[{"OA_place":"publisher","status":"public","OA_type":"hybrid","date_created":"2023-09-03T22:01:15Z","external_id":{"isi":["001065254200001"],"pmid":["37653226"]},"quality_controlled":"1","month":"07","ec_funded":1,"project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232","call_identifier":"FWF"},{"grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","call_identifier":"H2020"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"}],"date_updated":"2026-10-02T11:27:12Z","publication_status":"published","file_date_updated":"2025-01-09T07:48:01Z","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","publisher":"Springer Nature","has_accepted_license":"1","doi":"10.1038/s41587-023-01911-8","intvolume":"        42","author":[{"orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","first_name":"Julia M","full_name":"Michalska, Julia M"},{"first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431"},{"last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana","full_name":"Korinkova, Hana"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake","full_name":"Watson, Jake"},{"first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","first_name":"Alessandro"},{"full_name":"Roessler, Karl","first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","full_name":"Czech, Thomas","last_name":"Czech"},{"first_name":"Romana","full_name":"Höftberger, Romana","last_name":"Höftberger"},{"last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","first_name":"Sandra"},{"first_name":"Gaia","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G"}],"ddc":["570"],"citation":{"short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>."},"title":"Imaging brain tissue architecture across millimeter to nanometer scales","day":"01","publication":"Nature Biotechnology","scopus_import":"1","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","related_material":{"record":[{"status":"deleted","relation":"dissertation_contains","id":"18660"},{"id":"13126","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"18674","status":"public"}],"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}]},"page":"1051-1064","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2024-07-01T00:00:00Z","fulldoi":"https://doi.org/10.1038/s41587-023-01911-8","isi":1,"oa":1,"year":"2024","_id":"14257","oa_version":"Published Version","article_type":"original","volume":42,"type":"journal_article","file":[{"date_created":"2025-01-09T07:48:01Z","success":1,"access_level":"open_access","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","content_type":"application/pdf","file_size":26065165,"creator":"dernst","file_name":"2024_NatureBiotech_Michalska.pdf","relation":"main_file","date_updated":"2025-01-09T07:48:01Z","file_id":"18784"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","pmid":1},{"status":"public","OA_place":"repository","date_created":"2024-12-19T12:28:00Z","das_tickbox":"0","supplementarymaterial":"no","month":"02","ec_funded":1,"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF"},{"grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","_id":"269B5B22-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-10-02T11:27:43Z","publication_status":"draft","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.21.581330"}],"abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1101/2024.02.21.581330","author":[{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","first_name":"Sven M"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"orcid":"0009-0002-5890-120X","id":"F8660870-D756-11E9-98C5-34DFE5697425","last_name":"Inumella","first_name":"Syamala","full_name":"Inumella, Syamala"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba"},{"first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","first_name":"Jakob"},{"full_name":"Jahr, Wiebke","first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315","last_name":"Jahr"},{"first_name":"Marek","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","first_name":"Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G"}],"citation":{"ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>."},"title":"Super-resolution expansion microscopy in plant roots","day":"21","researchdata_availability":"no","publication":"bioRxiv","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"corr_author":"1","related_material":{"record":[{"status":"public","id":"19003","relation":"later_version"},{"status":"public","id":"18681","relation":"dissertation_contains"}]},"fulldoi":"https://doi.org/10.1101/2024.02.21.581330","date_published":"2024-02-21T00:00:00Z","oa":1,"_id":"18689","oa_version":"Preprint","year":"2024","type":"preprint","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript."},{"file_date_updated":"2024-12-18T14:41:53Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_processing_charge":"No","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","doi":"10.15479/at:ista:18674","author":[{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia"}],"citation":{"ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024.","ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>."},"ddc":["004"],"OA_place":"publisher","status":"public","das_tickbox":"0","date_created":"2024-12-18T14:24:43Z","supplementarymaterial":"no","doi_confirm":"1","month":"12","ec_funded":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"date_updated":"2026-10-02T11:27:13Z","publication_status":"published","year":"2024","oa_version":"Published Version","_id":"18674","supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G"}],"type":"dissertation","file":[{"file_id":"18675","date_updated":"2024-12-18T14:17:34Z","file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","relation":"main_file","creator":"jlyudchi","file_size":160536833,"content_type":"application/pdf","checksum":"1b42b8073e2bc09fc504da52372248c1","access_level":"open_access","success":1,"date_created":"2024-12-18T14:17:34Z"},{"file_id":"18676","date_updated":"2024-12-18T14:41:53Z","relation":"source_file","file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","creator":"jlyudchi","file_size":99172203,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","checksum":"b4da84624060745519723698f7ddf54b","date_created":"2024-12-18T14:21:06Z"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","day":"18","alternative_title":["ISTA Thesis"],"researchdata_availability":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-051-0"]},"page":"217","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13267","status":"public"},{"id":"14257","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18677","status":"public"}]},"corr_author":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2024-12-18T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:18674","degree_awarded":"PhD","oa":1},{"file_date_updated":"2026-07-28T08:33:51Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","doi":"10.15479/at:ista:18681","author":[{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","last_name":"Tavakoli"}],"ddc":["600","570"],"citation":{"short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>","apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>."},"status":"public","OA_place":"publisher","das_tickbox":"1","date_created":"2024-12-19T02:30:39Z","supplementarymaterial":"unclear","doi_confirm":"1","month":"12","project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-10-02T11:27:43Z","publication_status":"published","year":"2024","oa_version":"Published Version","_id":"18681","supervisor":[{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"file":[{"date_created":"2024-12-20T10:23:17Z","file_size":118593521,"creator":"mtavakol","access_level":"closed","checksum":"b61651d417cafddd740a8528f46068c5","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-12-20T10:31:37Z","file_id":"18699","file_name":"Thesis_Mojtaba Tavakoli_.docx","relation":"source_file"},{"date_created":"2024-12-20T10:25:12Z","file_id":"18700","date_updated":"2026-07-28T08:33:51Z","relation":"main_file","file_name":"Thesis_Mojtaba Tavakoli_.pdf","creator":"mtavakol","embargo_to":"open_access","file_size":63885521,"embargo":"2027-08-01","content_type":"application/pdf","access_level":"closed","checksum":"c80bcfd1a34c23afc3538052325283e5"}],"type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","alternative_title":["ISTA Thesis"],"OA_embargo":"20","day":"20","researchdata_availability":"unclear","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-048-0"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","page":"230","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18688","status":"public"},{"status":"public","id":"18689","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18677","status":"public"}]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2024-12-20T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:18681","degree_awarded":"PhD"},{"type":"preprint","acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}],"_id":"18677","oa_version":"Preprint","year":"2024","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"related_material":{"record":[{"relation":"later_version","id":"19704","status":"public"},{"relation":"dissertation_contains","id":"18674","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18681"}]},"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"fulldoi":"https://doi.org/10.1101/2024.03.01.582884","date_published":"2024-07-08T00:00:00Z","day":"08","title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","publication":"bioRxiv","researchdata_availability":"no","author":[{"last_name":"Tavakoli","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"},{"first_name":"Michał","full_name":"Januszewski, Michał","last_name":"Januszewski"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas"},{"full_name":"Vorlaufer, Jakob","first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"first_name":"Caroline","full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger"},{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira","first_name":"Bárbara","full_name":"Oliveira, Bárbara"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"},{"full_name":"Jain, Viren","first_name":"Viren","last_name":"Jain"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G"}],"doi":"10.1101/2024.03.01.582884","citation":{"short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.).","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. .","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>."},"main_file_link":[{"url":"https://doi.org/10.1101/2024.03.01.582884","open_access":"1"}],"abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner."}],"article_processing_charge":"No","department":[{"_id":"GaNo"},{"_id":"JoDa"}],"project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"ec_funded":1,"month":"07","publication_status":"draft","date_updated":"2026-10-02T11:27:43Z","date_created":"2024-12-18T14:48:24Z","das_tickbox":"0","status":"public","OA_place":"repository","supplementarymaterial":"no"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","related_material":{"record":[{"relation":"later_version","id":"18879","status":"public"},{"status":"public","relation":"dissertation_contains","id":"18681"}]},"fulldoi":"https://doi.org/10.1101/2024.05.02.592169","date_published":"2024-05-02T00:00:00Z","oa":1,"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","day":"02","publication":"bioRxiv","type":"preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","_id":"18688","oa_version":"Preprint","year":"2024","ec_funded":1,"month":"05","project":[{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"}],"date_updated":"2026-10-02T11:27:43Z","publication_status":"draft","status":"public","OA_place":"repository","date_created":"2024-12-19T11:35:08Z","doi":"10.1101/2024.05.02.592169","author":[{"full_name":"Watson, Jake F.","first_name":"Jake F.","last_name":"Watson"},{"full_name":"Vargas-Barroso, Victor","first_name":"Victor","last_name":"Vargas-Barroso"},{"full_name":"Morse-Mora, Rebecca J.","first_name":"Rebecca J.","last_name":"Morse-Mora"},{"first_name":"Andrea","full_name":"Navas-Olive, Andrea","last_name":"Navas-Olive"},{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854"},{"first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"first_name":"Matthias","full_name":"Tomschik, Matthias","last_name":"Tomschik"},{"full_name":"Rössler, Karl","first_name":"Karl","last_name":"Rössler"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"citation":{"short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>"},"department":[{"_id":"JoDa"},{"_id":"PeJo"}],"article_processing_charge":"No","abstract":[{"text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.05.02.592169"}]},{"date_published":"2024-06-11T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:17133","degree_awarded":"PhD","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"page":"161","related_material":{"record":[{"relation":"part_of_dissertation","id":"13227","status":"public"},{"id":"9928","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"corr_author":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"researchdata_availability":"no","title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","alternative_title":["ISTA Thesis"],"day":"11","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_main_final.pdf","relation":"main_file","date_updated":"2024-06-20T11:52:22Z","file_id":"17137","access_level":"open_access","checksum":"258c353d47fa37ea63ea43b1e10a34a0","content_type":"application/pdf","file_size":28370759,"creator":"fhassani","date_created":"2024-06-12T07:53:19Z"},{"file_id":"17138","date_updated":"2024-06-12T07:54:27Z","file_name":"Thesis_main.tex","relation":"source_file","creator":"fhassani","file_size":445735,"content_type":"text/x-tex","access_level":"closed","checksum":"deffa5d0db88093f74812fa71520d5e1","date_created":"2024-06-12T07:54:27Z"}],"type":"dissertation","keyword":["Quantum information","Qubits","Superconducting devices"],"supervisor":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"year":"2024","oa_version":"Published Version","_id":"17133","date_updated":"2026-10-02T11:28:17Z","publication_status":"published","month":"06","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"supplementarymaterial":"no","doi_confirm":"1","OA_place":"publisher","status":"public","date_created":"2024-06-11T18:20:05Z","das_tickbox":"0","citation":{"ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>"},"ddc":["530"],"doi":"10.15479/at:ista:17133","author":[{"orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"file_date_updated":"2024-06-20T11:52:22Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_processing_charge":"No","abstract":[{"lang":"eng","text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing."}]},{"quality_controlled":"1","supplementarymaterial":"no","external_id":{"isi":["001133672400004"],"arxiv":["2305.07044"]},"das_tickbox":"1","date_created":"2024-01-22T08:22:17Z","status":"public","publication_status":"published","date_updated":"2026-10-02T11:29:18Z","issue":"4","month":"02","publisher":"Oxford University Press","has_accepted_license":"1","article_processing_charge":"Yes","abstract":[{"text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 &amp;lt; z &amp;lt; 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JoMa"}],"file_date_updated":"2024-01-23T12:30:45Z","citation":{"short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>.","apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;527(4):9853-9871. doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>","ieee":"I. Kramarenko <i>et al.</i>, “Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>."},"ddc":["520"],"author":[{"orcid":"0000-0001-5346-6048","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","last_name":"Kramarenko","first_name":"Ivan","full_name":"Kramarenko, Ivan"},{"last_name":"Kerutt","first_name":"J","full_name":"Kerutt, J"},{"full_name":"Verhamme, A","first_name":"A","last_name":"Verhamme"},{"first_name":"P A","full_name":"Oesch, P A","last_name":"Oesch"},{"last_name":"Barrufet","full_name":"Barrufet, L","first_name":"L"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"last_name":"Kusakabe","full_name":"Kusakabe, H","first_name":"H"},{"last_name":"Goovaerts","first_name":"I","full_name":"Goovaerts, I"},{"full_name":"Thai, T T","first_name":"T T","last_name":"Thai"}],"doi":"10.1093/mnras/stad3853","intvolume":"       527","researchdata_availability":"upon request","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","title":"Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape","isi":1,"oa":1,"date_published":"2024-02-01T00:00:00Z","fulldoi":"https://doi.org/10.1093/mnras/stad3853","corr_author":"1","page":"9853-9871","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"year":"2024","arxiv":1,"oa_version":"Published Version","_id":"14852","acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","dataavailabilitystatement":"Raw MUSE data cubes are available from the ESO Science Archive Facility.2 The MUSE-Wide data from the first data release, which covers 44 fields in GOODS-S/CDFS, are available on the MUSE-Wide project page.3 The MUSE HUDF data from the second data release are available via the Advanced MUSE Data products (AMUSED) web interface.4 The stacked spectra in a machine-readable format and the spectral line measurements will be shared upon request to the corresponding author.","language":[{"iso":"eng"}],"type":"journal_article","file":[{"file_id":"14879","date_updated":"2024-01-23T12:30:45Z","relation":"main_file","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","creator":"dernst","file_size":4521738,"content_type":"application/pdf","access_level":"open_access","checksum":"9d02df4035c4951cf63dee0db1e462e9","success":1,"date_created":"2024-01-23T12:30:45Z"}],"volume":527,"DOAJ_listed":"1"},{"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"ec_funded":1,"month":"10","publication_status":"published","issue":"4","date_updated":"2026-10-02T11:30:08Z","das_tickbox":"0","date_created":"2024-10-09T07:02:20Z","OA_type":"closed access","status":"public","quality_controlled":"1","external_id":{"isi":["001328875900001"]},"supplementarymaterial":"unclear","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oliu-Barton","full_name":"Oliu-Barton, Miquel","first_name":"Miquel"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J"}],"intvolume":"        50","doi":"10.1287/moor.2022.0332","citation":{"mla":"Chatterjee, Krishnendu, et al. “Value-Positivity for Matrix Games.” <i>Mathematics of Operations Research</i>, vol. 50, no. 4, Institute for Operations Research and the Management Sciences, 2024, pp. 2433–3282, doi:<a href=\"https://doi.org/10.1287/moor.2022.0332\">10.1287/moor.2022.0332</a>.","ama":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. Value-positivity for matrix games. <i>Mathematics of Operations Research</i>. 2024;50(4):2433-3282. doi:<a href=\"https://doi.org/10.1287/moor.2022.0332\">10.1287/moor.2022.0332</a>","ieee":"K. Chatterjee, M. Oliu-Barton, and R. J. Saona Urmeneta, “Value-positivity for matrix games,” <i>Mathematics of Operations Research</i>, vol. 50, no. 4. Institute for Operations Research and the Management Sciences, pp. 2433–3282, 2024.","apa":"Chatterjee, K., Oliu-Barton, M., &#38; Saona Urmeneta, R. J. (2024). Value-positivity for matrix games. <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences. <a href=\"https://doi.org/10.1287/moor.2022.0332\">https://doi.org/10.1287/moor.2022.0332</a>","chicago":"Chatterjee, Krishnendu, Miquel Oliu-Barton, and Raimundo J Saona Urmeneta. “Value-Positivity for Matrix Games.” <i>Mathematics of Operations Research</i>. Institute for Operations Research and the Management Sciences, 2024. <a href=\"https://doi.org/10.1287/moor.2022.0332\">https://doi.org/10.1287/moor.2022.0332</a>.","ista":"Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. 2024. Value-positivity for matrix games. Mathematics of Operations Research. 50(4), 2433–3282.","short":"K. Chatterjee, M. Oliu-Barton, R.J. Saona Urmeneta, Mathematics of Operations Research 50 (2024) 2433–3282."},"abstract":[{"text":"Matrix games are the most basic model in game theory, and yet robustness with respect to small perturbations of the matrix entries is not fully understood. In this paper, we introduce value positivity and uniform value positivity, two properties that refine the notion of optimality in the context of polynomially perturbed matrix games. The first concept captures how the value depends on the perturbation parameter, and the second consists of the existence of a fixed strategy that guarantees the value of the unperturbed matrix game for every sufficiently small positive parameter. We provide polynomial-time algorithms to check whether a polynomially perturbed matrix game satisfies these properties. We further provide the functional form for a parameterized optimal strategy and the value function. Finally, we translate our results to linear programming and stochastic games, where value positivity is related to the existence of robust solutions.","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Institute for Operations Research and the Management Sciences","corr_author":"1","page":"2433-3282","related_material":{"record":[{"status":"public","id":"20234","relation":"dissertation_contains"}]},"scopus_import":"1","publication_identifier":{"eissn":["1526-5471"],"issn":["0364-765X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"fulldoi":"https://doi.org/10.1287/moor.2022.0332","date_published":"2024-10-01T00:00:00Z","day":"01","title":"Value-positivity for matrix games","publication":"Mathematics of Operations Research","researchdata_availability":"unclear","type":"journal_article","volume":50,"acknowledgement":"This research was supported by Fondation CFM pour la Recherche, the H2020 European Research Council [Grant ERC-CoG-863818 (ForM-SMArt)], the Austrian Science Fund [Grant 10.55776/COE12], ANID Chile [Grant ACT210005], and Agence Nationale de la Recherche [Grant ANR-21-CE40-0020].","language":[{"iso":"eng"}],"_id":"18266","oa_version":"None","year":"2024","article_type":"original"},{"intvolume":"        13","doi":"10.1142/s2010326324500072","author":[{"last_name":"Dubach","orcid":"0000-0001-6892-8137","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Guillaume","full_name":"Dubach, Guillaume"},{"full_name":"Reker, Jana","first_name":"Jana","last_name":"Reker","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9"}],"citation":{"ista":"Dubach G, Reker J. 2024. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. 13(2), 2450007.","short":"G. Dubach, J. Reker, Random Matrices: Theory and Applications 13 (2024).","mla":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2, 2450007, World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>.","chicago":"Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>.","apa":"Dubach, G., &#38; Reker, J. (2024). Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s2010326324500072\">https://doi.org/10.1142/s2010326324500072</a>","ama":"Dubach G, Reker J. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. <i>Random Matrices: Theory and Applications</i>. 2024;13(2). doi:<a href=\"https://doi.org/10.1142/s2010326324500072\">10.1142/s2010326324500072</a>","ieee":"G. Dubach and J. Reker, “Dynamics of a rank-one multiplicative perturbation of a unitary matrix,” <i>Random Matrices: Theory and Applications</i>, vol. 13, no. 2. World Scientific Publishing, 2024."},"department":[{"_id":"GradSch"},{"_id":"LaEr"}],"article_processing_charge":"No","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2212.14638","open_access":"1"}],"abstract":[{"text":"We provide a dynamical study of a model of multiplicative perturbation of a unitary matrix introduced by Fyodorov. In particular, we identify a flow of deterministic domains that bound the spectrum with high probability, separating the outlier from the typical eigenvalues at all sub-critical timescales. These results are obtained under generic assumptions on U that hold for a variety of unitary random matrix models.","lang":"eng"}],"publisher":"World Scientific Publishing","month":"04","ec_funded":1,"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"issue":"2","date_updated":"2026-10-02T11:31:29Z","publication_status":"published","OA_place":"repository","status":"public","das_tickbox":"0","date_created":"2024-05-23T08:31:57Z","OA_type":"green","supplementarymaterial":"unclear","external_id":{"isi":["001229295200002"],"arxiv":["2212.14638"]},"quality_controlled":"1","volume":13,"type":"journal_article","language":[{"iso":"eng"}],"_id":"17047","oa_version":"Preprint","year":"2024","arxiv":1,"article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2010-3271"],"issn":["2010-3263"]},"scopus_import":"1","corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17164"}]},"fulldoi":"https://doi.org/10.1142/s2010326324500072","date_published":"2024-04-01T00:00:00Z","oa":1,"isi":1,"article_number":"2450007","title":"Dynamics of a rank-one multiplicative perturbation of a unitary matrix","day":"01","publication":"Random Matrices: Theory and Applications","researchdata_availability":"unclear"},{"_id":"18891","oa_version":"Published Version","year":"2024","arxiv":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","volume":37,"file":[{"date_updated":"2025-02-04T08:11:25Z","file_id":"18989","file_name":"2024_NeurIPS_Sukenik.pdf","relation":"main_file","file_size":1784118,"creator":"dernst","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","access_level":"open_access","content_type":"application/pdf","success":1,"date_created":"2025-02-04T08:11:25Z"}],"type":"conference","researchdata_availability":"no","publication":"38th Annual Conference on Neural Information Processing Systems","title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","day":"01","alternative_title":["Advances in Neural Information Processing Systems"],"date_published":"2024-12-01T00:00:00Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","publisher":"Neural Information Processing Systems Foundation","has_accepted_license":"1","file_date_updated":"2025-02-04T08:11:25Z","department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"abstract":[{"text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent.","lang":"eng"}],"article_processing_charge":"No","ddc":["000"],"citation":{"chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37."},"intvolume":"        37","author":[{"id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník","first_name":"Peter","full_name":"Súkeník, Peter"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020"}],"conference":{"location":"Vancouver, Canada","end_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16"},"supplementarymaterial":"no","external_id":{"arxiv":["2405.14468"]},"quality_controlled":"1","OA_place":"publisher","status":"public","date_created":"2025-01-27T11:15:18Z","das_tickbox":"0","OA_type":"gold","date_updated":"2026-10-02T11:34:35Z","publication_status":"published","month":"12","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}]},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations."}],"article_processing_charge":"No","file_date_updated":"2024-11-07T10:59:42Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"ddc":["576"],"citation":{"mla":"Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>.","ieee":"P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.","apa":"Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic variation and barriers to gene exchange</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>","ama":"Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18515\">10.15479/at:ista:18515</a>","chicago":"Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18515\">https://doi.org/10.15479/at:ista:18515</a>.","short":"P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.","ista":"Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria."},"author":[{"last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy","first_name":"Parvathy"}],"doi":"10.15479/at:ista:18515","doi_confirm":"1","supplementarymaterial":"no","date_created":"2024-11-06T21:25:37Z","das_tickbox":"1","OA_type":"gold","status":"public","OA_place":"publisher","publication_status":"published","date_updated":"2026-10-02T11:36:48Z","project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"month":"11","supervisor":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"_id":"18515","oa_version":"Published Version","year":"2024","acknowledgement":"I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"success":1,"date_created":"2024-11-07T10:59:29Z","date_updated":"2024-11-07T10:59:29Z","file_id":"18519","relation":"main_file","file_name":"PhD_Thesis__Parvathy_071124_PDFA.pdf","file_size":37019760,"creator":"psurendr","access_level":"open_access","checksum":"c32cf7bc75748d9c551d8eb70178bbec","content_type":"application/pdf"},{"file_name":"PhD Thesis- Parvathy_071124.zip","relation":"source_file","file_id":"18520","date_updated":"2024-11-07T10:59:42Z","content_type":"application/zip","checksum":"4417e02d54084d89e75734e18caaa96d","access_level":"closed","creator":"psurendr","file_size":41198857,"date_created":"2024-11-07T10:59:42Z"}],"type":"dissertation","researchdata_availability":"yes","alternative_title":["ISTA Thesis"],"day":"07","title":"Effect of population structure on neutral genetic variation and barriers to gene exchange","degree_awarded":"PhD","oa":1,"fulldoi":"https://doi.org/10.15479/at:ista:18515","date_published":"2024-11-07T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"corr_author":"1","page":"219","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2663-337X"]}},{"researchdata_availability":"no","publication":"Physical Review Research","day":"10","article_number":"033277","title":"Theory of angular momentum transfer from light to molecules","oa":1,"fulldoi":"https://doi.org/10.1103/physrevresearch.6.033277","date_published":"2024-09-10T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19048"}]},"scopus_import":"1","publication_identifier":{"eissn":["2643-1564"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","_id":"18087","oa_version":"Published Version","year":"2024","arxiv":1,"acknowledgement":"We are grateful to Emilio Pisanty and Philipp Lunt for valuable discussions. This research was funded wholly or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). O.H.H. acknowledges support by the Austrian Science Fund (FWF) [10.55776/P36040]. Furthermore, the financial support by the Austrian Federal Ministry for Digital and Economic Affairs, the National Foundation for Research, Technology and Development, and the Christian Doppler Research Association is gratefully acknowledged.","language":[{"iso":"eng"}],"type":"journal_article","file":[{"file_size":1563824,"creator":"dernst","access_level":"open_access","checksum":"8f744d94956a1683b473b1cf9b411a37","content_type":"application/pdf","date_updated":"2024-09-23T09:46:20Z","file_id":"18125","relation":"main_file","file_name":"2024_PhysicalReviewResearch_Maslov.pdf","date_created":"2024-09-23T09:46:20Z","success":1}],"DOAJ_listed":"1","volume":6,"quality_controlled":"1","external_id":{"arxiv":["2310.00095"]},"supplementarymaterial":"yes","das_tickbox":"0","date_created":"2024-09-18T11:43:16Z","APC_amount":"3028,31 EUR","OA_type":"gold","OA_place":"publisher","status":"public","publication_status":"published","issue":"3","date_updated":"2026-10-02T11:36:24Z","project":[{"_id":"7c040762-9f16-11ee-852c-dd79eeee4ab3","name":"Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions","grant_number":"F100403"},{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"ec_funded":1,"month":"09","publisher":"American Physical Society","has_accepted_license":"1","article_processing_charge":"Yes","abstract":[{"text":"We present a theory describing the interaction of structured light, such as light carrying orbital angular momentum, with molecules. The light-matter interaction Hamiltonian we derive is expressed through couplings between spherical gradients of the electric field and the (transition) electric multipole moments of a particle of any nontrivial rotation point group. Our model can therefore accommodate an arbitrary complexity of the molecular and electric field structure, and it can be straightforwardly extended to atoms or nanostructures. Applying this framework to rovibrational spectroscopy of molecules, we uncover the general mechanism of angular momentum exchange between the spin and orbital angular momenta of light, molecular rotation, and its center-of-mass motion. We show that the nonzero vorticity of Laguerre-Gaussian beams can strongly enhance certain rovibrational transitions that are considered forbidden in the case of nonhelical light. We discuss the experimental requirements for the observation of these forbidden transitions in state-of-the-art spatially resolved spectroscopy measurements.","lang":"eng"}],"department":[{"_id":"GradSch"},{"_id":"MiLe"}],"file_date_updated":"2024-09-23T09:46:20Z","ddc":["530"],"citation":{"ista":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. 2024. Theory of angular momentum transfer from light to molecules. Physical Review Research. 6(3), 033277.","short":"M. Maslov, G. Koutentakis, M. Hrast, O.H. Heckl, M. Lemeshko, Physical Review Research 6 (2024).","mla":"Maslov, Mikhail, et al. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>, vol. 6, no. 3, 033277, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>.","ieee":"M. Maslov, G. Koutentakis, M. Hrast, O. H. Heckl, and M. Lemeshko, “Theory of angular momentum transfer from light to molecules,” <i>Physical Review Research</i>, vol. 6, no. 3. American Physical Society, 2024.","ama":"Maslov M, Koutentakis G, Hrast M, Heckl OH, Lemeshko M. Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. 2024;6(3). doi:<a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">10.1103/physrevresearch.6.033277</a>","apa":"Maslov, M., Koutentakis, G., Hrast, M., Heckl, O. H., &#38; Lemeshko, M. (2024). Theory of angular momentum transfer from light to molecules. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>","chicago":"Maslov, Mikhail, Georgios Koutentakis, Mateja Hrast, Oliver H. Heckl, and Mikhail Lemeshko. “Theory of Angular Momentum Transfer from Light to Molecules.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevresearch.6.033277\">https://doi.org/10.1103/physrevresearch.6.033277</a>."},"author":[{"last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail","first_name":"Mikhail"},{"first_name":"Georgios","full_name":"Koutentakis, Georgios","last_name":"Koutentakis","id":"d7b23d3a-9e21-11ec-b482-f76739596b95"},{"full_name":"Hrast, Mateja","first_name":"Mateja","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","last_name":"Hrast"},{"last_name":"Heckl","full_name":"Heckl, Oliver H.","first_name":"Oliver H."},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"intvolume":"         6","doi":"10.1103/physrevresearch.6.033277"},{"supplementarymaterial":"no","doi_confirm":"1","date_created":"2024-02-23T14:02:04Z","das_tickbox":"0","status":"public","OA_place":"publisher","publication_status":"published","date_updated":"2026-10-02T11:40:30Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"ec_funded":1,"month":"02","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2024-02-23T14:20:16Z","citation":{"short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>."},"ddc":["576","519"],"author":[{"first_name":"Michal","full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/at:ista:15020","researchdata_availability":"no","alternative_title":["ISTA Thesis"],"day":"23","title":"Genetic information and biological optimization","degree_awarded":"PhD","oa":1,"date_published":"2024-02-23T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:15020","page":"158","related_material":{"record":[{"relation":"part_of_dissertation","id":"7606","status":"public"},{"status":"public","id":"12081","relation":"part_of_dissertation"},{"id":"7553","relation":"part_of_dissertation","status":"public"}]},"corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"],"year":"2024","_id":"15020","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"file":[{"creator":"mhledik","file_size":7102089,"content_type":"application/pdf","checksum":"b2d3da47c98d481577a4baf68944fe41","access_level":"open_access","file_id":"15021","date_updated":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","relation":"main_file","date_created":"2024-02-23T13:50:53Z","success":1},{"date_created":"2024-02-23T13:50:54Z","creator":"mhledik","file_size":14014790,"content_type":"application/zip","access_level":"closed","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_id":"15022","date_updated":"2024-02-23T14:20:16Z","relation":"source_file","file_name":"hledik thesis source.zip"}],"type":"dissertation"},{"supervisor":[{"first_name":"Onur","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"}],"year":"2024","_id":"17225","oa_version":"Published Version","language":[{"iso":"eng"}],"file":[{"file_id":"17228","date_updated":"2024-07-11T10:26:22Z","file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","relation":"main_file","creator":"vli","file_size":6729761,"content_type":"application/pdf","access_level":"open_access","checksum":"15b2dbe8d2c9ed7ca5dd413827928077","success":1,"date_created":"2024-07-11T10:26:22Z"},{"relation":"source_file","file_name":"PhD Thesis Vyacheslav Li.zip","date_updated":"2024-07-11T10:26:22Z","file_id":"17229","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","access_level":"closed","content_type":"application/x-zip-compressed","file_size":9542859,"creator":"vli","date_created":"2024-07-11T10:26:22Z"}],"type":"dissertation","researchdata_availability":"no","title":"Towards a quantum entanglement enhanced atom interferomter","alternative_title":["ISTA Thesis"],"day":"11","date_published":"2024-07-11T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:17225","oa":1,"degree_awarded":"PhD","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"11438","relation":"part_of_dissertation","status":"public"}]},"page":"79","corr_author":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-07-11T10:26:22Z","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"article_processing_charge":"No","abstract":[{"text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence.","lang":"eng"}],"citation":{"ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024.","mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>.","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>.","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>"},"ddc":["530"],"doi":"10.15479/at:ista:17225","author":[{"first_name":"Vyacheslav","full_name":"Li, Vyacheslav","last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"}],"supplementarymaterial":"no","doi_confirm":"1","status":"public","OA_place":"publisher","das_tickbox":"0","date_created":"2024-07-11T09:46:48Z","date_updated":"2026-10-02T11:41:41Z","publication_status":"published","month":"07","project":[{"name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics","grant_number":"101087907","_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6"}]},{"supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"}],"oa_version":"Published Version","_id":"18135","year":"2024","language":[{"iso":"eng"}],"type":"dissertation","file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"c7bc3b31e430d57c65393051ca439575","creator":"alaurits","file_size":3648831,"file_name":"Lauritsen-thesis-final.pdf","relation":"main_file","file_id":"18147","date_updated":"2024-09-26T13:11:24Z","date_created":"2024-09-26T13:11:24Z","success":1},{"file_name":"Lauritsen-thesis-source.zip","relation":"source_file","date_updated":"2024-09-26T13:12:55Z","file_id":"18148","access_level":"closed","checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","content_type":"application/x-zip-compressed","file_size":1625888,"creator":"alaurits","date_created":"2024-09-26T13:12:55Z"}],"researchdata_availability":"no","day":"23","alternative_title":["ISTA Thesis"],"title":"Energies of dilute Fermi gases and universalities in BCS theory","degree_awarded":"PhD","oa":1,"fulldoi":"https://doi.org/10.15479/at:ista:18135","date_published":"2024-09-23T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11732"},{"id":"17240","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"14931","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"14542","status":"public"},{"id":"18107","relation":"part_of_dissertation","status":"public"}]},"corr_author":"1","page":"353","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","article_processing_charge":"No","abstract":[{"text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$.","lang":"eng"}],"file_date_updated":"2024-09-26T13:12:55Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024."},"ddc":["515","539"],"author":[{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard"}],"doi":"10.15479/at:ista:18135","doi_confirm":"1","supplementarymaterial":"no","das_tickbox":"0","date_created":"2024-09-24T10:56:25Z","status":"public","OA_place":"publisher","publication_status":"published","date_updated":"2026-10-02T11:43:01Z","project":[{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"},{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"09","ec_funded":1},{"scopus_import":"1","publication_identifier":{"eissn":["1793-6659"],"issn":["0129-055X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"19540","status":"public"},{"relation":"dissertation_contains","id":"18135","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_published":"2024-10-01T00:00:00Z","fulldoi":"https://doi.org/10.1142/s0129055x2360005x","isi":1,"oa":1,"title":"Universality in low-dimensional BCS theory","article_number":"2360005 ","day":"01","researchdata_availability":"no","publication":"Reviews in Mathematical Physics","volume":36,"file":[{"file_name":"2024_ReviewsmathPhysics_Henheik.pdf","relation":"main_file","date_updated":"2025-01-09T07:56:28Z","file_id":"18786","checksum":"2b053a4223b4db14b90520999ec56054","access_level":"open_access","content_type":"application/pdf","file_size":503910,"creator":"dernst","success":1,"date_created":"2025-01-09T07:56:28Z"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges  partial  financial  support  by  the  ERC  Advanced  Grant  “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","year":"2024","arxiv":1,"oa_version":"Published Version","_id":"14542","article_type":"original","ec_funded":1,"month":"10","project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"date_updated":"2026-10-02T11:43:00Z","issue":"9","publication_status":"published","status":"public","OA_place":"publisher","OA_type":"hybrid","das_tickbox":"0","date_created":"2023-11-15T23:48:14Z","external_id":{"arxiv":["2301.05621"],"isi":["001099640300002"]},"supplementarymaterial":"no","quality_controlled":"1","doi":"10.1142/s0129055x2360005x","intvolume":"        36","author":[{"last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","first_name":"Sven Joscha"},{"full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288"},{"id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","last_name":"Roos","full_name":"Roos, Barbara","first_name":"Barbara"}],"citation":{"short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics 36 (2024).","ista":"Henheik SJ, Lauritsen AB, Roos B. 2024. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 36(9), 2360005.","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>, vol. 36, no. 9, 2360005, World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>.","ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. 2024;36(9). doi:<a href=\"https://doi.org/10.1142/s0129055x2360005x\">10.1142/s0129055x2360005x</a>","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” <i>Reviews in Mathematical Physics</i>, vol. 36, no. 9. World Scientific Publishing, 2024.","apa":"Henheik, S. J., Lauritsen, A. B., &#38; Roos, B. (2024). Universality in low-dimensional BCS theory. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/s0129055x2360005x\">https://doi.org/10.1142/s0129055x2360005x</a>."},"ddc":["510"],"file_date_updated":"2025-01-09T07:56:28Z","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.","lang":"eng"}],"publisher":"World Scientific Publishing","has_accepted_license":"1"},{"date_created":"2024-02-04T23:00:53Z","das_tickbox":"1","status":"public","quality_controlled":"1","external_id":{"arxiv":["2301.04894"],"isi":["001170294000001"]},"supplementarymaterial":"no","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"month":"04","ec_funded":1,"publication_status":"published","issue":"7","date_updated":"2026-10-02T11:43:00Z","abstract":[{"text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"RoSe"}],"file_date_updated":"2024-07-22T11:11:56Z","publisher":"Elsevier","has_accepted_license":"1","author":[{"first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"},{"first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       286","doi":"10.1016/j.jfa.2024.110320","citation":{"short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>, vol. 286, no. 7, 110320, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>.","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. 2024;286(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” <i>Journal of Functional Analysis</i>, vol. 286, no. 7. Elsevier, 2024.","apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>"},"ddc":["510"],"day":"01","article_number":"110320","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","researchdata_availability":"not applicable","publication":"Journal of Functional Analysis","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"corr_author":"1","related_material":{"record":[{"status":"public","id":"18135","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"scopus_import":"1","oa":1,"isi":1,"fulldoi":"https://doi.org/10.1016/j.jfa.2024.110320","date_published":"2024-04-01T00:00:00Z","_id":"14931","oa_version":"Published Version","arxiv":1,"year":"2024","article_type":"original","file":[{"content_type":"application/pdf","checksum":"ee203cf2dc4420ad90d3c9970d246a78","access_level":"open_access","creator":"dernst","file_size":1381063,"file_name":"2024_JourFunctAnalysis_Lauritsen.pdf","relation":"main_file","file_id":"17305","date_updated":"2024-07-22T11:11:56Z","date_created":"2024-07-22T11:11:56Z","success":1}],"type":"journal_article","volume":286,"dataavailabilitystatement":"No data was used for the research described in the article.","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","language":[{"iso":"eng"}]},{"date_created":"2024-09-20T12:25:25Z","das_tickbox":"0","status":"public","quality_controlled":"1","external_id":{"arxiv":["2407.05990"],"isi":["001307817400001"]},"supplementarymaterial":"no","project":[{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427"}],"month":"09","publication_status":"published","date_updated":"2026-10-02T11:43:00Z","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"We consider a dilute fully spin-polarized Fermi gas at positive temperature in dimensions  d∈{1,2,3} . We show that the pressure of the interacting gas is bounded from below by that of the free gas plus, to leading order, an explicit term of order  adρ2+2/d, where a is the p-wave scattering length of the repulsive interaction and  ρ  is the particle density. The results are valid for a wide range of repulsive interactions, including that of a hard core, and uniform in temperatures at most of the order of the Fermi temperature. A central ingredient in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin, Gillespie and Ripka (Nucl. Phys. A, 176.2 (1971), pp. 237–260)."}],"file_date_updated":"2024-09-23T09:56:17Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"has_accepted_license":"1","publisher":"Cambridge University Press","author":[{"first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert"}],"doi":"10.1017/fms.2024.56","intvolume":"        12","citation":{"ista":"Lauritsen AB, Seiringer R. 2024. Pressure of a dilute spin-polarized Fermi gas: Lower bound. Forum of Mathematics, Sigma. 12, e78.","short":"A.B. Lauritsen, R. Seiringer, Forum of Mathematics, Sigma 12 (2024).","ieee":"A. B. Lauritsen and R. Seiringer, “Pressure of a dilute spin-polarized Fermi gas: Lower bound,” <i>Forum of Mathematics, Sigma</i>, vol. 12. Cambridge University Press, 2024.","ama":"Lauritsen AB, Seiringer R. Pressure of a dilute spin-polarized Fermi gas: Lower bound. <i>Forum of Mathematics, Sigma</i>. 2024;12. doi:<a href=\"https://doi.org/10.1017/fms.2024.56\">10.1017/fms.2024.56</a>","apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Pressure of a dilute spin-polarized Fermi gas: Lower bound. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2024.56\">https://doi.org/10.1017/fms.2024.56</a>","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute Spin-Polarized Fermi Gas: Lower Bound.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2024. <a href=\"https://doi.org/10.1017/fms.2024.56\">https://doi.org/10.1017/fms.2024.56</a>.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Pressure of a Dilute Spin-Polarized Fermi Gas: Lower Bound.” <i>Forum of Mathematics, Sigma</i>, vol. 12, e78, Cambridge University Press, 2024, doi:<a href=\"https://doi.org/10.1017/fms.2024.56\">10.1017/fms.2024.56</a>."},"ddc":["510"],"day":"09","article_number":"e78","title":"Pressure of a dilute spin-polarized Fermi gas: Lower bound","researchdata_availability":"no","publication":"Forum of Mathematics, Sigma","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18135"}]},"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","publication_identifier":{"issn":["2050-5094"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"oa":1,"date_published":"2024-09-09T00:00:00Z","fulldoi":"https://doi.org/10.1017/fms.2024.56","year":"2024","arxiv":1,"_id":"18107","oa_version":"Published Version","article_type":"original","type":"journal_article","file":[{"file_id":"18126","date_updated":"2024-09-23T09:56:17Z","file_name":"2024_ForumMath_Lauritsen.pdf","relation":"main_file","creator":"dernst","file_size":599886,"content_type":"application/pdf","checksum":"330b881240013213a8e08538fec13d29","access_level":"open_access","success":1,"date_created":"2024-09-23T09:56:17Z"}],"volume":12,"acknowledgement":"Financial support by the Austrian Science Fund (FWF) through grant DOI: 10.55776/I6427 (as part of the SFB/TRR 352) is gratefully acknowledged.","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"type":"dissertation","file":[{"file_id":"18467","date_updated":"2024-10-23T14:42:45Z","file_name":"MASisak_dissertation.pdf","relation":"main_file","creator":"msisak","file_size":1672547,"content_type":"application/pdf","access_level":"open_access","checksum":"8c4893e726aaa4b3efb82758da9b6851","success":1,"date_created":"2024-10-23T14:42:45Z"},{"file_id":"18468","date_updated":"2024-10-24T08:09:13Z","file_name":"MASisak_source.zip","relation":"source_file","creator":"msisak","file_size":617913,"content_type":"application/x-zip-compressed","access_level":"closed","checksum":"1831b072e861a1e5481024ca9d02b036","date_created":"2024-10-23T14:43:56Z"}],"keyword":["hyperkaehler geometry","branes","mirror symmetry","T-duality"],"supervisor":[{"first_name":"Tamás","full_name":"Hausel, Tamás","last_name":"Hausel","orcid":"0000-0002-9582-2634","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","_id":"18443","oa_version":"Published Version","date_published":"2024-10-24T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:18443","degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"178","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"researchdata_availability":"no","title":"T-dual branes on hyperkähler manifolds","day":"24","alternative_title":["ISTA Thesis"],"citation":{"short":"M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science and Technology Austria, 2024.","ista":"Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science and Technology Austria.","mla":"Sisak, Maria A. <i>T-Dual Branes on Hyperkähler Manifolds</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>.","ieee":"M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science and Technology Austria, 2024.","apa":"Sisak, M. A. (2024). <i>T-dual branes on hyperkähler manifolds</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>","ama":"Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18443\">10.15479/at:ista:18443</a>","chicago":"Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18443\">https://doi.org/10.15479/at:ista:18443</a>."},"ddc":["516"],"doi":"10.15479/at:ista:18443","author":[{"last_name":"Sisak","id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","full_name":"Sisak, Maria A","first_name":"Maria A"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file_date_updated":"2024-10-24T08:09:13Z","department":[{"_id":"GradSch"},{"_id":"TaHa"}],"article_processing_charge":"No","abstract":[{"text":"In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli spaces. As a consequence, they\r\nconjecture an equivalence between categories of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler structures and the\r\ncorresponding branes on affine torus bundles. We use the techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles and connections. This T-duality in the appropriate context specializes to\r\nT-duality between BBB and BAA-branes.\r\n","lang":"eng"}],"date_updated":"2026-10-02T11:43:57Z","publication_status":"published","month":"10","project":[{"_id":"6286e8c4-2b32-11ec-9570-f5297902f67f","grant_number":"26069","name":"Branes on hyperkähler manifolds"}],"supplementarymaterial":"no","doi_confirm":"1","OA_place":"publisher","status":"public","OA_type":"free access","date_created":"2024-10-19T12:00:37Z","das_tickbox":"0"}]