[{"intvolume":"       130","isi":1,"oa":1,"publisher":"American Physical Society","language":[{"iso":"eng"}],"publication":"Physical Review Letters","arxiv":1,"oa_version":"Preprint","type":"journal_article","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["General Physics and Astronomy"],"doi":"10.1103/physrevlett.130.106901","article_number":"106901","month":"03","author":[{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"last_name":"Lorenc","full_name":"Lorenc, Dusan","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","last_name":"Ashourishokri","full_name":"Ashourishokri, Younes"},{"last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A."},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","scopus_import":"1","abstract":[{"lang":"eng","text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order."}],"date_published":"2023-03-10T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","date_created":"2023-03-14T13:11:59Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"citation":{"ieee":"A. Volosniev <i>et al.</i>, “Spin-electric coupling in lead halide perovskites,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>.","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>"},"date_updated":"2023-08-01T13:39:04Z","_id":"12723","year":"2023","issue":"10","volume":130,"title":"Spin-electric coupling in lead halide perovskites","day":"10","external_id":{"arxiv":["2203.09443"],"isi":["000982435900002"]}},{"abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"date_published":"2023-03-15T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","article_number":"125201","month":"03","author":[{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","full_name":"Lorenc, Dusan","last_name":"Lorenc"},{"full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes"},{"first_name":"Ayan","full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov"},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek"}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"arxiv":1,"oa_version":"Preprint","publication":"Physical Review B","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"doi":"10.1103/physrevb.107.125201","intvolume":"       107","isi":1,"publisher":"American Physical Society","oa":1,"volume":107,"title":"Effective model for studying optical properties of lead halide perovskites","day":"15","external_id":{"arxiv":["2204.04022"],"isi":["000972602200006"]},"year":"2023","issue":"12","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"citation":{"chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. 2023;107(12). doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","ieee":"A. Volosniev <i>et al.</i>, “Effective model for studying optical properties of lead halide perovskites,” <i>Physical Review B</i>, vol. 107, no. 12. American Physical Society, 2023."},"date_updated":"2023-08-01T13:39:47Z","_id":"12724","date_created":"2023-03-14T13:13:05Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2204.04022"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"oa_version":"None","related_material":{"record":[{"relation":"part_of_dissertation","id":"10703","status":"public"},{"relation":"part_of_dissertation","id":"10791","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7932"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"new_edition","id":"14530"}]},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/at:ista:12726","degree_awarded":"PhD","page":"260","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex.","lang":"eng"}],"ddc":["530"],"date_published":"2023-03-23T00:00:00Z","file":[{"file_size":63734746,"access_level":"closed","content_type":"application/pdf","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_id":"12745","date_updated":"2023-11-24T11:57:46Z","file_name":"Thesis_Riedl_2023.pdf","relation":"main_file","date_created":"2023-03-23T12:49:23Z","creator":"cchlebak","checksum":"eba0e19fe57a8c15e7aeab55a845efb7"},{"embargo_to":"open_access","date_updated":"2023-09-24T22:30:03Z","file_name":"Thesis_Riedl_2023_source.rar","access_level":"closed","file_size":339473651,"file_id":"12746","content_type":"application/octet-stream","creator":"cchlebak","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","date_created":"2023-03-23T12:54:34Z","relation":"source_file"}],"status":"public","has_accepted_license":"1","month":"03","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael","full_name":"Riedl, Michael","last_name":"Riedl"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"citation":{"ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>"},"file_date_updated":"2023-11-24T11:57:46Z","date_updated":"2023-11-30T10:55:13Z","_id":"12726","date_created":"2023-03-15T13:22:13Z","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Synchronization in collectively moving active matter","day":"23","supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"year":"2023"},{"doi":"10.15479/at:ista:12732","page":"158","degree_awarded":"PhD","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"11470","relation":"part_of_dissertation"},{"status":"public","id":"8308","relation":"part_of_dissertation"},{"id":"11469","relation":"part_of_dissertation","status":"public"},{"id":"12750","relation":"part_of_dissertation","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"None","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Institute of Science and Technology Austria","oa":1,"status":"public","file":[{"file_name":"Thesis_sub_PBrighi.zip","date_updated":"2023-03-23T16:42:56Z","file_id":"12753","content_type":"application/zip","access_level":"closed","file_size":42167561,"checksum":"5d2de651ef9449c1b8dc27148ca74777","creator":"pbrighi","date_created":"2023-03-23T16:42:56Z","relation":"source_file"},{"checksum":"7caa153d4a5b0873a79358787d2dfe1e","creator":"pbrighi","date_created":"2023-03-23T16:43:14Z","relation":"main_file","date_updated":"2023-03-23T16:43:14Z","file_name":"Thesis_PBrighi.pdf","success":1,"file_id":"12754","content_type":"application/pdf","access_level":"open_access","file_size":13977000}],"abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"ddc":["530"],"date_published":"2023-03-21T00:00:00Z","article_processing_charge":"No","month":"03","author":[{"first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","last_name":"Brighi","full_name":"Brighi, Pietro"}],"has_accepted_license":"1","date_updated":"2023-09-20T10:44:12Z","_id":"12732","project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"file_date_updated":"2023-03-23T16:43:14Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"citation":{"ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>.","mla":"Brighi, Pietro. <i>Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>.","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","apa":"Brighi, P. (2023). <i>Ergodicity breaking in disordered and kinetically constrained quantum many-body systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-03-17T13:30:48Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","day":"21","year":"2023","supervisor":[{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}]},{"month":"02","author":[{"last_name":"Aksenov","full_name":"Aksenov, Vitaly","first_name":"Vitaly"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","full_name":"Fedorov, Alexander","last_name":"Fedorov"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"article_processing_charge":"No","year":"2023","title":"Unexpected scaling in path copying trees","quality_controlled":"1","day":"25","status":"public","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"date_published":"2023-02-25T00:00:00Z","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"publication_status":"published","date_created":"2023-03-19T23:00:58Z","publisher":"Association for Computing Machinery","oa":1,"type":"conference_poster","conference":{"start_date":"2023-02-25","location":"Montreal, QB, Canada","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01"},"publication_identifier":{"isbn":["9798400700156"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-03-20T07:57:27Z","_id":"12736","page":"438-440","doi":"10.1145/3572848.3577512","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","oa_version":"Published Version","citation":{"mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 438–40, doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. <i>Unexpected Scaling in Path Copying Trees</i>. Association for Computing Machinery; 2023:438-440. doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. <i>Unexpected Scaling in Path Copying Trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., &#38; Kokorin, I. (2023). <i>Unexpected scaling in path copying trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, <i>Unexpected scaling in path copying trees</i>. Association for Computing Machinery, 2023, pp. 438–440."}},{"publication_status":"published","date_created":"2023-03-26T22:01:08Z","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"file_date_updated":"2023-08-16T12:39:57Z","_id":"12762","date_updated":"2023-08-16T12:41:53Z","citation":{"ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>, vol. 3, Springer Nature, 2023, pp. 254–63, doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. 2023;3:254-263. doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263."},"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"year":"2023","day":"20","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","external_id":{"arxiv":["2108.06686"]},"volume":3,"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         3","oa":1,"publisher":"Springer Nature","publication_identifier":{"eissn":["2662-8457"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1038/s43588-023-00410-9","page":"254-263","arxiv":1,"oa_version":"Published Version","publication":"Nature Computational Science","ec_funded":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio"},{"full_name":"Pepic, Selver","last_name":"Pepic","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","first_name":"Selver"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"},{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele"}],"month":"03","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","quality_controlled":"1","article_type":"original","status":"public","date_published":"2023-03-20T00:00:00Z","ddc":["570"],"abstract":[{"text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"file":[{"relation":"main_file","date_created":"2023-08-16T12:39:57Z","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","creator":"dernst","content_type":"application/pdf","file_id":"14073","file_size":4474284,"access_level":"open_access","file_name":"2023_NatureCompScience_Lombardi.pdf","date_updated":"2023-08-16T12:39:57Z","success":1}]},{"supervisor":[{"last_name":"Sazanov","full_name":"Sazanov, Leonid A","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"year":"2023","title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","day":"23","publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-03-31T12:24:42Z","project":[{"name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541"},{"name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3","call_identifier":"H2020","grant_number":"101020697"}],"file_date_updated":"2023-04-20T07:02:59Z","date_updated":"2023-08-04T08:54:51Z","_id":"12781","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"citation":{"ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023.","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>."},"month":"03","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk"}],"article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["570","572"],"abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"date_published":"2023-03-23T00:00:00Z","file":[{"file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","date_updated":"2023-04-19T14:33:41Z","embargo_to":"local","file_size":6071553,"access_level":"closed","content_type":"application/pdf","file_id":"12852","creator":"vkravchu","checksum":"5ebb6345cb4119f93460c81310265a6d","embargo":"2024-04-20","relation":"main_file","date_created":"2023-04-19T14:33:41Z"},{"checksum":"c12055c48411d030d2afa51de2166221","creator":"vkravchu","relation":"source_file","date_created":"2023-04-19T14:33:52Z","embargo":"2024-04-20","date_updated":"2023-04-20T07:02:59Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","embargo_to":"local","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12853","file_size":19468766,"access_level":"closed"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-029-9"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/at:ista:12781","page":"127","degree_awarded":"PhD","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"12138","status":"public"}]}},{"alternative_title":["ISTA Master's Thesis"],"publication_status":"published","date_created":"2023-04-04T18:57:11Z","date_updated":"2023-06-02T22:30:05Z","_id":"12800","file_date_updated":"2023-06-02T22:30:04Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"citation":{"short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023."},"year":"2023","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","day":"05","publisher":"Institute of Science and Technology Austria","oa":1,"page":"21","doi":"10.15479/at:ista:12800","degree_awarded":"MS","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2791-4585"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","month":"04","author":[{"full_name":"Julseth, Mara","last_name":"Julseth","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara"}],"has_accepted_license":"1","status":"public","file":[{"checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","creator":"mjulseth","relation":"supplementary_material","date_created":"2023-04-06T06:09:40Z","file_name":"Dispersaldata.xlsx","date_updated":"2023-06-02T22:30:04Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"12805","file_size":52795,"access_level":"closed"},{"file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","date_updated":"2023-06-02T22:30:04Z","file_size":787239,"access_level":"open_access","content_type":"application/vnd.wolfram.nb","file_id":"12806","creator":"mjulseth","checksum":"5a13b6d204371572e249f03795bc0d04","embargo":"2023-06-01","relation":"supplementary_material","date_created":"2023-04-06T06:11:27Z"},{"checksum":"c3ec842839ed1e66bf2618ae33047df8","creator":"mjulseth","date_created":"2023-04-06T08:26:12Z","relation":"source_file","embargo_to":"open_access","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.docx","file_id":"12812","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":1061763},{"relation":"main_file","date_created":"2023-04-06T08:26:37Z","embargo":"2023-06-01","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","creator":"mjulseth","content_type":"application/pdf","file_id":"12813","file_size":1741364,"access_level":"open_access","date_updated":"2023-06-02T22:30:04Z","file_name":"ThesisMaraJulseth_04_23.pdf"}],"abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"ddc":["576"],"date_published":"2023-04-05T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","month":"04","author":[{"first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","full_name":"Alcarva, Catarina"}],"file":[{"file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_updated":"2023-04-07T06:16:06Z","embargo_to":"open_access","content_type":"application/pdf","file_id":"12814","file_size":9881969,"access_level":"closed","checksum":"35b5997d2b0acb461f9d33d073da0df5","creator":"cchlebak","relation":"main_file","date_created":"2023-04-07T06:16:06Z","embargo":"2024-04-07"},{"date_created":"2023-04-07T06:17:11Z","relation":"source_file","checksum":"81198f63c294890f6d58e8b29782efdc","creator":"cchlebak","file_id":"12815","content_type":"application/pdf","access_level":"closed","file_size":44201583,"file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_updated":"2023-04-07T06:17:11Z"},{"date_updated":"2023-04-07T06:18:05Z","file_name":"Thesis_CatarinaAlcarva_final.docx","access_level":"closed","file_size":84731244,"file_id":"12816","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak","checksum":"0317bf7f457bb585f99d453ffa69eb53","date_created":"2023-04-07T06:18:05Z","relation":"source_file"}],"ddc":["570"],"abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"date_published":"2023-04-06T00:00:00Z","status":"public","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"115","doi":"10.15479/at:ista:12809","degree_awarded":"PhD","type":"dissertation","publication_identifier":{"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2023","supervisor":[{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","day":"06","date_created":"2023-04-06T07:54:09Z","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RySh"}],"citation":{"short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023."},"date_updated":"2023-04-26T12:16:56Z","_id":"12809","file_date_updated":"2023-04-07T06:18:05Z","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}]},{"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-04-14T14:56:04Z","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"file_date_updated":"2023-04-20T09:26:51Z","_id":"12826","date_updated":"2023-06-23T09:47:36Z","citation":{"ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","apa":"Pokusaeva, V. (2023). <i>Neural control of optic flow-based navigation in Drosophila melanogaster</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>","mla":"Pokusaeva, Victoria. <i>Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12826\">10.15479/at:ista:12826</a>.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12826\">https://doi.org/10.15479/at:ista:12826</a>."},"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330"}],"year":"2023","day":"18","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","page":"106","degree_awarded":"PhD","doi":"10.15479/at:ista:12826","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva"}],"month":"04","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2023-04-18T00:00:00Z","ddc":["570","571"],"abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"file":[{"date_updated":"2023-04-20T09:26:51Z","file_name":"Thesis_Pokusaeva.docx","access_level":"closed","file_size":14507243,"file_id":"12857","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vpokusae","checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z","relation":"source_file"},{"relation":"main_file","date_created":"2023-04-20T09:14:44Z","creator":"vpokusae","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","file_size":10090711,"access_level":"open_access","content_type":"application/pdf","file_id":"12858","success":1,"date_updated":"2023-04-20T09:14:44Z","file_name":"Thesis_Pokusaeva.pdf"}]},{"publication_status":"submitted","main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"date_created":"2023-04-18T19:16:06Z","oa":1,"type":"preprint","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-04-25T06:51:21Z","_id":"12846","doi":"10.48550/arXiv.2303.14555","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"language":[{"iso":"eng"}],"publication":"arXiv","arxiv":1,"oa_version":"Preprint","citation":{"ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” <i>arXiv</i>. .","short":"A. Chern, S. Ishida, ArXiv (n.d.).","apa":"Chern, A., &#38; Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, 2303.14555, doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>."},"month":"03","author":[{"full_name":"Chern, Albert","last_name":"Chern","first_name":"Albert"},{"full_name":"Ishida, Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"}],"article_processing_charge":"No","article_number":"2303.14555","year":"2023","title":"Area formula for spherical polygons via prequantization","day":"25","status":"public","external_id":{"arxiv":["2303.14555"]},"abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"date_published":"2023-03-25T00:00:00Z","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA)."},{"publisher":"ML Research Press","oa":1,"intvolume":"       202","related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 40th International Conference on Machine Learning","arxiv":1,"oa_version":"Preprint","page":"2738-2776","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","month":"10","author":[{"last_name":"Bombari","full_name":"Bombari, Simone","first_name":"Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa"},{"first_name":"Shayan","id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","last_name":"Kiyani","full_name":"Kiyani, Shayan"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"}],"abstract":[{"lang":"eng","text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10)."}],"date_published":"2023-10-27T00:00:00Z","status":"public","quality_controlled":"1","date_created":"2023-04-23T16:11:03Z","alternative_title":["PMLR"],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2302.01629"}],"department":[{"_id":"GradSch"},{"_id":"MaMo"}],"citation":{"ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:2738-2776.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 2738–76.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:2738–76. ML Research Press, 2023.","apa":"Bombari, S., Kiyani, S., &#38; Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776."},"date_updated":"2024-09-10T13:03:19Z","_id":"12859","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"conference":{"start_date":"2023-07-23","location":"Honolulu, HI, United States","name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29"},"year":"2023","acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","volume":202,"external_id":{"arxiv":["2302.01629"]},"title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","day":"27"},{"date_published":"2023-04-26T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage.  We first analyse the model  with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. "}],"ddc":["000"],"acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","file":[{"success":1,"date_updated":"2023-04-26T12:30:06Z","file_name":"README.md","access_level":"open_access","file_size":4567,"file_id":"12870","content_type":"application/octet-stream","creator":"alaurits","checksum":"85ede12d38bb8d944022a8cba4d719f5","date_created":"2023-04-26T12:30:06Z","relation":"main_file"},{"creator":"alaurits","checksum":"25bf79452ae895f9c8a20571a096b4c3","date_created":"2023-04-26T12:27:34Z","relation":"main_file","success":1,"file_name":"simulations_era=10_flux_varied_europe.zip","date_updated":"2023-04-26T12:27:34Z","access_level":"open_access","file_size":732586731,"file_id":"12871","content_type":"application/x-zip-compressed"},{"checksum":"bca48d80ece73eb169aee7211a4a751a","creator":"alaurits","relation":"main_file","date_created":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","date_updated":"2023-04-26T12:29:53Z","success":1,"content_type":"application/x-zip-compressed","file_id":"12872","file_size":1743893150,"access_level":"open_access"},{"content_type":"application/x-zip-compressed","file_id":"12873","file_size":878391851,"access_level":"open_access","file_name":"simulations_era=10_R_varied_torus.zip","date_updated":"2023-04-26T12:29:19Z","success":1,"relation":"main_file","date_created":"2023-04-26T12:29:19Z","checksum":"e77a655db15486a387a36362fbf0b665","creator":"alaurits"},{"creator":"alaurits","checksum":"8556406513adc4aa2e0417f46680f627","date_created":"2023-04-26T12:30:05Z","relation":"main_file","success":1,"date_updated":"2023-04-26T12:30:05Z","file_name":"simulations_era=100.zip","access_level":"open_access","file_size":201652478,"file_id":"12874","content_type":"application/x-zip-compressed"}],"day":"26","title":"Research data for: A stochastic cellular automaton model of culture formation","status":"public","has_accepted_license":"1","year":"2023","author":[{"first_name":"Frederik Ravn","full_name":"Klausen, Frederik Ravn","last_name":"Klausen"},{"last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"month":"04","article_processing_charge":"No","citation":{"short":"F.R. Klausen, A.B. Lauritsen, (2023).","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>.","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. <i>Research Data for: A Stochastic Cellular Automaton Model of Culture Formation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023."},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"related_material":{"record":[{"relation":"used_in_publication","id":"14505","status":"for_moderation"},{"relation":"used_in_publication","id":"12890","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-04-26T12:30:06Z","type":"research_data","doi":"10.15479/AT:ISTA:12869","_id":"12869","date_updated":"2023-11-13T07:47:29Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa":1,"date_created":"2023-04-26T12:34:49Z","publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"date_created":"2023-05-02T07:58:57Z","alternative_title":["ISTA Thesis"],"publication_status":"published","citation":{"ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"MaIb"}],"_id":"12885","date_updated":"2023-08-14T07:25:26Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"file_date_updated":"2023-05-02T07:43:18Z","year":"2023","supervisor":[{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria"}],"day":"28","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","publisher":"Institute of Science and Technology Austria","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"10806","status":"public"},{"relation":"part_of_dissertation","id":"10042","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"12237"},{"relation":"part_of_dissertation","id":"9118","status":"public"},{"id":"10123","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:12885","page":"82","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"type":"dissertation","has_accepted_license":"1","article_processing_charge":"No","author":[{"full_name":"Calcabrini, Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano"}],"month":"04","file":[{"relation":"source_file","date_created":"2023-05-02T07:43:18Z","creator":"mcalcabr","checksum":"9347b0e09425f56fdcede5d3528404dc","file_size":99627036,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12887","file_name":"Thesis_Calcabrini.docx","date_updated":"2023-05-02T07:43:18Z"},{"checksum":"2d188b76621086cd384f0b9264b0a576","creator":"mcalcabr","date_created":"2023-05-02T07:42:45Z","relation":"main_file","date_updated":"2023-05-02T07:42:45Z","file_name":"Thesis_Calcabrini_pdfa.pdf","success":1,"file_id":"12888","content_type":"application/pdf","access_level":"open_access","file_size":8742220}],"date_published":"2023-04-28T00:00:00Z","ddc":["546","541"],"abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"status":"public"},{"date_created":"2023-05-04T08:35:01Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.02153"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023."},"date_updated":"2023-11-13T07:47:30Z","_id":"12890","year":"2023","issue":"5","acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","volume":108,"title":"Stochastic cellular automaton model of culture formation","day":"08","external_id":{"arxiv":["2305.02153"]},"intvolume":"       108","oa":1,"publisher":"American Physical Society","language":[{"iso":"eng"}],"arxiv":1,"oa_version":"Preprint","publication":"Physical Review E","related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"relation":"research_data","id":"12869","status":"public"}]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"doi":"10.1103/PhysRevE.108.054307","article_number":"054307","month":"11","author":[{"last_name":"Klausen","full_name":"Klausen, Frederik Ravn","first_name":"Frederik Ravn"},{"first_name":"Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"}],"article_processing_charge":"No","scopus_import":"1","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.","lang":"eng"}],"date_published":"2023-11-08T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original"},{"has_accepted_license":"1","author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra"}],"month":"05","article_processing_charge":"No","date_published":"2023-05-05T00:00:00Z","abstract":[{"text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context.","lang":"eng"}],"ddc":["570"],"file":[{"date_created":"2023-05-05T13:01:14Z","relation":"main_file","embargo":"2024-05-05","checksum":"59b0303dc483f40a96a610a90aab7ee9","creator":"aschauer","file_id":"12907","content_type":"application/pdf","access_level":"closed","file_size":31434230,"embargo_to":"open_access","file_name":"Thesis_Schauer_final.pdf","date_updated":"2023-05-05T13:01:14Z"},{"checksum":"25f54e12479b6adaabd129a20568e6c1","creator":"aschauer","date_created":"2023-05-05T13:04:15Z","relation":"source_file","file_name":"Thesis_Schauer_final.docx","date_updated":"2023-05-05T13:04:15Z","file_id":"12908","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":43809109}],"status":"public","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8966","status":"public"},{"relation":"part_of_dissertation","id":"7888","status":"public"}]},"publication_identifier":{"issn":["2663 - 337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"type":"dissertation","page":"190","doi":"10.15479/at:ista:12891","degree_awarded":"PhD","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"year":"2023","day":"05","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","date_created":"2023-05-05T08:48:20Z","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239"}],"file_date_updated":"2023-05-05T13:04:15Z","_id":"12891","date_updated":"2023-08-21T06:25:48Z"},{"oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"M-Shop"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"type":"dissertation","page":"180","doi":"10.15479/at:ista:12897","degree_awarded":"PhD","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"9817","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7117"},{"status":"public","relation":"dissertation_contains","id":"13188"}]},"author":[{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"month":"05","article_processing_charge":"No","has_accepted_license":"1","status":"public","date_published":"2023-05-05T00:00:00Z","ddc":["516","004","518","531"],"abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"file":[{"file_size":50714445,"access_level":"open_access","content_type":"application/pdf","file_id":"12942","date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-hafner-2023may11-a2b.pdf","embargo":"2023-12-07","relation":"main_file","date_created":"2023-05-11T10:43:20Z","creator":"chafner","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a"},{"file_size":265319,"access_level":"closed","content_type":"application/pdf","file_id":"12943","date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-release-form.pdf","embargo_to":"open_access","relation":"source_file","date_created":"2023-05-11T10:43:44Z","creator":"chafner","checksum":"a6b51334be2b81672357b1549afab40c"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"date_created":"2023-05-05T10:40:14Z","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2023-12-08T23:30:04Z","_id":"12897","date_updated":"2024-01-29T10:47:51Z","citation":{"chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023."},"department":[{"_id":"GradSch"},{"_id":"BeBi"}],"supervisor":[{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel"}],"year":"2023","day":"05","title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models"},{"status":"public","file":[{"creator":"rsahu","checksum":"8cbdab9c37ee55e591092a6f66b272c4","relation":"source_file","date_created":"2023-05-09T08:45:14Z","date_updated":"2023-06-06T22:30:03Z","file_name":"thesis.zip","embargo_to":"open_access","file_size":36767177,"access_level":"closed","content_type":"application/x-zip-compressed","file_id":"12928"},{"file_name":"thesis_pdfa_final.pdf","date_updated":"2023-07-06T11:37:40Z","file_size":17501990,"access_level":"closed","content_type":"application/pdf","file_id":"12929","creator":"rsahu","checksum":"439659ead46618147309be39d9dd5a8c","relation":"main_file","date_created":"2023-05-09T08:51:17Z"}],"date_published":"2023-05-05T00:00:00Z","ddc":["537","535","539"],"abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","last_name":"Sahu","full_name":"Sahu, Rishabh"}],"month":"05","has_accepted_license":"1","degree_awarded":"PhD","page":"190","doi":"10.15479/at:ista:12900","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"type":"dissertation","related_material":{"record":[{"status":"public","id":"9114","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"10924"},{"id":"13175","relation":"new_edition","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"publisher":"Institute of Science and Technology Austria","day":"05","title":"Cavity quantum electrooptics","year":"2023","supervisor":[{"full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"_id":"12900","date_updated":"2024-10-29T09:11:05Z","file_date_updated":"2023-07-06T11:37:40Z","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"citation":{"ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>"},"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-05-05T11:08:50Z"},{"contributor":[{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"file_date_updated":"2023-05-11T12:50:18Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T12:15:36Z","_id":"12933","doi":"10.15479/AT:ISTA:12933","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"citation":{"short":"G. Puixeu Sala, (2023).","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>.","mla":"Puixeu Sala, Gemma. <i>Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023."},"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"14058","status":"public"},{"status":"public","id":"14077","relation":"used_in_publication"}]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-05-10T10:00:49Z","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","day":"15","status":"public","ddc":["570"],"abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"date_published":"2023-05-15T00:00:00Z","file":[{"file_size":8029982,"access_level":"open_access","content_type":"text/csv","file_id":"12934","success":1,"file_name":"Dataset_S1.csv","date_updated":"2023-05-10T09:41:43Z","relation":"main_file","date_created":"2023-05-10T09:41:43Z","creator":"gpuixeus","checksum":"0ba0bcd0bb8b18d84792136a4370df90"},{"file_size":13667640,"access_level":"open_access","content_type":"text/csv","file_id":"12935","success":1,"date_updated":"2023-05-10T09:41:43Z","file_name":"Dataset_S2.csv","relation":"main_file","date_created":"2023-05-10T09:41:43Z","creator":"gpuixeus","checksum":"a62aa9a6d4904e0fdb699cf752640863"},{"date_updated":"2023-05-10T09:41:48Z","file_name":"Dataset_S3.csv","success":1,"content_type":"text/csv","file_id":"12936","file_size":8369141,"access_level":"open_access","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","creator":"gpuixeus","relation":"main_file","date_created":"2023-05-10T09:41:48Z"},{"file_size":19543247,"access_level":"open_access","content_type":"text/csv","file_id":"12937","success":1,"date_updated":"2023-05-10T09:41:50Z","file_name":"Dataset_S4.csv","relation":"main_file","date_created":"2023-05-10T09:41:50Z","creator":"gpuixeus","checksum":"f6156e5fc44446c907ddd0d7289d4cf8"},{"creator":"gpuixeus","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","date_created":"2023-05-11T12:50:18Z","relation":"main_file","success":1,"date_updated":"2023-05-11T12:50:18Z","file_name":"readme.txt","access_level":"open_access","file_size":4566,"file_id":"12944","content_type":"text/plain"}],"month":"05","author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma"}],"article_processing_charge":"No","has_accepted_license":"1","year":"2023"},{"date_created":"2023-05-15T14:52:36Z","alternative_title":["ISTA Thesis"],"publication_status":"published","citation":{"ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>.","mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>","ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"EdHa"}],"_id":"12964","date_updated":"2023-08-04T11:02:40Z","file_date_updated":"2023-05-19T07:04:25Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2023","supervisor":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"}],"day":"17","title":"Mechanochemical pattern formation across biological scales","publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"related_material":{"record":[{"status":"public","id":"8602","relation":"part_of_dissertation"}]},"oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12964","page":"146","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"type":"dissertation","has_accepted_license":"1","article_processing_charge":"No","author":[{"id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","first_name":"Daniel R","full_name":"Boocock, Daniel R","last_name":"Boocock"}],"month":"05","file":[{"creator":"dboocock","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","embargo":"2024-05-17","relation":"main_file","date_created":"2023-05-17T13:39:54Z","file_name":"thesis_boocock.pdf","date_updated":"2023-05-19T07:04:25Z","embargo_to":"open_access","file_size":40414730,"access_level":"closed","content_type":"application/pdf","file_id":"12988"},{"creator":"dboocock","checksum":"581a2313ffeb40fe77e8a122a25a7795","relation":"source_file","date_created":"2023-05-17T13:39:53Z","date_updated":"2023-05-17T14:35:13Z","file_name":"thesis_boocock.zip","file_size":34338567,"access_level":"closed","content_type":"application/zip","file_id":"12989"}],"date_published":"2023-05-17T00:00:00Z","ddc":["530"],"abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"status":"public"}]