[{"page":"9853-9871","doi":"10.1093/mnras/stad3853","date_published":"2024-02-01T00:00:00Z","date_created":"2024-01-22T08:22:17Z","has_accepted_license":"1","year":"2024","day":"01","publication":"Monthly Notices of the Royal Astronomical Society","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","author":[{"full_name":"Kramarenko, Ivan","last_name":"Kramarenko","first_name":"Ivan","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4"},{"first_name":"J","full_name":"Kerutt, J","last_name":"Kerutt"},{"first_name":"A","full_name":"Verhamme, A","last_name":"Verhamme"},{"last_name":"Oesch","full_name":"Oesch, P A","first_name":"P A"},{"full_name":"Barrufet, L","last_name":"Barrufet","first_name":"L"},{"first_name":"Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee"},{"full_name":"Kusakabe, H","last_name":"Kusakabe","first_name":"H"},{"last_name":"Goovaerts","full_name":"Goovaerts, I","first_name":"I"},{"full_name":"Thai, T T","last_name":"Thai","first_name":"T T"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2305.07044"]},"title":"Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape","citation":{"mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:10.1093/mnras/stad3853.","short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","ieee":"I. Kramarenko et al., “Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape,” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 2024;527(4):9853-9871. doi:10.1093/mnras/stad3853","apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad3853","chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stad3853.","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":527,"issue":"4","license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2024-01-23T12:30:45Z","file_size":4521738,"date_created":"2024-01-23T12:30:45Z","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9d02df4035c4951cf63dee0db1e462e9","file_id":"14879","success":1}],"language":[{"iso":"eng"}],"month":"02","intvolume":" 527","abstract":[{"text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 < z < 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2024-01-23T12:30:45Z","department":[{"_id":"GradSch"},{"_id":"JoMa"}],"date_updated":"2024-01-23T12:33:50Z","ddc":["520"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"14852"},{"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation","grant_number":"P32896"},{"name":"Polygenic Adaptation in a Metapopulation","grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"article_processing_charge":"No","author":[{"orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"title":"Local adaptation, genetic load and extinction in metapopulations","citation":{"mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Institute of Science and Technology Austria","page":"183","date_created":"2023-12-26T22:49:53Z","date_published":"2024-01-19T00:00:00Z","doi":"10.15479/at:ista:14711","year":"2024","has_accepted_license":"1","day":"19","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","_id":"14711","file_date_updated":"2024-01-03T18:31:34Z","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2024-01-26T12:00:54Z","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jitka","full_name":"Polechova, Jitka","last_name":"Polechova"},{"first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"}],"ddc":["576"],"alternative_title":["ISTA Thesis"],"month":"01","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10658","status":"public"},{"relation":"part_of_dissertation","id":"10787","status":"public"},{"relation":"part_of_dissertation","id":"14732","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2024-01-03T18:30:13Z","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","date_updated":"2024-01-03T18:30:13Z","file_size":16986244,"creator":"oolusany","file_id":"14730","checksum":"de179b1c6758f182ff0c70d8b38c1501","content_type":"application/zip","access_level":"closed","relation":"source_file"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_id":"14731","success":1,"date_updated":"2024-01-03T18:31:34Z","file_size":6460403,"creator":"oolusany","date_created":"2024-01-03T18:31:34Z","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf"}]},{"publisher":"Institute of Science and Technology Austria","day":"19","has_accepted_license":"1","year":"2024","date_published":"2024-01-19T00:00:00Z","doi":"10.15479/at:ista:14821","date_created":"2024-01-16T14:25:21Z","page":"89","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821.","apa":"Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria."},"title":"Adaptive hierarchical representations in the hippocampus","author":[{"full_name":"Chiossi, Heloisa","last_name":"Chiossi","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","first_name":"Heloisa"}],"article_processing_charge":"No","oa_version":"Published Version","month":"01","alternative_title":["ISTA Thesis"],"file":[{"checksum":"d3fa3de1abd5af5204c13e9d55375615","file_id":"14838","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_Thesis_190124.docx","date_created":"2024-01-19T11:04:05Z","creator":"hchiossi","file_size":8656268,"date_updated":"2024-01-19T11:04:05Z"},{"embargo":"2025-01-19","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","file_id":"14839","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","file_name":"PhD_Thesis_190124.pdf","date_created":"2024-01-19T11:03:59Z","file_size":6567275,"date_updated":"2024-01-19T11:03:59Z","creator":"hchiossi"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","ec_funded":1,"_id":"14821","status":"public","type":"dissertation","ddc":["570"],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"date_updated":"2024-02-01T09:50:29Z","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"file_date_updated":"2024-01-19T11:04:05Z"},{"acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","oa":1,"quality_controlled":"1","publisher":"Ubiquity Press","publication":"International Journal of the Commons","day":"11","year":"2024","has_accepted_license":"1","date_created":"2024-01-30T11:58:02Z","doi":"10.5334/ijc.1275","date_published":"2024-01-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.","ieee":"K. Nomura et al., “Tipping points of space debris in low earth orbit,” International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., & Falk, D. (2024). Tipping points of space debris in low earth orbit. International Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024, doi:10.5334/ijc.1275."},"title":"Tipping points of space debris in low earth orbit","article_processing_charge":"Yes","author":[{"first_name":"Keiko","last_name":"Nomura","full_name":"Nomura, Keiko"},{"first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon","last_name":"Rella"},{"last_name":"Merritt","full_name":"Merritt, Haily","first_name":"Haily"},{"full_name":"Baltussen, Mathieu","last_name":"Baltussen","first_name":"Mathieu"},{"first_name":"Darcy","full_name":"Bird, Darcy","last_name":"Bird"},{"first_name":"Annika","full_name":"Tjuka, Annika","last_name":"Tjuka"},{"full_name":"Falk, Dan","last_name":"Falk","first_name":"Dan"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"intvolume":" 18","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2024-02-05T10:06:35Z","file_name":"2023_IntJourCommons_Nomura.pdf","date_updated":"2024-02-05T10:06:35Z","file_size":1305786,"creator":"dernst","file_id":"14939","checksum":"b80ebc889033c365d8f8c05a0c655382","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["1875-0281"]},"volume":18,"issue":"1","_id":"14901","keyword":["Sociology and Political Science"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["550"],"date_updated":"2024-02-05T10:10:27Z","file_date_updated":"2024-02-05T10:06:35Z","department":[{"_id":"GradSch"},{"_id":"GaTk"}]},{"_id":"14705","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"citation":{"chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","short":"M.N. Elkrewi, (2024)."},"date_updated":"2024-02-26T09:59:29Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"}],"article_processing_charge":"No","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","file_date_updated":"2023-12-22T14:14:06Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01","has_accepted_license":"1","year":"2024","file":[{"file_name":"readme.txt.txt","date_created":"2023-12-22T13:54:21Z","creator":"melkrewi","file_size":847,"date_updated":"2023-12-22T13:54:21Z","success":1,"file_id":"14707","checksum":"bdaf1392867786634ec5466d528c36ca","relation":"main_file","access_level":"open_access","content_type":"text/plain"},{"creator":"melkrewi","file_size":343632753,"date_updated":"2023-12-22T14:14:06Z","file_name":"data_artemia_franciscana_genome.zip","date_created":"2023-12-22T14:14:06Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"file_id":"14708","checksum":"973e1cbdab923a71709782177980829f"}],"day":"02","date_published":"2024-01-02T00:00:00Z","doi":"10.15479/AT:ISTA:14705","related_material":{"record":[{"id":"15009","status":"public","relation":"used_in_publication"}]},"date_created":"2023-12-22T13:40:48Z","contributor":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","last_name":"Bett"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","contributor_type":"project_member","last_name":"Macon"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","contributor_type":"supervisor"},{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","contributor_type":"researcher","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}]},{"author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B."},{"last_name":"Garlovsky","full_name":"Garlovsky, Martin D.","first_name":"Martin D."},{"last_name":"Pal","full_name":"Pal, Arka","orcid":"0000-0002-4530-8469","first_name":"Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"last_name":"Lifchitz","full_name":"Lifchitz, Hila","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"first_name":"Erica","full_name":"Leder, Erica","last_name":"Leder"},{"first_name":"James","full_name":"Reeve, James","last_name":"Reeve"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_processing_charge":"No","external_id":{"pmid":["38175895"]},"title":"The genetic basis of a recent transition to live-bearing in marine snails","citation":{"ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"114-119","date_published":"2024-01-05T00:00:00Z","doi":"10.1126/science.adi2982","date_created":"2024-01-14T23:00:56Z","year":"2024","day":"05","publication":"Science","quality_controlled":"1","publisher":"American Association for the Advancement of Science","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"date_updated":"2024-03-05T09:35:25Z","type":"journal_article","article_type":"original","status":"public","_id":"14796","issue":"6678","volume":383,"related_material":{"record":[{"relation":"research_data","status":"public","id":"14812"}],"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/the-snail-or-the-egg/"}]},"publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 383","abstract":[{"text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.","lang":"eng"}],"oa_version":"None","pmid":1},{"type":"dissertation","status":"public","keyword":["Theoretical biology","Optimality","Evolution","Information"],"_id":"15020","file_date_updated":"2024-02-23T14:20:16Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"date_updated":"2024-03-06T14:22:52Z","ddc":["576","519"],"alternative_title":["ISTA Thesis"],"month":"02","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7553"},{"relation":"part_of_dissertation","status":"public","id":"12081"},{"relation":"part_of_dissertation","status":"public","id":"7606"}]},"ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"date_created":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"creator":"mhledik","checksum":"b2d3da47c98d481577a4baf68944fe41","file_id":"15021","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"hledik thesis source.zip","date_created":"2024-02-23T13:50:54Z","creator":"mhledik","file_size":14014790,"date_updated":"2024-02-23T14:20:16Z"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"author":[{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Genetic information and biological optimization","citation":{"chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","oa":1,"page":"158","doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","date_created":"2024-02-23T14:02:04Z","has_accepted_license":"1","year":"2024","day":"23"},{"date_published":"2024-03-11T00:00:00Z","doi":"10.15479/at:ista:15101","date_created":"2024-03-11T10:09:54Z","page":"84","day":"11","has_accepted_license":"1","year":"2024","publisher":"Institute of Science and Technology Austria","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","author":[{"last_name":"Chen","full_name":"Chen, JingJing","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101"},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00312"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232"},{"_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"15104","checksum":"db4947474ffa271e66c254b6fe876a55","creator":"jchen","file_size":11271363,"date_updated":"2024-03-12T07:12:17Z","file_name":"Thesis_Jingjing CHEN.docx","date_created":"2024-03-11T14:10:58Z"},{"file_size":16627311,"date_updated":"2024-03-11T14:11:06Z","creator":"jchen","file_name":"Thesis_Jingjing CHEN_merged.pdf","date_created":"2024-03-11T14:11:06Z","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-04-01","file_id":"15105","checksum":"a5eeae8b5702cd540f5d03469bc33dde"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"department":[{"_id":"GradSch"},{"_id":"PeJo"}],"file_date_updated":"2024-03-12T07:12:17Z","ddc":["570"],"supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"date_updated":"2024-03-14T13:14:19Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"15101"},{"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2021-09-27T10:54:51Z","date_updated":"2024-03-19T08:20:31Z","ddc":["004"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"_id":"10045","publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]},"publication_status":"epub_ahead","file":[{"file_name":"Generalized-0-Ext.pdf","date_created":"2021-09-27T10:54:51Z","file_size":603672,"date_updated":"2021-09-27T10:54:51Z","creator":"mdvorak","success":1,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","file_id":"10046","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"03","abstract":[{"text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n","lang":"eng"}],"oa_version":"Preprint","author":[{"first_name":"Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","last_name":"Dvorak"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2109.10203"]},"title":"Generalized minimum 0-extension problem and discrete convexity","citation":{"ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2109.10203","doi":"10.1007/s10107-024-02064-5","date_published":"2024-03-07T00:00:00Z","date_created":"2021-09-27T10:48:23Z","has_accepted_license":"1","year":"2024","day":"07","publication":"Mathematical Programming","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria)."},{"author":[{"first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera di Montesano"}],"article_processing_charge":"No","title":"Persistence and Morse theory for discrete geometric structures","citation":{"mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00342"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Discretization in Geometry and Dynamics","grant_number":"I4887"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"page":"108","doi":"10.15479/at:ista:15094","date_published":"2024-03-08T00:00:00Z","date_created":"2024-03-08T15:28:10Z","has_accepted_license":"1","year":"2024","day":"08","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2024-03-14T14:14:35Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"date_updated":"2024-03-20T09:36:57Z","ddc":["514","500","516"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"15094","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11660"},{"status":"public","id":"11658","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13182","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"15090"},{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","id":"15093","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"success":1,"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_id":"15112","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis Sebastiano.pdf","date_created":"2024-03-14T08:55:07Z","file_size":4106872,"date_updated":"2024-03-14T08:55:07Z","creator":"scultrer"},{"date_updated":"2024-03-14T14:14:35Z","file_size":4746234,"creator":"scultrer","date_created":"2024-03-14T08:56:24Z","file_name":"Thesis (1).zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_id":"15113"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"oa_version":"Published Version"},{"date_published":"2023-02-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch173","date_created":"2023-02-24T12:20:47Z","page":"4590-4605","day":"01","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","year":"2023","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X"},{"full_name":"Svoboda, Jakub","last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173."},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781611977554"]},"publication_status":"published","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2023-02-27T09:01:16Z","status":"public","type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22","end_date":"2023-01-25","location":"Florence, Italy"},"_id":"12676"},{"_id":"12736","status":"public","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","location":"Montreal, QB, Canada","end_date":"2023-03-01","start_date":"2023-02-25"},"type":"conference_poster","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512."},"date_updated":"2023-03-20T07:57:27Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"title":"Unexpected scaling in path copying trees","article_processing_charge":"No","author":[{"first_name":"Vitaly","full_name":"Aksenov, Vitaly","last_name":"Aksenov"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"25","year":"2023","publication_status":"published","publication_identifier":{"isbn":["9798400700156"]},"date_created":"2023-03-19T23:00:58Z","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","page":"438-440"},{"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","article_processing_charge":"No","author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716"},"project":[{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"date_created":"2023-03-08T15:19:45Z","doi":"10.15479/at:ista:12716","date_published":"2023-03-10T00:00:00Z","page":"178","day":"10","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-03-08T15:08:46Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"ddc":["599","573"],"date_updated":"2023-04-05T10:59:04Z","supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"status":"public","type":"dissertation","_id":"12716","ec_funded":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-03-08T15:08:46Z","file_name":"Burnett_Thesis_2023.docx","date_updated":"2023-03-08T15:08:46Z","file_size":23029260,"creator":"lburnett","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_id":"12717","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z","creator":"lburnett","file_size":11959869,"date_updated":"2023-03-08T15:08:46Z"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}]},{"month":"03","main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"oa":1,"oa_version":"Preprint","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"doi":"10.48550/arXiv.2303.14555","date_published":"2023-03-25T00:00:00Z","date_created":"2023-04-18T19:16:06Z","day":"25","language":[{"iso":"eng"}],"publication":"arXiv","year":"2023","publication_status":"submitted","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"status":"public","type":"preprint","article_number":"2303.14555","_id":"12846","title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"author":[{"first_name":"Albert","last_name":"Chern","full_name":"Chern, Albert"},{"last_name":"Ishida","full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"}],"external_id":{"arxiv":["2303.14555"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","short":"A. Chern, S. Ishida, ArXiv (n.d.).","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555"},"date_updated":"2023-04-25T06:51:21Z"},{"day":"06","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:12809","date_published":"2023-04-06T00:00:00Z","date_created":"2023-04-06T07:54:09Z","page":"115","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023."},"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","author":[{"first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina","last_name":"Alcarva"}],"article_processing_charge":"No","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"file":[{"embargo":"2024-04-07","file_id":"12814","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_created":"2023-04-07T06:16:06Z","file_size":9881969,"date_updated":"2023-04-07T06:16:06Z","creator":"cchlebak"},{"file_size":44201583,"date_updated":"2023-04-07T06:17:11Z","creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_created":"2023-04-07T06:17:11Z","content_type":"application/pdf","relation":"source_file","access_level":"closed","file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"0317bf7f457bb585f99d453ffa69eb53","file_id":"12816","date_updated":"2023-04-07T06:18:05Z","file_size":84731244,"creator":"cchlebak","date_created":"2023-04-07T06:18:05Z","file_name":"Thesis_CatarinaAlcarva_final.docx"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"month":"04","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"date_updated":"2023-04-26T12:16:56Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2023-04-07T06:18:05Z","_id":"12809","status":"public","type":"dissertation"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d."},"date_updated":"2023-06-01T12:54:45Z","title":"CrAM: A Compression-Aware Minimizer","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"article_processing_charge":"No","external_id":{"arxiv":["2207.14200"]},"author":[{"full_name":"Peste, Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"},{"last_name":"Kurtic","full_name":"Kurtic, Eldar","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"_id":"13053","status":"public","project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2023-05-01","end_date":"2023-05-05","location":"Kigali, Rwanda "},"type":"conference","publication":"11th International Conference on Learning Representations ","language":[{"iso":"eng"}],"publication_status":"accepted","year":"2023","ec_funded":1,"date_created":"2023-05-23T11:36:18Z","related_material":{"record":[{"id":"13074","status":"public","relation":"dissertation_contains"}]},"date_published":"2023-05-01T00:00:00Z","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"05","main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"oa":1,"quality_controlled":"1"},{"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"file_date_updated":"2023-04-20T09:26:51Z","date_updated":"2023-06-23T09:47:36Z","supervisor":[{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570","571"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"12826","ec_funded":1,"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-04-20T09:14:38Z","file_name":"Thesis_Pokusaeva.docx","date_updated":"2023-04-20T09:26:51Z","file_size":14507243,"creator":"vpokusae","checksum":"5f589a9af025f7eeebfd0c186209913e","file_id":"12857","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"},{"creator":"vpokusae","file_size":10090711,"date_updated":"2023-04-20T09:14:44Z","file_name":"Thesis_Pokusaeva.pdf","date_created":"2023-04-20T09:14:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"bbeed76db45a996b4c91a9abe12ce0ec","file_id":"12858"}],"alternative_title":["ISTA Thesis"],"month":"04","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria"}],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","citation":{"mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"page":"106","date_created":"2023-04-14T14:56:04Z","date_published":"2023-04-18T00:00:00Z","doi":"10.15479/at:ista:12826","year":"2023","has_accepted_license":"1","day":"18","oa":1,"publisher":"Institute of Science and Technology Austria"},{"page":"349-370","date_published":"2023-04-21T00:00:00Z","doi":"10.1007/978-3-031-30829-1_17","date_created":"2023-01-31T07:23:56Z","has_accepted_license":"1","year":"2023","day":"21","publication":"26th International Conference Foundations of Software Science and Computation Structures","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.11175"]},"title":"Quantitative safety and liveness","citation":{"ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"volume":13992,"ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308284"]},"publication_status":"published","file":[{"date_created":"2023-01-31T07:22:21Z","file_name":"qsl.pdf","creator":"esarac","date_updated":"2023-01-31T07:22:21Z","file_size":449027,"file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_size":1048171,"date_updated":"2023-06-19T10:28:09Z","creator":"dernst","file_name":"2023_LNCS_HenzingerT.pdf","date_created":"2023-06-19T10:28:09Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","file_id":"13153"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"month":"04","intvolume":" 13992","abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2023-06-19T10:28:09Z","date_updated":"2023-07-14T11:20:27Z","ddc":["000"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27"},"status":"public","_id":"12467"},{"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavol","last_name":"Kebis","full_name":"Kebis, Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"last_name":"Sarac","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2305.03447"]},"title":"Regular methods for operator precedence languages","citation":{"chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","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.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"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","page":"129:1--129:20","doi":"10.4230/LIPIcs.ICALP.2023.129","date_published":"2023-07-05T00:00:00Z","date_created":"2023-07-24T15:11:41Z","has_accepted_license":"1","year":"2023","day":"05","publication":"50th International Colloquium on Automata, Languages, and Programming","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2023-07-10","end_date":"2023-07-14","location":"Paderborn, Germany","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"status":"public","_id":"13292","file_date_updated":"2023-07-24T15:11:05Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_updated":"2023-07-31T08:38:38Z","ddc":["000"],"alternative_title":["LIPIcs"],"month":"07","intvolume":" 261","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":261,"ec_funded":1,"publication_identifier":{"isbn":["9783959772785"],"eissn":["1868-8969"]},"publication_status":"published","file":[{"file_id":"13293","checksum":"5d4c8932ef3450615a53b9bb15d92eb2","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-07-24T15:11:05Z","file_name":"icalp23.pdf","creator":"esarac","date_updated":"2023-07-24T15:11:05Z","file_size":859379}],"language":[{"iso":"eng"}]},{"_id":"13262","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2023-06-17","end_date":"2023-06-19","location":"Orlando, FL, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"type":"conference","status":"public","date_updated":"2023-07-31T10:54:32Z","ddc":["000"],"file_date_updated":"2023-07-31T10:53:08Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"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"}],"oa_version":"Published Version","scopus_import":"1","month":"06","publication_status":"published","publication_identifier":{"isbn":["9781450395458"]},"language":[{"iso":"eng"}],"file":[{"checksum":"72e312aabf0c5248c99b5cd3a88e4c88","file_id":"13334","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-07-31T10:53:08Z","file_name":"2023_SPAA_Fedorov.pdf","date_updated":"2023-07-31T10:53:08Z","file_size":2087937,"creator":"dernst"}],"citation":{"chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","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.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 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.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2304.09331"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","first_name":"Diba","full_name":"Hashemi, Diba","last_name":"Hashemi"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"}],"title":"Provably-efficient and internally-deterministic parallel Union-Find","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2023","has_accepted_license":"1","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","day":"17","page":"261-271","date_created":"2023-07-23T22:01:12Z","doi":"10.1145/3558481.3591082","date_published":"2023-06-17T00:00:00Z"},{"article_number":"014608","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608."},"title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"article_processing_charge":"No","author":[{"first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega","full_name":"Rojas Vega, Mauricio Nicolas"},{"last_name":"De Castro","full_name":"De Castro, Pablo","first_name":"Pablo"},{"full_name":"Soto, Rodrigo","last_name":"Soto","first_name":"Rodrigo"}],"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review E","day":"24","year":"2023","isi":1,"date_created":"2023-02-12T23:00:59Z","date_published":"2023-01-24T00:00:00Z","doi":"10.1103/PhysRevE.107.014608","_id":"12545","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-08-01T13:09:45Z","department":[{"_id":"GradSch"}],"oa_version":"Preprint","abstract":[{"text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.","lang":"eng"}],"intvolume":" 107","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"volume":107,"issue":"1"},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_published":"2023-03-10T00:00:00Z","doi":"10.1103/physrevlett.130.106901","date_created":"2023-03-14T13:11:59Z","isi":1,"year":"2023","day":"10","publication":"Physical Review Letters","article_number":"106901","author":[{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"},{"last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan"},{"full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes"},{"full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov","first_name":"Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203"}],"article_processing_charge":"No","external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"title":"Spin-electric coupling in lead halide perovskites","citation":{"short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"month":"03","intvolume":" 130","abstract":[{"text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.","lang":"eng"}],"oa_version":"Preprint","issue":"10","volume":130,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","keyword":["General Physics and Astronomy"],"_id":"12723","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"date_updated":"2023-08-01T13:39:04Z"},{"date_updated":"2023-08-01T13:39:47Z","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"_id":"12724","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","volume":107,"issue":"12","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"month":"03","intvolume":" 107","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201."},"title":"Effective model for studying optical properties of lead halide perovskites","author":[{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"last_name":"Ashourishokri","full_name":"Ashourishokri, Younes","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov","first_name":"Ayan"},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek"}],"article_processing_charge":"No","external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"article_number":"125201","day":"15","publication":"Physical Review B","isi":1,"year":"2023","doi":"10.1103/physrevb.107.125201","date_published":"2023-03-15T00:00:00Z","date_created":"2023-03-14T13:13:05Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"file":[{"creator":"dernst","date_updated":"2023-06-26T09:58:53Z","file_size":4844149,"date_created":"2023-06-26T09:58:53Z","file_name":"2023_ScientificReports_Vetrova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","file_id":"13170","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","volume":13,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans."}],"month":"06","intvolume":" 13","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-02T06:17:18Z","department":[{"_id":"GradSch"}],"file_date_updated":"2023-06-26T09:58:53Z","_id":"13166","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"09","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-06-09T00:00:00Z","doi":"10.1038/s41598-023-35979-8","date_created":"2023-06-25T22:00:46Z","acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382.","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8."},"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","author":[{"last_name":"Vetrova","full_name":"Vetrova, Alexandra A.","first_name":"Alexandra A."},{"first_name":"Daria M.","full_name":"Kupaeva, Daria M.","last_name":"Kupaeva"},{"id":"a521c60b-0815-11ed-9b02-b8bd522477c8","first_name":"Alena","full_name":"Kizenko, Alena","last_name":"Kizenko"},{"last_name":"Lebedeva","full_name":"Lebedeva, Tatiana S.","first_name":"Tatiana S."},{"last_name":"Walentek","full_name":"Walentek, Peter","first_name":"Peter"},{"first_name":"Nikoloz","full_name":"Tsikolia, Nikoloz","last_name":"Tsikolia"},{"full_name":"Kremnyov, Stanislav V.","last_name":"Kremnyov","first_name":"Stanislav V."}],"article_processing_charge":"No","external_id":{"isi":["001006690200045"],"pmid":["37296138"]},"article_number":"9382"},{"abstract":[{"lang":"eng","text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"scopus_import":"1","intvolume":" 107","month":"05","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"volume":107,"issue":"18","_id":"13138","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-02T06:16:02Z","department":[{"_id":"GradSch"}],"acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2023","isi":1,"publication":"Physical Review B","day":"01","date_created":"2023-06-18T22:00:46Z","date_published":"2023-05-01T00:00:00Z","doi":"10.1103/PhysRevB.107.184312","article_number":"184312","citation":{"ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["2303.00729"],"isi":["001003686900004"]},"author":[{"last_name":"Orlov","full_name":"Orlov, Pavel","first_name":"Pavel"},{"first_name":"Anastasiia","full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina"},{"first_name":"Rustem","full_name":"Sharipov, Rustem","last_name":"Sharipov"},{"first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","full_name":"Petrova, Elena","last_name":"Petrova"},{"first_name":"Vladimir","full_name":"Gritsev, Vladimir","last_name":"Gritsev"},{"full_name":"Kurlov, Denis V.","last_name":"Kurlov","first_name":"Denis V."}],"title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain"},{"year":"2023","has_accepted_license":"1","day":"23","page":"127","date_created":"2023-03-31T12:24:42Z","doi":"10.15479/at:ista:12781","date_published":"2023-03-23T00:00:00Z","publisher":"Institute of Science and Technology Austria","citation":{"apa":"Kravchuk, V. (2023). Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12781","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:10.15479/at:ista:12781","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","mla":"Kravchuk, Vladyslav. Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12781.","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12781."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"}],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines","grant_number":"101020697"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"language":[{"iso":"eng"}],"file":[{"checksum":"5ebb6345cb4119f93460c81310265a6d","file_id":"12852","embargo":"2024-04-20","content_type":"application/pdf","embargo_to":"local","access_level":"closed","relation":"main_file","date_created":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_updated":"2023-04-19T14:33:41Z","file_size":6071553,"creator":"vkravchu"},{"creator":"vkravchu","date_updated":"2023-04-20T07:02:59Z","file_size":19468766,"date_created":"2023-04-19T14:33:52Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"local","checksum":"c12055c48411d030d2afa51de2166221","file_id":"12853","embargo":"2024-04-20"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12138"}]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","date_updated":"2023-08-04T08:54:51Z","supervisor":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570","572"],"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"file_date_updated":"2023-04-20T07:02:59Z","_id":"12781","type":"dissertation","status":"public"},{"supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-08-04T10:33:27Z","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"file_date_updated":"2023-05-24T16:12:59Z","_id":"13074","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13087","checksum":"6b3354968403cb9d48cc5a83611fb571","success":1,"date_updated":"2023-05-24T16:11:16Z","file_size":2152072,"creator":"epeste","date_created":"2023-05-24T16:11:16Z","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf"},{"file_name":"PhD_Thesis_APeste.zip","date_created":"2023-05-24T16:12:59Z","creator":"epeste","file_size":1658293,"date_updated":"2023-05-24T16:12:59Z","file_id":"13088","checksum":"8d0df94bbcf4db72c991f22503b3fd60","relation":"source_file","access_level":"closed","content_type":"application/zip"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"11458","status":"public"},{"status":"public","id":"13053","relation":"part_of_dissertation"},{"id":"12299","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","citation":{"ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra","last_name":"Peste"}],"article_processing_charge":"No","title":"Efficiency and generalization of sparse neural networks","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2023","day":"23","page":"147","date_published":"2023-05-23T00:00:00Z","doi":"10.15479/at:ista:13074","date_created":"2023-05-23T17:07:53Z","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"12964","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","date_updated":"2023-08-04T11:02:40Z","supervisor":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"file_date_updated":"2023-05-19T07:04:25Z","abstract":[{"lang":"eng","text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-032-9"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"thesis_boocock.pdf","date_created":"2023-05-17T13:39:54Z","creator":"dboocock","file_size":40414730,"date_updated":"2023-05-19T07:04:25Z","embargo":"2024-05-17","file_id":"12988","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"},{"file_id":"12989","checksum":"581a2313ffeb40fe77e8a122a25a7795","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"thesis_boocock.zip","date_created":"2023-05-17T13:39:53Z","creator":"dboocock","file_size":34338567,"date_updated":"2023-05-17T14:35:13Z"}],"ec_funded":1,"related_material":{"record":[{"id":"8602","status":"public","relation":"part_of_dissertation"}]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12964.","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","mla":"Boocock, Daniel R. Mechanochemical Pattern Formation across Biological Scales. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12964.","apa":"Boocock, D. R. (2023). Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12964","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:10.15479/at:ista:12964","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"last_name":"Boocock","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"}],"title":"Mechanochemical pattern formation across biological scales","publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"17","page":"146","date_created":"2023-05-15T14:52:36Z","date_published":"2023-05-17T00:00:00Z","doi":"10.15479/at:ista:12964"},{"page":"82","date_published":"2023-04-28T00:00:00Z","doi":"10.15479/at:ista:12885","date_created":"2023-05-02T07:58:57Z","has_accepted_license":"1","year":"2023","day":"28","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877"}],"article_processing_charge":"No","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","citation":{"ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"related_material":{"record":[{"status":"public","id":"10806","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"id":"12237","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9118","status":"public"},{"id":"10123","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_size":99627036,"date_updated":"2023-05-02T07:43:18Z","creator":"mcalcabr","file_name":"Thesis_Calcabrini.docx","date_created":"2023-05-02T07:43:18Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"12887","checksum":"9347b0e09425f56fdcede5d3528404dc"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12888","checksum":"2d188b76621086cd384f0b9264b0a576","success":1,"date_updated":"2023-05-02T07:42:45Z","file_size":8742220,"creator":"mcalcabr","date_created":"2023-05-02T07:42:45Z","file_name":"Thesis_Calcabrini_pdfa.pdf"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"04","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2023-05-02T07:43:18Z","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"supervisor":[{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-14T07:25:26Z","ddc":["546","541"],"type":"dissertation","status":"public","_id":"12885"},{"citation":{"mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","article_number":"qrac004","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Evolution Letters","date_published":"2023-02-01T00:00:00Z","doi":"10.1093/evlett/qrac004","date_created":"2023-02-06T13:59:12Z","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"date_updated":"2023-08-16T11:44:32Z","ddc":["570"],"file_date_updated":"2023-08-16T11:43:33Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"_id":"12521","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"publication_identifier":{"issn":["2056-3744"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","creator":"dernst","file_size":2592189,"date_updated":"2023-08-16T11:43:33Z","file_name":"2023_EvLetters_Mrnjavac.pdf","date_created":"2023-08-16T11:43:33Z"}],"language":[{"iso":"eng"}],"volume":7,"issue":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 7"},{"publication":"Nature Computational Science","day":"20","year":"2023","has_accepted_license":"1","date_created":"2023-03-26T22:01:08Z","doi":"10.1038/s43588-023-00410-9","date_published":"2023-03-20T00:00:00Z","page":"254-263","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263."},"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","external_id":{"arxiv":["2108.06686"]},"article_processing_charge":"No","author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"last_name":"Pepic","full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver"},{"last_name":"Shriki","full_name":"Shriki, Oren","first_name":"Oren"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14073","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_NatureCompScience_Lombardi.pdf","date_created":"2023-08-16T12:39:57Z","file_size":4474284,"date_updated":"2023-08-16T12:39:57Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["2662-8457"]},"ec_funded":1,"volume":3,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"intvolume":" 3","month":"03","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-16T12:41:53Z","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"file_date_updated":"2023-08-16T12:39:57Z","_id":"12762","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article"},{"publisher":"Institute of Science and Technology Austria","day":"05","has_accepted_license":"1","year":"2023","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12891","date_created":"2023-05-05T08:48:20Z","page":"190","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12891.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","mla":"Schauer, Alexandra. Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12891.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","apa":"Schauer, A. (2023). Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12891","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:10.15479/at:ista:12891"},"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","author":[{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"file_id":"12907","checksum":"59b0303dc483f40a96a610a90aab7ee9","embargo":"2024-05-05","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-05-05T13:01:14Z","file_name":"Thesis_Schauer_final.pdf","creator":"aschauer","date_updated":"2023-05-05T13:01:14Z","file_size":31434230},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"12908","checksum":"25f54e12479b6adaabd129a20568e6c1","file_size":43809109,"date_updated":"2023-05-05T13:04:15Z","creator":"aschauer","file_name":"Thesis_Schauer_final.docx","date_created":"2023-05-05T13:04:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"status":"public","id":"8966","relation":"part_of_dissertation"},{"status":"public","id":"7888","relation":"part_of_dissertation"}]},"ec_funded":1,"_id":"12891","status":"public","type":"dissertation","ddc":["570"],"supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2023-08-21T06:25:48Z","file_date_updated":"2023-05-05T13:04:15Z","department":[{"_id":"GradSch"},{"_id":"CaHe"}]},{"file_date_updated":"2023-07-06T11:35:15Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ddc":["537","535","539"],"supervisor":[{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-24T11:16:35Z","status":"public","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"13175","related_material":{"record":[{"status":"public","id":"12900","relation":"old_edition"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"status":"public","id":"9114","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"success":1,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","file_id":"13176","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"thesis_pdfa.pdf","date_created":"2023-06-30T08:17:25Z","creator":"cchlebak","file_size":18688376,"date_updated":"2023-06-30T08:17:25Z"},{"content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"13196","checksum":"c3b45317ae58e0527533f98c202d81b7","date_updated":"2023-07-06T11:35:15Z","file_size":37847025,"creator":"cchlebak","date_created":"2023-07-06T11:35:15Z","file_name":"thesis.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"degree_awarded":"PhD","publication_status":"published","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"title":"Cavity quantum electrooptics","author":[{"last_name":"Sahu","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023."},"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","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:13175","date_created":"2023-06-30T08:07:43Z","page":"202","day":"05","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1},{"keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"12900","file_date_updated":"2023-07-06T11:37:40Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"ddc":["537","535","539"],"date_updated":"2023-08-24T11:16:35Z","supervisor":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"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. "}],"ec_funded":1,"related_material":{"record":[{"relation":"new_edition","status":"public","id":"13175"},{"status":"public","id":"10924","relation":"part_of_dissertation"},{"id":"9114","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"8cbdab9c37ee55e591092a6f66b272c4","file_id":"12928","embargo_to":"open_access","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"thesis.zip","date_created":"2023-05-09T08:45:14Z","file_size":36767177,"date_updated":"2023-06-06T22:30:03Z","creator":"rsahu"},{"file_id":"12929","checksum":"439659ead46618147309be39d9dd5a8c","access_level":"closed","relation":"main_file","content_type":"application/pdf","date_created":"2023-05-09T08:51:17Z","file_name":"thesis_pdfa_final.pdf","creator":"rsahu","date_updated":"2023-07-06T11:37:40Z","file_size":17501990}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"title":"Cavity quantum electrooptics","article_processing_charge":"No","author":[{"orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900."},"publisher":"Institute of Science and Technology Austria","date_created":"2023-05-05T11:08:50Z","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12900","page":"190","day":"05","year":"2023","has_accepted_license":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17."},"title":"Monitoring algorithmic fairness","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","first_name":"Mahyar","last_name":"Karimi","full_name":"Karimi, Mahyar","orcid":"0009-0005-0820-1696"},{"id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","last_name":"Kueffner","full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542"},{"first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","last_name":"Mallik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2305.15979"]},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"day":"18","publication":"Computer Aided Verification","has_accepted_license":"1","year":"2023","doi":"10.1007/978-3-031-37703-7_17","date_published":"2023-07-18T00:00:00Z","date_created":"2023-07-25T18:32:40Z","page":"358–382","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"ddc":["000"],"date_updated":"2023-09-05T15:14:00Z","file_date_updated":"2023-07-31T08:11:20Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"_id":"13310","status":"public","type":"conference","conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_size":647760,"date_updated":"2023-07-31T08:11:20Z","creator":"dernst","file_name":"2023_LNCS_CAV_HenzingerT.pdf","date_created":"2023-07-31T08:11:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"ccaf94bf7d658ba012c016e11869b54c","file_id":"13327"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783031377037"],"isbn":["9783031377020"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","volume":13965,"ec_funded":1,"oa_version":"Published Version","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."}],"month":"07","intvolume":" 13965","alternative_title":["LNCS"]},{"file_date_updated":"2023-09-06T07:32:39Z","department":[{"_id":"GradSch"}],"date_updated":"2023-09-06T11:04:31Z","ddc":["530","540"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14261","volume":14,"issue":"33","publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","file":[{"file_size":4986859,"date_updated":"2023-09-06T07:32:39Z","creator":"dernst","file_name":"2023_JourPhysChemistry_Gamper.pdf","date_created":"2023-09-06T07:32:39Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14272","checksum":"637454e2b3a357498d8d622d241c4bf6"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 14","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","author":[{"first_name":"Jakob","last_name":"Gamper","full_name":"Gamper, Jakob"},{"full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"last_name":"Weiss","full_name":"Weiss, Alexander K.H.","first_name":"Alexander K.H."},{"last_name":"Hofer","full_name":"Hofer, Thomas S.","first_name":"Thomas S."}],"external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"article_processing_charge":"Yes (in subscription journal)","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","citation":{"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.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.","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.","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.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","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,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & 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. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707","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. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"7395-7403","doi":"10.1021/acs.jpclett.3c01707","date_published":"2023-08-11T00:00:00Z","date_created":"2023-09-03T22:01:16Z","has_accepted_license":"1","isi":1,"year":"2023","day":"11","publication":"Journal of Physical Chemistry Letters","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"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."},{"year":"2023","has_accepted_license":"1","day":"21","page":"158","date_created":"2023-03-17T13:30:48Z","date_published":"2023-03-21T00:00:00Z","doi":"10.15479/at:ista:12732","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","apa":"Brighi, P. (2023). Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12732","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:10.15479/at:ista:12732","mla":"Brighi, Pietro. Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12732.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12732."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"}],"title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"5d2de651ef9449c1b8dc27148ca74777","file_id":"12753","date_updated":"2023-03-23T16:42:56Z","file_size":42167561,"creator":"pbrighi","date_created":"2023-03-23T16:42:56Z","file_name":"Thesis_sub_PBrighi.zip"},{"file_name":"Thesis_PBrighi.pdf","date_created":"2023-03-23T16:43:14Z","file_size":13977000,"date_updated":"2023-03-23T16:43:14Z","creator":"pbrighi","success":1,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","file_id":"12754","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"11470","status":"public"},{"relation":"part_of_dissertation","id":"8308","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"11469"},{"relation":"part_of_dissertation","id":"12750","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings."}],"oa_version":"None","alternative_title":["ISTA Thesis"],"month":"03","date_updated":"2023-09-20T10:44:12Z","supervisor":[{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2023-03-23T16:43:14Z","_id":"12732","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public"},{"_id":"13120","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Bialystok, Poland","end_date":"2023-08-04","start_date":"2023-07-31","name":"ITP: International Conference on Interactive Theorem Proving"},"type":"conference","status":"public","date_updated":"2023-09-25T11:04:29Z","ddc":["000"],"department":[{"_id":"GradSch"},{"_id":"VlKo"}],"file_date_updated":"2023-08-07T11:55:43Z","abstract":[{"lang":"eng","text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 268","month":"07","publication_status":"published","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"13982","checksum":"773a0197f05b67feaa6cb1e17ec3642d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_LIPIcS_Dvorak.pdf","date_created":"2023-08-07T11:55:43Z","file_size":715976,"date_updated":"2023-08-07T11:55:43Z","creator":"dernst"}],"related_material":{"link":[{"url":"https://github.com/madvorak/grammars/tree/publish","relation":"software"}]},"volume":268,"article_number":"15","citation":{"ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15.","chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In 14th International Conference on Interactive Theorem Proving, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ITP.2023.15.","short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in 14th International Conference on Interactive Theorem Proving, Bialystok, Poland, 2023, vol. 268.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: 14th International Conference on Interactive Theorem Proving. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ITP.2023.15","apa":"Dvorak, M., & Blanchette, J. (2023). Closure properties of general grammars - formally verified. In 14th International Conference on Interactive Theorem Proving (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITP.2023.15","mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” 14th International Conference on Interactive Theorem Proving, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ITP.2023.15."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2302.06420"]},"article_processing_charge":"No","author":[{"last_name":"Dvorak","orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin","first_name":"Martin","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"first_name":"Jasmin","last_name":"Blanchette","full_name":"Blanchette, Jasmin"}],"title":"Closure properties of general grammars - formally verified","acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2023","has_accepted_license":"1","publication":"14th International Conference on Interactive Theorem Proving","day":"27","date_created":"2023-06-05T07:29:05Z","date_published":"2023-07-27T00:00:00Z","doi":"10.4230/LIPIcs.ITP.2023.15"},{"publisher":"Institute of Science and Technology Austria","day":"23","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:13081","date_published":"2023-05-23T00:00:00Z","date_created":"2023-05-23T19:10:42Z","page":"93","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"L. Bocanegra, Epithelial Dynamics during Mouse Neural Tube Development, Institute of Science and Technology Austria, 2023.","ieee":"L. Bocanegra, “Epithelial dynamics during mouse neural tube development,” Institute of Science and Technology Austria, 2023.","ama":"Bocanegra L. Epithelial dynamics during mouse neural tube development. 2023. doi:10.15479/at:ista:13081","apa":"Bocanegra, L. (2023). Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13081","mla":"Bocanegra, Laura. Epithelial Dynamics during Mouse Neural Tube Development. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13081.","ista":"Bocanegra L. 2023. Epithelial dynamics during mouse neural tube development. Institute of Science and Technology Austria.","chicago":"Bocanegra, Laura. “Epithelial Dynamics during Mouse Neural Tube Development.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13081."},"title":"Epithelial dynamics during mouse neural tube development","author":[{"first_name":"Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","full_name":"Bocanegra, Laura","last_name":"Bocanegra"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.","lang":"eng"}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"74f3f89e59a0189bee53ebfad9c1b9af","file_id":"13089","creator":"lbocaneg","file_size":25615534,"date_updated":"2023-05-25T06:32:12Z","file_name":"Thesis_final_LauraBocanegra.docx","date_created":"2023-05-25T06:32:12Z"},{"file_name":"TotalFinal_Thesis_LauraBocanegraArx.pdf","date_created":"2023-05-25T06:32:16Z","creator":"lbocaneg","file_size":12386046,"date_updated":"2023-05-25T06:32:16Z","embargo":"2024-05-31","checksum":"c6cdef6323eacfb4b7a8af20f32eae97","file_id":"13090","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9349"},{"id":"12837","status":"public","relation":"part_of_dissertation"}]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"13081","status":"public","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"supervisor":[{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"date_updated":"2023-10-04T11:14:04Z","file_date_updated":"2023-05-25T06:32:16Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","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).","date_created":"2023-01-23T14:14:19Z","doi":"10.1038/s41593-023-01280-0","date_published":"2023-04-01T00:00:00Z","page":"606-614","publication":"Nature Neuroscience","day":"01","year":"2023","isi":1,"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"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"},{"_id":"266D407A-B435-11E9-9278-68D0E5697425","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","grant_number":"LT000256"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"title":"Panoramic visual statistics shape retina-wide organization of receptive fields","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"author":[{"last_name":"Gupta","orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","last_name":"Sumser"},{"first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","orcid":"0000-0003-2012-9947","last_name":"Symonova"},{"id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","first_name":"Jan","full_name":"Svaton, Jan","orcid":"0000-0002-6198-2939","last_name":"Svaton"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","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,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0.","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.","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.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0."},"intvolume":" 26","month":"04","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"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. 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However, the equality case has not been settled yet. 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CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 17.","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Automata.” In 34th International Conference on Concurrency Theory, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17.","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Safety and liveness of quantitative automata. In 34th International Conference on Concurrency Theory (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2023.17","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative automata. In: 34th International Conference on Concurrency Theory. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.CONCUR.2023.17","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.","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative automata,” in 34th International Conference on Concurrency Theory, Antwerp, Belgium, 2023, vol. 279.","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Automata.” 34th International Conference on Concurrency Theory, vol. 279, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.CONCUR.2023.17."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"article_number":"17","doi":"10.4230/LIPIcs.CONCUR.2023.17","date_published":"2023-09-01T00:00:00Z","date_created":"2023-07-14T10:00:15Z","has_accepted_license":"1","year":"2023","day":"01","publication":"34th International Conference on Concurrency Theory","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"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."},{"department":[{"_id":"GradSch"}],"date_updated":"2023-10-17T09:15:17Z","status":"public","keyword":["Algebra","Number Theory"],"type":"journal_article","article_type":"original","_id":"12406","volume":207,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0065-1036"],"eissn":["1730-6264"]},"publication_status":"published","month":"01","intvolume":" 207","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.","lang":"eng"}],"title":"Density of the union of positive diagonal binary quadratic forms","author":[{"id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","first_name":"Yijie","orcid":"0000-0002-4989-5330","full_name":"Diao, Yijie","last_name":"Diao"}],"external_id":{"arxiv":["2103.08268"],"isi":["000912903000001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” Acta Arithmetica, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17.","apa":"Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. Instytut Matematyczny. https://doi.org/10.4064/aa210830-24-11","ama":"Diao Y. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 2023;207:1-17. doi:10.4064/aa210830-24-11","mla":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:10.4064/aa210830-24-11.","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17.","chicago":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” Acta Arithmetica. Instytut Matematyczny, 2023. https://doi.org/10.4064/aa210830-24-11."},"date_published":"2023-01-09T00:00:00Z","doi":"10.4064/aa210830-24-11","date_created":"2023-01-26T21:17:04Z","page":"1-17","day":"09","publication":"Acta Arithmetica","isi":1,"year":"2023","quality_controlled":"1","publisher":"Instytut Matematyczny","oa":1,"acknowledgement":"This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n"},{"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"file_date_updated":"2023-10-18T07:56:08Z","supervisor":[{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P"}],"date_updated":"2023-10-18T09:20:56Z","ddc":["610"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"14422","related_material":{"record":[{"relation":"part_of_dissertation","id":"9633","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"cchlebak","file_size":30599717,"date_updated":"2023-10-12T14:54:52Z","file_name":"Confavreux_Thesis_2A.pdf","date_created":"2023-10-12T14:53:50Z","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","embargo":"2024-10-12","checksum":"7f636555eae7803323df287672fd13ed","file_id":"14424"},{"checksum":"725e85946db92290a4583a0de9779e1b","file_id":"14440","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"Confavreux Thesis.zip","date_created":"2023-10-18T07:38:34Z","file_size":68406739,"date_updated":"2023-10-18T07:56:08Z","creator":"cchlebak"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"C7610134-B532-11EA-BD9F-F5753DDC885E","first_name":"Basile J","last_name":"Confavreux","full_name":"Confavreux, Basile J"}],"article_processing_charge":"No","title":"Synapseek: Meta-learning synaptic plasticity rules","citation":{"ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.","apa":"Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","mla":"Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020"}],"page":"148","doi":"10.15479/at:ista:14422","date_published":"2023-10-12T00:00:00Z","date_created":"2023-10-12T14:13:25Z","has_accepted_license":"1","year":"2023","day":"12","publisher":"Institute of Science and Technology Austria"},{"title":"Boundary superconductivity in BCS theory","article_processing_charge":"No","author":[{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","last_name":"Roos"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14374.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:10.15479/at:ista:14374","apa":"Roos, B. (2023). Boundary superconductivity in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14374","mla":"Roos, Barbara. Boundary Superconductivity in BCS Theory. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14374."},"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"date_created":"2023-09-28T14:23:04Z","doi":"10.15479/at:ista:14374","date_published":"2023-09-30T00:00:00Z","page":"206","day":"30","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file_date_updated":"2023-10-06T11:38:01Z","ddc":["515","539"],"date_updated":"2023-10-27T10:37:30Z","supervisor":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","_id":"14374","ec_funded":1,"related_material":{"record":[{"status":"public","id":"13207","relation":"part_of_dissertation"},{"status":"public","id":"10850","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"phd-thesis-draft_pdfa_acrobat.pdf","date_created":"2023-10-06T11:35:56Z","creator":"broos","file_size":2365702,"date_updated":"2023-10-06T11:35:56Z","checksum":"ef039ffc3de2cb8dee5b14110938e9b6","file_id":"14398","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"81dcac33daeefaf0111db52f41bb1fd0","file_id":"14399","creator":"broos","date_updated":"2023-10-06T11:38:01Z","file_size":4691734,"date_created":"2023-10-06T11:38:01Z","file_name":"Version5.zip"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}]},{"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Hainzl, Christian, et al. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory, vol. 12, no. 4, EMS Press, 2023, pp. 1507–1540, doi:10.4171/JST/439.","short":"C. Hainzl, B. Roos, R. Seiringer, Journal of Spectral Theory 12 (2023) 1507–1540.","ieee":"C. Hainzl, B. Roos, and R. Seiringer, “Boundary superconductivity in the BCS model,” Journal of Spectral Theory, vol. 12, no. 4. EMS Press, pp. 1507–1540, 2023.","apa":"Hainzl, C., Roos, B., & Seiringer, R. (2023). Boundary superconductivity in the BCS model. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/439","ama":"Hainzl C, Roos B, Seiringer R. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 2023;12(4):1507–1540. doi:10.4171/JST/439","chicago":"Hainzl, Christian, Barbara Roos, and Robert Seiringer. “Boundary Superconductivity in the BCS Model.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/439.","ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540."},"title":"Boundary superconductivity in the BCS model","author":[{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"last_name":"Roos","full_name":"Roos, Barbara","orcid":"0000-0002-9071-5880","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"external_id":{"isi":["000997933500008"],"arxiv":["2201.08090"]},"article_processing_charge":"No","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.","publisher":"EMS Press","quality_controlled":"1","oa":1,"day":"18","publication":"Journal of Spectral Theory","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.4171/JST/439","date_published":"2023-05-18T00:00:00Z","date_created":"2023-07-10T16:35:45Z","page":"1507–1540","_id":"13207","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-10-27T10:37:29Z","file_date_updated":"2023-07-11T08:19:15Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"05","intvolume":" 12","file":[{"success":1,"checksum":"5501da33be010b5c81440438287584d5","file_id":"13208","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_EMS_Hainzl.pdf","date_created":"2023-07-11T08:19:15Z","creator":"alisjak","file_size":304619,"date_updated":"2023-07-11T08:19:15Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"publication_status":"published","related_material":{"record":[{"id":"14374","status":"public","relation":"dissertation_contains"}]},"issue":"4","volume":12,"ec_funded":1},{"citation":{"short":"V. Aksenov, M. Anoprenko, A. Fedorov, M. Spear, in:, 37th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"V. Aksenov, M. Anoprenko, A. Fedorov, and M. Spear, “Brief announcement: BatchBoost: Universal batching for concurrent data structures,” in 37th International Symposium on Distributed Computing, L’Aquila, Italy, 2023, vol. 281.","apa":"Aksenov, V., Anoprenko, M., Fedorov, A., & Spear, M. (2023). Brief announcement: BatchBoost: Universal batching for concurrent data structures. In 37th International Symposium on Distributed Computing (Vol. 281). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2023.35","ama":"Aksenov V, Anoprenko M, Fedorov A, Spear M. Brief announcement: BatchBoost: Universal batching for concurrent data structures. In: 37th International Symposium on Distributed Computing. Vol 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.DISC.2023.35","mla":"Aksenov, Vitaly, et al. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” 37th International Symposium on Distributed Computing, vol. 281, 35, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.DISC.2023.35.","ista":"Aksenov V, Anoprenko M, Fedorov A, Spear M. 2023. Brief announcement: BatchBoost: Universal batching for concurrent data structures. 37th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 281, 35.","chicago":"Aksenov, Vitaly, Michael Anoprenko, Alexander Fedorov, and Michael Spear. “Brief Announcement: BatchBoost: Universal Batching for Concurrent Data Structures.” In 37th International Symposium on Distributed Computing, Vol. 281. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.DISC.2023.35."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vitaly","full_name":"Aksenov, Vitaly","last_name":"Aksenov"},{"last_name":"Anoprenko","full_name":"Anoprenko, Michael","first_name":"Michael"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"first_name":"Michael","last_name":"Spear","full_name":"Spear, Michael"}],"article_processing_charge":"Yes","title":"Brief announcement: BatchBoost: Universal batching for concurrent data structures","article_number":"35","has_accepted_license":"1","year":"2023","day":"01","publication":"37th International Symposium on Distributed Computing","date_published":"2023-10-01T00:00:00Z","doi":"10.4230/LIPIcs.DISC.2023.35","date_created":"2023-11-05T23:00:53Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"date_updated":"2023-11-07T07:48:01Z","ddc":["000"],"file_date_updated":"2023-11-06T11:45:21Z","department":[{"_id":"GradSch"}],"_id":"14485","type":"conference","conference":{"name":"DISC: Symposium on Distributed Computing","start_date":"2023-10-09","location":"L'Aquila, Italy","end_date":"2023-10-13"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773010"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14492","checksum":"d9f8d2915cccdf2df5905b7cd1b4a560","success":1,"date_updated":"2023-11-06T11:45:21Z","file_size":646665,"creator":"dernst","date_created":"2023-11-06T11:45:21Z","file_name":"2023_LIPIcs_Aksenov.pdf"}],"language":[{"iso":"eng"}],"volume":281,"abstract":[{"text":"Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching.\r\nIn this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct \"data\" and \"index\" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is \"close\" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"month":"10","intvolume":" 281"},{"acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","oa_version":"Published Version","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. 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Klausen, A.B. Lauritsen, (2023).","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869."},"date_updated":"2023-11-13T07:47:29Z","title":"Research data for: A stochastic cellular automaton model of culture formation","file_date_updated":"2023-04-26T12:30:06Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen"}]},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"month":"11","intvolume":" 108","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders."}],"oa_version":"Preprint","related_material":{"link":[{"url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation","relation":"software"}],"record":[{"relation":"research_data","id":"12869","status":"public"}]},"volume":108,"issue":"5","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"12890","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_updated":"2023-11-13T07:47:30Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","doi":"10.1103/PhysRevE.108.054307","date_published":"2023-11-08T00:00:00Z","date_created":"2023-05-04T08:35:01Z","year":"2023","day":"08","publication":"Physical Review E","article_number":"054307","author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard"}],"article_processing_charge":"No","external_id":{"arxiv":["2305.02153"]},"title":"Stochastic cellular automaton model of culture formation","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.108.054307.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” Physical Review E, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:10.1103/PhysRevE.108.054307.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. Physical Review E. 2023;108(5). doi:10.1103/PhysRevE.108.054307","apa":"Klausen, F. R., & Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.108.054307","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awad380"}],"month":"11","date_updated":"2023-11-20T10:17:32Z","extern":"1","department":[{"_id":"GradSch"}],"_id":"14543","type":"journal_article","article_type":"original","status":"public","keyword":["Neurology (clinical)"],"year":"2023","day":"10","publication":"Brain","doi":"10.1093/brain/awad380","date_published":"2023-11-10T00:00:00Z","date_created":"2023-11-16T12:36:51Z","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"citation":{"ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380.","ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2023. doi:10.1093/brain/awad380","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380","ieee":"R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain. Oxford University Press, 2023.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380, Oxford University Press, 2023, doi:10.1093/brain/awad380."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Rauan","full_name":"Kaiyrzhanov, Rauan","last_name":"Kaiyrzhanov"},{"last_name":"Rad","full_name":"Rad, Aboulfazl","first_name":"Aboulfazl"},{"last_name":"Lin","full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia"},{"first_name":"Aida","full_name":"Bertoli-Avella, Aida","last_name":"Bertoli-Avella"},{"full_name":"Kallemeijn, Wouter W","last_name":"Kallemeijn","first_name":"Wouter W"},{"full_name":"Godwin, Annie","last_name":"Godwin","first_name":"Annie"},{"last_name":"Zaki","full_name":"Zaki, Maha S","first_name":"Maha S"},{"orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","last_name":"Huang","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3"},{"full_name":"Lau, Tracy","last_name":"Lau","first_name":"Tracy"},{"first_name":"Cassidy","last_name":"Petree","full_name":"Petree, Cassidy"},{"last_name":"Efthymiou","full_name":"Efthymiou, Stephanie","first_name":"Stephanie"},{"first_name":"Ehsan","full_name":"Ghayoor Karimiani, Ehsan","last_name":"Ghayoor Karimiani"},{"first_name":"Maja","last_name":"Hempel","full_name":"Hempel, Maja"},{"first_name":"Elizabeth A","full_name":"Normand, Elizabeth A","last_name":"Normand"},{"last_name":"Rudnik-Schöneborn","full_name":"Rudnik-Schöneborn, Sabine","first_name":"Sabine"},{"first_name":"Ulrich A","full_name":"Schatz, Ulrich A","last_name":"Schatz"},{"full_name":"Baggelaar, Marc P","last_name":"Baggelaar","first_name":"Marc P"},{"first_name":"Muhammad","full_name":"Ilyas, Muhammad","last_name":"Ilyas"},{"first_name":"Tipu","last_name":"Sultan","full_name":"Sultan, Tipu"},{"last_name":"Alvi","full_name":"Alvi, Javeria Raza","first_name":"Javeria Raza"},{"first_name":"Manizha","last_name":"Ganieva","full_name":"Ganieva, Manizha"},{"first_name":"Ben","full_name":"Fowler, Ben","last_name":"Fowler"},{"last_name":"Aanicai","full_name":"Aanicai, Ruxandra","first_name":"Ruxandra"},{"last_name":"Akay Tayfun","full_name":"Akay Tayfun, Gulsen","first_name":"Gulsen"},{"first_name":"Abdulaziz","last_name":"Al Saman","full_name":"Al Saman, Abdulaziz"},{"first_name":"Abdulrahman","full_name":"Alswaid, Abdulrahman","last_name":"Alswaid"},{"full_name":"Amiri, Nafise","last_name":"Amiri","first_name":"Nafise"},{"first_name":"Nilufar","last_name":"Asilova","full_name":"Asilova, Nilufar"},{"first_name":"Vorasuk","full_name":"Shotelersuk, Vorasuk","last_name":"Shotelersuk"},{"first_name":"Patra","last_name":"Yeetong","full_name":"Yeetong, Patra"},{"full_name":"Azam, Matloob","last_name":"Azam","first_name":"Matloob"},{"last_name":"Babaei","full_name":"Babaei, Meisam","first_name":"Meisam"},{"full_name":"Bahrami Monajemi, Gholamreza","last_name":"Bahrami Monajemi","first_name":"Gholamreza"},{"full_name":"Mohammadi, Pouria","last_name":"Mohammadi","first_name":"Pouria"},{"last_name":"Samie","full_name":"Samie, Saeed","first_name":"Saeed"},{"last_name":"Banu","full_name":"Banu, Selina Husna","first_name":"Selina Husna"},{"last_name":"Basto","full_name":"Basto, Jorge Pinto","first_name":"Jorge Pinto"},{"first_name":"Fanny","last_name":"Kortüm","full_name":"Kortüm, Fanny"},{"full_name":"Bauer, Mislen","last_name":"Bauer","first_name":"Mislen"},{"last_name":"Bauer","full_name":"Bauer, Peter","first_name":"Peter"},{"first_name":"Christian","last_name":"Beetz","full_name":"Beetz, Christian"},{"first_name":"Masoud","last_name":"Garshasbi","full_name":"Garshasbi, Masoud"},{"first_name":"Awatif","full_name":"Hameed Issa, Awatif","last_name":"Hameed Issa"},{"first_name":"Wafaa","full_name":"Eyaid, Wafaa","last_name":"Eyaid"},{"full_name":"Ahmed, Hind","last_name":"Ahmed","first_name":"Hind"},{"first_name":"Narges","last_name":"Hashemi","full_name":"Hashemi, Narges"},{"first_name":"Kazem","full_name":"Hassanpour, Kazem","last_name":"Hassanpour"},{"last_name":"Herman","full_name":"Herman, Isabella","first_name":"Isabella"},{"first_name":"Sherozjon","full_name":"Ibrohimov, Sherozjon","last_name":"Ibrohimov"},{"full_name":"Abdul-Majeed, Ban A","last_name":"Abdul-Majeed","first_name":"Ban A"},{"full_name":"Imdad, Maria","last_name":"Imdad","first_name":"Maria"},{"first_name":"Maksudjon","last_name":"Isrofilov","full_name":"Isrofilov, Maksudjon"},{"full_name":"Kaiyal, Qassem","last_name":"Kaiyal","first_name":"Qassem"},{"first_name":"Suliman","last_name":"Khan","full_name":"Khan, Suliman"},{"full_name":"Kirmse, Brian","last_name":"Kirmse","first_name":"Brian"},{"first_name":"Janet","full_name":"Koster, Janet","last_name":"Koster"},{"last_name":"Lourenço","full_name":"Lourenço, Charles Marques","first_name":"Charles Marques"},{"first_name":"Tadahiro","last_name":"Mitani","full_name":"Mitani, Tadahiro"},{"first_name":"Oana","full_name":"Moldovan, Oana","last_name":"Moldovan"},{"first_name":"David","full_name":"Murphy, David","last_name":"Murphy"},{"last_name":"Najafi","full_name":"Najafi, Maryam","first_name":"Maryam"},{"full_name":"Pehlivan, Davut","last_name":"Pehlivan","first_name":"Davut"},{"first_name":"Maria Eugenia","last_name":"Rocha","full_name":"Rocha, Maria Eugenia"},{"full_name":"Salpietro, Vincenzo","last_name":"Salpietro","first_name":"Vincenzo"},{"first_name":"Miriam","last_name":"Schmidts","full_name":"Schmidts, Miriam"},{"first_name":"Adel","full_name":"Shalata, Adel","last_name":"Shalata"},{"first_name":"Mohammad","last_name":"Mahroum","full_name":"Mahroum, Mohammad"},{"full_name":"Talbeya, Jawabreh Kassem","last_name":"Talbeya","first_name":"Jawabreh Kassem"},{"first_name":"Robert W","last_name":"Taylor","full_name":"Taylor, Robert W"},{"first_name":"Dayana","full_name":"Vazquez, Dayana","last_name":"Vazquez"},{"first_name":"Annalisa","full_name":"Vetro, Annalisa","last_name":"Vetro"},{"last_name":"Waterham","full_name":"Waterham, Hans R","first_name":"Hans R"},{"first_name":"Mashaya","last_name":"Zaman","full_name":"Zaman, Mashaya"},{"first_name":"Tina A","full_name":"Schrader, Tina A","last_name":"Schrader"},{"first_name":"Wendy K","last_name":"Chung","full_name":"Chung, Wendy K"},{"first_name":"Renzo","last_name":"Guerrini","full_name":"Guerrini, Renzo"},{"last_name":"Lupski","full_name":"Lupski, James R","first_name":"James R"},{"first_name":"Joseph","full_name":"Gleeson, Joseph","last_name":"Gleeson"},{"full_name":"Suri, Mohnish","last_name":"Suri","first_name":"Mohnish"},{"full_name":"Jamshidi, Yalda","last_name":"Jamshidi","first_name":"Yalda"},{"first_name":"Kailash P","full_name":"Bhatia, Kailash P","last_name":"Bhatia"},{"full_name":"Vona, Barbara","last_name":"Vona","first_name":"Barbara"},{"last_name":"Schrader","full_name":"Schrader, Michael","first_name":"Michael"},{"first_name":"Mariasavina","full_name":"Severino, Mariasavina","last_name":"Severino"},{"first_name":"Matthew","full_name":"Guille, Matthew","last_name":"Guille"},{"first_name":"Edward W","last_name":"Tate","full_name":"Tate, Edward W"},{"first_name":"Gaurav K","last_name":"Varshney","full_name":"Varshney, Gaurav K"},{"first_name":"Henry","last_name":"Houlden","full_name":"Houlden, Henry"},{"last_name":"Maroofian","full_name":"Maroofian, Reza","first_name":"Reza"}],"article_processing_charge":"No","title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","article_number":"awad380"},{"article_number":"2360005 ","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"citation":{"chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, 2360005, World Scientific Publishing, 2023, doi:10.1142/s0129055x2360005x.","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing, 2023.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x","apa":"Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2301.05621"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha"},{"last_name":"Lauritsen","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"},{"first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara","last_name":"Roos"}],"title":"Universality in low-dimensional BCS theory","acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","year":"2023","has_accepted_license":"1","publication":"Reviews in Mathematical Physics","day":"31","date_created":"2023-11-15T23:48:14Z","doi":"10.1142/s0129055x2360005x","date_published":"2023-10-31T00:00:00Z","_id":"14542","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-11-20T10:04:38Z","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1142/S0129055X2360005X"}],"scopus_import":"1","month":"10","publication_status":"epub_ahead","publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"language":[{"iso":"eng"}],"ec_funded":1},{"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios."}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"9969","status":"public"},{"status":"public","id":"13238","relation":"part_of_dissertation"},{"status":"public","id":"14490","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"14598","checksum":"521c72818d720a52b377207b2ee87b6a","creator":"cchlebak","file_size":3037720,"date_updated":"2023-11-23T10:29:55Z","file_name":"thesis_yeo.zip","date_created":"2023-11-23T10:29:55Z"},{"success":1,"file_id":"14599","checksum":"0ed5d16899687aecf13d843c9878c9f2","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"thesis_yeo.pdf","date_created":"2023-11-23T10:30:08Z","file_size":2717256,"date_updated":"2023-11-23T10:30:08Z","creator":"cchlebak"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"status":"public","type":"dissertation","_id":"14506","file_date_updated":"2023-11-23T10:30:08Z","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"ddc":["000"],"date_updated":"2023-11-30T10:54:51Z","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-11-10T08:10:43Z","date_published":"2023-11-10T00:00:00Z","doi":"10.15479/14506","page":"162","day":"10","year":"2023","has_accepted_license":"1","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"title":"Advances in efficiency and privacy in payment channel network analysis","article_processing_charge":"No","author":[{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023."}},{"file":[{"file_id":"12745","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","content_type":"application/pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","relation":"main_file","access_level":"closed","file_name":"Thesis_Riedl_2023.pdf","date_created":"2023-03-23T12:49:23Z","file_size":63734746,"date_updated":"2023-11-24T11:57:46Z","creator":"cchlebak"},{"creator":"cchlebak","file_size":339473651,"date_updated":"2023-09-24T22:30:03Z","file_name":"Thesis_Riedl_2023_source.rar","date_created":"2023-03-23T12:54:34Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/octet-stream","file_id":"12746","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10703"},{"id":"10791","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"relation":"part_of_dissertation","id":"461","status":"public"},{"relation":"new_edition","status":"public","id":"14530"}]},"oa_version":"None","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}],"month":"03","alternative_title":["ISTA Thesis"],"ddc":["530"],"supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"date_updated":"2023-11-30T10:55:13Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2023-11-24T11:57:46Z","_id":"12726","status":"public","type":"dissertation","day":"23","has_accepted_license":"1","year":"2023","date_published":"2023-03-23T00:00:00Z","doi":"10.15479/at:ista:12726","date_created":"2023-03-15T13:22:13Z","page":"260","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria."},"title":"Synchronization in collectively moving active matter","author":[{"last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No"},{"_id":"14530","type":"dissertation","status":"public","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"supervisor":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"date_updated":"2023-11-30T10:55:13Z","ddc":["530","570"],"file_date_updated":"2023-11-15T09:52:54Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"Updated Version","alternative_title":["ISTA Thesis"],"month":"11","publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14536","checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","success":1,"date_updated":"2023-11-15T09:52:54Z","file_size":36743942,"creator":"mriedl","date_created":"2023-11-15T09:52:54Z","file_name":"Thesis_Riedl_2023_corr.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"relation":"part_of_dissertation","status":"public","id":"7932"},{"relation":"part_of_dissertation","id":"461","status":"public"},{"relation":"old_edition","id":"12726","status":"public"}]},"citation":{"ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"article_processing_charge":"No","title":"Synchronization in collectively moving active matter","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"16","page":"260","date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14530","date_created":"2023-11-15T09:59:03Z"},{"month":"11","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"abstract":[{"text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.","lang":"eng"}],"related_material":{"record":[{"id":"10851","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"13264","relation":"part_of_dissertation"}]},"file":[{"creator":"pduc","file_size":34828019,"date_updated":"2023-11-22T09:46:06Z","file_name":"Phan_Thesis_pdfa.pdf","date_created":"2023-11-17T13:36:44Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"db0c37d213bc002125bd59690e9db246","file_id":"14548"},{"creator":"pduc","date_updated":"2023-11-17T13:47:54Z","file_size":279319709,"date_created":"2023-11-17T13:44:53Z","file_name":"dissertation_src.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","file_id":"14549"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"14547","file_date_updated":"2023-11-22T09:46:06Z","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"ddc":["530"],"supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"date_updated":"2023-11-30T10:56:04Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14547","date_created":"2023-11-17T13:45:26Z","page":"80","day":"16","has_accepted_license":"1","year":"2023","title":"Resonant microwave spectroscopy of Al-InAs","author":[{"full_name":"Phan, Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547."}},{"file_date_updated":"2023-12-04T08:04:14Z","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"ddc":["531","006"],"date_updated":"2023-12-04T08:09:05Z","keyword":["Computer Graphics and Computer-Aided Design"],"status":"public","article_type":"original","type":"journal_article","_id":"14628","issue":"5","volume":42,"language":[{"iso":"eng"}],"file":[{"checksum":"0192f597d7a2ceaf89baddfd6190d4c8","file_id":"14630","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/zip","date_created":"2023-11-29T15:16:01Z","file_name":"tog-22-0089-File004.zip","creator":"yichen","date_updated":"2023-11-29T15:16:01Z","file_size":95467870},{"success":1,"checksum":"7fb024963be81933494f38de191e4710","file_id":"14631","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"tog-22-0089-File005.zip","date_created":"2023-11-29T15:16:01Z","creator":"yichen","file_size":103731880,"date_updated":"2023-11-29T15:16:01Z"},{"creator":"dernst","file_size":57067476,"date_updated":"2023-12-04T08:04:14Z","file_name":"2023_ACMToG_Makatura.pdf","date_created":"2023-12-04T08:04:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_id":"14638"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301","1557-7368"]},"intvolume":" 42","month":"10","oa_version":"Published Version","abstract":[{"text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.","lang":"eng"}],"title":"Procedural metamaterials: A unified procedural graph for metamaterial design","article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Makatura, Liane","last_name":"Makatura","first_name":"Liane"},{"last_name":"Wang","full_name":"Wang, Bohan","first_name":"Bohan"},{"last_name":"Chen","full_name":"Chen, Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu"},{"first_name":"Bolei","full_name":"Deng, Bolei","last_name":"Deng"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.","ieee":"L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389."},"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"article_number":"168","date_created":"2023-11-29T15:02:03Z","doi":"10.1145/3605389","date_published":"2023-10-01T00:00:00Z","publication":"ACM Transactions on Graphics","day":"01","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program."},{"acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","oa":1,"quality_controlled":"1","publisher":"Elsevier","publication":"International Journal of Mass Spectrometry","day":"23","year":"2023","date_created":"2023-12-10T23:00:57Z","date_published":"2023-11-23T00:00:00Z","doi":"10.1016/j.ijms.2023.117168","article_number":"117168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2023. https://doi.org/10.1016/j.ijms.2023.117168.","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2023.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023).","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168."},"title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl"},{"first_name":"Anna","last_name":"Ploner","full_name":"Ploner, Anna"},{"first_name":"Christina","full_name":"Meisenbichler, Christina","last_name":"Meisenbichler"},{"first_name":"Robert","last_name":"Konrat","full_name":"Konrat, Robert"},{"last_name":"Müller","full_name":"Müller, Thomas","first_name":"Thomas"}],"oa_version":"Published Version","abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"intvolume":" 495","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ijms.2023.117168"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1387-3806"]},"volume":495,"_id":"14653","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-12-11T08:16:35Z","department":[{"_id":"GradSch"}]},{"issue":"3","volume":131,"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05098","open_access":"1"}],"intvolume":" 131","month":"07","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."}],"oa_version":"Preprint","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_updated":"2023-12-13T11:40:19Z","article_type":"original","type":"journal_article","keyword":["General Physics and Astronomy"],"status":"public","_id":"13274","date_created":"2023-07-24T09:43:59Z","doi":"10.1103/physrevlett.131.034002","date_published":"2023-07-21T00:00:00Z","year":"2023","isi":1,"publication":"Physical Review Letters","day":"21","oa":1,"publisher":"American Physical Society","quality_controlled":"1","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.).","external_id":{"isi":["001052929900004"],"arxiv":["2306.05098"]},"article_processing_charge":"No","author":[{"last_name":"Paranjape","full_name":"Paranjape, Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","first_name":"Chaitanya S"},{"last_name":"Yalniz","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"full_name":"Duguet, Yohann","last_name":"Duguet","first_name":"Yohann"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"title":"Direct path from turbulence to time-periodic solutions","citation":{"mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:10.1103/physrevlett.131.034002.","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” Physical Review Letters, vol. 131, no. 3. American Physical Society, 2023.","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023).","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023). Direct path from turbulence to time-periodic solutions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.131.034002","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002","chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"034002"},{"file_date_updated":"2023-08-18T10:47:55Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"date_updated":"2023-12-13T12:15:36Z","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"14058","ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9803"},{"relation":"research_data","id":"12933","status":"public"},{"status":"public","id":"6831","relation":"part_of_dissertation"},{"status":"public","id":"14077","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","file_size":10891454,"date_created":"2023-08-16T18:15:17Z","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"14075","checksum":"4e44e169f2724ee8c9324cd60bcc2b71"},{"file_name":"PhDThesis_PuixeuG.pdf","date_created":"2023-08-18T10:47:55Z","file_size":19856686,"date_updated":"2023-08-18T10:47:55Z","creator":"gpuixeus","success":1,"file_id":"14079","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"alternative_title":["ISTA Thesis"],"month":"08","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."}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"}],"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","citation":{"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.","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.","apa":"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. https://doi.org/10.15479/at:ista:14058","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:10.15479/at:ista:14058","mla":"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, doi:10.15479/at:ista:14058.","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.","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. https://doi.org/10.15479/at:ista:14058."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"page":"230","date_created":"2023-08-15T10:20:40Z","doi":"10.15479/at:ista:14058","date_published":"2023-08-15T00:00:00Z","year":"2023","has_accepted_license":"1","day":"15","oa":1,"publisher":"Institute of Science and Technology Austria"},{"issue":"8","volume":13,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12933"},{"status":"public","id":"14058","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_id":"14498","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_G3_Puixeu.pdf","date_created":"2023-11-07T09:00:19Z","creator":"dernst","file_size":845642,"date_updated":"2023-11-07T09:00:19Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2160-1836"]},"publication_status":"published","month":"08","intvolume":" 13","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"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."}],"file_date_updated":"2023-11-07T09:00:19Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"ddc":["570"],"date_updated":"2023-12-13T12:15:37Z","status":"public","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14077","doi":"10.1093/g3journal/jkad121","date_published":"2023-08-01T00:00:00Z","date_created":"2023-08-18T06:52:14Z","day":"01","publication":"G3: Genes, Genomes, Genetics","isi":1,"has_accepted_license":"1","year":"2023","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"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).","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","author":[{"full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001002997200001"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121.","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. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","apa":"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. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","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,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (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.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121."},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications"}]},{"article_processing_charge":"No","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2023-05-11T12:50:18Z","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","date_updated":"2023-12-13T12:15:36Z","citation":{"mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","short":"G. Puixeu Sala, (2023).","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933."},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","status":"public","_id":"12933","date_created":"2023-05-10T10:00:49Z","contributor":[{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"doi":"10.15479/AT:ISTA:12933","related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"status":"public","id":"14077","relation":"used_in_publication"}]},"date_published":"2023-05-15T00:00:00Z","year":"2023","has_accepted_license":"1","day":"15","file":[{"date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S1.csv","creator":"gpuixeus","date_updated":"2023-05-10T09:41:43Z","file_size":8029982,"checksum":"0ba0bcd0bb8b18d84792136a4370df90","file_id":"12934","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/csv"},{"creator":"gpuixeus","file_size":13667640,"date_updated":"2023-05-10T09:41:43Z","file_name":"Dataset_S2.csv","date_created":"2023-05-10T09:41:43Z","relation":"main_file","access_level":"open_access","content_type":"text/csv","success":1,"file_id":"12935","checksum":"a62aa9a6d4904e0fdb699cf752640863"},{"content_type":"text/csv","relation":"main_file","access_level":"open_access","success":1,"checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","file_id":"12936","file_size":8369141,"date_updated":"2023-05-10T09:41:48Z","creator":"gpuixeus","file_name":"Dataset_S3.csv","date_created":"2023-05-10T09:41:48Z"},{"success":1,"file_id":"12937","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","relation":"main_file","access_level":"open_access","content_type":"text/csv","file_name":"Dataset_S4.csv","date_created":"2023-05-10T09:41:50Z","creator":"gpuixeus","file_size":19543247,"date_updated":"2023-05-10T09:41:50Z"},{"success":1,"file_id":"12944","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"readme.txt","date_created":"2023-05-11T12:50:18Z","creator":"gpuixeus","file_size":4566,"date_updated":"2023-05-11T12:50:18Z"}],"oa":1,"publisher":"Institute of Science and Technology Austria","month":"05","abstract":[{"lang":"eng","text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\"."}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14352","checksum":"eb747420e6a88a7796fa934151957676","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_ForumMathematics_Cipolloni.pdf","date_created":"2023-09-20T11:09:35Z","file_size":852652,"date_updated":"2023-09-20T11:09:35Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["2050-5094"]},"ec_funded":1,"volume":11,"oa_version":"Published Version","abstract":[{"text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation.","lang":"eng"}],"intvolume":" 11","month":"08","scopus_import":"1","ddc":["510"],"date_updated":"2023-12-13T12:24:23Z","file_date_updated":"2023-09-20T11:09:35Z","department":[{"_id":"LaEr"},{"_id":"GradSch"}],"_id":"14343","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","publication":"Forum of Mathematics, Sigma","day":"23","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-09-17T22:01:09Z","doi":"10.1017/fms.2023.70","date_published":"2023-08-23T00:00:00Z","acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge University Press, 2023, doi:10.1017/fms.2023.70.","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.70","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023.","chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70.","ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74."},"title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","external_id":{"isi":["001051980200001"],"arxiv":["2301.05181"]},"article_processing_charge":"Yes","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","last_name":"Henheik"},{"first_name":"Oleksii","id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61","last_name":"Kolupaiev","full_name":"Kolupaiev, Oleksii"}],"article_number":"e74","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}]},{"oa":1,"publisher":"IOP Publishing","quality_controlled":"1","acknowledgement":"J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331.","date_created":"2023-10-12T12:42:53Z","doi":"10.1088/1751-8121/acfe62","date_published":"2023-10-11T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Journal of Physics A: Mathematical and Theoretical","day":"11","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"article_number":"445201","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001080908000001"],"arxiv":["2211.16606"]},"author":[{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"first_name":"Roderich","full_name":"Tumulka, Roderich","last_name":"Tumulka"}],"title":"Creation rate of Dirac particles at a point source","citation":{"chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.","ista":"Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62.","short":"S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).","ieee":"S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44. IOP Publishing, 2023.","ama":"Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62","apa":"Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 56","month":"10","abstract":[{"lang":"eng","text":"Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\\in\\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission)."}],"oa_version":"Published Version","ec_funded":1,"issue":"44","volume":56,"publication_status":"published","publication_identifier":{"eissn":["1751-8121"],"issn":["1751-8113"]},"language":[{"iso":"eng"}],"file":[{"file_size":721399,"date_updated":"2023-10-16T07:07:24Z","creator":"dernst","file_name":"2023_JourPhysics_Henheik.pdf","date_created":"2023-10-16T07:07:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"5b68de147dd4c608b71a6e0e844d2ce9","file_id":"14429"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14421","file_date_updated":"2023-10-16T07:07:24Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"date_updated":"2023-12-13T13:01:25Z","ddc":["510"]},{"_id":"14425","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["540","000"],"date_updated":"2023-12-13T13:02:07Z","file_date_updated":"2023-10-16T07:34:49Z","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.","lang":"eng"}],"intvolume":" 14","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-10-16T07:34:49Z","file_size":3194116,"date_created":"2023-10-16T07:34:49Z","file_name":"2023_NatureComm_Zeng.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7d1dffd36b672ec679f08f70ce79da87","file_id":"14432","success":1}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/TiO2-water"}]},"volume":14,"article_number":"6131","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131.","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41865-8.","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 2023;14. doi:10.1038/s41467-023-41865-8","apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., & Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41865-8","short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023).","ieee":"Z. Zeng et al., “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications, vol. 14, 6131, Springer Nature, 2023, doi:10.1038/s41467-023-41865-8."},"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","article_processing_charge":"Yes","external_id":{"isi":["001084354900008"],"pmid":["37783698"],"arxiv":["2303.07433"]},"author":[{"last_name":"Zeng","full_name":"Zeng, Zezhu","first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"last_name":"Wodaczek","full_name":"Wodaczek, Felix","orcid":"0009-0000-1457-795X","first_name":"Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e"},{"last_name":"Liu","full_name":"Liu, Keyang","first_name":"Keyang"},{"first_name":"Frederick","full_name":"Stein, Frederick","last_name":"Stein"},{"first_name":"Jürg","last_name":"Hutter","full_name":"Hutter, Jürg"},{"full_name":"Chen, Ji","last_name":"Chen","first_name":"Ji"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","day":"02","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-10-15T22:01:10Z","date_published":"2023-10-02T00:00:00Z","doi":"10.1038/s41467-023-41865-8"},{"language":[{"iso":"eng"}],"file":[{"file_size":11947523,"date_updated":"2023-12-01T11:10:46Z","creator":"ssack","file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-11-30","checksum":"068fd3570506ec42b2faa390de784bc4","file_id":"14635"},{"file_name":"PhD Thesis (1).zip","date_created":"2023-11-30T15:54:11Z","creator":"ssack","file_size":18422964,"date_updated":"2023-12-01T11:10:46Z","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_id":"14636","relation":"source_file","access_level":"closed","content_type":"application/zip"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"id":"11471","status":"public","relation":"part_of_dissertation"},{"id":"13125","status":"public","relation":"part_of_dissertation"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","month":"11","alternative_title":["ISTA Thesis"],"ddc":["530"],"date_updated":"2023-12-13T14:47:25Z","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"file_date_updated":"2023-12-01T11:10:46Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"_id":"14622","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","day":"30","year":"2023","has_accepted_license":"1","date_created":"2023-11-28T10:58:13Z","date_published":"2023-11-30T00:00:00Z","doi":"10.15479/at:ista:14622","page":"142","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria."},"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","article_processing_charge":"No","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508"}],"project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}]},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"6328","status":"public"},{"relation":"part_of_dissertation","id":"7885","status":"public"},{"status":"public","id":"12272","relation":"part_of_dissertation"},{"id":"14274","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"ec_funded":1,"file":[{"embargo":"2024-12-20","file_id":"14699","checksum":"457927165d5d556305d3086f6b83e5c7","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","file_name":"Thesis.pdf","date_created":"2023-12-20T09:35:34Z","creator":"jstopp","file_size":51585778,"date_updated":"2023-12-20T09:35:34Z"},{"file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-12-20T09:35:35Z","file_name":"Thesis.docx","creator":"jstopp","date_updated":"2023-12-20T10:41:42Z","file_size":69625950}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"file_date_updated":"2023-12-20T10:41:42Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"ddc":["570"],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"date_updated":"2023-12-21T14:30:02Z","status":"public","type":"dissertation","_id":"14697","date_published":"2023-12-20T00:00:00Z","doi":"10.15479/at:ista:14697","date_created":"2023-12-18T19:14:28Z","page":"226","day":"20","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","full_name":"Stopp, Julian A","last_name":"Stopp"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697."},"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"page":"96","date_published":"2023-12-12T00:00:00Z","doi":"10.15479/at:ista:14651","date_created":"2023-12-11T19:30:37Z","has_accepted_license":"1","year":"2023","day":"12","publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"}],"article_processing_charge":"No","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","citation":{"ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11411"}]},"ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"success":1,"checksum":"520bdb61e95e66070e02824947d2c5fa","file_id":"14684","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Phd_Thesis_LA.pdf","date_created":"2023-12-13T15:37:55Z","file_size":34101468,"date_updated":"2023-12-13T15:37:55Z","creator":"larathoo"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"14685","checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","file_size":31052872,"creator":"larathoo","date_created":"2023-12-13T15:42:23Z","file_name":"Phd_Thesis_LA.zip"},{"file_name":"Supplementary_Materials.zip","date_created":"2023-12-11T19:24:59Z","file_size":10713896,"date_updated":"2023-12-14T08:58:18Z","creator":"larathoo","checksum":"9a778c949932286f4519e1f1fca2820d","file_id":"14681","content_type":"application/zip","relation":"supplementary_material","access_level":"closed"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"12","abstract":[{"text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-12-14T08:58:18Z","supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2023-12-22T11:04:45Z","ddc":["570"],"type":"dissertation","status":"public","_id":"14651"},{"date_created":"2023-12-21T10:14:37Z","doi":"10.48550/arXiv.2312.12213","date_published":"2023-12-19T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","day":"19","publication_status":"submitted","year":"2023","month":"12","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.12213","open_access":"1"}],"oa":1,"acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.","oa_version":"Preprint","abstract":[{"text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","external_id":{"arxiv":["2312.12213"]},"article_processing_charge":"No","author":[{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"first_name":"Hugo","full_name":"Lavenant, Hugo","last_name":"Lavenant"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213.","ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. .","short":"S. Ishida, H. Lavenant, ArXiv (n.d.).","apa":"Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213","chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213.","ista":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213."},"date_updated":"2023-12-27T13:44:33Z","keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"status":"public","type":"preprint","article_number":"2312.12213","_id":"14703"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs."}],"month":"12","intvolume":" 13950","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://eprint.iacr.org/2022/1554","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031477539"],"eissn":["0302-9743"],"issn":["1611-3349"],"eisbn":["9783031477546"]},"publication_status":"published","volume":13950,"_id":"14735","status":"public","type":"conference","conference":{"start_date":"2023-05-01","location":"Bol, Brac, Croatia","end_date":"2023-05-05","name":"FC: Financial Cryptography and Data Security"},"date_updated":"2024-01-08T09:28:14Z","department":[{"_id":"ElKo"},{"_id":"GradSch"}],"acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"27th International Conference on Financial Cryptography and Data Security","year":"2023","date_published":"2023-12-01T00:00:00Z","doi":"10.1007/978-3-031-47754-6_1","date_created":"2024-01-08T09:17:38Z","page":"3-20","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20.","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1.","ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1","apa":"Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","mla":"Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1."},"title":"Executing and proving over dirty ledgers","author":[{"full_name":"Stefo, Christos","last_name":"Stefo","first_name":"Christos","id":"a20e8902-32b0-11ee-9fa8-b23fa638b793"},{"first_name":"Zhuolun","last_name":"Xiang","full_name":"Xiang, Zhuolun"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"}],"article_processing_charge":"No"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","apa":"Zikelic, D. (2023). Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539","mla":"Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539.","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539."},"title":"Automated verification and control of infinite state stochastic systems","article_processing_charge":"No","author":[{"last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"day":"15","year":"2023","date_created":"2023-11-15T13:39:10Z","doi":"10.15479/14539","date_published":"2023-11-15T00:00:00Z","page":"256","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["000"],"date_updated":"2024-01-16T11:58:15Z","supervisor":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"file_date_updated":"2023-11-15T13:44:24Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"_id":"14539","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_updated":"2023-11-15T13:43:28Z","file_size":2116426,"creator":"cchlebak","date_created":"2023-11-15T13:43:28Z","file_name":"main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14540","checksum":"f23e002b0059ca78e1fbb864da52dd7e","success":1},{"date_updated":"2023-11-15T13:44:24Z","file_size":35884057,"creator":"cchlebak","date_created":"2023-11-15T13:44:24Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_id":"14541","checksum":"80ca37618a3c7b59866875f8be9b15ed"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1194","relation":"part_of_dissertation"},{"id":"12000","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9644","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12511","status":"public"},{"relation":"part_of_dissertation","id":"14600","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14601"},{"status":"public","id":"10414","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"month":"11","alternative_title":["ISTA Thesis"]},{"oa":1,"publisher":"European Geosciences Union","month":"04","oa_version":"Published Version","date_created":"2024-01-22T12:08:12Z","date_published":"2023-04-13T00:00:00Z","doi":"10.5194/egusphere-egu23-6157","publication_status":"published","year":"2023","has_accepted_license":"1","publication":"EGU General Assembly 2023","language":[{"iso":"eng"}],"day":"13","file":[{"file_name":"2023_EGU_Polesello.pdf","date_created":"2024-01-24T11:19:54Z","creator":"dernst","file_size":296769,"date_updated":"2024-01-24T11:19:54Z","success":1,"checksum":"8cb88c1bc80ccee328478a62064d98f7","file_id":"14883","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"conference":{"start_date":"2023-04-23","location":"Vienna, Austria & Virtual","end_date":"2023-04-28","name":"EGU General Assembly"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference_abstract","status":"public","_id":"14863","article_number":"EGU23-6157","article_processing_charge":"No","author":[{"first_name":"Andrea","id":"74c777f4-32da-11ee-b498-874db0835561","full_name":"Polesello, Andrea","last_name":"Polesello"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"last_name":"Pasquero","full_name":"Pasquero, Claudia","first_name":"Claudia"},{"first_name":"Agostino N.","last_name":"Meroni","full_name":"Meroni, Agostino N."}],"department":[{"_id":"CaMu"},{"_id":"GradSch"}],"title":"Intensification mechanisms of tropical cyclones","file_date_updated":"2024-01-24T11:19:54Z","date_updated":"2024-01-24T11:25:07Z","citation":{"short":"A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023.","ieee":"A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023.","apa":"Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157","ama":"Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157","mla":"Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157.","ista":"Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157.","chicago":"Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"]},{"issue":"4","volume":42,"ec_funded":1,"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"13156","checksum":"a0b0ba3b36f43a94388e8824613d812a","success":1,"creator":"dernst","date_updated":"2023-06-19T11:02:23Z","file_size":78940724,"date_created":"2023-06-19T11:02:23Z","file_name":"2023_ACMToG_Freire.pdf"},{"checksum":"b9206bbb67af82df49b7e7cdbde3410c","file_id":"13157","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-06-20T12:20:51Z","file_name":"2023_ACMToG_SuppMaterial_Freire.pdf","date_updated":"2023-06-20T12:20:51Z","file_size":34345905,"creator":"dernst"}],"language":[{"iso":"eng"}],"month":"07","intvolume":" 42","abstract":[{"lang":"eng","text":"We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. \r\nOur approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.\r\nOur technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"oa_version":"Submitted Version","file_date_updated":"2023-06-20T12:20:51Z","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"date_updated":"2024-01-29T10:30:49Z","ddc":["006"],"type":"journal_article","article_type":"original","conference":{"start_date":"2023-08-06","end_date":"2023-08-10","location":"Los Angeles, CA, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"status":"public","keyword":["PCB design and layout","Mesh geometry models"],"_id":"13049","date_published":"2023-07-26T00:00:00Z","doi":"10.1145/3592411","date_created":"2023-05-22T08:37:04Z","has_accepted_license":"1","isi":1,"year":"2023","day":"26","publication":"Transactions on Graphics","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"We thank the reviewers for the valuable feedback. We also thank the Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication and assembly. This project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 715767 – MATERIALIZABLE).","author":[{"first_name":"Marco","full_name":"Freire, Marco","last_name":"Freire"},{"full_name":"Bhargava, Manas","orcid":"0009-0007-6138-6890","last_name":"Bhargava","first_name":"Manas","id":"FF8FA64C-AA6A-11E9-99AD-50D4E5697425"},{"last_name":"Schreck","full_name":"Schreck, Camille","first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pierre-Alexandre","full_name":"Hugron, Pierre-Alexandre","last_name":"Hugron"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"last_name":"Lefebvre","full_name":"Lefebvre, Sylvain","first_name":"Sylvain"}],"article_processing_charge":"No","external_id":{"isi":["001044671300108"]},"title":"PCBend: Light up your 3D shapes with foldable circuit boards","citation":{"chicago":"Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron, Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592411.","ista":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 42(4), 142.","mla":"Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics, vol. 42, no. 4, 142, Association for Computing Machinery, 2023, doi:10.1145/3592411.","short":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre, Transactions on Graphics 42 (2023).","ieee":"M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre, “PCBend: Light up your 3D shapes with foldable circuit boards,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.","apa":"Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., & Lefebvre, S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592411","ama":"Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 2023;42(4). doi:10.1145/3592411"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"142"},{"title":"Superconductivity from a melted insulator in Josephson junction arrays","external_id":{"isi":["001054563800006"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","first_name":"Soham","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","last_name":"Senior","orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L"},{"first_name":"Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714","full_name":"Saez Mollejo, Jaime","last_name":"Saez Mollejo"},{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise","orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","last_name":"Puglia"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","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.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w","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.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023."},"project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"name":"Protected states of quantum matter","_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344"}],"date_created":"2023-08-11T07:41:17Z","date_published":"2023-11-01T00:00:00Z","doi":"10.1038/s41567-023-02161-w","page":"1630-1635","publication":"Nature Physics","day":"01","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","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.).","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"file_date_updated":"2024-01-29T11:25:38Z","ddc":["530"],"date_updated":"2024-01-29T11:27:49Z","keyword":["General Physics and Astronomy"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14032","ec_funded":1,"volume":19,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"1fc86d71bfbf836e221c1e925343adc5","file_id":"14899","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","date_created":"2024-01-29T11:25:38Z","file_size":1977706,"date_updated":"2024-01-29T11:25:38Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"intvolume":" 19","month":"11","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"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.","lang":"eng"}]},{"date_updated":"2024-01-29T11:00:46Z","department":[{"_id":"GradSch"}],"_id":"13128","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"publication_status":"published","volume":66,"issue":"4","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We also study some related questions on moderate expanders over matrix rings, namely, for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, ForumMath., 31, 951–970).\r\n"}],"month":"12","intvolume":" 66","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:10.4153/S000843952300036X.","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” Canadian Mathematical Bulletin, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","apa":"Mohammadi, A., Pham, T., & Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. Cambridge University Press. https://doi.org/10.4153/S000843952300036X","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 2023;66(4):1280-1295. doi:10.4153/S000843952300036X","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin. Cambridge University Press, 2023. https://doi.org/10.4153/S000843952300036X.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295."},"title":"An energy decomposition theorem for matrices and related questions","author":[{"first_name":"Ali","full_name":"Mohammadi, Ali","last_name":"Mohammadi"},{"first_name":"Thang","full_name":"Pham, Thang","last_name":"Pham"},{"last_name":"Wang","full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X","first_name":"Yiting","id":"1917d194-076e-11ed-97cd-837255f88785"}],"external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"article_processing_charge":"No","day":"01","publication":"Canadian Mathematical Bulletin","isi":1,"year":"2023","doi":"10.4153/S000843952300036X","date_published":"2023-12-01T00:00:00Z","date_created":"2023-06-11T22:00:40Z","page":"1280-1295","quality_controlled":"1","publisher":"Cambridge University Press","oa":1},{"status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14087","department":[{"_id":"GradSch"}],"file_date_updated":"2024-01-30T12:48:24Z","ddc":["540"],"date_updated":"2024-01-30T12:49:24Z","month":"09","intvolume":" 39","scopus_import":"1","oa_version":"Published Version","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"}],"volume":39,"file":[{"success":1,"checksum":"b936747170d0b708172b518078c4081a","file_id":"14908","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_SoftMatter_Ronning.pdf","date_created":"2024-01-30T12:48:24Z","creator":"dernst","file_size":7660662,"date_updated":"2024-01-30T12:48:24Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"publication_status":"published","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","author":[{"last_name":"Rønning","full_name":"Rønning, Jonas","first_name":"Jonas"},{"last_name":"Renaud","full_name":"Renaud, Julian B","first_name":"Julian B","id":"7af6767d-14eb-11ed-b536-a32449ae867c"},{"full_name":"Doostmohammadi, Amin","last_name":"Doostmohammadi","first_name":"Amin"},{"first_name":"Luiza","full_name":"Angheluta, Luiza","last_name":"Angheluta"}],"external_id":{"isi":["001035766100001"],"arxiv":["2303.07063"]},"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 2023;39:7513-7527. doi:10.1039/d3sm00316g","apa":"Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g","ieee":"J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.","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.” Soft Matter, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g.","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.","chicago":"Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g."},"quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"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.","date_published":"2023-09-01T00:00:00Z","doi":"10.1039/d3sm00316g","date_created":"2023-08-20T22:01:15Z","page":"7513-7527","day":"01","publication":"Soft Matter","has_accepted_license":"1","isi":1,"year":"2023"},{"title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","article_processing_charge":"No","external_id":{"arxiv":["2302.01629"]},"author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","first_name":"Simone","last_name":"Bombari","full_name":"Bombari, Simone"},{"id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","first_name":"Shayan","full_name":"Kiyani, Shayan","last_name":"Kiyani"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In Proceedings of the 40th International Conference on Machine Learning, 202:2738–76. ML Research Press, 2023.","ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:2738-2776.","apa":"Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press."},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"date_created":"2023-04-23T16:11:03Z","date_published":"2023-10-27T00:00:00Z","page":"2738-2776","publication":"Proceedings of the 40th International Conference on Machine Learning","day":"27","year":"2023","oa":1,"quality_controlled":"1","publisher":"ML Research Press","acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"date_updated":"2024-02-06T07:42:00Z","status":"public","conference":{"start_date":"2023-07-23","end_date":"2023-07-29","location":"Honolulu, HI, United States","name":"ICML: International Conference on Machine Learning"},"type":"conference","_id":"12859","related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}]},"volume":202,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 202","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"alternative_title":["PMLR"],"oa_version":"Preprint","abstract":[{"text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).","lang":"eng"}]},{"_id":"13107","status":"public","type":"dissertation","ddc":["570"],"date_updated":"2024-02-07T08:03:33Z","supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-06-07T08:41:49Z","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans."}],"month":"05","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"date_created":"2023-06-01T13:48:41Z","file_name":"Thesis_Lisa Knaus_approved_final.docx","creator":"lknaus","date_updated":"2023-06-01T13:48:41Z","file_size":12991551,"checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_id":"13112","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"13114","checksum":"6903d152aa01181d87a696085af31c83","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","date_created":"2023-06-02T09:47:29Z","creator":"lknaus","file_size":9309015,"date_updated":"2023-06-07T08:41:49Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"id":"12802","status":"public","relation":"part_of_dissertation"}]},"project":[{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","apa":"Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107","mla":"Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107."},"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","article_processing_charge":"No","author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","first_name":"Lisa","full_name":"Knaus, Lisa","last_name":"Knaus"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"31","year":"2023","has_accepted_license":"1","date_created":"2023-06-01T09:05:24Z","doi":"10.15479/at:ista:13107","date_published":"2023-05-31T00:00:00Z","page":"147"},{"article_number":"A21","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"}],"citation":{"chicago":"Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2023.780.","ista":"Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. 974, A21.","mla":"Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics, vol. 974, A21, Cambridge University Press, 2023, doi:10.1017/jfm.2023.780.","ieee":"E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows,” Journal of Fluid Mechanics, vol. 974. Cambridge University Press, 2023.","short":"E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023).","apa":"Marensi, E., Yalniz, G., & Hof, B. (2023). Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2023.780","ama":"Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. 2023;974. doi:10.1017/jfm.2023.780"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena","orcid":"0000-0001-7173-4923"},{"full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2212.12406"],"isi":["001088363700001"]},"title":"Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH).","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"10","publication":"Journal of Fluid Mechanics","doi":"10.1017/jfm.2023.780","date_published":"2023-11-10T00:00:00Z","date_created":"2023-10-30T09:32:28Z","_id":"14466","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["turbulence","transition to turbulence","patterns"],"date_updated":"2024-02-15T09:06:23Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2024-02-15T09:05:21Z","abstract":[{"lang":"eng","text":"The first long-lived turbulent structures observable in planar shear flows take the form of localized stripes, inclined with respect to the mean flow direction. The dynamics of these stripes is central to transition, and recent studies proposed an analogy to directed percolation where the stripes’ proliferation is ultimately responsible for the turbulence becoming sustained. In the present study we focus on the internal stripe dynamics as well as on the eventual stripe expansion, and we compare the underlying mechanisms in pressure- and shear-driven planar flows, respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities of the overall laminar–turbulence patterns, the stripe proliferation processes in the two cases are fundamentally different. Starting from the growth and sustenance of individual stripes, we find that in plane-Couette flow new streaks are created stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation is deterministic and occurs locally at the downstream tip. Because of the up/downstream symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and two strong laminar turbulent interfaces. These differences in symmetry as well as in internal growth give rise to two fundamentally different stripe splitting mechanisms. In plane-Poiseuille flow splitting is connected to the elongational growth of the original stripe, and it results from a break-off/shedding of the stripe's tail. In plane-Couette flow splitting follows from a broadening of the original stripe and a division along the stripe into two slimmer stripes."}],"oa_version":"Published Version","month":"11","intvolume":" 974","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2024-02-15T09:05:21Z","file_size":2804641,"date_created":"2024-02-15T09:05:21Z","file_name":"2023_JourFluidMechanics_Marensi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"17c64c1fb0d5f73252364bf98b0b9e1a","file_id":"14996","success":1}],"language":[{"iso":"eng"}],"volume":974},{"department":[{"_id":"StFr"},{"_id":"GradSch"}],"title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","article_processing_charge":"Yes (via OA deal)","author":[{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","last_name":"Jethwa"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","first_name":"Soumyadip","full_name":"Mondal, Soumyadip","last_name":"Mondal"},{"last_name":"Pant","full_name":"Pant, Bhargavi","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","first_name":"Bhargavi"},{"orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2023. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition., e202316476.","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202316476.","ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 2023. doi:10.1002/anie.202316476","apa":"Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2023). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition (2023).","ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” Angewandte Chemie International Edition. Wiley, 2023.","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition, e202316476, Wiley, 2023, doi:10.1002/anie.202316476."},"date_updated":"2024-02-15T14:43:05Z","keyword":["General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"review","article_number":"e202316476","_id":"14687","date_created":"2023-12-15T16:10:13Z","doi":"10.1002/anie.202316476","date_published":"2023-12-14T00:00:00Z","publication":"Angewandte Chemie International Edition","language":[{"iso":"eng"}],"day":"14","publication_status":"epub_ahead","year":"2023","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"month":"12","oa":1,"main_file_link":[{"url":" https://doi.org/10.1002/anie.202316476","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","publisher":"Wiley","oa_version":"Published Version","abstract":[{"text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity.","lang":"eng"}]},{"month":"05","intvolume":" 62","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture."}],"related_material":{"record":[{"relation":"other","id":"14861","status":"public"},{"relation":"research_data","id":"12497","status":"public"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/","description":"News on ISTA website"}]},"issue":"19","volume":62,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14072","checksum":"7dd083ed8850faa55c34e411ed390de9","success":1,"date_updated":"2023-08-16T12:33:31Z","file_size":1422445,"creator":"dernst","date_created":"2023-08-16T12:33:31Z","file_name":"2023_AngewChemInt_Becker.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published","status":"public","keyword":["General Chemistry","Catalysis"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"12675","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"file_date_updated":"2023-08-16T12:33:31Z","ddc":["540"],"date_updated":"2024-02-21T12:14:06Z","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","date_published":"2023-05-01T00:00:00Z","doi":"10.1002/anie.202219314","date_created":"2023-02-24T10:45:01Z","day":"01","publication":"Angewandte Chemie International Edition","has_accepted_license":"1","isi":1,"year":"2023","article_number":"e202219314","title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","author":[{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","last_name":"Becker","full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151"},{"first_name":"Mélanie","full_name":"Berbon, Mélanie","last_name":"Berbon"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"first_name":"Estelle","full_name":"Morvan, Estelle","last_name":"Morvan"},{"full_name":"Bardiaux, Benjamin","last_name":"Bardiaux","first_name":"Benjamin"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman","first_name":"Roman"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"first_name":"Antoine","last_name":"Loquet","full_name":"Loquet, Antoine"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}],"external_id":{"isi":["000956919900001"],"pmid":["36738230"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314.","ieee":"L. M. Becker et al., “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte Chemie International Edition, vol. 62, no. 19. Wiley, 2023.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023).","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202219314","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314."}},{"day":"23","file":[{"date_created":"2023-03-23T10:03:16Z","file_name":"Research_Data.zip","date_updated":"2023-03-24T09:34:20Z","file_size":87018103,"creator":"lbecker","checksum":"fd9a28620a81a82991fb70f4fd6591d9","file_id":"12743","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"file_name":"README.txt","date_created":"2023-03-24T07:13:55Z","file_size":747,"date_updated":"2023-03-24T09:42:03Z","creator":"dernst","file_id":"12755","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","content_type":"text/plain","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","year":"2023","date_published":"2023-03-23T00:00:00Z","related_material":{"record":[{"id":"12675","status":"public","relation":"used_in_publication"}]},"doi":"10.15479/AT:ISTA:12497","contributor":[{"last_name":"Berbon","contributor_type":"researcher","first_name":"Mélanie"},{"last_name":"Vallet","first_name":"Alicia","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Axelle","last_name":"Grelard"},{"contributor_type":"researcher","first_name":"Estelle","last_name":"Morvan"},{"contributor_type":"researcher","first_name":"Benjamin","last_name":"Bardiaux"},{"last_name":"Lichtenecker","contributor_type":"researcher","first_name":"Roman"},{"first_name":"Matthias","contributor_type":"researcher","last_name":"Ernst"},{"first_name":"Antoine","contributor_type":"researcher","last_name":"Loquet"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","contributor_type":"contact_person","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"last_name":"Becker","orcid":"0000-0002-6401-5151","contributor_type":"researcher","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"}],"date_created":"2023-02-03T08:08:02Z","oa_version":"Published Version","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:14:06Z","citation":{"mla":"Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497","short":"L.M. Becker, P. Schanda, (2023).","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497."},"file_date_updated":"2023-03-24T09:42:03Z","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","author":[{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","_id":"12497","status":"public","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"}},{"department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"file_date_updated":"2024-01-30T14:28:30Z","ddc":["530"],"date_updated":"2024-02-21T12:19:08Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13314","ec_funded":1,"related_material":{"record":[{"status":"public","id":"13116","relation":"research_data"}]},"volume":19,"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-01-30T14:28:30Z","file_size":22471673,"date_created":"2024-01-30T14:28:30Z","file_name":"2023_NaturePhysics_Dunajova.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14916","checksum":"bc7673ca07d37309013a86166577b2f7","success":1}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"intvolume":" 19","month":"12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Chiral and nematic phases of flexible active filaments","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38075437"]},"author":[{"last_name":"Dunajova","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"full_name":"Prats Mateu, Batirtze","last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze"},{"last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lim, Keesiang","last_name":"Lim","first_name":"Keesiang"},{"full_name":"Brandis, Dörte","last_name":"Brandis","id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","first_name":"Dörte"},{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","full_name":"Wong, Richard W.","first_name":"Richard W."},{"first_name":"Jens","last_name":"Elgeti","full_name":"Elgeti, Jens"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","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.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","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.","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.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w."},"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"date_created":"2023-07-27T14:44:45Z","doi":"10.1038/s41567-023-02218-w","date_published":"2023-12-01T00:00:00Z","page":"1916-1926","publication":"Nature Physics","day":"01","year":"2023","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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)."},{"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14280","date_published":"2023-09-25T00:00:00Z","date_created":"2023-09-06T10:58:25Z","page":"156","day":"25","has_accepted_license":"1","year":"2023","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_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"},{"name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","author":[{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280."},"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","id":"11373","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7387","status":"public"},{"status":"public","id":"10934","relation":"research_data"}]},"ec_funded":1,"file":[{"date_updated":"2023-10-04T10:28:35Z","file_size":114932847,"creator":"pradler","date_created":"2023-10-04T10:11:53Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"87eef11fbc5c7df0826f12a3a629b444","file_id":"14390"},{"embargo":"2024-10-04","file_id":"14391","checksum":"3253e099b7126469d941fd9419d68b4f","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_created":"2023-10-04T10:11:21Z","creator":"pradler","file_size":37838778,"date_updated":"2023-10-04T10:28:35Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"publication_status":"published","degree_awarded":"PhD","status":"public","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14280","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"file_date_updated":"2023-10-04T10:28:35Z","ddc":["572"],"supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"date_updated":"2024-02-21T12:35:18Z"},{"citation":{"ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286","apa":"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. https://doi.org/10.15479/at:ista:13286","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.","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.","mla":"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, doi:10.15479/at:ista:13286.","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.","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. https://doi.org/10.15479/at:ista:13286."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Valentini","full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco"}],"article_processing_charge":"No","title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Conventional and unconventional topological superconductors","grant_number":"F8606"}],"has_accepted_license":"1","year":"2023","day":"21","page":"184","doi":"10.15479/at:ista:13286","date_published":"2023-07-21T00:00:00Z","date_created":"2023-07-24T14:10:45Z","publisher":"Institute of Science and Technology Austria","oa":1,"supervisor":[{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-21T12:35:34Z","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"GeKa"}],"file_date_updated":"2023-08-11T14:39:17Z","_id":"13286","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"mvalenti","file_size":56121429,"date_updated":"2023-08-11T10:01:34Z","file_name":"PhD_thesis_Valentini_final.zip","date_created":"2023-08-11T09:27:39Z","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","checksum":"666ee31c7eade89679806287c062fa14","file_id":"14033"},{"file_id":"14035","checksum":"0992f2ebef152dee8e70055350ebbb55","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"PhD_thesis_Valentini_final_validated.pdf","date_created":"2023-08-11T14:39:17Z","creator":"mvalenti","file_size":38199711,"date_updated":"2023-08-11T14:39:17Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"13312","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12118","status":"public"},{"status":"public","id":"8910","relation":"part_of_dissertation"},{"relation":"research_data","id":"12522","status":"public"}]},"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"07"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169. doi:10.1007/978-3-031-37706-8_8","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8","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 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 156–169.","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.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.","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.","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 35th International Conference on Computer Aided Verification , 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8."},"title":"Lincheck: A practical framework for testing concurrent data structures on JVM","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita"},{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander","last_name":"Fedorov"},{"first_name":"Maria","full_name":"Sokolova, Maria","last_name":"Sokolova"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"publication":"35th International Conference on Computer Aided Verification ","day":"17","year":"2023","has_accepted_license":"1","date_created":"2023-09-03T22:01:16Z","date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37706-8_8","page":"156-169","oa":1,"publisher":"Springer Nature","quality_controlled":"1","ddc":["000"],"date_updated":"2024-02-27T07:46:52Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"file_date_updated":"2023-09-06T08:16:25Z","_id":"14260","status":"public","conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","location":"Paris, France","end_date":"2023-07-22"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","language":[{"iso":"eng"}],"file":[{"file_size":421408,"date_updated":"2023-09-06T08:16:25Z","creator":"dernst","file_name":"2023_LNCS_Koval.pdf","date_created":"2023-09-06T08:16:25Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14275","checksum":"c346016393123a0a2338ad4d976f61bc"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"related_material":{"record":[{"id":"14995","status":"public","relation":"research_data"}]},"volume":13964,"oa_version":"Published Version","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."}],"intvolume":" 13964","month":"07","alternative_title":["LNCS"],"scopus_import":"1"},{"status":"public","type":"dissertation","_id":"13984","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"file_date_updated":"2024-03-01T12:58:14Z","ddc":["570","577"],"date_updated":"2024-03-01T15:25:17Z","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-08-08","file_id":"13986","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","file_size":10797612,"date_updated":"2024-03-01T08:51:42Z","creator":"afransch","file_name":"Thesis_AnnaFranschitz_202308.pdf","date_created":"2023-08-08T18:01:28Z"},{"creator":"afransch","date_updated":"2023-08-09T07:25:27Z","file_size":2619085,"date_created":"2023-08-08T18:02:25Z","file_name":"Thesis_AnnaFranschitz_202308.docx","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"13987","checksum":"40abf7ccca14a3893f72dc7fb88585d6"},{"file_name":"Addendum_AnnaFranschitz202402.pdf","title":"Addendum","date_created":"2024-03-01T08:37:15Z","creator":"cchlebak","file_size":85956,"date_updated":"2024-03-01T12:13:29Z","embargo":"2024-08-08","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","file_id":"15042","relation":"erratum","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","description":"Minor modifications and clarifications - Feb 2024"},{"file_name":"Addendum_AnnaFranschitz202402.docx","title":"Addendum - source file","date_created":"2024-03-01T08:39:20Z","file_size":11818,"date_updated":"2024-03-01T08:51:42Z","creator":"cchlebak","file_id":"15043","checksum":"66745aa01f960f17472c024875c049ed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"file_id":"15044","checksum":"55c876b73d49db15228a7f571592ec77","content_type":"application/pdf","description":"For printing purposes","access_level":"closed","relation":"other","title":"Print Version","date_created":"2024-03-01T08:56:06Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","date_updated":"2024-03-01T12:58:14Z","file_size":10416761,"creator":"cchlebak"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663 - 337X"]},"title":"Individual and social immunity against viral infections in ants","article_processing_charge":"No","author":[{"full_name":"Franschitz, Anna","last_name":"Franschitz","id":"480826C8-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","short":"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:10.15479/at:ista:13984","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984"},"publisher":"Institute of Science and Technology Austria","date_created":"2023-08-08T15:33:29Z","doi":"10.15479/at:ista:13984","date_published":"2023-08-08T00:00:00Z","page":"89","day":"08","year":"2023","has_accepted_license":"1"},{"day":"10","publication":"arXiv","language":[{"iso":"eng"}],"year":"2023","publication_status":"submitted","doi":"10.48550/ARXIV.2311.06103","date_published":"2023-11-10T00:00:00Z","date_created":"2024-02-28T17:59:32Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system's inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL."}],"month":"11","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.06103","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-04T07:02:39Z","citation":{"ista":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103.","chicago":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2311.06103.","apa":"Prach, B., & Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. arXiv. https://doi.org/10.48550/ARXIV.2311.06103","ama":"Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv. doi:10.48550/ARXIV.2311.06103","ieee":"B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” arXiv. .","short":"B. Prach, C. Lampert, ArXiv (n.d.).","mla":"Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, 2311.06103, doi:10.48550/ARXIV.2311.06103."},"title":"1-Lipschitz neural networks are more expressive with N-activations","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"author":[{"first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","last_name":"Prach"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"article_processing_charge":"No","external_id":{"arxiv":["2311.06103"]},"article_number":"2311.06103","_id":"15039","status":"public","type":"preprint"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323.","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","mla":"Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323","apa":"Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323"},"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","author":[{"last_name":"Kuzmicz-Kowalska","full_name":"Kuzmicz-Kowalska, Katarzyna","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"day":"13","has_accepted_license":"1","year":"2023","date_published":"2023-09-13T00:00:00Z","doi":"10.15479/at:ista:14323","date_created":"2023-09-13T10:07:18Z","page":"151","publisher":"Institute of Science and Technology Austria","ddc":["570"],"supervisor":[{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-07T15:02:59Z","file_date_updated":"2023-09-13T10:08:25Z","department":[{"_id":"GradSch"},{"_id":"AnKi"}],"_id":"14323","status":"public","type":"dissertation","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"file":[{"access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","checksum":"bd83596869c814b24aeff7077d031c0e","file_id":"14324","embargo":"2025-03-13","creator":"kkuzmicz","date_updated":"2023-09-13T10:08:25Z","file_size":10147911,"date_created":"2023-09-13T09:52:52Z","file_name":"PhDThesis_KK_final_pdfA.pdf"},{"date_created":"2023-09-13T09:53:29Z","file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2023-09-13T09:53:29Z","file_size":103980668,"creator":"kkuzmicz","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","file_id":"14325","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7883"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"]},{"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","first_name":"Mike","full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen"}],"title":"Adaptive mutation in E. coli modulated by luxS","publisher":"Institute of Science and Technology Austria","year":"2023","has_accepted_license":"1","day":"30","page":"104","date_created":"2023-12-04T13:17:37Z","date_published":"2023-11-30T00:00:00Z","doi":"10.15479/at:ista:14641","_id":"14641","type":"dissertation","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"status":"public","date_updated":"2024-03-22T13:21:17Z","supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2024-03-20T13:19:36Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/vnd.oasis.opendocument.text","access_level":"closed","relation":"source_file","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","file_id":"14648","date_updated":"2023-12-06T13:13:26Z","file_size":46405919,"creator":"mhenness","date_created":"2023-12-06T13:13:26Z","file_name":"mike_thesis_v06-12-2023.odt"},{"checksum":"f5203a61eddaf35235bbc51904d73982","file_id":"14649","embargo":"2024-11-30","access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","date_created":"2023-12-06T13:14:15Z","file_name":"mike_thesis_v06-12-2023.pdf","creator":"mhenness","date_updated":"2023-12-06T13:14:15Z","file_size":21282155},{"content_type":"application/pdf","access_level":"closed","relation":"other","file_id":"15145","checksum":"9f7b4d646f1cfb57e3b9106a8a9cdd9d","date_updated":"2024-03-20T13:19:36Z","file_size":2930287,"creator":"cchlebak","date_created":"2024-03-20T13:19:36Z","file_name":"2023_Hennessey_Michael_Thesis_from_source.pdf"}],"ec_funded":1},{"ddc":["515"],"supervisor":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}],"date_updated":"2024-03-22T13:21:28Z","file_date_updated":"2024-03-20T12:28:32Z","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"_id":"14587","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"creator":"amarvegg","file_size":2881100,"date_updated":"2023-11-29T09:09:31Z","file_name":"thesis_Marveggio.pdf","date_created":"2023-11-29T09:09:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14626","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4"},{"file_id":"14627","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis_Marveggio.zip","date_created":"2023-11-29T09:10:19Z","creator":"amarvegg","file_size":10189696,"date_updated":"2024-03-20T12:28:32Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"11842","status":"public","relation":"part_of_dissertation"},{"id":"14597","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}],"month":"11","alternative_title":["ISTA Thesis"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria."},"title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","author":[{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice","last_name":"Marveggio"}],"article_processing_charge":"No","project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"day":"21","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:14587","date_published":"2023-11-21T00:00:00Z","date_created":"2023-11-21T11:41:05Z","page":"228","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","publisher":"Institute of Science and Technology Austria","oa":1},{"abstract":[{"lang":"eng","text":"We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\\zeta)$ and a general class of related quantities involving two resolvents\r\nat nearby spectral parameters. "}],"oa_version":"Preprint","acknowledgement":"Supported by the ERC Advanced Grant ”RMTBeyond” No. 101020331","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01712"}],"oa":1,"month":"01","year":"2023","publication_status":"submitted","day":"04","language":[{"iso":"eng"}],"publication":"arXiv","date_published":"2023-01-04T00:00:00Z","doi":"10.48550/arXiv.2301.01712","ec_funded":1,"date_created":"2024-03-20T09:41:04Z","_id":"15128","article_number":"2301.01712","type":"preprint","status":"public","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"citation":{"ista":"Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. arXiv, 2301.01712.","chicago":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2301.01712.","short":"V. Riabov, ArXiv (n.d.).","ieee":"V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” arXiv. .","apa":"Riabov, V. (n.d.). Mesoscopic eigenvalue statistics for Wigner-type matrices. arXiv. https://doi.org/10.48550/arXiv.2301.01712","ama":"Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. arXiv. doi:10.48550/arXiv.2301.01712","mla":"Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.” ArXiv, 2301.01712, doi:10.48550/arXiv.2301.01712."},"date_updated":"2024-03-25T12:48:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","first_name":"Volodymyr","last_name":"Riabov","full_name":"Riabov, Volodymyr"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.01712"]},"title":"Mesoscopic eigenvalue statistics for Wigner-type matrices","department":[{"_id":"GradSch"},{"_id":"LaEr"}]},{"type":"dissertation","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"status":"public","_id":"12491","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"file_date_updated":"2024-02-08T23:30:04Z","date_updated":"2024-03-25T23:30:05Z","supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"02","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"8586","status":"public"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12527","checksum":"069d87f025e0799bf9e3c375664264f2","embargo":"2024-02-07","creator":"bzens","date_updated":"2024-02-08T23:30:04Z","file_size":23082464,"date_created":"2023-02-07T13:07:38Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf"},{"file_id":"12528","checksum":"8c66ed203495d6e078ed1002a866520c","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"PhDThesis_BettinaZens_2023_final.docx","date_created":"2023-02-07T13:09:05Z","file_size":106169509,"date_updated":"2024-02-08T23:30:04Z","creator":"bzens"}],"project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"article_processing_charge":"No","author":[{"full_name":"Zens, Bettina","orcid":"0000-0002-9561-1239","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina"}],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","citation":{"mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"publisher":"Institute of Science and Technology Austria","page":"187","date_created":"2023-02-02T14:50:20Z","date_published":"2023-02-02T00:00:00Z","doi":"10.15479/at:ista:12491","year":"2023","has_accepted_license":"1","day":"02"},{"month":"08","alternative_title":["ISTA Master's Thesis"],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"14227","checksum":"453caf851d75c3478c10ed09bd242a91","creator":"cchlebak","file_size":15501411,"date_updated":"2024-02-26T23:30:03Z","file_name":"documents-export-2023-08-24.zip","date_created":"2023-08-24T13:02:49Z"},{"date_created":"2023-08-24T13:03:42Z","file_name":"thesis_pdf_a.pdf","creator":"cchlebak","date_updated":"2024-02-26T23:30:03Z","file_size":6854783,"file_id":"14228","checksum":"7349d29963d6695e555e171748648d9a","embargo":"2024-02-25","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"degree_awarded":"MS","publication_status":"published","publication_identifier":{"issn":["2791-4585"]},"status":"public","type":"dissertation","_id":"14226","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file_date_updated":"2024-02-26T23:30:03Z","ddc":["500"],"date_updated":"2024-02-26T23:30:04Z","supervisor":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-08-24T13:01:18Z","doi":"10.15479/at:ista:14226","date_published":"2023-08-24T00:00:00Z","page":"43","day":"24","year":"2023","has_accepted_license":"1","title":"Generalizing medial axes with homology switches","article_processing_charge":"No","author":[{"orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226."}},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 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Institute of Science and Technology Austria.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470."},"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","article_processing_charge":"No","author":[{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"day":"09","year":"2023","has_accepted_license":"1","date_created":"2023-01-31T15:10:53Z","date_published":"2023-01-09T00:00:00Z","doi":"10.15479/at:ista:12470","page":"201","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["610"],"date_updated":"2023-08-31T12:26:58Z","supervisor":[{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"file_date_updated":"2023-07-27T22:30:54Z","_id":"12470","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_created":"2023-01-31T15:11:42Z","file_name":"20230109_PhD_thesis_JM_final.pdf","creator":"cchlebak","date_updated":"2023-07-27T22:30:54Z","file_size":41771714,"checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_id":"12471","embargo":"2023-07-09","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_id":"12472","checksum":"0bebbdee0773443959e1f6ab8caf281f","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2023-01-31T15:11:51Z","file_name":"20230109_PhD_thesis_JM_final.docx","creator":"cchlebak","date_updated":"2023-07-10T22:30:04Z","file_size":66983464}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11943"},{"relation":"part_of_dissertation","id":"11950","status":"public"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"month":"01","alternative_title":["ISTA Thesis"]},{"article_processing_charge":"No","author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia","full_name":"Kirillova, Kseniia","last_name":"Kirillova"}],"title":"Panoramic functional gradients across the mouse retina","citation":{"ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"46","date_created":"2023-02-09T07:45:05Z","doi":"10.15479/at:ista:12531","date_published":"2023-02-08T00:00:00Z","year":"2023","has_accepted_license":"1","day":"08","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-02-09T23:30:03Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2024-02-09T23:30:04Z","supervisor":[{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","_id":"12531","degree_awarded":"MS","publication_status":"published","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"file":[{"creator":"cchlebak","date_updated":"2024-02-09T23:30:03Z","file_size":8369317,"date_created":"2023-02-09T08:03:32Z","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"12532","checksum":"57d8da3a6c749eb1556b7435fe266a5f","embargo":"2024-02-08"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/x-zip-compressed","file_id":"12535","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","creator":"cchlebak","file_size":11204408,"date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","date_created":"2023-02-10T09:32:06Z"}],"alternative_title":["ISTA Master's Thesis"],"month":"02","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"oa_version":"Published Version"},{"oa":1,"publisher":"Institute of Science and Technology Austria","day":"05","year":"2023","has_accepted_license":"1","date_created":"2023-04-04T18:57:11Z","date_published":"2023-04-05T00:00:00Z","doi":"10.15479/at:ista:12800","page":"21","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023."},"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","article_processing_charge":"No","author":[{"full_name":"Julseth, Mara","last_name":"Julseth","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1"}],"oa_version":"Published Version","abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. 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Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"ddc":["516","004","518","531"],"supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-01-29T10:47:51Z","file_date_updated":"2023-12-08T23:30:04Z","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"_id":"12897","status":"public","type":"dissertation","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12942","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","embargo":"2023-12-07","date_updated":"2023-12-08T23:30:04Z","file_size":50714445,"creator":"chafner","date_created":"2023-05-11T10:43:20Z","file_name":"thesis-hafner-2023may11-a2b.pdf"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","checksum":"a6b51334be2b81672357b1549afab40c","file_id":"12943","creator":"chafner","file_size":265319,"date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-release-form.pdf","date_created":"2023-05-11T10:43:44Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"9817","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7117"},{"id":"13188","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}],"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"05","alternative_title":["ISTA Thesis"],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12897.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","mla":"Hafner, Christian. Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12897.","apa":"Hafner, C. (2023). Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12897","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:10.15479/at:ista:12897","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023."},"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"article_processing_charge":"No","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"day":"05","has_accepted_license":"1","year":"2023","date_published":"2023-05-05T00:00:00Z","doi":"10.15479/at:ista:12897","date_created":"2023-05-05T10:40:14Z","page":"180","publisher":"Institute of Science and Technology Austria","oa":1}]