[{"file_date_updated":"2023-07-06T11:35:15Z","ec_funded":1,"page":"202","publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"_id":"13175","title":"Cavity quantum electrooptics","alternative_title":["ISTA Thesis"],"date_created":"2023-06-30T08:07:43Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publication_status":"published","ddc":["537","535","539"],"citation":{"chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>."},"year":"2023","date_updated":"2024-10-29T09:11:06Z","abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"day":"05","doi":"10.15479/at:ista:13175","degree_awarded":"PhD","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"05","project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"oa_version":"Published Version","related_material":{"record":[{"id":"12900","relation":"old_edition","status":"public"},{"status":"public","id":"9114","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10924"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_name":"thesis_pdfa.pdf","content_type":"application/pdf","date_updated":"2023-06-30T08:17:25Z","file_size":18688376,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","date_created":"2023-06-30T08:17:25Z","creator":"cchlebak","file_id":"13176","relation":"main_file","success":1,"access_level":"open_access"},{"access_level":"closed","relation":"source_file","file_id":"13196","creator":"cchlebak","date_created":"2023-07-06T11:35:15Z","checksum":"c3b45317ae58e0527533f98c202d81b7","file_size":37847025,"date_updated":"2023-07-06T11:35:15Z","file_name":"thesis.zip","content_type":"application/x-zip-compressed"}],"type":"dissertation","date_published":"2023-05-05T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"supervisor":[{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]}},{"article_type":"original","publisher":"EMS Press","file_date_updated":"2023-07-11T08:19:15Z","page":"1507–1540","ec_funded":1,"quality_controlled":"1","title":"Boundary superconductivity in the BCS model","intvolume":"        12","publication_status":"published","date_created":"2023-07-10T16:35:45Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","_id":"13207","ddc":["530"],"volume":12,"acknowledgement":"We thank Egor Babaev for encouraging us to study this problem, and Rupert Frank for many fruitful discussions. scussions. Funding. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (Barbara Roos and Robert Seiringer) is gratefully acknowledged.","abstract":[{"lang":"eng","text":"We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity."}],"doi":"10.4171/JST/439","arxiv":1,"day":"18","isi":1,"external_id":{"arxiv":["2201.08090"],"isi":["000997933500008"]},"date_updated":"2023-10-27T10:37:29Z","year":"2023","citation":{"ieee":"C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” <i>Journal of Spectral Theory</i>, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023.","chicago":"Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” <i>Journal of Spectral Theory</i>. EMS Press, 2023. <a href=\"https://doi.org/10.4171/JST/439\">https://doi.org/10.4171/JST/439</a>.","apa":"Hainzl, C., Roos, B., &#38; Seiringer, R. (2023). Boundary superconductivity in the BCS model. <i>Journal of Spectral Theory</i>. EMS Press. <a href=\"https://doi.org/10.4171/JST/439\">https://doi.org/10.4171/JST/439</a>","ama":"Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. <i>Journal of Spectral Theory</i>. 2023;12(4):1507–1540. doi:<a href=\"https://doi.org/10.4171/JST/439\">10.4171/JST/439</a>","ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540.","short":"C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.","mla":"Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” <i>Journal of Spectral Theory</i>, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:<a href=\"https://doi.org/10.4171/JST/439\">10.4171/JST/439</a>."},"language":[{"iso":"eng"}],"month":"05","oa_version":"Published Version","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Journal of Spectral Theory","has_accepted_license":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14374"}]},"file":[{"access_level":"open_access","success":1,"relation":"main_file","creator":"alisjak","file_id":"13208","checksum":"5501da33be010b5c81440438287584d5","file_size":304619,"date_created":"2023-07-11T08:19:15Z","content_type":"application/pdf","file_name":"2023_EMS_Hainzl.pdf","date_updated":"2023-07-11T08:19:15Z"}],"oa":1,"publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"date_published":"2023-05-18T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"citation":{"mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” <i>34th International Conference on Concurrency Theory</i>, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">10.4230/LIPIcs.CONCUR.2023.17</a>.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Safety and liveness of quantitative automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: <i>34th International Conference on Concurrency Theory</i>. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">10.4230/LIPIcs.CONCUR.2023.17</a>","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Safety and liveness of quantitative automata. In <i>34th International Conference on Concurrency Theory</i> (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.17</a>","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In <i>34th International Conference on Concurrency Theory</i>, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.17\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.17</a>.","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in <i>34th International Conference on Concurrency Theory</i>, Antwerp, Belgium, 2023, vol. 279."},"year":"2023","date_updated":"2023-10-09T07:14:03Z","external_id":{"arxiv":["2307.06016"]},"day":"01","doi":"10.4230/LIPIcs.CONCUR.2023.17","arxiv":1,"abstract":[{"lang":"eng","text":"The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications."}],"volume":279,"acknowledgement":"We thank Christof Löding for pointing us to some results on PSpace-hardess of universality problems and the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22.","ddc":["000"],"_id":"13221","author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mazzocchi","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_created":"2023-07-14T10:00:15Z","publication_status":"published","intvolume":"       279","alternative_title":["LIPIcs"],"title":"Safety and liveness of quantitative automata","ec_funded":1,"quality_controlled":"1","file_date_updated":"2023-07-14T12:03:48Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"conference","date_published":"2023-09-01T00:00:00Z","publication_identifier":{"isbn":["9783959772990"],"eissn":["1868-8969"]},"oa":1,"file":[{"checksum":"d40e57a04448ea5c77d7e1cfb9590a81","file_size":755529,"date_created":"2023-07-14T12:03:48Z","file_name":"CONCUR23.pdf","content_type":"application/pdf","date_updated":"2023-07-14T12:03:48Z","relation":"main_file","access_level":"open_access","success":1,"creator":"esarac","file_id":"13224"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publication":"34th International Conference on Concurrency Theory","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"oa_version":"Published Version","article_number":"17","month":"09","language":[{"iso":"eng"}],"conference":{"name":"CONCUR: Conference on Concurrency Theory","start_date":"2023-09-18","end_date":"2023-09-23","location":"Antwerp, Belgium"}},{"_id":"13262","scopus_import":"1","author":[{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","first_name":"Alexander","full_name":"Fedorov, Alexander"},{"full_name":"Hashemi, Diba","first_name":"Diba","last_name":"Hashemi","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783"},{"first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"publication_status":"published","date_created":"2023-07-23T22:01:12Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"article_processing_charge":"Yes (in subscription journal)","title":"Provably-efficient and internally-deterministic parallel Union-Find","page":"261-271","quality_controlled":"1","file_date_updated":"2023-07-31T10:53:08Z","publisher":"Association for Computing Machinery","date_updated":"2023-07-31T10:54:32Z","citation":{"apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271."},"year":"2023","external_id":{"arxiv":["2304.09331"]},"doi":"10.1145/3558481.3591082","arxiv":1,"day":"17","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"ddc":["000"],"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","has_accepted_license":"1","oa_version":"Published Version","month":"06","language":[{"iso":"eng"}],"conference":{"location":"Orlando, FL, United States","end_date":"2023-06-19","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2023-06-17"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-06-17T00:00:00Z","type":"conference","publication_identifier":{"isbn":["9781450395458"]},"oa":1,"file":[{"date_updated":"2023-07-31T10:53:08Z","file_name":"2023_SPAA_Fedorov.pdf","content_type":"application/pdf","date_created":"2023-07-31T10:53:08Z","file_size":2087937,"checksum":"72e312aabf0c5248c99b5cd3a88e4c88","file_id":"13334","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy"],"publication":"Physical Review Letters","month":"07","article_number":"034002","oa_version":"Preprint","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05098","open_access":"1"}],"date_published":"2023-07-21T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"quality_controlled":"1","article_type":"original","publisher":"American Physical Society","author":[{"id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","full_name":"Paranjape, Chaitanya S","last_name":"Paranjape","first_name":"Chaitanya S"},{"full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"full_name":"Duguet, Yohann","first_name":"Yohann","last_name":"Duguet"},{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"}],"issue":"3","_id":"13274","title":"Direct path from turbulence to time-periodic solutions","intvolume":"       131","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_created":"2023-07-24T09:43:59Z","article_processing_charge":"No","volume":131,"acknowledgement":"We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.).","isi":1,"external_id":{"isi":["001052929900004"],"arxiv":["2306.05098"]},"date_updated":"2023-12-13T11:40:19Z","citation":{"chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>.","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” <i>Physical Review Letters</i>, vol. 131, no. 3. American Physical Society, 2023.","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. 2023;131(3). doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., &#38; Hof, B. (2023). Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>","ista":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.","mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>.","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023)."},"year":"2023","abstract":[{"lang":"eng","text":"Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics."}],"doi":"10.1103/physrevlett.131.034002","arxiv":1,"day":"21"},{"has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"F8606","name":"Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"}],"month":"07","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2023-07-21T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios"}],"oa":1,"file":[{"access_level":"closed","relation":"source_file","file_id":"14033","creator":"mvalenti","date_created":"2023-08-11T09:27:39Z","checksum":"666ee31c7eade89679806287c062fa14","file_size":56121429,"date_updated":"2023-08-11T10:01:34Z","content_type":"application/x-zip-compressed","file_name":"PhD_thesis_Valentini_final.zip"},{"date_created":"2023-08-11T14:39:17Z","file_size":38199711,"checksum":"0992f2ebef152dee8e70055350ebbb55","date_updated":"2023-08-11T14:39:17Z","content_type":"application/pdf","file_name":"PhD_thesis_Valentini_final_validated.pdf","access_level":"open_access","relation":"main_file","file_id":"14035","creator":"mvalenti"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"13312","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12118","status":"public"},{"relation":"part_of_dissertation","id":"8910","status":"public"},{"status":"public","id":"12522","relation":"research_data"}]},"status":"public","_id":"13286","author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco","full_name":"Valentini, Marco"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_created":"2023-07-24T14:10:45Z","title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","alternative_title":["ISTA Thesis"],"page":"184","ec_funded":1,"file_date_updated":"2023-08-11T14:39:17Z","publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T12:35:34Z","citation":{"ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","mla":"Valentini, Marco. <i>Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>.","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","apa":"Valentini, M. (2023). <i>Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>"},"year":"2023","doi":"10.15479/at:ista:13286","degree_awarded":"PhD","day":"21","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"ddc":["530"]},{"publication":"50th International Colloquium on Automata, Languages, and Programming","has_accepted_license":"1","month":"07","oa_version":"Published Version","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","end_date":"2023-07-14","location":"Paderborn, Germany"},"date_published":"2023-07-05T00:00:00Z","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"file_id":"13293","creator":"esarac","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2023-07-24T15:11:05Z","file_name":"icalp23.pdf","content_type":"application/pdf","date_created":"2023-07-24T15:11:05Z","file_size":859379,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2"}],"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kebis","first_name":"Pavol","full_name":"Kebis, Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"_id":"13292","title":"Regular methods for operator precedence languages","alternative_title":["LIPIcs"],"intvolume":"       261","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"article_processing_charge":"Yes","date_created":"2023-07-24T15:11:41Z","file_date_updated":"2023-07-24T15:11:05Z","page":"129:1--129:20","quality_controlled":"1","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["2305.03447"]},"date_updated":"2023-07-31T08:38:38Z","citation":{"short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Regular methods for operator precedence languages. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20."},"year":"2023","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"doi":"10.4230/LIPIcs.ICALP.2023.129","arxiv":1,"day":"05","ddc":["000"],"volume":261,"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n"},{"intvolume":"     13965","alternative_title":["LNCS"],"title":"Monitoring algorithmic fairness","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_created":"2023-07-25T18:32:40Z","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","orcid":"0009-0005-0820-1696","full_name":"Karimi, Mahyar","first_name":"Mahyar","last_name":"Karimi"},{"orcid":"0000-0001-8974-2542","full_name":"Kueffner, Konstantin","first_name":"Konstantin","last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","first_name":"Kaushik","last_name":"Mallik"}],"_id":"13310","publisher":"Springer Nature","file_date_updated":"2023-07-31T08:11:20Z","ec_funded":1,"quality_controlled":"1","page":"358–382","abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"day":"18","doi":"10.1007/978-3-031-37703-7_17","arxiv":1,"external_id":{"arxiv":["2305.15979"]},"citation":{"apa":"Henzinger, T. A., Karimi, M., Kueffner, K., &#38; Mallik, K. (2023). Monitoring algorithmic fairness. In <i>Computer Aided Verification</i> (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">https://doi.org/10.1007/978-3-031-37703-7_17</a>","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: <i>Computer Aided Verification</i>. Vol 13965. Springer Nature; 2023:358–382. doi:<a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">10.1007/978-3-031-37703-7_17</a>","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13965, pp. 358–382.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In <i>Computer Aided Verification</i>, 13965:358–382. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">https://doi.org/10.1007/978-3-031-37703-7_17</a>.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” <i>Computer Aided Verification</i>, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:<a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">10.1007/978-3-031-37703-7_17</a>.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382."},"year":"2023","date_updated":"2023-09-05T15:14:00Z","ddc":["000"],"acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","volume":13965,"month":"07","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Computer Aided Verification","conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","end_date":"2023-07-22","location":"Paris, France"},"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783031377037"],"isbn":["9783031377020"]},"type":"conference","date_published":"2023-07-18T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"file_name":"2023_LNCS_CAV_HenzingerT.pdf","content_type":"application/pdf","date_updated":"2023-07-31T08:11:20Z","file_size":647760,"checksum":"ccaf94bf7d658ba012c016e11869b54c","date_created":"2023-07-31T08:11:20Z","creator":"dernst","file_id":"13327","relation":"main_file","access_level":"open_access","success":1}]},{"volume":19,"acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","ddc":["530"],"doi":"10.1038/s41567-023-02218-w","day":"01","abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"date_updated":"2024-02-21T12:19:08Z","citation":{"mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. 2023;19:1916-1926. doi:<a href=\"https://doi.org/10.1038/s41567-023-02218-w\">10.1038/s41567-023-02218-w</a>","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02218-w\">https://doi.org/10.1038/s41567-023-02218-w</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1916–1926, 2023."},"year":"2023","external_id":{"pmid":["38075437"]},"publisher":"Springer Nature","article_type":"original","page":"1916-1926","quality_controlled":"1","ec_funded":1,"file_date_updated":"2024-01-30T14:28:30Z","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","date_created":"2023-07-27T14:44:45Z","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"title":"Chiral and nematic phases of flexible active filaments","intvolume":"        19","pmid":1,"_id":"13314","scopus_import":"1","author":[{"full_name":"Dunajova, Zuzana","first_name":"Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","first_name":"Batirtze","last_name":"Prats Mateu"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","first_name":"Philipp"},{"full_name":"Lim, Keesiang","last_name":"Lim","first_name":"Keesiang"},{"id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","full_name":"Brandis, Dörte","last_name":"Brandis","first_name":"Dörte"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","last_name":"Velicky","first_name":"Philipp","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Richard W.","last_name":"Wong","full_name":"Wong, Richard W."},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"file":[{"content_type":"application/pdf","file_name":"2023_NaturePhysics_Dunajova.pdf","date_updated":"2024-01-30T14:28:30Z","file_size":22471673,"checksum":"bc7673ca07d37309013a86166577b2f7","date_created":"2024-01-30T14:28:30Z","creator":"dernst","file_id":"14916","success":1,"relation":"main_file","access_level":"open_access"}],"related_material":{"record":[{"id":"13116","relation":"research_data","status":"public"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-12-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"month":"12","publication":"Nature Physics","has_accepted_license":"1"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"12680","relation":"part_of_dissertation"}]},"status":"public","file":[{"file_size":28684,"checksum":"96ee518d796d02af71395622c45de03c","date_created":"2023-07-31T10:16:32Z","file_name":"Exterior Algebra and Combinatorics.zip","content_type":"application/x-zip-compressed","date_updated":"2023-07-31T10:16:32Z","relation":"source_file","access_level":"closed","creator":"skoese","file_id":"13333"},{"success":1,"relation":"main_file","access_level":"open_access","file_id":"13480","creator":"skoese","date_created":"2023-08-03T15:28:55Z","checksum":"f610f4713f88bc477de576aaa46b114e","file_size":4953418,"date_updated":"2023-08-03T15:28:55Z","file_name":"thesis-pdfa.pdf","content_type":"application/pdf"}],"type":"dissertation","date_published":"2023-07-31T00:00:00Z","oa":1,"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"07","oa_version":"Published Version","ddc":["510","516"],"year":"2023","citation":{"apa":"Köse, S. (2023). <i>Exterior algebra and combinatorics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","mla":"Köse, Seyda. <i>Exterior Algebra and Combinatorics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>.","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria."},"date_updated":"2023-10-04T11:54:56Z","abstract":[{"lang":"eng","text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n"}],"day":"31","degree_awarded":"MS","doi":"10.15479/at:ista:13331","file_date_updated":"2023-08-03T15:28:55Z","page":"26","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Köse","first_name":"Seyda","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}],"_id":"13331","alternative_title":["ISTA Master's Thesis"],"title":"Exterior algebra and combinatorics","date_created":"2023-07-31T10:20:55Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"publication_status":"published"},{"type":"dissertation","date_published":"2023-08-08T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663 - 337X"]},"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"file":[{"file_id":"13986","creator":"afransch","relation":"main_file","access_level":"closed","date_updated":"2024-03-01T08:51:42Z","file_name":"Thesis_AnnaFranschitz_202308.pdf","content_type":"application/pdf","embargo":"2024-08-08","date_created":"2023-08-08T18:01:28Z","file_size":10797612,"checksum":"27220243d5d51c3b0d7d61c0879d7a0c","embargo_to":"open_access"},{"relation":"source_file","access_level":"closed","creator":"afransch","file_id":"13987","checksum":"40abf7ccca14a3893f72dc7fb88585d6","file_size":2619085,"date_created":"2023-08-08T18:02:25Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_AnnaFranschitz_202308.docx","date_updated":"2023-08-09T07:25:27Z"},{"date_updated":"2024-03-01T12:13:29Z","content_type":"application/pdf","file_name":"Addendum_AnnaFranschitz202402.pdf","date_created":"2024-03-01T08:37:15Z","embargo":"2024-08-08","embargo_to":"open_access","title":"Addendum","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_size":85956,"file_id":"15042","creator":"cchlebak","access_level":"closed","relation":"erratum","description":"Minor modifications and clarifications - Feb 2024"},{"relation":"source_file","access_level":"closed","creator":"cchlebak","file_id":"15043","title":"Addendum - source file","checksum":"66745aa01f960f17472c024875c049ed","file_size":11818,"date_created":"2024-03-01T08:39:20Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Addendum_AnnaFranschitz202402.docx","date_updated":"2024-03-01T08:51:42Z"},{"relation":"other","access_level":"closed","description":"For printing purposes","file_id":"15044","creator":"cchlebak","date_created":"2024-03-01T08:56:06Z","title":"Print Version","file_size":10416761,"checksum":"55c876b73d49db15228a7f571592ec77","date_updated":"2024-03-01T12:58:14Z","content_type":"application/pdf","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","month":"08","language":[{"iso":"eng"}],"citation":{"chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>","apa":"Franschitz, A. (2023). <i>Individual and social immunity against viral infections in ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","mla":"Franschitz, Anna. <i>Individual and Social Immunity against Viral Infections in Ants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>."},"year":"2023","date_updated":"2024-03-01T15:25:17Z","day":"08","doi":"10.15479/at:ista:13984","degree_awarded":"PhD","abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"ddc":["570","577"],"_id":"13984","author":[{"first_name":"Anna","last_name":"Franschitz","full_name":"Franschitz, Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_created":"2023-08-08T15:33:29Z","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Individual and social immunity against viral infections in ants","page":"89","file_date_updated":"2024-03-01T12:58:14Z","publisher":"Institute of Science and Technology Austria"},{"oa":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"type":"journal_article","date_published":"2023-11-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"1fc86d71bfbf836e221c1e925343adc5","file_size":1977706,"date_created":"2024-01-29T11:25:38Z","content_type":"application/pdf","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","date_updated":"2024-01-29T11:25:38Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"14899"}],"month":"11","project":[{"_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344","name":"Protected states of quantum matter"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Physics","keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator."}],"day":"01","doi":"10.1038/s41567-023-02161-w","external_id":{"isi":["001054563800006"]},"isi":1,"year":"2023","citation":{"ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>."},"date_updated":"2024-01-29T11:27:49Z","ddc":["530"],"volume":19,"acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","intvolume":"        19","title":"Superconductivity from a melted insulator in Josephson junction arrays","article_processing_charge":"Yes (in subscription journal)","date_created":"2023-08-11T07:41:17Z","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"publication_status":"published","author":[{"full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295","last_name":"Senior","first_name":"Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","first_name":"Jaime","last_name":"Saez Mollejo"},{"orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","first_name":"Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425"},{"full_name":"Zemlicka, Martin","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","first_name":"Andrew P"}],"scopus_import":"1","_id":"14032","article_type":"original","publisher":"Springer Nature","file_date_updated":"2024-01-29T11:25:38Z","quality_controlled":"1","ec_funded":1,"page":"1630-1635"},{"_id":"14058","author":[{"orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"date_created":"2023-08-15T10:20:40Z","article_processing_charge":"No","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","ec_funded":1,"page":"230","file_date_updated":"2023-08-18T10:47:55Z","publisher":"Institute of Science and Technology Austria","year":"2023","citation":{"short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023."},"date_updated":"2023-12-13T12:15:36Z","day":"15","doi":"10.15479/at:ista:14058","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"ddc":["576"],"has_accepted_license":"1","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","month":"08","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"dissertation","date_published":"2023-08-15T00:00:00Z","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_updated":"2023-08-17T06:55:24Z","content_type":"application/zip","file_name":"Thesis_latex_forpdfa.zip","date_created":"2023-08-16T18:15:17Z","file_size":10891454,"checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_id":"14075","creator":"gpuixeus","access_level":"closed","relation":"source_file"},{"relation":"main_file","success":1,"access_level":"open_access","file_id":"14079","creator":"gpuixeus","date_created":"2023-08-18T10:47:55Z","file_size":19856686,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_updated":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","content_type":"application/pdf"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"status":"public","id":"12933","relation":"research_data"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14077","status":"public"}]}},{"doi":"10.1093/g3journal/jkad121","day":"01","abstract":[{"lang":"eng","text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns."}],"date_updated":"2023-12-13T12:15:37Z","year":"2023","citation":{"ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8)."},"isi":1,"external_id":{"isi":["001002997200001"]},"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","volume":13,"ddc":["570"],"publication_status":"published","date_created":"2023-08-18T06:52:14Z","article_processing_charge":"Yes","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","intvolume":"        13","_id":"14077","scopus_import":"1","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"full_name":"Macon, Ariana","first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"issue":"8","publisher":"Oxford University Press","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2023-11-07T09:00:19Z","publication_identifier":{"issn":["2160-1836"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-08-01T00:00:00Z","type":"journal_article","file":[{"relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"14498","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_size":845642,"date_created":"2023-11-07T09:00:19Z","file_name":"2023_G3_Puixeu.pdf","content_type":"application/pdf","date_updated":"2023-11-07T09:00:19Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"relation":"dissertation_contains","id":"14058","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"month":"08","publication":"G3: Genes, Genomes, Genetics","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology"]},{"month":"09","oa_version":"Published Version","has_accepted_license":"1","publication":"Soft Matter","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"type":"journal_article","date_published":"2023-09-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"b936747170d0b708172b518078c4081a","file_size":7660662,"date_created":"2024-01-30T12:48:24Z","file_name":"2023_SoftMatter_Ronning.pdf","content_type":"application/pdf","date_updated":"2024-01-30T12:48:24Z","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"14908"}],"intvolume":"        39","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","department":[{"_id":"GradSch"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-08-20T22:01:15Z","publication_status":"published","author":[{"last_name":"Rønning","first_name":"Jonas","full_name":"Rønning, Jonas"},{"full_name":"Renaud, Julian B","first_name":"Julian B","last_name":"Renaud","id":"7af6767d-14eb-11ed-b536-a32449ae867c"},{"full_name":"Doostmohammadi, Amin","last_name":"Doostmohammadi","first_name":"Amin"},{"first_name":"Luiza","last_name":"Angheluta","full_name":"Angheluta, Luiza"}],"scopus_import":"1","_id":"14087","article_type":"original","publisher":"Royal Society of Chemistry","file_date_updated":"2024-01-30T12:48:24Z","quality_controlled":"1","page":"7513-7527","abstract":[{"text":"Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter.","lang":"eng"}],"day":"01","doi":"10.1039/d3sm00316g","arxiv":1,"external_id":{"isi":["001035766100001"],"arxiv":["2303.07063"]},"isi":1,"citation":{"short":"J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527.","mla":"Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>.","ista":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 39, 7513–7527.","ama":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. 2023;39:7513-7527. doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>","apa":"Rønning, J., Renaud, J. B., Doostmohammadi, A., &#38; Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>","ieee":"J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” <i>Soft Matter</i>, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.","chicago":"Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>."},"year":"2023","date_updated":"2024-01-30T12:49:24Z","ddc":["540"],"volume":39,"acknowledgement":"J. Rø and L. A. acknowledge support from the Research Council of Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab). A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142 and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them."},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"creator":"cchlebak","file_id":"14227","relation":"source_file","access_level":"closed","file_name":"documents-export-2023-08-24.zip","content_type":"application/x-zip-compressed","date_updated":"2024-02-26T23:30:03Z","embargo_to":"open_access","file_size":15501411,"checksum":"453caf851d75c3478c10ed09bd242a91","date_created":"2023-08-24T13:02:49Z"},{"content_type":"application/pdf","file_name":"thesis_pdf_a.pdf","date_updated":"2024-02-26T23:30:03Z","file_size":6854783,"checksum":"7349d29963d6695e555e171748648d9a","date_created":"2023-08-24T13:03:42Z","embargo":"2024-02-25","creator":"cchlebak","file_id":"14228","access_level":"open_access","relation":"main_file"}],"type":"dissertation","date_published":"2023-08-24T00:00:00Z","oa":1,"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner"}],"publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"08","oa_version":"Published Version","ddc":["500"],"citation":{"ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","mla":"Stephenson, Elizabeth R. <i>Generalizing Medial Axes with Homology Switches</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14226\">10.15479/at:ista:14226</a>","apa":"Stephenson, E. R. (2023). <i>Generalizing medial axes with homology switches</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14226\">https://doi.org/10.15479/at:ista:14226</a>"},"year":"2023","date_updated":"2024-02-26T23:30:04Z","abstract":[{"lang":"eng","text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes."}],"day":"24","degree_awarded":"MS","doi":"10.15479/at:ista:14226","file_date_updated":"2024-02-26T23:30:03Z","page":"43","publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}],"_id":"14226","title":"Generalizing medial axes with homology switches","alternative_title":["ISTA Master's Thesis"],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_created":"2023-08-24T13:01:18Z","publication_status":"published"},{"oa_version":"Published Version","month":"07","publication":"35th International Conference on Computer Aided Verification ","has_accepted_license":"1","conference":{"end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification","start_date":"2023-07-17"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031377051"],"eissn":["1611-3349"],"issn":["0302-9743"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-07-17T00:00:00Z","type":"conference","file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"14275","creator":"dernst","date_created":"2023-09-06T08:16:25Z","file_size":421408,"checksum":"c346016393123a0a2338ad4d976f61bc","date_updated":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","content_type":"application/pdf"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"research_data","id":"14995"}]},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"date_created":"2023-09-03T22:01:16Z","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","alternative_title":["LNCS"],"intvolume":"     13964","_id":"14260","scopus_import":"1","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"full_name":"Sokolova, Maria","last_name":"Sokolova","first_name":"Maria"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"publisher":"Springer Nature","page":"156-169","quality_controlled":"1","file_date_updated":"2023-09-06T08:16:25Z","doi":"10.1007/978-3-031-37706-8_8","day":"17","abstract":[{"lang":"eng","text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness."}],"date_updated":"2024-02-27T07:46:52Z","citation":{"apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169."},"year":"2023","volume":13964,"ddc":["000"]},{"file":[{"date_updated":"2023-09-06T07:32:39Z","content_type":"application/pdf","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_created":"2023-09-06T07:32:39Z","checksum":"637454e2b3a357498d8d622d241c4bf6","file_size":4986859,"file_id":"14272","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1948-7185"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-08-11T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"08","publication":"Journal of Physical Chemistry Letters","has_accepted_license":"1","volume":14,"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","ddc":["530","540"],"doi":"10.1021/acs.jpclett.3c01707","day":"11","abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"date_updated":"2023-09-06T11:04:31Z","year":"2023","citation":{"short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>.","ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>."},"isi":1,"external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"publisher":"American Chemical Society","article_type":"original","page":"7395-7403","quality_controlled":"1","file_date_updated":"2023-09-06T07:32:39Z","publication_status":"published","department":[{"_id":"GradSch"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-09-03T22:01:16Z","title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","intvolume":"        14","pmid":1,"_id":"14261","scopus_import":"1","author":[{"full_name":"Gamper, Jakob","first_name":"Jakob","last_name":"Gamper"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","first_name":"Florian","full_name":"Kluibenschedl, Florian"},{"first_name":"Alexander K.H.","last_name":"Weiss","full_name":"Weiss, Alexander K.H."},{"full_name":"Hofer, Thomas S.","last_name":"Hofer","first_name":"Thomas S."}],"issue":"33"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"11373","relation":"part_of_dissertation"},{"status":"public","id":"7387","relation":"part_of_dissertation"},{"relation":"research_data","id":"10934","status":"public"}]},"status":"public","file":[{"date_created":"2023-10-04T10:11:53Z","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_size":114932847,"date_updated":"2023-10-04T10:28:35Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD Thesis_Philipp Radler_20231004.docx","relation":"source_file","access_level":"closed","file_id":"14390","creator":"pradler"},{"file_size":37838778,"checksum":"3253e099b7126469d941fd9419d68b4f","embargo_to":"open_access","embargo":"2024-10-04","date_created":"2023-10-04T10:11:21Z","content_type":"application/pdf","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_updated":"2023-10-04T10:28:35Z","relation":"main_file","access_level":"closed","creator":"pradler","file_id":"14391"}],"date_published":"2023-09-25T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"supervisor":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"language":[{"iso":"eng"}],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"has_accepted_license":"1","month":"09","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"},{"grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis"}],"ddc":["572"],"date_updated":"2024-02-21T12:35:18Z","year":"2023","citation":{"ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>."},"abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"doi":"10.15479/at:ista:14280","degree_awarded":"PhD","day":"25","file_date_updated":"2023-10-04T10:28:35Z","page":"156","ec_funded":1,"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"}],"_id":"14280","title":"Spatiotemporal signaling during assembly of the bacterial divisome","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"date_created":"2023-09-06T10:58:25Z","article_processing_charge":"No"},{"file":[{"creator":"dernst","file_id":"14395","relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureNeuroscience_Gupta.pdf","date_updated":"2023-10-04T11:40:51Z","checksum":"a33d91e398e548f34003170e10988368","file_size":6144866,"date_created":"2023-10-04T11:40:51Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"research_data","id":"12370","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-04-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"oa":1,"language":[{"iso":"eng"}],"publication":"Nature Neuroscience","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"month":"04","acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","volume":26,"ddc":["570"],"date_updated":"2023-10-04T11:41:05Z","citation":{"ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>"},"year":"2023","isi":1,"external_id":{"pmid":["36959418"],"isi":["000955258300002"]},"doi":"10.1038/s41593-023-01280-0","day":"01","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types."}],"page":"606-614","quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-10-04T11:40:51Z","publisher":"Springer Nature","article_type":"original","_id":"12349","pmid":1,"scopus_import":"1","author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh","first_name":"Divyansh","last_name":"Gupta"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser","first_name":"Anton L","full_name":"Sumser, Anton L","orcid":"0000-0002-4792-1881"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova","first_name":"Olga"},{"id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","last_name":"Svaton","first_name":"Jan","full_name":"Svaton, Jan","orcid":"0000-0002-6198-2939"},{"last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-01-23T14:14:19Z","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","intvolume":"        26"}]