[{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"OA_place":"publisher","oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/at:ista:12826","supervisor":[{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"_id":"12826","publication_status":"published","date_published":"2023-04-18T00:00:00Z","month":"04","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","article_processing_charge":"No","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"ec_funded":1,"citation":{"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.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","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.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","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","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023."},"type":"dissertation","doi":"10.15479/at:ista:12826","file_date_updated":"2023-04-20T09:26:51Z","status":"public","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria"}],"ddc":["570","571"],"corr_author":"1","alternative_title":["ISTA Thesis"],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2023-04-14T14:56:04Z","year":"2023","page":"106","license":"https://creativecommons.org/licenses/by/4.0/","day":"18","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","date_updated":"2026-04-07T13:26:49Z","language":[{"iso":"eng"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file":[{"file_size":14507243,"relation":"source_file","file_name":"Thesis_Pokusaeva.docx","date_updated":"2023-04-20T09:26:51Z","access_level":"closed","file_id":"12857","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vpokusae","checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z"},{"relation":"main_file","file_size":10090711,"content_type":"application/pdf","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"creator":"vpokusae","file_id":"12858","date_created":"2023-04-20T09:14:44Z","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","date_updated":"2023-04-20T09:14:44Z"}]},{"year":"2023","month":"04","date_published":"2023-04-26T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"14505"},{"id":"12890","status":"public","relation":"used_in_publication"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","title":"Research data for: A stochastic cellular automaton model of culture formation","date_updated":"2025-09-09T12:26:01Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"day":"26","citation":{"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.","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869","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","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.","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.","short":"F.R. Klausen, A.B. Lauritsen, (2023)."},"file":[{"date_created":"2023-04-26T12:30:06Z","success":1,"checksum":"85ede12d38bb8d944022a8cba4d719f5","content_type":"application/octet-stream","creator":"alaurits","file_id":"12870","access_level":"open_access","date_updated":"2023-04-26T12:30:06Z","file_name":"README.md","relation":"main_file","file_size":4567},{"relation":"main_file","file_size":732586731,"date_created":"2023-04-26T12:27:34Z","file_id":"12871","creator":"alaurits","checksum":"25bf79452ae895f9c8a20571a096b4c3","content_type":"application/x-zip-compressed","success":1,"date_updated":"2023-04-26T12:27:34Z","file_name":"simulations_era=10_flux_varied_europe.zip","access_level":"open_access"},{"file_size":1743893150,"relation":"main_file","date_updated":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","access_level":"open_access","date_created":"2023-04-26T12:29:53Z","file_id":"12872","checksum":"bca48d80ece73eb169aee7211a4a751a","success":1,"creator":"alaurits","content_type":"application/x-zip-compressed"},{"relation":"main_file","file_size":878391851,"success":1,"creator":"alaurits","checksum":"e77a655db15486a387a36362fbf0b665","content_type":"application/x-zip-compressed","file_id":"12873","date_created":"2023-04-26T12:29:19Z","access_level":"open_access","file_name":"simulations_era=10_R_varied_torus.zip","date_updated":"2023-04-26T12:29:19Z"},{"relation":"main_file","file_size":201652478,"date_created":"2023-04-26T12:30:05Z","file_id":"12874","creator":"alaurits","content_type":"application/x-zip-compressed","success":1,"checksum":"8556406513adc4aa2e0417f46680f627","date_updated":"2023-04-26T12:30:05Z","file_name":"simulations_era=100.zip","access_level":"open_access"}],"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 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. "}],"status":"public","doi":"10.15479/AT:ISTA:12869","file_date_updated":"2023-04-26T12:30:06Z","type":"research_data","has_accepted_license":"1","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"publisher":"Institute of Science and Technology Austria","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:12869","ddc":["000"],"author":[{"full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn","last_name":"Klausen"},{"full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288"}],"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. ","_id":"12869","date_created":"2023-04-26T12:34:49Z"},{"date_created":"2023-05-04T08:35:01Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"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.","issue":"5","author":[{"full_name":"Klausen, Frederik Ravn","last_name":"Klausen","first_name":"Frederik Ravn"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"}],"corr_author":"1","type":"journal_article","status":"public","doi":"10.1103/PhysRevE.108.054307","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."}],"article_number":"054307","day":"08","date_updated":"2025-09-09T12:26:01Z","title":"Stochastic cellular automaton model of culture formation","oa_version":"Preprint","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2305.02153"],"isi":["001106396300005"],"pmid":["38115445"]},"year":"2023","publication":"Physical Review E","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"_id":"12890","pmid":1,"fulldoi":"https://doi.org/10.1103/PhysRevE.108.054307","publisher":"American Physical Society","scopus_import":"1","oa":1,"arxiv":1,"volume":108,"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.","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","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.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” Physical Review E, vol. 108, no. 5. American Physical Society, 2023."},"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"status":"public","id":"12869","relation":"research_data"}]},"date_published":"2023-11-08T00:00:00Z","publication_status":"published","month":"11"},{"ddc":["537","535","539"],"author":[{"full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"alternative_title":["ISTA Thesis"],"corr_author":"1","date_created":"2023-05-05T11:08:50Z","type":"dissertation","status":"public","file_date_updated":"2023-07-06T11:37:40Z","doi":"10.15479/at:ista:12900","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"date_updated":"2026-04-15T06:43:26Z","title":"Cavity quantum electrooptics","day":"05","language":[{"iso":"eng"}],"oa_version":"Published Version","file":[{"file_size":36767177,"relation":"source_file","access_level":"closed","file_name":"thesis.zip","date_updated":"2023-06-06T22:30:03Z","embargo_to":"open_access","date_created":"2023-05-09T08:45:14Z","checksum":"8cbdab9c37ee55e591092a6f66b272c4","creator":"rsahu","content_type":"application/x-zip-compressed","file_id":"12928"},{"date_updated":"2023-07-06T11:37:40Z","file_name":"thesis_pdfa_final.pdf","access_level":"closed","date_created":"2023-05-09T08:51:17Z","file_id":"12929","content_type":"application/pdf","creator":"rsahu","checksum":"439659ead46618147309be39d9dd5a8c","file_size":17501990,"relation":"main_file"}],"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"}],"year":"2023","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"page":"190","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","fulldoi":"https://doi.org/10.15479/at:ista:12900","supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-030-5"]},"_id":"12900","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"article_processing_charge":"No","citation":{"ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:12900","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12900.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12900","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12900.","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."},"ec_funded":1,"date_published":"2023-05-05T00:00:00Z","publication_status":"published","month":"05","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"13175","relation":"new_edition"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9114","status":"public"}]}},{"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"article_processing_charge":"No","day":"15","date_updated":"2026-04-07T13:25:33Z","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","oa_version":"Published Version","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\"."}],"file":[{"relation":"main_file","file_size":8029982,"file_id":"12934","content_type":"text/csv","success":1,"creator":"gpuixeus","checksum":"0ba0bcd0bb8b18d84792136a4370df90","date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S1.csv","date_updated":"2023-05-10T09:41:43Z","access_level":"open_access"},{"relation":"main_file","file_size":13667640,"date_created":"2023-05-10T09:41:43Z","file_id":"12935","checksum":"a62aa9a6d4904e0fdb699cf752640863","creator":"gpuixeus","content_type":"text/csv","success":1,"file_name":"Dataset_S2.csv","date_updated":"2023-05-10T09:41:43Z","access_level":"open_access"},{"date_updated":"2023-05-10T09:41:48Z","file_name":"Dataset_S3.csv","access_level":"open_access","date_created":"2023-05-10T09:41:48Z","file_id":"12936","success":1,"creator":"gpuixeus","content_type":"text/csv","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","file_size":8369141,"relation":"main_file"},{"relation":"main_file","file_size":19543247,"file_id":"12937","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","success":1,"creator":"gpuixeus","content_type":"text/csv","date_created":"2023-05-10T09:41:50Z","date_updated":"2023-05-10T09:41:50Z","file_name":"Dataset_S4.csv","access_level":"open_access"},{"checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","content_type":"text/plain","creator":"gpuixeus","success":1,"file_id":"12944","date_created":"2023-05-11T12:50:18Z","access_level":"open_access","file_name":"readme.txt","date_updated":"2023-05-11T12:50:18Z","relation":"main_file","file_size":4566}],"citation":{"short":"G. Puixeu Sala, (2023).","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","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.","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.","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.","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"},"date_published":"2023-05-15T00:00:00Z","month":"05","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14077"},{"id":"14058","status":"public","relation":"used_in_publication"}]},"contributor":[{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:12933","corr_author":"1","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2023-05-10T10:00:49Z","_id":"12933","type":"research_data","doi":"10.15479/AT:ISTA:12933","file_date_updated":"2023-05-11T12:50:18Z","status":"public","oa":1,"has_accepted_license":"1"},{"abstract":[{"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 .","lang":"eng"}],"file":[{"access_level":"open_access","date_updated":"2024-07-22T09:09:45Z","file_name":"2023_ICLR_Peste.pdf","date_created":"2024-07-22T09:09:45Z","checksum":"a6eec897e13a91cdc3eeaf309801752c","content_type":"application/pdf","creator":"dernst","success":1,"file_id":"17294","file_size":458201,"relation":"main_file"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","date_updated":"2026-04-07T13:30:19Z","title":"CrAM: A Compression-Aware Minimizer","quality_controlled":"1","year":"2023","external_id":{"arxiv":["2207.14200"]},"main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"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).","date_created":"2023-05-23T11:36:18Z","corr_author":"1","author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","last_name":"Peste","full_name":"Peste, Elena-Alexandra"},{"full_name":"Vladu, Adrian","first_name":"Adrian","last_name":"Vladu"},{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar","last_name":"Kurtic","full_name":"Kurtic, Eldar"},{"full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"acknowledged_ssus":[{"_id":"ScienComp"}],"conference":{"end_date":"2023-05-05","location":"Kigali, Rwanda ","name":"ICLR: International Conference on Learning Representations","start_date":"2023-05-01"},"status":"public","file_date_updated":"2024-07-22T09:09:45Z","type":"conference","ec_funded":1,"citation":{"ieee":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda , 2023.","short":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , OpenReview, 2023.","apa":"Krumes, A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (2023). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda : OpenReview.","ista":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. 2023. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","mla":"Krumes, Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations , OpenReview, 2023.","ama":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations . OpenReview; 2023.","chicago":"Krumes, Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations . OpenReview, 2023."},"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"article_processing_charge":"No","related_material":{"record":[{"id":"13074","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://github.com/IST-DASLab/CrAM","relation":"software"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","date_published":"2023-05-01T00:00:00Z","publication_status":"published","_id":"13053","publication":"11th International Conference on Learning Representations ","publisher":"OpenReview","has_accepted_license":"1","oa":1,"arxiv":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}]},{"month":"05","publication_status":"published","date_published":"2023-05-31T00:00:00Z","degree_awarded":"PhD","related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"citation":{"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.","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","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.","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.","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","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."},"ec_funded":1,"OA_place":"publisher","project":[{"call_identifier":"H2020","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"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets","call_identifier":"FWF"}],"has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","fulldoi":"https://doi.org/10.15479/at:ista:13107","supervisor":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"}],"publication_identifier":{"issn":["2663-337X"]},"_id":"13107","year":"2023","page":"147","language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2026-04-14T08:34:36Z","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","day":"31","file":[{"file_size":12991551,"relation":"source_file","file_name":"Thesis_Lisa Knaus_approved_final.docx","date_updated":"2023-06-01T13:48:41Z","access_level":"closed","date_created":"2023-06-01T13:48:41Z","file_id":"13112","creator":"lknaus","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3"},{"file_size":9309015,"relation":"main_file","access_level":"open_access","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","date_updated":"2023-06-07T08:41:49Z","date_created":"2023-06-02T09:47:29Z","content_type":"application/pdf","creator":"lknaus","checksum":"6903d152aa01181d87a696085af31c83","file_id":"13114"}],"abstract":[{"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.","lang":"eng"}],"doi":"10.15479/at:ista:13107","file_date_updated":"2023-06-07T08:41:49Z","status":"public","type":"dissertation","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","ddc":["570"],"author":[{"full_name":"Knaus, Lisa","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus"}],"date_created":"2023-06-01T09:05:24Z"},{"external_id":{"isi":["001011963000001"],"arxiv":["2106.07328"]},"year":"2023","isi":1,"page":"1280-1295","quality_controlled":"1","day":"01","date_updated":"2026-04-08T13:04:49Z","title":"An energy decomposition theorem for matrices and related questions","language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":" 66","abstract":[{"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\r\nmax{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 \r\nWe also study some related questions on moderate expanders over matrix rings, namely, for 𝐴,𝐵,𝐶 ⊆𝐺𝐿2(𝔽𝑞), we have\r\n|𝐴𝐵+𝐶|, |(𝐴+𝐵)𝐶|≫𝑞4,\r\n 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).","lang":"eng"}],"type":"journal_article","doi":"10.4153/S000843952300036X","status":"public","author":[{"full_name":"Mohammadi, Ali","last_name":"Mohammadi","first_name":"Ali"},{"full_name":"Pham, Thang","last_name":"Pham","first_name":"Thang"},{"full_name":"Wang, Yiting","first_name":"Yiting","id":"1917d194-076e-11ed-97cd-837255f88785","orcid":"0000-0002-2856-767X","last_name":"Wang"}],"date_created":"2023-06-11T22:00:40Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"issue":"4","publication_status":"published","date_published":"2023-12-01T00:00:00Z","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","department":[{"_id":"GradSch"}],"article_processing_charge":"No","volume":66,"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.","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","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","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.","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.","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"},"arxiv":1,"oa":1,"fulldoi":"https://doi.org/10.4153/S000843952300036X","scopus_import":"1","publisher":"Cambridge University Press","publication":"Canadian Mathematical Bulletin","_id":"13128","publication_identifier":{"issn":["0008-4395"],"eissn":["1496-4287"]}},{"publication":"Physical Review B","_id":"13138","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"fulldoi":"https://doi.org/10.1103/PhysRevB.107.184312","publisher":"American Physical Society","scopus_import":"1","oa":1,"arxiv":1,"volume":107,"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).","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.","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","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.","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.","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"},"article_processing_charge":"No","department":[{"_id":"GradSch"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2023-05-01T00:00:00Z","publication_status":"published","month":"05","date_created":"2023-06-18T22:00:46Z","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. ","issue":"18","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.00729","open_access":"1"}],"author":[{"full_name":"Orlov, Pavel","first_name":"Pavel","last_name":"Orlov"},{"last_name":"Tiutiakina","first_name":"Anastasiia","full_name":"Tiutiakina, Anastasiia"},{"full_name":"Sharipov, Rustem","last_name":"Sharipov","first_name":"Rustem"},{"first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","full_name":"Petrova, Elena"},{"full_name":"Gritsev, Vladimir","first_name":"Vladimir","last_name":"Gritsev"},{"full_name":"Kurlov, Denis V.","last_name":"Kurlov","first_name":"Denis V."}],"type":"journal_article","status":"public","doi":"10.1103/PhysRevB.107.184312","intvolume":" 107","article_number":"184312","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-08-02T06:16:02Z","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","day":"01","language":[{"iso":"eng"}],"oa_version":"Preprint","isi":1,"quality_controlled":"1","external_id":{"isi":["001003686900004"],"arxiv":["2303.00729"]},"year":"2023"},{"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1038/s41598-023-35979-8","scopus_import":"1","publisher":"Springer Nature","publication":"Scientific Reports","_id":"13166","publication_identifier":{"eissn":["2045-2322"]},"pmid":1,"publication_status":"published","date_published":"2023-06-09T00:00:00Z","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","department":[{"_id":"GradSch"}],"article_processing_charge":"No","volume":13,"citation":{"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.","short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (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.","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","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.","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"},"type":"journal_article","doi":"10.1038/s41598-023-35979-8","status":"public","file_date_updated":"2023-06-26T09:58:53Z","ddc":["570"],"author":[{"full_name":"Vetrova, Alexandra A.","first_name":"Alexandra A.","last_name":"Vetrova"},{"full_name":"Kupaeva, Daria M.","first_name":"Daria M.","last_name":"Kupaeva"},{"full_name":"Kizenko, Alena","first_name":"Alena","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","last_name":"Kizenko"},{"full_name":"Lebedeva, Tatiana S.","last_name":"Lebedeva","first_name":"Tatiana S."},{"first_name":"Peter","last_name":"Walentek","full_name":"Walentek, Peter"},{"first_name":"Nikoloz","last_name":"Tsikolia","full_name":"Tsikolia, Nikoloz"},{"full_name":"Kremnyov, Stanislav V.","first_name":"Stanislav V.","last_name":"Kremnyov"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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.).","external_id":{"pmid":["37296138"],"isi":["001006690200045"]},"year":"2023","isi":1,"quality_controlled":"1","title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","date_updated":"2023-08-02T06:17:18Z","day":"09","language":[{"iso":"eng"}],"oa_version":"Published Version","intvolume":" 13","file":[{"date_created":"2023-06-26T09:58:53Z","success":1,"content_type":"application/pdf","checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","creator":"dernst","file_id":"13170","access_level":"open_access","date_updated":"2023-06-26T09:58:53Z","file_name":"2023_ScientificReports_Vetrova.pdf","relation":"main_file","file_size":4844149}],"article_number":"9382","abstract":[{"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.","lang":"eng"}]},{"citation":{"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.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175."},"ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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"}]},"degree_awarded":"PhD","date_published":"2023-05-05T00:00:00Z","publication_status":"published","month":"05","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663-337X"]},"_id":"13175","fulldoi":"https://doi.org/10.15479/at:ista:13175","supervisor":[{"orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"OA_place":"publisher","file":[{"access_level":"open_access","date_updated":"2023-06-30T08:17:25Z","file_name":"thesis_pdfa.pdf","creator":"cchlebak","content_type":"application/pdf","success":1,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","file_id":"13176","date_created":"2023-06-30T08:17:25Z","file_size":18688376,"relation":"main_file"},{"file_name":"thesis.zip","date_updated":"2023-07-06T11:35:15Z","access_level":"closed","date_created":"2023-07-06T11:35:15Z","file_id":"13196","content_type":"application/x-zip-compressed","checksum":"c3b45317ae58e0527533f98c202d81b7","creator":"cchlebak","file_size":37847025,"relation":"source_file"}],"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"}],"date_updated":"2026-04-15T06:43:26Z","title":"Cavity quantum electrooptics","day":"05","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"202","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"year":"2023","date_created":"2023-06-30T08:07:43Z","ddc":["537","535","539"],"author":[{"full_name":"Sahu, Rishabh","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","last_name":"Sahu"}],"alternative_title":["ISTA Thesis"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"corr_author":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"type":"dissertation","doi":"10.15479/at:ista:13175","file_date_updated":"2023-07-06T11:35:15Z","status":"public"},{"year":"2023","external_id":{"arxiv":["2201.08090"],"isi":["000997933500008"]},"quality_controlled":"1","page":"1507–1540","isi":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","date_updated":"2026-04-07T13:27:39Z","title":"Boundary superconductivity in the BCS model","day":"18","file":[{"date_created":"2023-07-11T08:19:15Z","checksum":"5501da33be010b5c81440438287584d5","content_type":"application/pdf","creator":"alisjak","success":1,"file_id":"13208","access_level":"open_access","file_name":"2023_EMS_Hainzl.pdf","date_updated":"2023-07-11T08:19:15Z","relation":"main_file","file_size":304619}],"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"}],"intvolume":" 12","doi":"10.4171/JST/439","file_date_updated":"2023-07-11T08:19:15Z","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","ddc":["530"],"author":[{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","first_name":"Barbara","last_name":"Roos","orcid":"0000-0002-9071-5880","full_name":"Roos, Barbara"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert"}],"issue":"4","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.","date_created":"2023-07-10T16:35:45Z","month":"05","publication_status":"published","date_published":"2023-05-18T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"14374","status":"public"}]},"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"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.","ista":"Hainzl C, Roos B, Seiringer R. 2023. Boundary superconductivity in the BCS model. Journal of Spectral Theory. 12(4), 1507–1540.","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","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.","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."},"ec_funded":1,"volume":12,"arxiv":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"scopus_import":"1","publisher":"EMS Press","fulldoi":"https://doi.org/10.4171/JST/439","_id":"13207","publication_identifier":{"issn":["1664-039X"],"eissn":["1664-0403"]},"publication":"Journal of Spectral Theory"},{"oa":1,"has_accepted_license":"1","arxiv":1,"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","publication_identifier":{"isbn":["9781450395458"]},"_id":"13262","fulldoi":"https://doi.org/10.1145/3558481.3591082","publisher":"Association for Computing Machinery","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","date_published":"2023-06-17T00:00:00Z","month":"06","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.","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","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.","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","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.","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.","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."},"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"conference":{"end_date":"2023-06-19","start_date":"2023-06-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Orlando, FL, United States"},"type":"conference","status":"public","doi":"10.1145/3558481.3591082","file_date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-23T22:01:12Z","ddc":["000"],"author":[{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"last_name":"Hashemi","first_name":"Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","full_name":"Hashemi, Diba"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","orcid":"0000-0001-5634-0731","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","page":"261-271","isi":1,"quality_controlled":"1","external_id":{"arxiv":["2304.09331"],"isi":["001108889000024"]},"year":"2023","file":[{"file_size":2087937,"relation":"main_file","date_updated":"2023-07-31T10:53:08Z","file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","date_created":"2023-07-31T10:53:08Z","file_id":"13334","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1,"creator":"dernst","content_type":"application/pdf"}],"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"}],"date_updated":"2025-09-09T12:43:18Z","title":"Provably-efficient and internally-deterministic parallel Union-Find","day":"17","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"fulldoi":"https://doi.org/10.15479/at:ista:13286","supervisor":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"_id":"13286","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors"}],"OA_place":"publisher","oa":1,"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"article_processing_charge":"No","citation":{"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.","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.","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","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.","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","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."},"ec_funded":1,"publication_status":"published","date_published":"2023-07-21T00:00:00Z","month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","related_material":{"record":[{"relation":"research_data","status":"public","id":"12522"},{"relation":"part_of_dissertation","status":"public","id":"12118"},{"relation":"part_of_dissertation","id":"8910","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"13312"}]},"ddc":["530"],"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","full_name":"Valentini, Marco"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"alternative_title":["ISTA Thesis"],"corr_author":"1","date_created":"2023-07-24T14:10:45Z","type":"dissertation","status":"public","doi":"10.15479/at:ista:13286","file_date_updated":"2023-08-11T14:39:17Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","date_updated":"2026-06-03T07:16:01Z","day":"21","language":[{"iso":"eng"}],"oa_version":"Published Version","file":[{"file_size":56121429,"relation":"source_file","file_name":"PhD_thesis_Valentini_final.zip","date_updated":"2023-08-11T10:01:34Z","access_level":"closed","date_created":"2023-08-11T09:27:39Z","file_id":"14033","checksum":"666ee31c7eade89679806287c062fa14","content_type":"application/x-zip-compressed","creator":"mvalenti"},{"file_size":38199711,"relation":"main_file","date_updated":"2023-08-11T14:39:17Z","file_name":"PhD_thesis_Valentini_final_validated.pdf","access_level":"open_access","date_created":"2023-08-11T14:39:17Z","file_id":"14035","creator":"mvalenti","content_type":"application/pdf","checksum":"0992f2ebef152dee8e70055350ebbb55"}],"abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"year":"2023","page":"184"},{"oa":1,"has_accepted_license":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"arxiv":1,"publication":"50th International Colloquium on Automata, Languages, and Programming","_id":"13292","publication_identifier":{"isbn":["9783959772785"],"eissn":["1868-8969"]},"fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2023.129","scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-07-05T00:00:00Z","publication_status":"published","month":"07","volume":261,"ec_funded":1,"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.","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","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: 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.","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","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.","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."},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"article_processing_charge":"Yes","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","name":"ICALP: Automata, Languages and Programming","start_date":"2023-07-10"},"type":"conference","file_date_updated":"2023-07-24T15:11:05Z","status":"public","doi":"10.4230/LIPIcs.ICALP.2023.129","date_created":"2023-07-24T15:11:41Z","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","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","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"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"ddc":["000"],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LIPIcs"],"page":"129:1--129:20","quality_controlled":"1","external_id":{"arxiv":["2305.03447"]},"year":"2023","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."}],"file":[{"file_name":"icalp23.pdf","date_updated":"2023-07-24T15:11:05Z","access_level":"open_access","date_created":"2023-07-24T15:11:05Z","file_id":"13293","content_type":"application/pdf","checksum":"5d4c8932ef3450615a53b9bb15d92eb2","creator":"esarac","success":1,"file_size":859379,"relation":"main_file"}],"day":"05","title":"Regular methods for operator precedence languages","date_updated":"2025-07-10T11:50:41Z","oa_version":"Published Version","language":[{"iso":"eng"}]},{"type":"dissertation","doi":"10.15479/at:ista:13331","status":"public","file_date_updated":"2023-08-03T15:28:55Z","date_created":"2023-07-31T10:20:55Z","author":[{"full_name":"Köse, Seyda","orcid":"0009-0008-0457-9730","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda"}],"ddc":["510","516"],"corr_author":"1","alternative_title":["ISTA Master's Thesis"],"page":"26","year":"2023","abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"file":[{"file_id":"13333","checksum":"96ee518d796d02af71395622c45de03c","content_type":"application/x-zip-compressed","creator":"skoese","date_created":"2023-07-31T10:16:32Z","date_updated":"2023-07-31T10:16:32Z","file_name":"Exterior Algebra and Combinatorics.zip","access_level":"closed","relation":"source_file","file_size":28684},{"access_level":"open_access","file_name":"thesis-pdfa.pdf","date_updated":"2023-08-03T15:28:55Z","date_created":"2023-08-03T15:28:55Z","creator":"skoese","checksum":"f610f4713f88bc477de576aaa46b114e","content_type":"application/pdf","success":1,"file_id":"13480","file_size":4953418,"relation":"main_file"}],"day":"31","date_updated":"2026-04-07T13:29:29Z","title":"Exterior algebra and combinatorics","language":[{"iso":"eng"}],"oa_version":"Published Version","oa":1,"has_accepted_license":"1","OA_place":"publisher","_id":"13331","publication_identifier":{"issn":["2791-4585"]},"fulldoi":"https://doi.org/10.15479/at:ista:13331","supervisor":[{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","id":"12680","status":"public"}]},"degree_awarded":"MS","date_published":"2023-07-31T00:00:00Z","publication_status":"published","month":"07","citation":{"mla":"Köse, Seyda. Exterior Algebra and Combinatorics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13331.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","apa":"Köse, S. (2023). Exterior algebra and combinatorics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13331","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13331.","ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:10.15479/at:ista:13331"},"department":[{"_id":"GradSch"},{"_id":"UlWa"}],"article_processing_charge":"No"},{"has_accepted_license":"1","oa":1,"OA_place":"publisher","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"_id":"14058","publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"fulldoi":"https://doi.org/10.15479/at:ista:14058","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"id":"12933","status":"public","relation":"research_data"},{"id":"6831","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14077","status":"public"}]},"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"08","date_published":"2023-08-15T00:00:00Z","publication_status":"published","ec_funded":1,"citation":{"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","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.","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.","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.","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","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."},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"article_processing_charge":"No","status":"public","file_date_updated":"2023-08-18T10:47:55Z","doi":"10.15479/at:ista:14058","type":"dissertation","date_created":"2023-08-15T10:20:40Z","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["ISTA Thesis"],"author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"}],"ddc":["576"],"page":"230","year":"2023","abstract":[{"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.","lang":"eng"}],"file":[{"relation":"source_file","file_size":10891454,"date_created":"2023-08-16T18:15:17Z","file_id":"14075","creator":"gpuixeus","content_type":"application/zip","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_name":"Thesis_latex_forpdfa.zip","date_updated":"2023-08-17T06:55:24Z","access_level":"closed"},{"file_size":19856686,"relation":"main_file","date_updated":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","date_created":"2023-08-18T10:47:55Z","file_id":"14079","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","creator":"gpuixeus","success":1,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"15","date_updated":"2026-04-07T13:25:34Z","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation"},{"type":"journal_article","file_date_updated":"2023-11-07T09:00:19Z","status":"public","doi":"10.1093/g3journal/jkad121","acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"ddc":["570"],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2023-08-18T06:52:14Z","issue":"8","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).","external_id":{"pmid":["37259621"],"isi":["001002997200001"]},"year":"2023","isi":1,"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"quality_controlled":"1","day":"01","date_updated":"2026-04-07T13:25:34Z","title":"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"}],"intvolume":" 13","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":[{"relation":"main_file","file_size":845642,"date_created":"2023-11-07T09:00:19Z","file_id":"14498","creator":"dernst","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","success":1,"content_type":"application/pdf","date_updated":"2023-11-07T09:00:19Z","file_name":"2023_G3_Puixeu.pdf","access_level":"open_access"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"oa":1,"has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/g3journal/jkad121","publisher":"Oxford University Press","scopus_import":"1","publication":"G3: Genes, Genomes, Genetics","_id":"14077","publication_identifier":{"issn":["2160-1836"]},"pmid":1,"publication_status":"published","date_published":"2023-08-01T00:00:00Z","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","related_material":{"record":[{"status":"public","id":"12933","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"article_processing_charge":"Yes","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"volume":13,"ec_funded":1,"citation":{"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","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","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","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.","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."}},{"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"GradSch"}],"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","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.","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.","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","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.","short":"J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527.","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."},"volume":39,"month":"09","publication_status":"published","date_published":"2023-09-01T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publisher":"Royal Society of Chemistry","fulldoi":"https://doi.org/10.1039/d3sm00316g","_id":"14087","pmid":1,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"publication":"Soft Matter","arxiv":1,"has_accepted_license":"1","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","date_updated":"2025-04-23T13:03:12Z","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"}],"file":[{"file_size":7660662,"relation":"main_file","file_name":"2023_SoftMatter_Ronning.pdf","date_updated":"2024-01-30T12:48:24Z","access_level":"open_access","date_created":"2024-01-30T12:48:24Z","file_id":"14908","checksum":"b936747170d0b708172b518078c4081a","content_type":"application/pdf","success":1,"creator":"dernst"}],"intvolume":" 39","year":"2023","external_id":{"pmid":["37493084"],"isi":["001035766100001"],"arxiv":["2303.07063"]},"quality_controlled":"1","isi":1,"page":"7513-7527","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Jonas","last_name":"Rønning","full_name":"Rønning, Jonas"},{"last_name":"Renaud","id":"7af6767d-14eb-11ed-b536-a32449ae867c","first_name":"Julian B","full_name":"Renaud, Julian B"},{"last_name":"Doostmohammadi","first_name":"Amin","full_name":"Doostmohammadi, Amin"},{"full_name":"Angheluta, Luiza","first_name":"Luiza","last_name":"Angheluta"}],"ddc":["540"],"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_created":"2023-08-20T22:01:15Z","file_date_updated":"2024-01-30T12:48:24Z","doi":"10.1039/d3sm00316g","status":"public","type":"journal_article"},{"file_date_updated":"2023-09-06T07:32:39Z","doi":"10.1021/acs.jpclett.3c01707","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Gamper, Jakob","last_name":"Gamper","first_name":"Jakob"},{"full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"last_name":"Hofer","first_name":"Thomas S.","full_name":"Hofer, Thomas S."}],"ddc":["530","540"],"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.","issue":"33","date_created":"2023-09-03T22:01:16Z","year":"2023","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"quality_controlled":"1","isi":1,"page":"7395-7403","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"11","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","date_updated":"2023-09-06T11:04:31Z","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"}],"file":[{"file_size":4986859,"relation":"main_file","date_updated":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","access_level":"open_access","file_id":"14272","creator":"dernst","content_type":"application/pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","success":1,"date_created":"2023-09-06T07:32:39Z"}],"intvolume":" 14","has_accepted_license":"1","oa":1,"scopus_import":"1","publisher":"American Chemical Society","fulldoi":"https://doi.org/10.1021/acs.jpclett.3c01707","publication_identifier":{"eissn":["1948-7185"]},"_id":"14261","pmid":1,"publication":"Journal of Physical Chemistry Letters","month":"08","date_published":"2023-08-11T00:00:00Z","publication_status":"published","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"}],"article_processing_charge":"Yes (in subscription journal)","citation":{"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.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","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","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.","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","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."},"volume":14}]