[{"oa_version":"Published Version","supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"file_date_updated":"2024-02-26T23:30:03Z","doi":"10.15479/at:ista:14226","day":"24","publication_identifier":{"issn":["2791-4585"]},"has_accepted_license":"1","article_processing_charge":"No","month":"08","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2023-08-24T00:00:00Z","status":"public","type":"dissertation","year":"2023","file":[{"creator":"cchlebak","access_level":"closed","file_size":15501411,"file_name":"documents-export-2023-08-24.zip","file_id":"14227","checksum":"453caf851d75c3478c10ed09bd242a91","date_updated":"2024-02-26T23:30:03Z","relation":"source_file","embargo_to":"open_access","date_created":"2023-08-24T13:02:49Z","content_type":"application/x-zip-compressed"},{"embargo":"2024-02-25","creator":"cchlebak","file_name":"thesis_pdf_a.pdf","date_updated":"2024-02-26T23:30:03Z","file_id":"14228","checksum":"7349d29963d6695e555e171748648d9a","file_size":6854783,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-24T13:03:42Z"}],"degree_awarded":"MS","_id":"14226","OA_place":"publisher","title":"Generalizing medial axes with homology switches","fulldoi":"https://doi.org/10.15479/at:ista:14226","citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226"},"page":"43","corr_author":"1","alternative_title":["ISTA Master's Thesis"],"publisher":"Institute of Science and Technology Austria","date_created":"2023-08-24T13:01:18Z","language":[{"iso":"eng"}],"date_updated":"2026-04-07T14:02:30Z","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"ddc":["500"],"author":[{"last_name":"Stephenson","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"}],"oa":1},{"_id":"14510","degree_awarded":"PhD","year":"2023","file":[{"creator":"ngnyliuk","access_level":"closed","file_size":20824903,"checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","date_updated":"2024-11-23T23:30:38Z","relation":"source_file","embargo_to":"open_access","date_created":"2023-11-20T09:18:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"access_level":"open_access","file_size":24871844,"checksum":"bfc96d47fc4e7e857dd71656097214a4","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","file_id":"14568","date_updated":"2024-11-23T23:30:38Z","creator":"ngnyliuk","embargo":"2024-11-23","date_created":"2023-11-20T09:23:11Z","content_type":"application/pdf","relation":"main_file"}],"related_material":{"record":[{"id":"14591","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9887","relation":"part_of_dissertation"},{"status":"public","id":"8139","relation":"part_of_dissertation"}]},"type":"dissertation","status":"public","date_published":"2023-11-10T00:00:00Z","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","OA_place":"publisher","day":"10","doi":"10.15479/at:ista:14510","file_date_updated":"2024-11-23T23:30:38Z","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"11","article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"date_updated":"2026-11-08T23:30:45Z","ec_funded":1,"oa":1,"author":[{"last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"corr_author":"1","page":"180","citation":{"mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"fulldoi":"https://doi.org/10.15479/at:ista:14510","date_created":"2023-11-10T09:10:06Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","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"}},{"citation":{"chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523"},"fulldoi":"https://doi.org/10.1101/2023.10.09.561523","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"corr_author":"1","publication":"bioRxiv","doi":"10.1101/2023.10.09.561523","day":"10","article_processing_charge":"No","month":"10","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"draft","project":[{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-22T10:17:49Z","date_published":"2023-10-10T00:00:00Z","type":"preprint","related_material":{"record":[{"relation":"later_version","id":"15330","status":"public"},{"id":"14510","status":"public","relation":"dissertation_contains"}]},"status":"public","_id":"14591","year":"2023","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:30:44Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","OA_place":"repository","author":[{"last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","orcid":"0000-0002-2198-0509"},{"last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nagel","full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","full_name":"Monzer, Aline","last_name":"Monzer"},{"last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria","first_name":"Annamaria"},{"full_name":"Isono, Erika","first_name":"Erika","last_name":"Isono"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"}],"oa":1,"ec_funded":1},{"OA_place":"publisher","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","year":"2023","degree_awarded":"PhD","file":[{"creator":"cchlebak","embargo":"2023-07-09","file_size":41771714,"date_updated":"2023-07-27T22:30:54Z","file_id":"12471","file_name":"20230109_PhD_thesis_JM_final.pdf","checksum":"1a2306e5f59f52df598e7ecfadf921ac","access_level":"open_access","relation":"main_file","date_created":"2023-01-31T15:11:42Z","content_type":"application/pdf"},{"date_updated":"2023-07-10T22:30:04Z","file_id":"12472","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"access_level":"closed","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-01-31T15:11:51Z","embargo_to":"open_access","relation":"source_file"}],"_id":"12470","date_published":"2023-01-09T00:00:00Z","status":"public","related_material":{"record":[{"status":"public","id":"11943","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"type":"dissertation","publication_status":"published","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"isbn":["978-3-99078-026-8"],"issn":["2663-337X"]},"has_accepted_license":"1","article_processing_charge":"No","month":"01","file_date_updated":"2023-07-27T22:30:54Z","doi":"10.15479/at:ista:12470","day":"09","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"supervisor":[{"orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"oa":1,"ec_funded":1,"ddc":["610"],"author":[{"last_name":"Michalska","first_name":"Julia M","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"language":[{"iso":"eng"}],"date_updated":"2026-07-06T12:50:45Z","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"date_created":"2023-01-31T15:10:53Z","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"],"fulldoi":"https://doi.org/10.15479/at:ista:12470","citation":{"chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470"},"page":"201","corr_author":"1"},{"page":"142","corr_author":"1","citation":{"chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622"},"fulldoi":"https://doi.org/10.15479/at:ista:14622","alternative_title":["ISTA Thesis"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"date_created":"2023-11-28T10:58:13Z","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"date_updated":"2026-09-14T08:36:32Z","language":[{"iso":"eng"}],"author":[{"full_name":"Sack, Stefan","first_name":"Stefan","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack"}],"ddc":["530"],"ec_funded":1,"oa":1,"abstract":[{"text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation.","lang":"eng"}],"supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"oa_version":"Published Version","doi":"10.15479/at:ista:14622","day":"30","file_date_updated":"2024-11-30T23:30:03Z","month":"11","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi_confirm":"1","publication_status":"published","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"IBM PhD Nomination Fellowship - Stefan Sack"},{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"related_material":{"record":[{"id":"13125","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"11471","status":"public"},{"id":"9760","status":"public","relation":"part_of_dissertation"}]},"type":"dissertation","status":"public","date_published":"2023-11-30T00:00:00Z","_id":"14622","file":[{"embargo":"2024-11-30","creator":"ssack","access_level":"open_access","date_updated":"2024-11-30T23:30:03Z","file_name":"PhD_Thesis.pdf","checksum":"068fd3570506ec42b2faa390de784bc4","file_id":"14635","file_size":11947523,"relation":"main_file","content_type":"application/pdf","date_created":"2023-11-30T15:53:10Z"},{"relation":"source_file","embargo_to":"open_access","content_type":"application/zip","date_created":"2023-11-30T15:54:11Z","creator":"ssack","access_level":"closed","file_id":"14636","date_updated":"2024-11-30T23:30:03Z","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","file_name":"PhD Thesis (1).zip","file_size":18422964}],"degree_awarded":"PhD","year":"2023","title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","OA_place":"publisher"},{"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":"2023-06-07T06:57:32Z","publisher":"American Physical Society","corr_author":"1","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"citation":{"short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404.","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404"},"fulldoi":"https://doi.org/10.1103/physreva.107.062404","article_type":"original","isi":1,"intvolume":" 107","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","full_name":"Sack, Stefan","last_name":"Sack"},{"last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"last_name":"Kueng","first_name":"Richard","full_name":"Kueng, Richard"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"ddc":["530"],"ec_funded":1,"arxiv":1,"oa":1,"date_updated":"2026-11-08T23:31:03Z","language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"month":"06","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","project":[{"grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. ","lang":"eng"}],"oa_version":"Published Version","day":"02","doi":"10.1103/physreva.107.062404","issue":"6","file_date_updated":"2023-06-13T07:28:36Z","volume":107,"publication":"Physical Review A","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","scopus_import":"1","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17208"},{"relation":"dissertation_contains","id":"14622","status":"public"}]},"status":"public","date_published":"2023-06-02T00:00:00Z","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","_id":"13125","article_number":"062404","year":"2023","file":[{"content_type":"application/pdf","date_created":"2023-06-13T07:28:36Z","success":1,"relation":"main_file","file_name":"2023_PhysRevA_Sack.pdf","checksum":"0d71423888eeccaa60d8f41197f26306","file_id":"13131","date_updated":"2023-06-13T07:28:36Z","file_size":2524611,"access_level":"open_access","creator":"dernst"}]},{"project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461"}],"publication_status":"published","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"has_accepted_license":"1","article_processing_charge":"Yes","quality_controlled":"1","month":"12","publication":"Molecular Biology and Evolution","volume":40,"file_date_updated":"2024-01-02T11:39:38Z","issue":"12","doi":"10.1093/molbev/msad245","day":"01","oa_version":"Published Version","abstract":[{"text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","file":[{"creator":"dernst","access_level":"open_access","checksum":"47c1c72fb499f26ea52d216b242208c8","file_name":"2023_MolecularBioEvo_Lasne.pdf","date_updated":"2024-01-02T11:39:38Z","file_id":"14727","file_size":8623505,"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2024-01-02T11:39:38Z"}],"year":"2023","_id":"14613","article_number":"msad245","date_published":"2023-12-01T00:00:00Z","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","status":"public","related_material":{"record":[{"relation":"research_data","id":"14614","status":"public"},{"id":"19386","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","relation":"press_release","description":"News on ISTA webpage"}]},"type":"journal_article","publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2023-11-27T16:14:37Z","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"},"intvolume":" 40","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1093/molbev/msad245","citation":{"mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:10.1093/molbev/msad245.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., & Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution, vol. 40, no. 12. Oxford University Press, 2023.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245."},"corr_author":"1","external_id":{"isi":["001122489000003"],"pmid":["37988296"]},"oa":1,"ddc":["570"],"author":[{"first_name":"Clementine","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","last_name":"Lasne"},{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"last_name":"Layana Franco","orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"last_name":"Macon","full_name":"Macon, Ariana","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:31:05Z","department":[{"_id":"BeVi"}]},{"corr_author":"1","page":"1630-1635","external_id":{"isi":["001054563800006"]},"fulldoi":"https://doi.org/10.1038/s41567-023-02161-w","citation":{"mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023."},"isi":1,"article_type":"original","intvolume":" 19","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":"2023-08-11T07:41:17Z","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"date_updated":"2026-11-08T23:31:07Z","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","first_name":"Soham","orcid":"0000-0001-5263-5559"},{"orcid":"0000-0002-0672-9295","first_name":"Jorden L","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior"},{"last_name":"Saez Mollejo","id":"e0390f72-f6e0-11ea-865d-862393336714","first_name":"Jaime","full_name":"Saez Mollejo, Jaime"},{"last_name":"Puglia","orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","first_name":"Denise","id":"4D495994-AE37-11E9-AC72-31CAE5697425"},{"last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","first_name":"Martin","orcid":"0009-0005-0878-3032"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"ddc":["530"],"ec_funded":1,"oa":1,"abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"oa_version":"Published Version","day":"01","doi":"10.1038/s41567-023-02161-w","volume":19,"publication":"Nature Physics","file_date_updated":"2024-01-29T11:25:38Z","quality_controlled":"1","month":"11","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","project":[{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"status":"public","type":"journal_article","related_material":{"record":[{"id":"17881","status":"public","relation":"dissertation_contains"}]},"acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","date_published":"2023-11-01T00:00:00Z","year":"2023","file":[{"success":1,"relation":"main_file","date_created":"2024-01-29T11:25:38Z","content_type":"application/pdf","creator":"dernst","file_size":1977706,"file_id":"14899","checksum":"1fc86d71bfbf836e221c1e925343adc5","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","date_updated":"2024-01-29T11:25:38Z","access_level":"open_access"}],"_id":"14032","title":"Superconductivity from a melted insulator in Josephson junction arrays","scopus_import":"1","keyword":["General Physics and Astronomy"]},{"fulldoi":"https://doi.org/10.1093/evlett/qrac004","citation":{"ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004."},"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"corr_author":"1","intvolume":" 7","isi":1,"article_type":"original","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"},"publisher":"Oxford University Press","date_created":"2023-02-06T13:59:12Z","language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:31:09Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"ddc":["570"],"author":[{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea"},{"last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"oa":1,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"volume":7,"publication":"Evolution Letters","file_date_updated":"2023-08-16T11:43:33Z","issue":"1","doi":"10.1093/evlett/qrac004","day":"01","publication_identifier":{"issn":["2056-3744"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","quality_controlled":"1","month":"02","pmid":1,"project":[{"grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-02-01T00:00:00Z","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","status":"public","type":"journal_article","related_material":{"record":[{"status":"public","id":"18531","relation":"dissertation_contains"}]},"file":[{"creator":"dernst","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_name":"2023_EvLetters_Mrnjavac.pdf","file_id":"14068","date_updated":"2023-08-16T11:43:33Z","file_size":2592189,"access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2023-08-16T11:43:33Z"}],"year":"2023","article_number":"qrac004","_id":"12521","scopus_import":"1","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"]},{"abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}],"oa_version":"Preprint","day":"30","volume":202,"publication":"Proceedings of the 40th International Conference on Machine Learning","quality_controlled":"1","month":"07","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"status":"public","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"23072"},{"id":"17465","status":"public","relation":"dissertation_contains"}]},"type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","location":"Honolulu, Hawaii, HI, United States","end_date":"2023-07-29","start_date":"2023-07-23"},"acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","date_published":"2023-07-30T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"year":"2023","_id":"14459","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","scopus_import":"1","corr_author":"1","external_id":{"arxiv":["2212.13468"]},"page":"31151-31209","citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023."},"intvolume":" 202","alternative_title":["PMLR"],"date_created":"2023-10-29T23:01:17Z","publisher":"ML Research Press","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:31:11Z","author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","last_name":"Shevchenko"},{"full_name":"Kögler, Kevin","first_name":"Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"oa":1,"arxiv":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"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publisher":"Springer Nature","date_created":"2023-06-04T22:01:02Z","citation":{"mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998."},"fulldoi":"https://doi.org/10.1038/s41467-023-38761-6","corr_author":"1","external_id":{"arxiv":["2205.03293"],"pmid":["37225689"],"isi":["001001099700002"]},"intvolume":" 14","article_type":"original","isi":1,"ddc":["530"],"author":[{"last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","first_name":"Elena"},{"full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V.","last_name":"Poshakinskiy"},{"full_name":"Sett, Riya","first_name":"Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett"},{"last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0005-0878-3032","first_name":"Martin","full_name":"Zemlicka, Martin"},{"last_name":"Poddubny","full_name":"Poddubny, Alexander N.","first_name":"Alexander N."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"}],"oa":1,"arxiv":1,"ec_funded":1,"language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:31:15Z","department":[{"_id":"JoFi"}],"article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"eissn":["2041-1723"]},"month":"05","quality_controlled":"1","pmid":1,"project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"file_date_updated":"2023-06-06T07:31:20Z","publication":"Nature Communications","volume":14,"doi":"10.1038/s41467-023-38761-6","day":"24","scopus_import":"1","title":"Tunable directional photon scattering from a pair of superconducting qubits","date_published":"2023-05-24T00:00:00Z","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","related_material":{"record":[{"id":"13124","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"19533","status":"public"}]},"type":"journal_article","status":"public","_id":"13117","article_number":"2998","year":"2023","file":[{"relation":"main_file","success":1,"date_created":"2023-06-06T07:31:20Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_size":1654389,"file_id":"13123","date_updated":"2023-06-06T07:31:20Z","file_name":"2023_NaturePhysics_Redchenko.pdf","checksum":"a857df40f0882859c48a1ff1e2001ec2"}]},{"language":[{"iso":"eng"}],"date_updated":"2026-11-08T23:31:17Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"oa":1,"ec_funded":1,"ddc":["570"],"author":[{"last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","first_name":"Divyansh","full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F","first_name":"Wiktor F","last_name":"Mlynarski"},{"orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L","first_name":"Anton L","id":"3320A096-F248-11E8-B48F-1D18A9856A87","last_name":"Sumser"},{"last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","first_name":"Olga","full_name":"Symonova, Olga"},{"last_name":"Svaton","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","orcid":"0000-0002-6198-2939","full_name":"Svaton, Jan","first_name":"Jan"},{"first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"}],"intvolume":" 26","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1038/s41593-023-01280-0","citation":{"mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0.","short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023."},"corr_author":"1","page":"606-614","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-01-23T14:14:19Z","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"},"year":"2023","file":[{"date_updated":"2023-10-04T11:40:51Z","file_id":"14395","file_name":"2023_NatureNeuroscience_Gupta.pdf","checksum":"a33d91e398e548f34003170e10988368","file_size":6144866,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2023-10-04T11:40:51Z","success":1,"relation":"main_file"}],"_id":"12349","date_published":"2023-04-01T00:00:00Z","acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","status":"public","type":"journal_article","related_material":{"record":[{"relation":"research_data","status":"public","id":"12370"},{"relation":"dissertation_contains","id":"18574","status":"public"}]},"scopus_import":"1","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","volume":26,"publication":"Nature Neuroscience","file_date_updated":"2023-10-04T11:40:51Z","day":"01","doi":"10.1038/s41593-023-01280-0","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types."}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","call_identifier":"H2020"},{"grant_number":"LT000256","name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","quality_controlled":"1","month":"04"},{"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"date_updated":"2026-11-08T23:31:17Z","ec_funded":1,"oa":1,"author":[{"last_name":"Gupta","full_name":"Gupta, Divyansh","first_name":"Divyansh","orcid":"0000-0001-7400-6665","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4792-1881","first_name":"Anton L","full_name":"Sumser, Anton L","last_name":"Sumser"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch"}],"ddc":["571"],"corr_author":"1","citation":{"mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370","apa":"Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370."},"fulldoi":"https://doi.org/10.15479/AT:ISTA:12370","date_created":"2023-01-25T12:45:18Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA 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work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ","date_created":"2023-06-02T12:30:40Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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"},"corr_author":"1","citation":{"ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116.","mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116."},"fulldoi":"https://doi.org/10.15479/AT:ISTA:13116","ec_funded":1,"oa":1,"author":[{"full_name":"Dunajova, Zuzana","first_name":"Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova"},{"last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","full_name":"Prats Mateu, Batirtze"},{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler"},{"last_name":"Lim","full_name":"Lim, Keesiang","first_name":"Keesiang"},{"last_name":"Brandis","full_name":"Brandis, Dörte","first_name":"Dörte"},{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G"},{"last_name":"Wong","first_name":"Richard W.","full_name":"Wong, Richard W."},{"last_name":"Elgeti","full_name":"Elgeti, Jens","first_name":"Jens"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"ddc":["539"],"department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"date_updated":"2026-11-08T23:31:19Z"},{"publisher":"Springer Nature","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2023-07-27T14:44:45Z","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"},"intvolume":" 19","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1038/s41567-023-02218-w","citation":{"chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w"},"corr_author":"1","external_id":{"pmid":["38075437"],"isi":["001178645300041"]},"page":"1916-1926","oa":1,"ec_funded":1,"ddc":["530"],"author":[{"last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","full_name":"Dunajova, Zuzana","first_name":"Zuzana"},{"last_name":"Prats Mateu","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","full_name":"Prats Mateu, Batirtze"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","first_name":"Philipp","last_name":"Radler"},{"first_name":"Keesiang","full_name":"Lim, Keesiang","last_name":"Lim"},{"id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","full_name":"Brandis, Dörte","first_name":"Dörte","last_name":"Brandis"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"last_name":"Wong","first_name":"Richard W.","full_name":"Wong, Richard W."},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"}],"date_updated":"2026-11-08T23:31:19Z","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division"},{"_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360"}],"pmid":1,"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","month":"12","volume":19,"file_date_updated":"2024-01-30T14:28:30Z","publication":"Nature Physics","doi":"10.1038/s41567-023-02218-w","day":"01","oa_version":"Published Version","abstract":[{"text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.","lang":"eng"}],"scopus_import":"1","title":"Chiral and nematic phases of flexible active filaments","year":"2023","file":[{"success":1,"relation":"main_file","date_created":"2024-01-30T14:28:30Z","content_type":"application/pdf","creator":"dernst","file_size":22471673,"date_updated":"2024-01-30T14:28:30Z","checksum":"bc7673ca07d37309013a86166577b2f7","file_id":"14916","file_name":"2023_NaturePhysics_Dunajova.pdf","access_level":"open_access"}],"_id":"13314","date_published":"2023-12-01T00:00:00Z","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","status":"public","type":"journal_article","related_material":{"record":[{"relation":"research_data","id":"13116","status":"public"},{"status":"public","id":"21439","relation":"research_data"},{"status":"public","id":"21423","relation":"dissertation_contains"}]}},{"scopus_import":"1","title":"Control of tissue dimensions in the developing neural tube and somites","date_published":"2023-09-01T00:00:00Z","acknowledgement":"We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.","status":"public","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19763"}]},"year":"2023","file":[{"creator":"dernst","access_level":"open_access","file_size":598842,"date_updated":"2024-01-29T11:06:45Z","file_id":"14896","checksum":"8a75c4e29fd9b62e3c50663c2265b173","file_name":"2023_CurrOpSystBioloy_Minchington.pdf","relation":"main_file","success":1,"date_created":"2024-01-29T11:06:45Z","content_type":"application/pdf"}],"article_number":"100459","_id":"13136","publication_identifier":{"eissn":["2452-3100"]},"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","month":"09","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","abstract":[{"text":"Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.","lang":"eng"}],"file_date_updated":"2024-01-29T11:06:45Z","publication":"Current Opinion in Systems Biology","volume":35,"doi":"10.1016/j.coisb.2023.100459","day":"01","ddc":["570"],"author":[{"last_name":"Minchington","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","first_name":"Thomas","full_name":"Minchington, Thomas"},{"last_name":"Rus","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093","first_name":"Stefanie","full_name":"Rus, Stefanie"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"}],"oa":1,"date_updated":"2026-11-08T23:31:23Z","language":[{"iso":"eng"}],"department":[{"_id":"AnKi"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publisher":"Elsevier","date_created":"2023-06-18T22:00:46Z","fulldoi":"https://doi.org/10.1016/j.coisb.2023.100459","citation":{"mla":"Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35, 100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459.","short":"T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023).","chicago":"Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459.","ama":"Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459","apa":"Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2023.100459","ista":"Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459.","ieee":"T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” Current Opinion in Systems Biology, vol. 35. Elsevier, 2023."},"corr_author":"1","intvolume":" 35","article_type":"original"},{"file_date_updated":"2023-08-16T08:15:41Z","publication":"Molecular Ecology","volume":32,"issue":"6","day":"01","doi":"10.1111/mec.16793","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","month":"03","year":"2023","file":[{"access_level":"open_access","date_updated":"2023-08-16T08:15:41Z","file_id":"14062","file_name":"2023_MolecularEcology_Shipilina.pdf","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_size":7144607,"creator":"dernst","content_type":"application/pdf","date_created":"2023-08-16T08:15:41Z","relation":"main_file","success":1}],"_id":"12159","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","date_published":"2023-03-01T00:00:00Z","status":"public","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20694"}]},"type":"journal_article","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","title":"On the origin and structure of haplotype blocks","intvolume":" 32","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1111/mec.16793","citation":{"short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793"},"page":"1441-1457","corr_author":"1","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"publisher":"Wiley","date_created":"2023-01-12T12:09:17Z","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_updated":"2026-11-08T23:31:24Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"oa":1,"ddc":["570"],"author":[{"last_name":"Shipilina","first_name":"Daria","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka","first_name":"Arka","orcid":"0000-0002-4530-8469"},{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}]},{"fulldoi":"https://doi.org/10.1016/j.molp.2023.06.007","citation":{"short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier, 2023. https://doi.org/10.1016/j.molp.2023.06.007.","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007.","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier, pp. 1117–1119, 2023.","apa":"Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2023.06.007","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007"},"external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"page":"1117-1119","corr_author":"1","intvolume":" 16","isi":1,"article_type":"letter_note","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"publisher":"Elsevier","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2023-07-12T07:32:46Z","department":[{"_id":"JiFr"}],"date_updated":"2026-11-08T23:31:26Z","language":[{"iso":"eng"}],"ddc":["580"],"author":[{"last_name":"Chen","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","first_name":"Huihuang"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li"},{"first_name":"Minxia","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou"},{"last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"}],"oa":1,"ec_funded":1,"oa_version":"Published Version","das_tickbox":"1","abstract":[{"lang":"eng","text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast."}],"publication":"Molecular Plant","volume":16,"file_date_updated":"2024-01-29T10:37:05Z","issue":"7","doi":"10.1016/j.molp.2023.06.007","day":"01","publication_identifier":{"issn":["1752-9867"],"eissn":["1674-2052"]},"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","quality_controlled":"1","month":"07","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","date_published":"2023-07-01T00:00:00Z","status":"public","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"19478","status":"public"}]},"file":[{"file_id":"14894","date_updated":"2024-01-29T10:37:05Z","file_name":"2023_MolecularPlant_Chen.pdf","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","file_size":1000871,"access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_created":"2024-01-29T10:37:05Z","success":1,"relation":"main_file"}],"year":"2023","_id":"13212","scopus_import":"1","title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling."},{"month":"01","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"issn":["0894-1491"],"eissn":["1098-1136"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","pmid":1,"abstract":[{"lang":"eng","text":"Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses."}],"oa_version":"Published Version","doi":"10.1002/glia.24101","day":"01","issue":"1","file_date_updated":"2022-03-04T08:55:27Z","publication":"Glia","volume":70,"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","scopus_import":"1","keyword":["Cellular and Molecular Neuroscience","Neurology"],"type":"journal_article","status":"public","acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","date_published":"2022-01-01T00:00:00Z","_id":"10818","year":"2022","file":[{"date_created":"2022-03-04T08:55:27Z","content_type":"application/pdf","success":1,"relation":"main_file","file_size":5340294,"file_id":"10819","file_name":"2021_Glia_Basilico.pdf","date_updated":"2022-03-04T08:55:27Z","checksum":"f10a897290e66c0a062e04ba91db6c17","access_level":"open_access","creator":"dernst"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"date_created":"2022-03-04T08:53:37Z","publisher":"Wiley","external_id":{"isi":["000708025800001"],"pmid":["34661306"]},"corr_author":"1","page":"173-195","citation":{"ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 2022;70(1):173-195. doi:10.1002/glia.24101","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. Wiley. https://doi.org/10.1002/glia.24101","ieee":"B. Basilico et al., “Microglia control glutamatergic synapses in the adult mouse hippocampus,” Glia, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","ista":"Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 70(1), 173–195.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:10.1002/glia.24101.","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” Glia. Wiley, 2022. https://doi.org/10.1002/glia.24101.","short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195."},"fulldoi":"https://doi.org/10.1002/glia.24101","article_type":"original","isi":1,"intvolume":" 70","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico"},{"last_name":"Ferrucci","first_name":"Laura","full_name":"Ferrucci, Laura"},{"last_name":"Ratano","full_name":"Ratano, Patrizia","first_name":"Patrizia"},{"last_name":"Golia","full_name":"Golia, Maria T.","first_name":"Maria T."},{"first_name":"Alfonso","full_name":"Grimaldi, Alfonso","last_name":"Grimaldi"},{"last_name":"Rosito","first_name":"Maria","full_name":"Rosito, Maria"},{"last_name":"Ferretti","full_name":"Ferretti, Valentina","first_name":"Valentina"},{"last_name":"Reverte","first_name":"Ingrid","full_name":"Reverte, Ingrid"},{"full_name":"Sanchini, Caterina","first_name":"Caterina","last_name":"Sanchini"},{"first_name":"Maria C.","full_name":"Marrone, Maria C.","last_name":"Marrone"},{"last_name":"Giubettini","first_name":"Maria","full_name":"Giubettini, Maria"},{"full_name":"De Turris, Valeria","first_name":"Valeria","last_name":"De Turris"},{"last_name":"Salerno","full_name":"Salerno, Debora","first_name":"Debora"},{"first_name":"Stefano","full_name":"Garofalo, Stefano","last_name":"Garofalo"},{"last_name":"St‐Pierre","full_name":"St‐Pierre, Marie‐Kim","first_name":"Marie‐Kim"},{"last_name":"Carrier","first_name":"Micael","full_name":"Carrier, Micael"},{"last_name":"Renzi","full_name":"Renzi, Massimiliano","first_name":"Massimiliano"},{"last_name":"Pagani","full_name":"Pagani, Francesca","first_name":"Francesca"},{"first_name":"Brijesh","full_name":"Modi, Brijesh","last_name":"Modi"},{"full_name":"Raspa, Marcello","first_name":"Marcello","last_name":"Raspa"},{"last_name":"Scavizzi","full_name":"Scavizzi, Ferdinando","first_name":"Ferdinando"},{"last_name":"Gross","first_name":"Cornelius T.","full_name":"Gross, Cornelius T."},{"last_name":"Marinelli","first_name":"Silvia","full_name":"Marinelli, Silvia"},{"first_name":"Marie‐Ève","full_name":"Tremblay, Marie‐Ève","last_name":"Tremblay"},{"last_name":"Caprioli","full_name":"Caprioli, Daniele","first_name":"Daniele"},{"first_name":"Laura","full_name":"Maggi, Laura","last_name":"Maggi"},{"full_name":"Limatola, Cristina","first_name":"Cristina","last_name":"Limatola"},{"first_name":"Silvia","full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio"},{"last_name":"Ragozzino","first_name":"Davide","full_name":"Ragozzino, Davide"}],"ddc":["570"],"oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"date_updated":"2024-10-09T21:04:02Z"},{"author":[{"full_name":"Liu, Jianxin","first_name":"Jianxin","last_name":"Liu"},{"orcid":"0000-0001-7173-4923","first_name":"Elena","full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi"},{"first_name":"Xuesong","full_name":"Wu, Xuesong","last_name":"Wu"}],"date_updated":"2025-05-20T06:08:26Z","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"publisher":"Springer Nature","date_created":"2022-03-04T09:14:34Z","alternative_title":["IUTAM"],"intvolume":" 38","isi":1,"fulldoi":"https://doi.org/10.1007/978-3-030-67902-6_51","citation":{"mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” IUTAM Laminar-Turbulent Transition, vol. 38, Springer Nature, 2022, pp. 587–98, doi:10.1007/978-3-030-67902-6_51.","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In IUTAM Laminar-Turbulent Transition, 38:587–98. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-67902-6_51.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. Vol 38. Springer Nature; 2022:587-598. doi:10.1007/978-3-030-67902-6_51","apa":"Liu, J., Marensi, E., & Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In IUTAM Laminar-Turbulent Transition (Vol. 38, pp. 587–598). London, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-67902-6_51","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in IUTAM Laminar-Turbulent Transition, London, United Kingdom, 2022, vol. 38, pp. 587–598.","ista":"Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium, IUTAM, vol. 38, 587–598."},"page":"587-598","external_id":{"isi":["000709087600051"]},"OA_type":"closed access","scopus_import":"1","title":"Effects of streaky structures on the instability of supersonic boundary layers","year":"2022","_id":"10820","conference":{"end_date":"2019-09-06","name":"IUTAM Symposium","location":"London, United Kingdom","start_date":"2019-09-02"},"date_published":"2022-01-01T00:00:00Z","acknowledgement":"The work is supported by the National Key Research and Development Program of China (No. 2016YFA0401200), the National Natural Science Foundation of China (Grant Nos. 91952202 and 11402167).","status":"public","type":"conference","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["9783030679026"],"eissn":["1875-3493"],"issn":["1875-3507"],"isbn":["9783030679019"]},"article_processing_charge":"No","quality_controlled":"1","month":"01","volume":38,"publication":"IUTAM Laminar-Turbulent Transition","day":"01","doi":"10.1007/978-3-030-67902-6_51","oa_version":"None","abstract":[{"text":"Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.","lang":"eng"}]}]