[{"oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7435","status":"deleted"},{"status":"public","id":"7481","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9416"},{"relation":"part_of_dissertation","id":"7479","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"},{"_id":"E-Lib"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","doi":"10.15479/AT:ISTA:9418","degree_awarded":"PhD","page":"125","oa":1,"publisher":"Institute of Science and Technology Austria","date_published":"2021-05-30T00:00:00Z","ddc":["000"],"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."}],"file":[{"file_size":2673905,"access_level":"open_access","content_type":"application/pdf","file_id":"9419","success":1,"date_updated":"2021-05-24T11:22:29Z","file_name":"mph-thesis-v519-pdfimages.pdf","relation":"main_file","date_created":"2021-05-24T11:22:29Z","creator":"bphuong","checksum":"4f0abe64114cfed264f9d36e8d1197e3"},{"checksum":"f5699e876bc770a9b0df8345a77720a2","creator":"bphuong","date_created":"2021-05-24T11:56:02Z","relation":"source_file","date_updated":"2021-05-24T11:56:02Z","file_name":"thesis.zip","file_id":"9420","content_type":"application/zip","access_level":"closed","file_size":92995100}],"status":"public","has_accepted_license":"1","author":[{"last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"}],"month":"05","article_processing_charge":"No","citation":{"ieee":"M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021.","short":"M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021.","ista":"Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria.","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>.","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>","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>."},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file_date_updated":"2021-05-24T11:56:02Z","_id":"9418","date_updated":"2023-09-08T11:11:12Z","date_created":"2021-05-24T13:06:23Z","publication_status":"published","alternative_title":["ISTA Thesis"],"day":"30","title":"Underspecification in deep learning","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"year":"2021"},{"isi":1,"intvolume":"       126","oa":1,"publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"type":"journal_article","doi":"10.1103/PhysRevLett.126.244502","oa_version":"Preprint","publication":"Physical Review Letters","arxiv":1,"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/turbulent-flow-simplified/","relation":"press_release","description":"News on IST Homepage"}]},"author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312","first_name":"Gökhan","full_name":"Yalniz, Gökhan","last_name":"Yalniz"},{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"}],"month":"06","article_processing_charge":"No","article_number":"244502","quality_controlled":"1","article_type":"letter_note","status":"public","date_published":"2021-06-18T00:00:00Z","abstract":[{"lang":"eng","text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n"}],"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"date_created":"2021-06-16T15:45:36Z","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"_id":"9558","date_updated":"2023-08-08T14:08:36Z","citation":{"short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","apa":"Yalniz, G., Hof, B., &#38; Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>","ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>.","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. 2021;126(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>.","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” <i>Physical Review Letters</i>, vol. 126, no. 24. American Physical Society, 2021."},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"issue":"24","year":"2021","day":"18","title":"Coarse graining the state space of a turbulent flow using periodic orbits","external_id":{"isi":["000663310100008"],"arxiv":["2007.02584"]},"volume":126,"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster."},{"_id":"9562","date_updated":"2023-09-11T12:55:53Z","file_date_updated":"2022-07-02T22:30:04Z","citation":{"ieee":"D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,” Institute of Science and Technology Austria, 2021.","apa":"Kleindienst, D. (2021). <i>2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>","ista":"Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. Institute of Science and Technology Austria.","short":"D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning, Institute of Science and Technology Austria, 2021.","ama":"Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>","mla":"Kleindienst, David. <i>2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9562\">10.15479/at:ista:9562</a>.","chicago":"Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9562\">https://doi.org/10.15479/at:ista:9562</a>."},"department":[{"_id":"GradSch"},{"_id":"RySh"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2021-06-17T14:10:47Z","day":"01","title":"2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning","year":"2021","supervisor":[{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"doi":"10.15479/at:ista:9562","page":"124","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","related_material":{"record":[{"status":"public","id":"9756","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9437"},{"status":"public","id":"8532","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"612"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","oa":1,"status":"public","file":[{"file_name":"Thesis.pdf","date_updated":"2022-07-02T22:30:04Z","file_size":77299142,"access_level":"open_access","content_type":"application/pdf","file_id":"9563","creator":"dkleindienst","checksum":"659df5518db495f679cb1df9e9bd1d94","embargo":"2022-07-01","relation":"main_file","date_created":"2021-06-17T14:03:14Z"},{"checksum":"3bcf63a2b19e5b6663be051bea332748","creator":"dkleindienst","relation":"source_file","date_created":"2021-06-17T14:04:30Z","date_updated":"2022-07-02T22:30:04Z","file_name":"Thesis_source.zip","embargo_to":"open_access","content_type":"application/zip","file_id":"9564","file_size":369804895,"access_level":"closed"}],"date_published":"2021-06-01T00:00:00Z","ddc":["570"],"abstract":[{"text":"Left-right asymmetries can be considered a fundamental organizational principle of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell synaptic connection shows an input-side dependent asymmetry where the hemispheric location of the presynaptic CA3 neuron determines the synaptic properties. Left-input synapses terminating on apical dendrites in stratum radiatum have a higher density of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1 and smaller areas with less often perforated PSDs. On the other hand, left-input synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities than right-input ones. Apical and basal synapses further employ different signaling pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize synaptic membrane proteins with high sensitivity and resolution, and has been used to reveal the asymmetry at the electron microscopic level. However, it requires time-consuming manual demarcation of the synaptic surface for quantitative measurements. To facilitate the analysis of replica labeling, I first developed a software named Darea, which utilizes deep-learning to automatize this demarcation. With Darea I characterized the synaptic distribution of NMDA and AMPA receptors as well as the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I explored the role of GluN2B and its carboxy-terminus in the establishment of input-side dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were detected. We further discovered a previously unknown functional asymmetry of GluN2A, which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus plays a critical role in normal formation of input-side dependent asymmetry.","lang":"eng"}],"article_processing_charge":"No","author":[{"id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David","last_name":"Kleindienst"}],"month":"06","has_accepted_license":"1"},{"oa":1,"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png"},"language":[{"iso":"eng"}],"arxiv":1,"publication":"Proceedings of the 33rd Canadian Conference on Computational Geometry","oa_version":"Submitted Version","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","keyword":["convex grabbing game","graph grabbing game","combinatorial game","convex geometry"],"has_accepted_license":"1","article_processing_charge":"No","month":"06","author":[{"last_name":"Dvorak","full_name":"Dvorak, Martin","first_name":"Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X"},{"first_name":"Sara","full_name":"Nicholson, Sara","last_name":"Nicholson"}],"file":[{"file_size":381306,"access_level":"open_access","content_type":"application/pdf","file_id":"9616","success":1,"file_name":"Convex-Grabbing-Game_CCCG_proc_version.pdf","date_updated":"2021-06-28T20:23:13Z","relation":"main_file","date_created":"2021-06-28T20:23:13Z","creator":"mdvorak","checksum":"45accb1de9b7e0e4bb2fbfe5fd3e6239"},{"success":1,"date_updated":"2021-08-12T10:57:21Z","file_name":"Convex-Grabbing-Game_FULL-VERSION.pdf","access_level":"open_access","file_size":403645,"file_id":"9902","content_type":"application/pdf","creator":"kschuh","checksum":"9199cf18c65658553487458cc24d0ab2","date_created":"2021-08-12T10:57:21Z","relation":"main_file"}],"abstract":[{"text":"The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general.","lang":"eng"}],"ddc":["516"],"date_published":"2021-06-29T00:00:00Z","status":"public","quality_controlled":"1","date_created":"2021-06-22T15:57:11Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_status":"accepted","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"citation":{"mla":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>.","ama":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. In: <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>.","chicago":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, n.d.","ista":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. Proceedings of the 33rd Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry.","apa":"Dvorak, M., &#38; Nicholson, S. (n.d.). Massively winning configurations in the convex grabbing game on the plane. In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Halifax, NS, Canada.","short":"M. Dvorak, S. Nicholson, in:, Proceedings of the 33rd Canadian Conference on Computational Geometry, n.d.","ieee":"M. Dvorak and S. Nicholson, “Massively winning configurations in the convex grabbing game on the plane,” in <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Halifax, NS, Canada."},"date_updated":"2021-08-12T10:57:39Z","_id":"9592","file_date_updated":"2021-08-12T10:57:21Z","conference":{"name":"CCCG: Canadian Conference on Computational Geometry","end_date":"2021-08-12","start_date":"2021-08-10","location":"Halifax, NS, Canada"},"year":"2021","external_id":{"arxiv":["2106.11247"]},"title":"Massively winning configurations in the convex grabbing game on the plane","day":"29"},{"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"citation":{"ama":"Caballero Mancebo S. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>","mla":"Caballero Mancebo, Silvia. <i>Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9623\">10.15479/at:ista:9623</a>.","chicago":"Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>.","apa":"Caballero Mancebo, S. (2021). <i>Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9623\">https://doi.org/10.15479/at:ista:9623</a>","ista":"Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. Institute of Science and Technology Austria.","short":"S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes, Institute of Science and Technology Austria, 2021.","ieee":"S. Caballero Mancebo, “Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,” Institute of Science and Technology Austria, 2021."},"date_updated":"2023-09-07T13:33:27Z","_id":"9623","file_date_updated":"2022-07-02T22:30:06Z","date_created":"2021-07-01T14:50:17Z","alternative_title":["ISTA Thesis"],"publication_status":"published","title":"Fertilization-induced deformations are controlled by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes","year":"2021","supervisor":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"9750","status":"public"},{"status":"public","id":"9006","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"111","doi":"10.15479/at:ista:9623","degree_awarded":"PhD","type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication_identifier":{"isbn":["978-3-99078-012-1"],"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"file":[{"date_created":"2021-07-01T14:48:54Z","relation":"source_file","creator":"scaballe","checksum":"e039225a47ef32666d59bf35ddd30ecf","access_level":"closed","file_size":131946790,"file_id":"9624","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_updated":"2022-07-02T22:30:06Z","file_name":"PhDThesis_SCM.docx"},{"date_updated":"2022-07-02T22:30:06Z","file_name":"PhDThesis_SCM.pdf","file_size":17094958,"access_level":"open_access","content_type":"application/pdf","file_id":"9625","creator":"scaballe","checksum":"dd4d78962ea94ad95e97ca7d9af08f4b","embargo":"2022-07-01","relation":"main_file","date_created":"2021-07-01T14:46:25Z"}],"ddc":["570"],"abstract":[{"text":"Cytoplasmic reorganizations are essential for morphogenesis. In large cells like oocytes, these reorganizations become crucial in patterning the oocyte for later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm (ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization with the contraction of the actomyosin cortex along the animal-vegetal axis of the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER), maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here we have used the species Phallusia mammillata to investigate the changes in cell shape that accompany these reorganizations and the mechanochemical mechanisms underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV) axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show that the fast oscillation corresponds to a dynamic polarization of the actin cortex as a result of a fertilization-induced increase in cortical tension in the oocyte that triggers a rupture of the cortex at the animal pole and the establishment of vegetal-directed cortical flows. These flows are responsible for the vegetal accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion of the VP, leading to CP formation, correlates with a relaxation of the vegetal cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm is a solid-like layer that buckles under compression forces arising from the contracting actin cortex at the VP. Straightening of the myoplasm when actin flows stops, facilitates the expansion of the VP and the CP. Altogether, our results present a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation. \r\n","lang":"eng"}],"date_published":"2021-07-01T00:00:00Z","status":"public","has_accepted_license":"1","article_processing_charge":"No","month":"07","author":[{"last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346"}]},{"has_accepted_license":"1","month":"07","author":[{"id":"469E6004-F248-11E8-B48F-1D18A9856A87","first_name":"Nishchal","full_name":"Agrawal, Nishchal","last_name":"Agrawal"}],"article_processing_charge":"No","ddc":["532"],"abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"date_published":"2021-07-29T00:00:00Z","file":[{"date_created":"2021-07-28T13:32:02Z","relation":"source_file","creator":"nagrawal","checksum":"77436be3563a90435024307b1b5ee7e8","access_level":"closed","file_size":22859658,"file_id":"9744","content_type":"application/x-zip-compressed","embargo_to":"open_access","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","date_updated":"2022-07-29T22:30:05Z"},{"checksum":"72a891d7daba85445c29b868c22575ed","creator":"nagrawal","relation":"main_file","date_created":"2021-07-28T13:32:05Z","embargo":"2022-07-28","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","date_updated":"2022-07-29T22:30:05Z","content_type":"application/pdf","file_id":"9745","file_size":18658048,"access_level":"open_access"}],"status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"6189","relation":"part_of_dissertation"}]},"type":"dissertation","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"M-Shop"}],"page":"118","doi":"10.15479/at:ista:9728","degree_awarded":"PhD","supervisor":[{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"year":"2021","title":"Transition to turbulence and drag reduction in particle-laden pipe flows","day":"29","date_created":"2021-07-27T13:40:30Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"citation":{"ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria.","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021."},"file_date_updated":"2022-07-29T22:30:05Z","date_updated":"2024-02-28T13:14:39Z","_id":"9728"},{"file_date_updated":"2022-03-10T12:13:57Z","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"},{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"_id":"9733","date_updated":"2024-03-06T12:30:44Z","citation":{"short":"D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and Technology Austria, 2021.","apa":"Feliciangeli, D. (2021). <i>The polaron at strong coupling</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>","ista":"Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science and Technology Austria.","chicago":"Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9733\">https://doi.org/10.15479/at:ista:9733</a>.","mla":"Feliciangeli, Dario. <i>The Polaron at Strong Coupling</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>.","ama":"Feliciangeli D. The polaron at strong coupling. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9733\">10.15479/at:ista:9733</a>","ieee":"D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and Technology Austria, 2021."},"department":[{"_id":"GradSch"},{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2021-07-27T15:48:30Z","day":"20","title":"The polaron at strong coupling","supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"},{"full_name":"Maas, Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"year":"2021","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","doi":"10.15479/at:ista:9733","degree_awarded":"PhD","page":"180","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"9787","status":"public"},{"id":"9792","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"9225","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9781"},{"status":"public","relation":"part_of_dissertation","id":"9791"}]},"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","date_published":"2021-08-20T00:00:00Z","ddc":["515","519","539"],"abstract":[{"lang":"eng","text":"This thesis is the result of the research carried out by the author during his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich polaron model, specifically to its regime of strong coupling. This model, which is rigorously introduced and discussed in the introduction, has been of great interest in condensed matter physics and field theory for more than eighty years. It is used to describe an electron interacting with the atoms of a solid material (the strength of this interaction is modeled by the presence of a coupling constant α in the Hamiltonian of the system). The particular regime examined here, which is mathematically described by considering the limit α →∞, displays many interesting features related to the emergence of classical behavior, which allows for a simplified effective description of the system under analysis. The properties, the range of validity and a quantitative analysis of the precision of such classical approximations are the main object of the present work. We specify our investigation to the study of the ground state energy of the system, its dynamics and its effective mass. For each of these problems, we provide in the introduction an overview of the previously known results and a detailed account of the original contributions by the author."}],"file":[{"relation":"main_file","date_created":"2021-08-19T14:03:48Z","checksum":"e88bb8ca43948abe060eb2d2fa719881","creator":"dfelicia","content_type":"application/pdf","file_id":"9944","file_size":1958710,"access_level":"open_access","file_name":"Thesis_FeliciangeliA.pdf","date_updated":"2021-09-06T09:28:56Z"},{"content_type":"application/octet-stream","file_id":"9945","file_size":3771669,"access_level":"closed","date_updated":"2022-03-10T12:13:57Z","file_name":"thesis.7z","relation":"source_file","date_created":"2021-08-19T14:06:35Z","checksum":"72810843abee83705853505b3f8348aa","creator":"dfelicia"}],"author":[{"first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli","full_name":"Feliciangeli, Dario"}],"month":"08","article_processing_charge":"No","has_accepted_license":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2521-327X"]},"type":"journal_article","doi":"10.22331/Q-2021-07-01-491","publication":"Quantum","oa_version":"Published Version","arxiv":1,"ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"14622","relation":"dissertation_contains","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"intvolume":"         5","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","oa":1,"quality_controlled":"1","article_type":"original","status":"public","date_published":"2021-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing."}],"ddc":["530"],"file":[{"file_size":2312482,"access_level":"open_access","content_type":"application/pdf","file_id":"9774","file_name":"2021_Quantum_Sack.pdf","date_updated":"2021-08-06T06:44:31Z","relation":"main_file","date_created":"2021-08-06T06:44:31Z","creator":"cchlebak","checksum":"9706c2bb8e748e9b5b138381995a7f6f"}],"author":[{"full_name":"Sack, Stefan","last_name":"Sack","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"month":"07","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","article_number":"491","file_date_updated":"2021-08-06T06:44:31Z","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899"}],"_id":"9760","date_updated":"2023-12-13T14:47:25Z","citation":{"ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. 2021;5. doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:<a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">10.22331/Q-2021-07-01-491</a>.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>.","apa":"Sack, S., &#38; Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/Q-2021-07-01-491\">https://doi.org/10.22331/Q-2021-07-01-491</a>","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” <i>Quantum</i>, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021."},"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publication_status":"published","date_created":"2021-08-01T22:01:21Z","day":"01","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","external_id":{"isi":["000669830600001"],"arxiv":["2101.05742"]},"volume":5,"acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","year":"2021"},{"quality_controlled":"1","article_type":"original","status":"public","date_published":"2021-08-01T00:00:00Z","abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Sperl, Georg","last_name":"Sperl"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"month":"08","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","article_number":"168","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"type":"journal_article","doi":"10.1145/3450626.3459816","publication":"ACM Transactions on Graphics","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/knitting-virtual-yarn/"}],"record":[{"status":"public","id":"12358","relation":"dissertation_contains"},{"relation":"software","id":"9327","status":"public"}]},"isi":1,"intvolume":"        40","oa":1,"publisher":"Association for Computing Machinery","day":"01","title":"Mechanics-aware deformation of yarn pattern geometry","external_id":{"isi":["000674930900132"]},"volume":40,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","issue":"4","year":"2021","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"_id":"9818","date_updated":"2023-08-10T14:24:36Z","citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021."},"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3450626.3459816"}],"publication_status":"published","date_created":"2021-08-08T22:01:27Z"},{"oa":1,"publisher":"Springer Nature","intvolume":"     12704","language":[{"iso":"eng"}],"ec_funded":1,"publication":"Topics in Cryptology – CT-RSA 2021","oa_version":"Submitted Version","doi":"10.1007/978-3-030-75539-3_17","page":"399-421","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030755386"]},"article_processing_charge":"No","scopus_import":"1","month":"05","author":[{"first_name":"Benedikt","orcid":"0000-0002-7553-6606","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","full_name":"Auerbach, Benedikt"},{"first_name":"Suvradip","id":"B9CD0494-D033-11E9-B219-A439E6697425","last_name":"Chakraborty","full_name":"Chakraborty, Suvradip"},{"last_name":"Klein","full_name":"Klein, Karen","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","full_name":"Walter, Michael","last_name":"Walter"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X"}],"abstract":[{"lang":"eng","text":"Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices.\r\n\r\nWe propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks."}],"date_published":"2021-05-11T00:00:00Z","status":"public","quality_controlled":"1","date_created":"2021-08-08T22:01:30Z","alternative_title":["LNCS"],"publication_status":"published","main_file_link":[{"url":"https://eprint.iacr.org/2020/670","open_access":"1"}],"department":[{"_id":"KrPi"},{"_id":"GradSch"}],"citation":{"ieee":"B. Auerbach <i>et al.</i>, “Inverse-Sybil attacks in automated contact tracing,” in <i>Topics in Cryptology – CT-RSA 2021</i>, Virtual Event, 2021, vol. 12704, pp. 399–421.","apa":"Auerbach, B., Chakraborty, S., Klein, K., Pascual Perez, G., Pietrzak, K. Z., Walter, M., &#38; Yeo, M. X. (2021). Inverse-Sybil attacks in automated contact tracing. In <i>Topics in Cryptology – CT-RSA 2021</i> (Vol. 12704, pp. 399–421). Virtual Event: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>","ista":"Auerbach B, Chakraborty S, Klein K, Pascual Perez G, Pietrzak KZ, Walter M, Yeo MX. 2021. Inverse-Sybil attacks in automated contact tracing. Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference, LNCS, vol. 12704, 399–421.","short":"B. Auerbach, S. Chakraborty, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, M.X. Yeo, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021, pp. 399–421.","mla":"Auerbach, Benedikt, et al. “Inverse-Sybil Attacks in Automated Contact Tracing.” <i>Topics in Cryptology – CT-RSA 2021</i>, vol. 12704, Springer Nature, 2021, pp. 399–421, doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>.","ama":"Auerbach B, Chakraborty S, Klein K, et al. Inverse-Sybil attacks in automated contact tracing. In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:399-421. doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>","chicago":"Auerbach, Benedikt, Suvradip Chakraborty, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, Michael Walter, and Michelle X Yeo. “Inverse-Sybil Attacks in Automated Contact Tracing.” In <i>Topics in Cryptology – CT-RSA 2021</i>, 12704:399–421. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>."},"date_updated":"2023-02-23T14:09:56Z","_id":"9826","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"conference":{"start_date":"2021-05-17","location":"Virtual Event","name":"CT-RSA: Cryptographers’ Track at the RSA Conference","end_date":"2021-05-20"},"year":"2021","acknowledgement":"Guillermo Pascual-Perez and Michelle Yeo were funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie Grant Agreement No. 665385; the remaining contributors to this project have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","volume":12704,"title":"Inverse-Sybil attacks in automated contact tracing","day":"11"},{"_id":"9891","date_updated":"2023-08-11T10:29:48Z","file_date_updated":"2021-10-27T12:57:06Z","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>.","mla":"Lauritsen, Asbjørn Bækgaard. “Floating Wigner Crystal and Periodic Jellium Configurations.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8, 083305, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>.","ama":"Lauritsen AB. Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. 2021;62(8). doi:<a href=\"https://doi.org/10.1063/5.0053494\">10.1063/5.0053494</a>","short":"A.B. Lauritsen, Journal of Mathematical Physics 62 (2021).","apa":"Lauritsen, A. B. (2021). Floating Wigner crystal and periodic jellium configurations. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0053494\">https://doi.org/10.1063/5.0053494</a>","ista":"Lauritsen AB. 2021. Floating Wigner crystal and periodic jellium configurations. Journal of Mathematical Physics. 62(8), 083305.","ieee":"A. B. Lauritsen, “Floating Wigner crystal and periodic jellium configurations,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 8. AIP Publishing, 2021."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"publication_status":"published","date_created":"2021-08-12T07:08:36Z","external_id":{"isi":["000683960800003"],"arxiv":["2103.07975"]},"day":"01","title":"Floating Wigner crystal and periodic jellium configurations","volume":62,"acknowledgement":"The author would like to thank Robert Seiringer for guidance and many helpful comments on this project. The author would also like to thank Mathieu Lewin for his comments on the manuscript and Lorenzo Portinale for providing his lecture notes for the course “Mathematics of quantum many-body systems” in spring 2020, taught by Robert Seiringer. The Proof of Theorem III.1 is inspired by these lecture notes.","issue":"8","year":"2021","doi":"10.1063/5.0053494","publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"type":"journal_article","publication":"Journal of Mathematical Physics","oa_version":"Published Version","arxiv":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"AIP Publishing","oa":1,"isi":1,"intvolume":"        62","article_type":"original","status":"public","quality_controlled":"1","file":[{"checksum":"d035be2b894c4d50d90ac5ce252e27cd","creator":"cziletti","relation":"main_file","date_created":"2021-10-27T12:57:06Z","date_updated":"2021-10-27T12:57:06Z","file_name":"2021_JMathPhy_Lauritsen.pdf","success":1,"content_type":"application/pdf","file_id":"10188","file_size":4352640,"access_level":"open_access"}],"date_published":"2021-08-01T00:00:00Z","abstract":[{"text":"Extending on ideas of Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)], we present a modified “floating crystal” trial state for jellium (also known as the classical homogeneous electron gas) with density equal to a characteristic function. This allows us to show that three definitions of the jellium energy coincide in dimensions d ≥ 2, thus extending the result of Cotar and Petrache [“Equality of the Jellium and uniform electron gas next-order asymptotic terms for Coulomb and Riesz potentials,” arXiv: 1707.07664 (2019)] and Lewin, Lieb, and Seiringer [Phys. Rev. B 100, 035127 (2019)] that the three definitions coincide in dimension d ≥ 3. We show that the jellium energy is also equivalent to a “renormalized energy” studied in a series of papers by Serfaty and others, and thus, by the work of Bétermin and Sandier [Constr. Approximation 47, 39–74 (2018)], we relate the jellium energy to the order n term in the logarithmic energy of n points on the unit 2-sphere. We improve upon known lower bounds for this renormalized energy. Additionally, we derive formulas for the jellium energy of periodic configurations.","lang":"eng"}],"ddc":["530"],"scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288"}],"month":"08","article_number":"083305","has_accepted_license":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"American Physical Society","intvolume":"       127","isi":1,"doi":"10.1103/physrevlett.127.060602","type":"journal_article","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"oa_version":"Published Version","publication":"Physical Review Letters","article_processing_charge":"Yes (in subscription journal)","month":"08","author":[{"orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","first_name":"Volker","full_name":"Karle, Volker","last_name":"Karle"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","first_name":"Alexios","full_name":"Michailidis, Alexios","last_name":"Michailidis"}],"has_accepted_license":"1","article_number":"060602","status":"public","article_type":"letter_note","quality_controlled":"1","file":[{"creator":"mserbyn","checksum":"51218f302dcef99d90d1209809fcc874","relation":"main_file","date_created":"2021-08-13T09:28:08Z","success":1,"file_name":"PhysRevLett.127.060602_SOM.pdf","date_updated":"2021-08-13T09:28:08Z","file_size":5064231,"access_level":"open_access","content_type":"application/pdf","file_id":"9904"}],"ddc":["539"],"abstract":[{"text":"Eigenstate thermalization in quantum many-body systems implies that eigenstates at high energy are similar to random vectors. Identifying systems where at least some eigenstates are nonthermal is an outstanding question. In this Letter we show that interacting quantum models that have a nullspace—a degenerate subspace of eigenstates at zero energy (zero modes), which corresponds to infinite temperature, provide a route to nonthermal eigenstates. We analytically show the existence of a zero mode which can be represented as a matrix product state for a certain class of local Hamiltonians. In the more general case we use a subspace disentangling algorithm to generate an orthogonal basis of zero modes characterized by increasing entanglement entropy. We show evidence for an area-law entanglement scaling of the least-entangled zero mode in the broad parameter regime, leading to a conjecture that all local Hamiltonians with the nullspace feature zero modes with area-law entanglement scaling and, as such, break the strong thermalization hypothesis. Finally, we find zero modes in constrained models and propose a setup for observing their experimental signatures.","lang":"eng"}],"date_published":"2021-08-06T00:00:00Z","publication_status":"published","date_created":"2021-08-13T09:27:39Z","date_updated":"2023-08-11T10:43:27Z","_id":"9903","file_date_updated":"2021-08-13T09:28:08Z","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"department":[{"_id":"MaSe"},{"_id":"GradSch"},{"_id":"MiLe"}],"citation":{"ieee":"V. Karle, M. Serbyn, and A. Michailidis, “Area-law entangled eigenstates from nullspaces of local Hamiltonians,” <i>Physical Review Letters</i>, vol. 127, no. 6. American Physical Society, 2021.","ista":"Karle V, Serbyn M, Michailidis A. 2021. Area-law entangled eigenstates from nullspaces of local Hamiltonians. Physical Review Letters. 127(6), 060602.","apa":"Karle, V., Serbyn, M., &#38; Michailidis, A. (2021). Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>","short":"V. Karle, M. Serbyn, A. Michailidis, Physical Review Letters 127 (2021).","ama":"Karle V, Serbyn M, Michailidis A. Area-law entangled eigenstates from nullspaces of local Hamiltonians. <i>Physical Review Letters</i>. 2021;127(6). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>","mla":"Karle, Volker, et al. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>, vol. 127, no. 6, 060602, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.060602\">10.1103/physrevlett.127.060602</a>.","chicago":"Karle, Volker, Maksym Serbyn, and Alexios Michailidis. “Area-Law Entangled Eigenstates from Nullspaces of Local Hamiltonians.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.060602\">https://doi.org/10.1103/physrevlett.127.060602</a>."},"year":"2021","issue":"6","external_id":{"arxiv":["2102.13633"],"isi":["000684276000002"]},"title":"Area-law entangled eigenstates from nullspaces of local Hamiltonians","day":"06","acknowledgement":"We acknowledge useful discussions with V. Gritsev and A. Garkun and suggestions on implementation of the\r\nPPXPP model by D. Bluvstein. A. M. and M. S. were supported by the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899)","volume":127},{"year":"2021","issue":"9","external_id":{"isi":["000681754200001"],"pmid":["34357701 "]},"title":"Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture","day":"06","acknowledgement":"This work was supported by ANID—Millennium Science Initiative Program—ICN17_022, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía Avanzada UC (UMA UC).","volume":22,"publication_status":"published","date_created":"2021-08-15T22:01:30Z","pmid":1,"date_updated":"2024-03-25T23:30:22Z","_id":"9913","file_date_updated":"2021-10-05T13:36:42Z","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"citation":{"chicago":"Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös, Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>. Wiley, 2021. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>.","mla":"Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System Architecture.” <i>EMBO Reports</i>, vol. 22, no. 9, e51813, Wiley, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>.","ama":"Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. 2021;22(9). doi:<a href=\"https://doi.org/10.15252/embr.202051813\">10.15252/embr.202051813</a>","short":"A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková, S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).","ista":"Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Reports. 22(9), e51813.","apa":"Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez, R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. <i>EMBO Reports</i>. Wiley. <a href=\"https://doi.org/10.15252/embr.202051813\">https://doi.org/10.15252/embr.202051813</a>","ieee":"A. Vega <i>et al.</i>, “Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture,” <i>EMBO Reports</i>, vol. 22, no. 9. Wiley, 2021."},"article_processing_charge":"Yes","scopus_import":"1","month":"09","author":[{"last_name":"Vega","full_name":"Vega, Andrea","first_name":"Andrea"},{"full_name":"Fredes, Isabel","last_name":"Fredes","first_name":"Isabel"},{"first_name":"José","last_name":"O’Brien","full_name":"O’Brien, José"},{"last_name":"Shen","full_name":"Shen, Zhouxin","first_name":"Zhouxin"},{"full_name":"Ötvös, Krisztina","last_name":"Ötvös","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"last_name":"Abualia","full_name":"Abualia, Rashed","first_name":"Rashed","id":"4827E134-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9357-9415"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"full_name":"Briggs, Steven P.","last_name":"Briggs","first_name":"Steven P."},{"last_name":"Gutiérrez","full_name":"Gutiérrez, Rodrigo A.","first_name":"Rodrigo A."}],"article_number":"e51813","has_accepted_license":"1","status":"public","article_type":"original","quality_controlled":"1","file":[{"checksum":"750de03dc3b715c37090126c1548ba13","creator":"cchlebak","date_created":"2021-10-05T13:36:42Z","relation":"main_file","file_name":"2021_EmboR_Vega.pdf","date_updated":"2021-10-05T13:36:42Z","success":1,"file_id":"10090","content_type":"application/pdf","access_level":"open_access","file_size":3144854}],"abstract":[{"lang":"eng","text":"Nitrate commands genome-wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild-type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate."}],"ddc":["580"],"date_published":"2021-09-06T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publisher":"Wiley","oa":1,"intvolume":"        22","isi":1,"doi":"10.15252/embr.202051813","type":"journal_article","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"10303","relation":"dissertation_contains","status":"public"}]},"language":[{"iso":"eng"}],"publication":"EMBO Reports","oa_version":"Published Version"},{"month":"08","author":[{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","has_accepted_license":"1","status":"public","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"}],"ddc":["539"],"date_published":"2021-08-19T00:00:00Z","file":[{"relation":"source_file","date_created":"2021-08-16T09:33:21Z","checksum":"3cd1986efde5121d7581f6fcf9090da8","creator":"mperuzzo","content_type":"application/x-zip-compressed","file_id":"9924","file_size":151387283,"access_level":"closed","file_name":"GeometricSuperinductorsForCQED.zip","date_updated":"2021-09-06T08:39:47Z"},{"file_size":17596344,"access_level":"open_access","content_type":"application/pdf","file_id":"9939","file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-1b.pdf","date_updated":"2021-09-06T08:39:47Z","relation":"main_file","date_created":"2021-08-18T14:20:06Z","creator":"mperuzzo","checksum":"50928c621cdf0775d7a5906b9dc8602c"},{"file_id":"9940","description":"Extra copy of the thesis as PDF/A-2b","content_type":"application/pdf","access_level":"closed","file_size":17592425,"file_name":"GeometricSuperinductorsAndTheirApplicationsIncQED-2b.pdf","date_updated":"2021-09-06T08:39:47Z","date_created":"2021-08-18T14:20:09Z","relation":"other","checksum":"37f486aa1b622fe44af00d627ec13f6c","creator":"mperuzzo"}],"publisher":"Institute of Science and Technology Austria","oa":1,"type":"dissertation","keyword":["quantum computing","superinductor","quantum metrology"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-013-8"]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"149","degree_awarded":"PhD","doi":"10.15479/at:ista:9920","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"9928","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8755"}]},"supervisor":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"}],"year":"2021","title":"Geometric superinductors and their applications in circuit quantum electrodynamics","day":"19","publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2021-08-16T09:44:09Z","file_date_updated":"2021-09-06T08:39:47Z","date_updated":"2024-09-10T12:23:56Z","_id":"9920","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"citation":{"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>","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>.","ista":"Peruzzo M. 2021. Geometric superinductors and their applications in circuit quantum electrodynamics. Institute of Science and Technology Austria.","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>","short":"M. Peruzzo, Geometric Superinductors and Their Applications in Circuit Quantum Electrodynamics, Institute of Science and Technology Austria, 2021.","ieee":"M. Peruzzo, “Geometric superinductors and their applications in circuit quantum electrodynamics,” Institute of Science and Technology Austria, 2021."}},{"supervisor":[{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"year":"2021","title":"Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration","day":"02","date_created":"2021-08-29T12:36:50Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"citation":{"ieee":"A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration,” Institute of Science and Technology Austria, 2021.","ista":"Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. Institute of Science and Technology Austria.","apa":"Hansen, A. H. (2021). <i>Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>","short":"A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration, Institute of Science and Technology Austria, 2021.","ama":"Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>","mla":"Hansen, Andi H. <i>Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9962\">10.15479/at:ista:9962</a>.","chicago":"Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects in Radial Projection Neuron Migration.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9962\">https://doi.org/10.15479/at:ista:9962</a>."},"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}],"file_date_updated":"2022-09-03T22:30:04Z","date_updated":"2023-09-22T09:58:30Z","_id":"9962","has_accepted_license":"1","month":"09","author":[{"first_name":"Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H"}],"article_processing_charge":"No","abstract":[{"text":"The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.","lang":"eng"}],"ddc":["570"],"date_published":"2021-09-02T00:00:00Z","file":[{"date_updated":"2022-09-03T22:30:04Z","file_name":"Thesis_Hansen.docx","embargo_to":"open_access","file_size":10629190,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"9971","creator":"ahansen","checksum":"66b56f5b988b233dc66a4f4b4fb2cdfe","relation":"source_file","date_created":"2021-08-30T09:17:39Z"},{"checksum":"204fa40321a1c6289b68c473634c4bf3","creator":"ahansen","relation":"main_file","date_created":"2021-08-30T09:29:44Z","embargo":"2022-09-02","date_updated":"2022-09-03T22:30:04Z","file_name":"Thesis_Hansen_PDFA-1a.pdf","content_type":"application/pdf","file_id":"9972","file_size":13457469,"access_level":"open_access"}],"status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8569"},{"status":"public","id":"960","relation":"part_of_dissertation"}]},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["Neuronal migration","Non-cell-autonomous","Cell-autonomous","Neurodevelopmental disease"],"doi":"10.15479/at:ista:9962","page":"182","degree_awarded":"PhD"},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publisher":"Institute of Science and Technology Austria","oa":1,"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","page":"168","degree_awarded":"PhD","doi":"10.15479/at:ista:9992","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"6351","relation":"part_of_dissertation","status":"public"},{"id":"6943","relation":"part_of_dissertation","status":"public"},{"id":"8002","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","first_name":"Lukas"}],"month":"09","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2021-09-13T00:00:00Z","ddc":["575"],"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"file":[{"creator":"lhoermaye","checksum":"c763064adaa720e16066c1a4f9682bbb","date_created":"2021-09-09T07:29:48Z","relation":"source_file","embargo_to":"open_access","file_name":"Thesis_vupload.docx","date_updated":"2021-09-15T22:30:26Z","access_level":"closed","file_size":25179004,"file_id":"9993","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"embargo":"2021-09-09","relation":"main_file","date_created":"2021-09-09T14:25:08Z","creator":"lhoermaye","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","file_size":6246900,"access_level":"open_access","content_type":"application/pdf","file_id":"9996","date_updated":"2021-09-15T22:30:26Z","file_name":"Thesis_vfinal_pdfa.pdf"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2021-09-09T07:37:20Z","project":[{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file_date_updated":"2021-09-15T22:30:26Z","_id":"9992","date_updated":"2023-09-07T13:38:33Z","citation":{"apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021."},"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"year":"2021","day":"13","title":"Wound healing in the Arabidopsis root meristem"},{"publication_status":"published","pmid":1,"date_created":"2021-09-11T16:22:02Z","file_date_updated":"2021-09-13T10:31:21Z","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_updated":"2025-07-14T09:10:09Z","_id":"9997","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"citation":{"ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021."},"year":"2021","issue":"1","title":"The evolution of indirect reciprocity under action and assessment generosity","day":"31","external_id":{"isi":["000692406400018"],"pmid":["34465830"]},"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","volume":11,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        11","isi":1,"publisher":"Springer Nature","oa":1,"type":"journal_article","keyword":["Multidisciplinary"],"publication_identifier":{"eissn":["2045-2322"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41598-021-96932-1","language":[{"iso":"eng"}],"ec_funded":1,"publication":"Scientific Reports","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10293"}]},"month":"08","author":[{"last_name":"Schmid","full_name":"Schmid, Laura","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shati, Pouya","last_name":"Shati","first_name":"Pouya"},{"first_name":"Christian","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"}],"article_processing_charge":"Yes","has_accepted_license":"1","article_number":"17443","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.","lang":"eng"}],"ddc":["003"],"date_published":"2021-08-31T00:00:00Z","file":[{"relation":"main_file","date_created":"2021-09-13T10:31:21Z","checksum":"19df8816cf958b272b85841565c73182","creator":"cchlebak","content_type":"application/pdf","file_id":"10006","file_size":2424943,"access_level":"open_access","file_name":"2021_ScientificReports_Schmid.pdf","date_updated":"2021-09-13T10:31:21Z","success":1}]},{"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"citation":{"chicago":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” In <i>8th International Conference on Learning Representations</i>. ICLR, 2020.","ama":"Lechner M. Learning representations for binary-classification without backpropagation. In: <i>8th International Conference on Learning Representations</i>. ICLR; 2020.","mla":"Lechner, Mathias. “Learning Representations for Binary-Classification without Backpropagation.” <i>8th International Conference on Learning Representations</i>, ICLR, 2020.","short":"M. Lechner, in:, 8th International Conference on Learning Representations, ICLR, 2020.","ista":"Lechner M. 2020. Learning representations for binary-classification without backpropagation. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Lechner, M. (2020). Learning representations for binary-classification without backpropagation. In <i>8th International Conference on Learning Representations</i>. Virtual ; Addis Ababa, Ethiopia: ICLR.","ieee":"M. Lechner, “Learning representations for binary-classification without backpropagation,” in <i>8th International Conference on Learning Representations</i>, Virtual ; Addis Ababa, Ethiopia, 2020."},"date_updated":"2023-04-03T07:33:40Z","_id":"10672","file_date_updated":"2022-01-26T07:35:17Z","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"end_date":"2020-05-01","name":"ICLR: International Conference on Learning Representations","location":"Virtual ; Addis Ababa, Ethiopia","start_date":"2020-04-26"},"date_created":"2022-01-25T15:50:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","main_file_link":[{"url":"https://openreview.net/forum?id=Bke61krFvS","open_access":"1"}],"publication_status":"published","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award).\r\n","title":"Learning representations for binary-classification without backpropagation","day":"11","year":"2020","language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"8th International Conference on Learning Representations","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"ICLR","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"checksum":"ea13d42dd4541ddb239b6a75821fd6c9","creator":"mlechner","date_created":"2022-01-26T07:35:17Z","relation":"main_file","file_name":"iclr_2020.pdf","date_updated":"2022-01-26T07:35:17Z","success":1,"file_id":"10677","content_type":"application/pdf","access_level":"open_access","file_size":249431}],"abstract":[{"text":"The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity.","lang":"eng"}],"ddc":["000"],"date_published":"2020-03-11T00:00:00Z","status":"public","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","month":"03","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"}]},{"year":"2020","title":"A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits","acknowledgement":"RH and RG are partially supported by Horizon-2020 ECSEL Project grant No. 783163 (iDev40), Productive 4.0, and ATBMBFW CPS-IoT Ecosystem. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23\r\n(Wittgenstein Award). AA is supported by the National Science Foundation (NSF) Graduate Research Fellowship\r\nProgram. RH and DR are partially supported by The Boeing Company and JP Morgan Chase. This research work is\r\npartially drawn from the PhD dissertation of RH.\r\n","alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"http://proceedings.mlr.press/v119/hasani20a.html"}],"publication_status":"published","date_created":"2022-01-25T15:50:34Z","_id":"10673","date_updated":"2022-01-26T11:14:27Z","conference":{"name":"ML: Machine Learning","end_date":"2020-07-18","start_date":"2020-07-12","location":"Virtual"},"file_date_updated":"2022-01-26T11:08:51Z","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"citation":{"ieee":"R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, pp. 4082–4093.","mla":"Hasani, Ramin, et al. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, 2020, pp. 4082–93.","ama":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. PMLR. ; 2020:4082-4093.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “A Natural Lottery Ticket Winner: Reinforcement Learning with Ordinary Neural Circuits.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 4082–93. PMLR, 2020.","apa":"Hasani, R., Lechner, M., Amini, A., Rus, D., &#38; Grosu, R. (2020). A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (pp. 4082–4093). Virtual.","ista":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2020. A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits. Proceedings of the 37th International Conference on Machine Learning. ML: Machine LearningPMLR, PMLR, , 4082–4093.","short":"R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 4082–4093."},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"scopus_import":"1","article_processing_charge":"No","author":[{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"}],"has_accepted_license":"1","status":"public","quality_controlled":"1","series_title":"PMLR","file":[{"file_id":"10691","content_type":"application/pdf","access_level":"open_access","file_size":2329798,"date_updated":"2022-01-26T11:08:51Z","file_name":"2020_PMLR_Hasani.pdf","success":1,"date_created":"2022-01-26T11:08:51Z","relation":"main_file","checksum":"c9a4a29161777fc1a89ef451c040e3b1","creator":"cchlebak"}],"date_published":"2020-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level."}],"ddc":["000"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","short":"CC BY-NC-ND (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"page":"4082-4093","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2640-3498"]},"type":"conference","publication":"Proceedings of the 37th International Conference on Machine Learning","oa_version":"Published Version","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"ddc":["519"],"date_published":"2020-01-12T00:00:00Z","file":[{"date_created":"2020-01-12T11:49:49Z","relation":"source_file","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","creator":"jtkadlec","file_id":"7255","content_type":"application/zip","access_level":"closed","file_size":21100497,"file_name":"thesis.zip","date_updated":"2020-07-14T12:47:52Z"},{"creator":"dernst","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","date_created":"2020-01-28T07:32:42Z","relation":"main_file","date_updated":"2020-07-14T12:47:52Z","file_name":"2020_Tkadlec_Thesis.pdf","access_level":"open_access","file_size":11670983,"file_id":"7367","content_type":"application/pdf"}],"status":"public","has_accepted_license":"1","month":"01","author":[{"first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7210","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5751"},{"relation":"dissertation_contains","id":"7212","status":"public"}]},"type":"dissertation","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["2663-337X"]},"page":"144","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7196","oa":1,"publisher":"Institute of Science and Technology Austria","title":"A role of graphs in evolutionary processes","day":"12","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"year":"2020","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"citation":{"mla":"Tkadlec, Josef. <i>A Role of Graphs in Evolutionary Processes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7196\">10.15479/AT:ISTA:7196</a>","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","apa":"Tkadlec, J. (2020). <i>A role of graphs in evolutionary processes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7196\">https://doi.org/10.15479/AT:ISTA:7196</a>","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020."},"file_date_updated":"2020-07-14T12:47:52Z","date_updated":"2023-10-17T12:29:46Z","_id":"7196","date_created":"2019-12-20T12:26:36Z","publication_status":"published","alternative_title":["ISTA Thesis"]}]