00:00Z","month":"11","isi":1,"date_updated":"2026-04-08T07:10:43Z","author":[{"full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo"},{"full_name":"Hassani, Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"full_name":"Szep, Gregory","last_name":"Szep","first_name":"Gregory"},{"full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","full_name":"Redchenko, Elena"},{"last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin","full_name":"Zemlicka, Martin"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"article_type":"original","page":"040341","file_date_updated":"2022-01-18T11:29:33Z","volume":2,"date_created":"2021-08-17T08:14:18Z","scopus_import":"1","issue":"4","file":[{"file_name":"2021_PRXQuantum_Peruzzo.pdf","relation":"main_file","date_created":"2022-01-18T11:29:33Z","content_type":"application/pdf","file_id":"10641","checksum":"36eb41ea43d8ca22b0efab12419e4eb2","access_level":"open_access","file_size":4247422,"creator":"cchlebak","success":1,"date_updated":"2022-01-18T11:29:33Z"}],"project":[{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"2622978C-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2106.05882"],"isi":["000723015100001"]},"publication_status":"published","citation":{"apa":"Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., &#38; Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>","ieee":"M. Peruzzo <i>et al.</i>, “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction,” <i>PRX Quantum</i>, vol. 2, no. 4. American Physical Society, p. 040341, 2021.","ama":"Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. <i>PRX Quantum</i>. 2021;2(4):040341. doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>","ista":"Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. PRX Quantum. 2(4), 040341.","mla":"Peruzzo, Matilda, et al. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>, vol. 2, no. 4, American Physical Society, 2021, p. 040341, doi:<a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">10.1103/PRXQuantum.2.040341</a>.","short":"M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, PRX Quantum 2 (2021) 040341.","chicago":"Peruzzo, Matilda, Farid Hassani, Gregory Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” <i>PRX Quantum</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PRXQuantum.2.040341\">https://doi.org/10.1103/PRXQuantum.2.040341</a>."},"publication":"PRX Quantum","related_material":{"record":[{"relation":"research_data","status":"public","id":"13057"},{"status":"public","id":"17133","relation":"dissertation_contains"},{"status":"public","id":"9920","relation":"dissertation_contains"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021"},{"article_processing_charge":"No","status":"public","type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2021-08-19T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"_id":"9920","ddc":["539"],"publication_identifier":{"isbn":["978-3-99078-013-8"],"issn":["2663-337X"]},"title":"Geometric superinductors and their applications in circuit quantum electrodynamics","day":"19","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","keyword":["quantum computing","superinductor","quantum metrology"],"corr_author":"1","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"doi":"10.15479/at:ista:9920","oa_version":"Published Version","has_accepted_license":"1","supervisor":[{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"oa":1,"OA_place":"publisher","citation":{"ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","ama":"Peruzzo M. Geometric superinductors and their applications in circuit quantum electrodynamics. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021.","mla":"Peruzzo, Matilda. <i>Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9920\">10.15479/at:ista:9920</a>.","chicago":"Peruzzo, Matilda. “Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>.","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","apa":"Peruzzo, M. (2021). <i>Geometric superinductors and their applications in circuit quantum electrodynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9920\">https://doi.org/10.15479/at:ista:9920</a>"},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9928"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"year":"2021","language":[{"iso":"eng"}],"publication_status":"published","author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","full_name":"Peruzzo, Matilda"}],"file_date_updated":"2021-09-06T08:39:47Z","page":"149","degree_awarded":"PhD","date_created":"2021-08-16T09:44:09Z","file":[{"file_size":151387283,"date_updated":"2021-09-06T08:39:47Z","creator":"mperuzzo","relation":"source_file","file_name":"GeometricSuperinductorsForCQED.zip","checksum":"3cd1986efde5121d7581f6fcf9090da8","access_level":"closed","date_created":"2021-08-16T09:33:21Z","content_type":"application/x-zip-compressed","file_id":"9924"},{"relation":"main_file","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","checksum":"50928c621cdf0775d7a5906b9dc8602c","access_level":"open_access","date_created":"2021-08-18T14:20:06Z","content_type":"application/pdf","file_id":"9939","file_size":17596344,"date_updated":"2021-09-06T08:39:47Z","creator":"mperuzzo"},{"description":"Extra copy of the thesis as PDF/A-2b","file_size":17592425,"date_updated":"2021-09-06T08:39:47Z","creator":"mperuzzo","relation":"other","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","checksum":"37f486aa1b622fe44af00d627ec13f6c","access_level":"closed","date_created":"2021-08-18T14:20:09Z","content_type":"application/pdf","file_id":"9940"}],"month":"08","date_updated":"2026-04-08T07:10:43Z"},{"department":[{"_id":"BeBi"}],"ddc":["516"],"_id":"9817","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"ec_funded":1,"intvolume":"        40","title":"The design space of plane elastic curves","day":"19","article_processing_charge":"No","status":"public","type":"journal_article","date_published":"2021-07-19T00:00:00Z","doi":"10.1145/3450626.3459800","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_number":"126","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Association for Computing Machinery","abstract":[{"text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000674930900091"]},"publication_status":"published","citation":{"apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>."},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","relation":"press_release","description":"News on IST Website"}],"record":[{"relation":"dissertation_contains","id":"12897","status":"public"}]},"publication":"ACM Transactions on Graphics","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","month":"07","isi":1,"date_updated":"2026-04-09T22:30:04Z","conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","location":"Virtual","end_date":"2021-08-13","start_date":"2021-08-09"},"author":[{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"article_type":"original","file_date_updated":"2021-10-18T10:42:22Z","volume":40,"date_created":"2021-08-08T22:01:26Z","issue":"4","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"file":[{"file_size":17064290,"date_updated":"2021-10-18T10:42:15Z","success":1,"creator":"chafner","relation":"main_file","file_name":"elastic-curves-paper.pdf","access_level":"open_access","checksum":"7e5d08ce46b0451b3102eacd3d00f85f","content_type":"application/pdf","file_id":"10150","date_created":"2021-10-18T10:42:15Z"},{"relation":"supplementary_material","file_name":"elastic-curves-supp.pdf","access_level":"open_access","checksum":"0088643478be7c01a703b5b10767348f","file_id":"10151","content_type":"application/pdf","date_created":"2021-10-18T10:42:22Z","file_size":547156,"date_updated":"2021-10-18T10:42:22Z","creator":"chafner"}],"scopus_import":"1"},{"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/647800","open_access":"1"}],"has_accepted_license":"1","oa_version":"Submitted Version","doi":"10.1038/s43588-021-00157-1","oa":1,"publisher":"Springer Nature","corr_author":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","keyword":["general medicine"],"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks.","lang":"eng"}],"publication_identifier":{"issn":["2662-8457"]},"acknowledgement":"We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and T. Vogels for critically reading earlier versions of the manuscript. We are grateful to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished data. This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).","_id":"10816","ddc":["610"],"department":[{"_id":"PeJo"}],"day":"16","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","ec_funded":1,"intvolume":"         1","status":"public","article_processing_charge":"No","date_published":"2021-12-16T00:00:00Z","type":"journal_article","date_updated":"2025-10-09T22:30:54Z","isi":1,"month":"12","page":"830-842","file_date_updated":"2022-06-18T22:30:03Z","article_type":"original","author":[{"last_name":"Guzmán","first_name":"José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"first_name":"Claudia ","orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia "},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","first_name":"Xiaomin","orcid":"0000-0003-0256-6529","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"}],"file":[{"embargo":"2022-06-17","file_size":1699466,"date_updated":"2022-06-18T22:30:03Z","creator":"patrickd","relation":"main_file","file_name":"Guzmanetal2021.pdf","access_level":"open_access","checksum":"9fec5b667909ef52be96d502e4f8c2ae","content_type":"application/pdf","file_id":"11430","date_created":"2022-06-02T12:51:07Z"},{"file_size":3005651,"embargo":"2022-06-17","creator":"patrickd","title":"Supplementary Material","date_updated":"2022-06-18T22:30:03Z","file_name":"Guzmanetal2021Suppl.pdf","relation":"supplementary_material","date_created":"2022-06-02T12:53:47Z","content_type":"application/pdf","file_id":"11431","checksum":"52a005b13a114e3c3a28fa6bbe8b1a8d","access_level":"open_access"}],"issue":"12","scopus_import":"1","date_created":"2022-03-04T08:32:36Z","volume":1,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000888567500015"]},"citation":{"mla":"Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>, vol. 1, no. 12, Springer Nature, 2021, pp. 830–42, doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. 2021;1(12):830-842. doi:<a href=\"https://doi.org/10.1038/s43588-021-00157-1\">10.1038/s43588-021-00157-1</a>","ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network,” <i>Nature Computational Science</i>, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science. 1(12), 830–842.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, Nature Computational Science 1 (2021) 830–842.","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” <i>Nature Computational Science</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-021-00157-1\">https://doi.org/10.1038/s43588-021-00157-1</a>"},"year":"2021","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/spot-the-difference/"}],"record":[{"relation":"software","status":"public","id":"10110"}]},"publication":"Nature Computational Science"},{"file":[{"access_level":"open_access","checksum":"f92f8931cad0aa7e411c1715337bf408","file_id":"10114","content_type":"application/x-zip-compressed","date_created":"2021-10-08T08:46:04Z","relation":"main_file","file_name":"patternseparation-main (1).zip","date_updated":"2021-10-08T08:46:04Z","success":1,"creator":"cchlebak","file_size":332990101}],"date_created":"2021-10-08T06:44:22Z","abstract":[{"lang":"eng","text":"Pattern separation is a fundamental brain computation that converts small differences in input patterns into large differences in output patterns. Several synaptic mechanisms of pattern separation have been proposed, including code expansion, inhibition and plasticity; however, which of these mechanisms play a role in the entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation circuit, remains unclear. Here we show that a biologically realistic, full-scale EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator. Both external gamma-modulated inhibition and internal lateral inhibition mediated by PV+-INs substantially contributed to pattern separation. Both local connectivity and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness. Similarly, mossy fiber synapses with conditional detonator properties contributed to pattern separation. By contrast, perforant path synapses with Hebbian synaptic plasticity and direct EC–CA3 connection shifted the network towards pattern completion. Our results demonstrate that the specific properties of cells and synapses optimize higher-order computations in biological networks and might be useful to improve the deep learning capabilities of technical networks."}],"publisher":"IST Austria","file_date_updated":"2021-10-08T08:46:04Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"José","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","last_name":"Guzmán","full_name":"Guzmán, José"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"full_name":"Espinoza Martinez, Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez"},{"full_name":"Zhang, Xiaomin","last_name":"Zhang","orcid":"0000-0003-0256-6529","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"full_name":"Suter, Benjamin","last_name":"Suter","first_name":"Benjamin","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"}],"license":"https://opensource.org/licenses/GPL-3.0","date_updated":"2026-04-09T22:30:06Z","oa":1,"month":"12","has_accepted_license":"1","doi":"10.15479/AT:ISTA:10110","tmp":{"name":"GNU General Public License 3.0","legal_code_url":"https://www.gnu.org/licenses/gpl-3.0.en.html","short":"GPL 3.0"},"year":"2021","date_published":"2021-12-16T00:00:00Z","related_material":{"record":[{"relation":"used_for_analysis_in","id":"10816","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/spot-the-difference/","description":"News on IST Webpage","relation":"press_release"}]},"type":"software","status":"public","citation":{"ieee":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M. Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.","ama":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>","ista":"Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021. How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","mla":"Guzmán, José, et al. <i>How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10110\">10.15479/AT:ISTA:10110</a>.","short":"J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas, (2021).","chicago":"Guzmán, José, Alois Schlögl, Claudia  Espinoza Martinez, Xiaomin Zhang, Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3 Network.” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>.","apa":"Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &#38; Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10110\">https://doi.org/10.15479/AT:ISTA:10110</a>"},"day":"16","title":"How connectivity rules and synaptic properties shape the efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network","_id":"10110","ddc":["005"],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}]},{"related_material":{"record":[{"id":"12891","status":"public","relation":"dissertation_contains"}]},"publication":"Developmental Biology","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2021","citation":{"ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>"},"external_id":{"isi":["000639461800008"],"pmid":["33352181"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":474,"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","file":[{"relation":"main_file","file_name":"2021_DevBiology_Schauer.pdf","checksum":"fa2a5731fd16ab171b029f32f031c440","access_level":"open_access","date_created":"2021-08-11T10:28:06Z","file_id":"9880","content_type":"application/pdf","file_size":1440321,"date_updated":"2021-08-11T10:28:06Z","creator":"kschuh","success":1}],"date_created":"2020-12-22T09:53:34Z","author":[{"last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"article_type":"original","page":"71-81","file_date_updated":"2021-08-11T10:28:06Z","date_updated":"2026-04-09T22:30:07Z","month":"06","isi":1,"date_published":"2021-06-01T00:00:00Z","type":"journal_article","article_processing_charge":"Yes (via OA deal)","status":"public","ec_funded":1,"intvolume":"       474","day":"01","title":"Reassembling gastrulation","ddc":["570"],"_id":"8966","department":[{"_id":"CaHe"}],"publication_identifier":{"issn":["0012-1606"]},"acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","abstract":[{"lang":"eng","text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process."}],"pmid":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"publisher":"Elsevier","oa":1,"doi":"10.1016/j.ydbio.2020.12.014","has_accepted_license":"1","oa_version":"Published Version"},{"title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","day":"01","intvolume":"        16","ec_funded":1,"acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","publication_identifier":{"issn":["1754-2189"],"eissn":["1750-2799"]},"department":[{"_id":"PeJo"}],"_id":"9438","ddc":["570"],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","status":"public","article_processing_charge":"No","oa":1,"oa_version":"Submitted Version","has_accepted_license":"1","doi":"10.1038/s41596-021-00526-0","acknowledged_ssus":[{"_id":"M-Shop"}],"pmid":1,"abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"corr_author":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"language":[{"iso":"eng"}],"year":"2021","publication":"Nature Protocols","citation":{"apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>"},"isi":1,"month":"06","date_updated":"2025-04-22T22:30:43Z","date_created":"2021-05-30T22:01:24Z","file":[{"creator":"cziletti","date_updated":"2021-12-02T23:30:05Z","file_size":38574802,"embargo":"2021-12-01","file_id":"9639","content_type":"application/pdf","date_created":"2021-07-08T12:27:55Z","access_level":"open_access","checksum":"7eb580abd8893cdb0b410cf41bc8c263","file_name":"VandaeletalAuthorVersion2021.pdf","relation":"main_file"}],"scopus_import":"1","project":[{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"V00739","call_identifier":"FWF","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"issue":"6","volume":16,"article_type":"original","page":"2947–2967","file_date_updated":"2021-12-02T23:30:05Z","author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael"},{"last_name":"Okamoto","id":"3337E116-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0408-6094","first_name":"Yuji","full_name":"Okamoto, Yuji"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina"},{"last_name":"Vargas Barroso","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","full_name":"Vargas Barroso, Victor M"},{"last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9885-6936","first_name":"Benjamin","full_name":"Suter, Benjamin"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"}]},{"abstract":[{"lang":"eng","text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["General Chemistry","General Chemical Engineering"],"quality_controlled":"1","corr_author":"1","publisher":"Springer Nature","oa":1,"doi":"10.1038/s41557-021-00643-z","oa_version":"Submitted Version","has_accepted_license":"1","type":"journal_article","date_published":"2021-03-15T00:00:00Z","article_processing_charge":"No","status":"public","intvolume":"        13","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","day":"15","department":[{"_id":"StFr"}],"_id":"9250","ddc":["540"],"acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"volume":13,"date_created":"2021-03-16T11:12:20Z","issue":"5","file":[{"date_updated":"2021-09-16T22:30:03Z","creator":"dernst","embargo":"2021-09-15","file_size":1811448,"checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","access_level":"open_access","date_created":"2021-03-22T11:46:00Z","content_type":"application/pdf","file_id":"9276","relation":"main_file","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf"}],"scopus_import":"1","author":[{"full_name":"Petit, Yann K.","last_name":"Petit","first_name":"Yann K."},{"full_name":"Mourad, Eléonore","first_name":"Eléonore","last_name":"Mourad"},{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"full_name":"Leypold, Christian","last_name":"Leypold","first_name":"Christian"},{"full_name":"Windischbacher, Andreas","first_name":"Andreas","last_name":"Windischbacher"},{"full_name":"Mijailovic, Daniel","first_name":"Daniel","last_name":"Mijailovic"},{"last_name":"Slugovc","first_name":"Christian","full_name":"Slugovc, Christian"},{"last_name":"Borisov","first_name":"Sergey M.","full_name":"Borisov, Sergey M."},{"full_name":"Zojer, Egbert","first_name":"Egbert","last_name":"Zojer"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander"}],"page":"465-471","file_date_updated":"2021-09-16T22:30:03Z","article_type":"original","isi":1,"month":"03","date_updated":"2024-10-09T21:00:28Z","publication":"Nature Chemistry","year":"2021","citation":{"apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>.","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>"},"external_id":{"pmid":["33723377"],"isi":["000629296400001"]},"publication_status":"published","language":[{"iso":"eng"}]},{"article_processing_charge":"No","status":"public","type":"journal_article","date_published":"2021-06-01T00:00:00Z","department":[{"_id":"MaSe"}],"ddc":["539"],"_id":"9428","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","publication_identifier":{"eissn":["1745-2481"]},"intvolume":"        17","ec_funded":1,"title":"Quantum many-body scars and weak breaking of ergodicity","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"quality_controlled":"1","publisher":"Nature Research","abstract":[{"text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology.","lang":"eng"}],"doi":"10.1038/s41567-021-01230-2","oa_version":"Preprint","has_accepted_license":"1","oa":1,"citation":{"chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>.","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>"},"publication":"Nature Physics","year":"2021","language":[{"iso":"eng"}],"external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"publication_status":"published","author":[{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"}],"file_date_updated":"2021-12-02T23:30:03Z","article_type":"review","page":"675–685","volume":17,"date_created":"2021-05-28T09:03:50Z","scopus_import":"1","issue":"6","file":[{"date_updated":"2021-12-02T23:30:03Z","creator":"patrickd","embargo":"2021-12-01","file_size":10028836,"access_level":"open_access","checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_id":"10026","content_type":"application/pdf","date_created":"2021-09-20T09:27:43Z","relation":"main_file","file_name":"RevisedQMBSreview.pdf"}],"project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"month":"06","isi":1,"date_updated":"2025-04-14T07:52:09Z"},{"date_published":"2021-06-19T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No","day":"19","title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","intvolume":"       138","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","_id":"10167","ddc":["610"],"department":[{"_id":"BeVi"}],"pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"publisher":"Oxford University Press ","corr_author":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.1093/molbev/msab178","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication":"Molecular Biology and Evolution","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19386"}]},"citation":{"mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>"},"publication_status":"published","external_id":{"isi":["000741368600009"],"pmid":["34146097"]},"language":[{"iso":"eng"}],"issue":"12","file":[{"date_updated":"2022-05-06T09:47:18Z","success":1,"creator":"dernst","file_size":1008594,"access_level":"open_access","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","content_type":"application/pdf","file_id":"11352","date_created":"2022-05-06T09:47:18Z","relation":"main_file","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf"}],"project":[{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"scopus_import":"1","date_created":"2021-10-21T07:49:12Z","volume":138,"file_date_updated":"2022-05-06T09:47:18Z","article_type":"original","page":"5345-58","author":[{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","full_name":"Elkrewi, Marwan N"},{"last_name":"Moldovan","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"last_name":"Picard","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L","full_name":"Picard, Marion A L"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"date_updated":"2026-04-09T22:30:15Z","month":"06","isi":1},{"title":"Experimental observation of the origin and structure of elastoinertial turbulence","day":"03","intvolume":"       118","acknowledgement":"We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688.","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"department":[{"_id":"BjHo"}],"_id":"10299","type":"journal_article","date_published":"2021-11-03T00:00:00Z","status":"public","article_processing_charge":"No","article_number":"e2102350118","oa":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2103.00023","open_access":"1"}],"doi":"10.1073/pnas.2102350118","pmid":1,"abstract":[{"text":"Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number.","lang":"eng"}],"publisher":"National Academy of Sciences","corr_author":"1","keyword":["multidisciplinary","elastoinertial turbulence","viscoelastic flows","elastic instability","drag reduction"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"quality_controlled":"1","publication_status":"published","external_id":{"arxiv":["2103.00023"],"isi":["000720926900019"],"pmid":[" 34732570"]},"language":[{"iso":"eng"}],"year":"2021","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19906"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"apa":"Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., &#38; Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2102350118\">https://doi.org/10.1073/pnas.2102350118</a>.","short":"G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>.","ama":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(45). doi:<a href=\"https://doi.org/10.1073/pnas.2102350118\">10.1073/pnas.2102350118</a>","ieee":"G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 45. National Academy of Sciences, 2021.","ista":"Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences of the United States of America. 118(45), e2102350118."},"isi":1,"month":"11","date_updated":"2026-04-09T22:30:20Z","date_created":"2021-11-17T13:24:24Z","scopus_import":"1","project":[{"grant_number":"I04188","call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow in complex fluids"}],"issue":"45","volume":118,"article_type":"original","author":[{"full_name":"Choueiri, George H","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri"},{"full_name":"Lopez Alonso, Jose M","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso"},{"full_name":"Varshney, Atul","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","last_name":"Varshney"},{"last_name":"Sankar","first_name":"Sarath","full_name":"Sankar, Sarath"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}]},{"date_updated":"2026-04-09T22:30:32Z","month":"02","isi":1,"volume":17,"project":[{"grant_number":"P31639","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton"},{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","date_created":"2020-10-04T22:01:37Z","author":[{"full_name":"Boocock, Daniel R","first_name":"Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","last_name":"Boocock"},{"first_name":"Naoya","last_name":"Hino","full_name":"Hino, Naoya"},{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"article_type":"original","page":"267-274","external_id":{"isi":["000573519500002"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12964"}],"link":[{"url":"https://ist.ac.at/en/news/wound-healing-waves/","description":"News on IST Homepage","relation":"press_release"}]},"publication":"Nature Physics","year":"2021","citation":{"ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>"},"oa":1,"doi":"10.1038/s41567-020-01037-7","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.05.15.096479"}],"abstract":[{"lang":"eng","text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration."}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","publisher":"Springer Nature","intvolume":"        17","ec_funded":1,"day":"01","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","_id":"8602","department":[{"_id":"EdHa"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","date_published":"2021-02-01T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public"}]