[{"status":"public","keyword":["General Physics and Astronomy"],"isi":1,"scopus_import":"1","citation":{"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>.","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.","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>","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>","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."},"publication":"Physical Review Letters","corr_author":"1","issue":"10","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"pmid":1,"date_updated":"2025-04-23T08:53:33Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"title":"Spin-electric coupling in lead halide perovskites","article_number":"106901","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"volume":130,"date_published":"2023-03-10T00:00:00Z","year":"2023","oa":1,"arxiv":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."}],"publication_status":"published","article_type":"original","day":"10","oa_version":"Preprint","external_id":{"pmid":["36962044"],"isi":["000982435900002"],"arxiv":["2203.09443"]},"month":"03","doi":"10.1103/physrevlett.130.106901","author":[{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek"},{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","last_name":"Ashourishokri","first_name":"Younes"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"first_name":"Zhanybek","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"}],"date_created":"2023-03-14T13:11:59Z","intvolume":"       130","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.09443","open_access":"1"}],"publisher":"American Physical Society","_id":"12723"},{"department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"issue":"12","corr_author":"1","scopus_import":"1","isi":1,"publication":"Physical Review B","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>.","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.","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).","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>","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>","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."},"status":"public","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"article_number":"125201","article_processing_charge":"No","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"date_updated":"2024-10-09T21:04:46Z","title":"Effective model for studying optical properties of lead halide perovskites","month":"03","day":"15","external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"oa_version":"Preprint","publication_status":"published","article_type":"original","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."}],"oa":1,"year":"2023","volume":107,"date_published":"2023-03-15T00:00:00Z","arxiv":1,"publisher":"American Physical Society","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"_id":"12724","intvolume":"       107","type":"journal_article","doi":"10.1103/physrevb.107.125201","author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"last_name":"Shiva Kumar","first_name":"Abhishek","full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan"},{"last_name":"Ashourishokri","first_name":"Younes","full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334"},{"full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov","first_name":"Ayan"},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Zhanybek","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"}],"date_created":"2023-03-14T13:13:05Z"},{"status":"public","page":"260","citation":{"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>","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>","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <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.","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>.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023."},"degree_awarded":"PhD","corr_author":"1","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"title":"Synchronization in collectively moving active matter","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-07T13:29:13Z","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"year":"2023","date_published":"2023-03-23T00:00:00Z","file_date_updated":"2023-11-24T11:57:46Z","related_material":{"record":[{"id":"461","status":"public","relation":"part_of_dissertation"},{"id":"10791","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7932","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10703","status":"public"},{"relation":"new_edition","id":"14530","status":"public"}]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"publication_status":"published","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"}],"oa_version":"None","OA_place":"publisher","day":"23","month":"03","has_accepted_license":"1","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael"}],"date_created":"2023-03-15T13:22:13Z","doi":"10.15479/at:ista:12726","type":"dissertation","file":[{"description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","date_created":"2023-03-23T12:49:23Z","creator":"cchlebak","date_updated":"2023-11-24T11:57:46Z","file_id":"12745","relation":"main_file","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","access_level":"closed","file_size":63734746,"content_type":"application/pdf"},{"file_name":"Thesis_Riedl_2023_source.rar","date_created":"2023-03-23T12:54:34Z","creator":"cchlebak","date_updated":"2023-09-24T22:30:03Z","file_size":339473651,"access_level":"closed","embargo_to":"open_access","content_type":"application/octet-stream","file_id":"12746","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","relation":"source_file"}],"_id":"12726","supervisor":[{"first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"publisher":"Institute of Science and Technology Austria"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"ddc":["530"],"corr_author":"1","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"citation":{"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>.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","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>.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","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>","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>","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023."},"page":"158","degree_awarded":"PhD","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","date_updated":"2026-04-07T13:26:32Z","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","month":"03","oa_version":"Published Version","ec_funded":1,"day":"21","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"12750","relation":"part_of_dissertation"},{"status":"public","id":"11470","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8308"},{"relation":"part_of_dissertation","id":"11469","status":"public"}]},"file_date_updated":"2023-03-23T16:43:14Z","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"}],"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"date_published":"2023-03-21T00:00:00Z","oa":1,"year":"2023","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"}],"_id":"12732","publisher":"Institute of Science and Technology Austria","file":[{"creator":"pbrighi","file_name":"Thesis_sub_PBrighi.zip","date_created":"2023-03-23T16:42:56Z","date_updated":"2023-03-23T16:42:56Z","file_id":"12753","relation":"source_file","checksum":"5d2de651ef9449c1b8dc27148ca74777","access_level":"closed","file_size":42167561,"content_type":"application/zip"},{"creator":"pbrighi","date_created":"2023-03-23T16:43:14Z","file_name":"Thesis_PBrighi.pdf","date_updated":"2023-03-23T16:43:14Z","file_size":13977000,"access_level":"open_access","content_type":"application/pdf","file_id":"12754","checksum":"7caa153d4a5b0873a79358787d2dfe1e","success":1,"relation":"main_file"}],"type":"dissertation","date_created":"2023-03-17T13:30:48Z","author":[{"orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro","last_name":"Brighi","first_name":"Pietro"}],"doi":"10.15479/at:ista:12732","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}]},{"status":"public","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"107-118","citation":{"short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 107–18. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>.","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 107–18, doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>.","ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2023:107-118. doi:<a href=\"https://doi.org/10.1145/3572848.3577481\">10.1145/3572848.3577481</a>","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577481\">https://doi.org/10.1145/3572848.3577481</a>","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Montreal, QC, Canada, 2023, pp. 107–118."},"scopus_import":"1","department":[{"_id":"DaAl"}],"title":"Fast and scalable channels in Kotlin Coroutines","publication_identifier":{"isbn":["9798400700156"]},"date_updated":"2023-03-20T07:29:28Z","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2023-02-25","location":"Montreal, QC, Canada","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"quality_controlled":"1","arxiv":1,"year":"2023","oa":1,"date_published":"2023-02-25T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}],"external_id":{"arxiv":["2211.04986"]},"oa_version":"Preprint","day":"25","month":"02","author":[{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"},{"last_name":"Elizarov","first_name":"Roman","full_name":"Elizarov, Roman"}],"date_created":"2023-03-19T23:00:58Z","doi":"10.1145/3572848.3577481","type":"conference","_id":"12735","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"publisher":"Association for Computing Machinery"},{"doi":"10.1145/3572848.3577512","date_created":"2023-03-19T23:00:58Z","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown"},{"last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander"},{"last_name":"Kokorin","first_name":"Ilya","full_name":"Kokorin, Ilya"}],"type":"conference_poster","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"_id":"12736","date_published":"2023-02-25T00:00:00Z","year":"2023","oa":1,"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."}],"publication_status":"published","day":"25","oa_version":"Published Version","month":"02","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.","date_updated":"2026-06-18T17:29:03Z","publication_identifier":{"isbn":["9798400700156"]},"title":"Unexpected scaling in path copying trees","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Montreal, QB, Canada","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2023-02-25"},"language":[{"iso":"eng"}],"status":"public","scopus_import":"1","page":"438-440","citation":{"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.","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>","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>","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>.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. <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>.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023."},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","ddc":["000"],"department":[{"_id":"DaAl"},{"_id":"GradSch"}]},{"title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","publication_identifier":{"issn":["0020-1669"],"eissn":["1520-510X"]},"acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","date_updated":"2025-04-24T11:32:09Z","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","OA_type":"green","status":"public","publication":"Inorganic Chemistry","citation":{"ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. 2023;62(11):4625-4636. doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., &#38; Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. <i>Inorganic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>","ieee":"Á. García-Romero <i>et al.</i>, “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” <i>Inorganic Chemistry</i>, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” <i>Inorganic Chemistry</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">https://doi.org/10.1021/acs.inorgchem.3c00057</a>.","ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” <i>Inorganic Chemistry</i>, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:<a href=\"https://doi.org/10.1021/acs.inorgchem.3c00057\">10.1021/acs.inorgchem.3c00057</a>.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636."},"page":"4625-4636","scopus_import":"1","isi":1,"issue":"11","department":[{"_id":"StFr"}],"pmid":1,"author":[{"first_name":"Álvaro","last_name":"García-Romero","full_name":"García-Romero, Álvaro"},{"last_name":"Waters","first_name":"Jessica E.","full_name":"Waters, Jessica E."},{"last_name":"Jethwa","first_name":"Rajesh B","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","full_name":"Jethwa, Rajesh B"},{"full_name":"Bond, Andrew D.","first_name":"Andrew D.","last_name":"Bond"},{"last_name":"Colebatch","first_name":"Annie L.","full_name":"Colebatch, Annie L."},{"full_name":"García-Rodríguez, Raúl","last_name":"García-Rodríguez","first_name":"Raúl"},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."}],"date_created":"2023-03-19T23:00:59Z","doi":"10.1021/acs.inorgchem.3c00057","intvolume":"        62","type":"journal_article","_id":"12737","publisher":"American Chemical Society","main_file_link":[{"open_access":"1","url":"https://uvadoc.uva.es/handle/10324/59798"}],"oa":1,"year":"2023","volume":62,"date_published":"2023-03-08T00:00:00Z","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed."}],"external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"oa_version":"Submitted Version","OA_place":"repository","day":"08","month":"03"},{"keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"status":"public","publication":"Nature Metabolism","page":"495-515","citation":{"ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>, vol. 5, Springer Nature, 2023, pp. 495–515, doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>.","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” <i>Nature Metabolism</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515.","ieee":"D. Cikes <i>et al.</i>, “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” <i>Nature Metabolism</i>, vol. 5. Springer Nature, pp. 495–515, 2023.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-023-00766-2\">https://doi.org/10.1038/s42255-023-00766-2</a>","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. <i>Nature Metabolism</i>. 2023;5:495-515. doi:<a href=\"https://doi.org/10.1038/s42255-023-00766-2\">10.1038/s42255-023-00766-2</a>"},"scopus_import":"1","isi":1,"pmid":1,"department":[{"_id":"Bio"}],"title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","publication_identifier":{"issn":["2522-5812"]},"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","date_updated":"2023-11-28T07:31:33Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2023","volume":5,"date_published":"2023-03-20T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s42255-023-00791-1","relation":"erratum"}]},"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing."}],"external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"oa_version":"Preprint","day":"20","month":"03","date_created":"2023-03-23T12:58:43Z","author":[{"last_name":"Cikes","first_name":"Domagoj","full_name":"Cikes, Domagoj"},{"full_name":"Elsayad, Kareem","first_name":"Kareem","last_name":"Elsayad"},{"full_name":"Sezgin, Erdinc","last_name":"Sezgin","first_name":"Erdinc"},{"full_name":"Koitai, Erika","first_name":"Erika","last_name":"Koitai"},{"last_name":"Ferenc","first_name":"Torma","full_name":"Ferenc, Torma"},{"last_name":"Orthofer","first_name":"Michael","full_name":"Orthofer, Michael"},{"full_name":"Yarwood, Rebecca","first_name":"Rebecca","last_name":"Yarwood"},{"full_name":"Heinz, Leonhard X.","first_name":"Leonhard X.","last_name":"Heinz"},{"full_name":"Sedlyarov, Vitaly","last_name":"Sedlyarov","first_name":"Vitaly"},{"orcid":"0000-0002-8821-8236","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","full_name":"Darwish-Miranda, Nasser","last_name":"Darwish-Miranda","first_name":"Nasser"},{"full_name":"Taylor, Adrian","last_name":"Taylor","first_name":"Adrian"},{"last_name":"Grapentine","first_name":"Sophie","full_name":"Grapentine, Sophie"},{"full_name":"al-Murshedi, Fathiya","first_name":"Fathiya","last_name":"al-Murshedi"},{"full_name":"Abot, Anne","last_name":"Abot","first_name":"Anne"},{"first_name":"Adelheid","last_name":"Weidinger","full_name":"Weidinger, Adelheid"},{"last_name":"Kutchukian","first_name":"Candice","full_name":"Kutchukian, Candice"},{"last_name":"Sanchez","first_name":"Colline","full_name":"Sanchez, Colline"},{"full_name":"Cronin, Shane J. F.","last_name":"Cronin","first_name":"Shane J. F."},{"full_name":"Novatchkova, Maria","first_name":"Maria","last_name":"Novatchkova"},{"last_name":"Kavirayani","first_name":"Anoop","full_name":"Kavirayani, Anoop"},{"last_name":"Schuetz","first_name":"Thomas","full_name":"Schuetz, Thomas"},{"first_name":"Bernhard","last_name":"Haubner","full_name":"Haubner, Bernhard"},{"full_name":"Haas, Lisa","first_name":"Lisa","last_name":"Haas"},{"full_name":"Hagelkruys, Astrid","first_name":"Astrid","last_name":"Hagelkruys"},{"full_name":"Jackowski, Suzanne","last_name":"Jackowski","first_name":"Suzanne"},{"full_name":"Kozlov, Andrey","last_name":"Kozlov","first_name":"Andrey"},{"full_name":"Jacquemond, Vincent","last_name":"Jacquemond","first_name":"Vincent"},{"full_name":"Knauf, Claude","last_name":"Knauf","first_name":"Claude"},{"full_name":"Superti-Furga, Giulio","last_name":"Superti-Furga","first_name":"Giulio"},{"first_name":"Eric","last_name":"Rullman","full_name":"Rullman, Eric"},{"full_name":"Gustafsson, Thomas","last_name":"Gustafsson","first_name":"Thomas"},{"full_name":"McDermot, John","last_name":"McDermot","first_name":"John"},{"full_name":"Lowe, Martin","first_name":"Martin","last_name":"Lowe"},{"first_name":"Zsolt","last_name":"Radak","full_name":"Radak, Zsolt"},{"full_name":"Chamberlain, Jeffrey S.","last_name":"Chamberlain","first_name":"Jeffrey S."},{"last_name":"Bakovic","first_name":"Marica","full_name":"Bakovic, Marica"},{"full_name":"Banka, Siddharth","last_name":"Banka","first_name":"Siddharth"},{"last_name":"Penninger","first_name":"Josef M.","full_name":"Penninger, Josef M."}],"doi":"10.1038/s42255-023-00766-2","type":"journal_article","intvolume":"         5","_id":"12747","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"publisher":"Springer Nature"},{"status":"public","scopus_import":"1","isi":1,"publication":"Science Advances","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"},"citation":{"ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>.","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>."},"issue":"11","ddc":["570"],"corr_author":"1","pmid":1,"department":[{"_id":"AnSa"}],"publication_identifier":{"eissn":["2375-2548"]},"date_updated":"2025-04-23T08:50:02Z","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","article_number":"eade5224","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"year":"2023","date_published":"2023-03-17T00:00:00Z","volume":9,"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"file_date_updated":"2023-03-27T06:24:49Z","day":"17","ec_funded":1,"external_id":{"pmid":["36921039"],"isi":["000968083500010"]},"oa_version":"Published Version","month":"03","has_accepted_license":"1","doi":"10.1126/sciadv.ade5224","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"author":[{"last_name":"Hurtig","first_name":"Fredrik","full_name":"Hurtig, Fredrik"},{"first_name":"Thomas C.Q.","last_name":"Burgers","full_name":"Burgers, Thomas C.Q."},{"full_name":"Cezanne, Alice","last_name":"Cezanne","first_name":"Alice"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"full_name":"Mol, Frank N.","first_name":"Frank N.","last_name":"Mol"},{"full_name":"Traparić, Jovan","last_name":"Traparić","first_name":"Jovan"},{"full_name":"Pulschen, Andre Arashiro","last_name":"Pulschen","first_name":"Andre Arashiro"},{"full_name":"Nierhaus, Tim","last_name":"Nierhaus","first_name":"Tim"},{"last_name":"Tarrason-Risa","first_name":"Gabriel","full_name":"Tarrason-Risa, Gabriel"},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"first_name":"Jan","last_name":"Löwe","full_name":"Löwe, Jan"},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"first_name":"Rifka","last_name":"Vlijm","full_name":"Vlijm, Rifka"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"}],"date_created":"2023-03-26T22:01:06Z","type":"journal_article","intvolume":"         9","file":[{"file_name":"2023_ScienceAdvances_Hurtig.pdf","date_created":"2023-03-27T06:24:49Z","creator":"dernst","date_updated":"2023-03-27T06:24:49Z","access_level":"open_access","file_size":1826471,"content_type":"application/pdf","file_id":"12768","relation":"main_file","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5"}],"publisher":"American Association for the Advancement of Science","_id":"12756"},{"author":[{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"date_created":"2023-03-26T22:01:06Z","doi":"10.1042/BCJ20210285","type":"journal_article","intvolume":"       480","_id":"12757","publisher":"Portland Press","main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"date_published":"2023-03-15T00:00:00Z","volume":480,"oa":1,"year":"2023","abstract":[{"lang":"eng","text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues."}],"article_type":"review","publication_status":"published","oa_version":"Published Version","external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"day":"15","has_accepted_license":"1","month":"03","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","date_updated":"2024-10-09T21:04:50Z","publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"319-333","citation":{"apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. Portland Press. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>","ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. <i>The Biochemical Journal</i>. 2023;480(5):319-333. doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” <i>The Biochemical Journal</i>, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>. Portland Press, 2023. <a href=\"https://doi.org/10.1042/BCJ20210285\">https://doi.org/10.1042/BCJ20210285</a>.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” <i>The Biochemical Journal</i>, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:<a href=\"https://doi.org/10.1042/BCJ20210285\">10.1042/BCJ20210285</a>.","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333."},"publication":"The Biochemical Journal","isi":1,"scopus_import":"1","corr_author":"1","ddc":["570"],"issue":"5","pmid":1,"department":[{"_id":"LeSa"}]},{"pmid":1,"department":[{"_id":"FyKo"},{"_id":"MaRo"}],"issue":"3","ddc":["570"],"scopus_import":"1","isi":1,"publication":"PLoS ONE","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"},"citation":{"ieee":"M. A. Pak <i>et al.</i>, “Using AlphaFold to predict the impact of single mutations on protein stability and function,” <i>PLoS ONE</i>, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. 2023;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>.","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>."},"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e0282689","article_processing_charge":"No","publication_identifier":{"eissn":["1932-6203"]},"date_updated":"2025-04-23T08:50:30Z","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","month":"03","has_accepted_license":"1","day":"16","external_id":{"pmid":["36928239"],"isi":["000985134400106"]},"oa_version":"Published Version","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"file_date_updated":"2023-03-27T07:09:08Z","year":"2023","oa":1,"date_published":"2023-03-16T00:00:00Z","volume":18,"publisher":"Public Library of Science","_id":"12758","file":[{"date_updated":"2023-03-27T07:09:08Z","creator":"dernst","date_created":"2023-03-27T07:09:08Z","file_name":"2023_PLoSOne_Pak.pdf","content_type":"application/pdf","access_level":"open_access","file_size":856625,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","success":1,"relation":"main_file","file_id":"12771"}],"type":"journal_article","intvolume":"        18","doi":"10.1371/journal.pone.0282689","author":[{"first_name":"Marina A.","last_name":"Pak","full_name":"Pak, Marina A."},{"last_name":"Markhieva","first_name":"Karina A.","full_name":"Markhieva, Karina A."},{"full_name":"Novikova, Mariia S.","last_name":"Novikova","first_name":"Mariia S."},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"full_name":"Vorobyev, Ilya S.","last_name":"Vorobyev","first_name":"Ilya S."},{"first_name":"Ekaterina","last_name":"Maksimova","full_name":"Maksimova, Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"last_name":"Ivankov","first_name":"Dmitry N.","full_name":"Ivankov, Dmitry N."}],"date_created":"2023-03-26T22:01:07Z"},{"_id":"12759","publisher":"Public Library of Science","file":[{"file_size":7290413,"access_level":"open_access","content_type":"application/pdf","file_id":"12770","success":1,"relation":"main_file","checksum":"2380331ec27cc87808826fc64419ac1c","creator":"dernst","date_created":"2023-03-27T06:51:09Z","file_name":"2023_PLoSOne_Rothman.pdf","date_updated":"2023-03-27T06:51:09Z"}],"type":"journal_article","intvolume":"        18","date_created":"2023-03-26T22:01:07Z","author":[{"full_name":"Rothman, Jason Seth","last_name":"Rothman","first_name":"Jason Seth"},{"first_name":"Carolina","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"full_name":"Angus Silver, R.","first_name":"R.","last_name":"Angus Silver"}],"doi":"10.1371/journal.pone.0277148","project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits"},{"grant_number":"V00739","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"month":"03","has_accepted_license":"1","ec_funded":1,"external_id":{"pmid":["36930689"],"isi":["001024737400001"]},"oa_version":"Published Version","day":"17","file_date_updated":"2023-03-27T06:51:09Z","article_type":"original","publication_status":"published","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"year":"2023","oa":1,"volume":18,"date_published":"2023-03-17T00:00:00Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","article_number":"e0277148","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","publication_identifier":{"eissn":["1932-6203"]},"date_updated":"2025-04-23T08:50:50Z","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","department":[{"_id":"PeJo"}],"pmid":1,"issue":"3 March","ddc":["570"],"publication":"PLoS ONE","citation":{"ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>.","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” <i>PLoS ONE</i>, vol. 18, no. 3 March. Public Library of Science, 2023.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. 2023;18(3 March). doi:<a href=\"https://doi.org/10.1371/journal.pone.0277148\">10.1371/journal.pone.0277148</a>","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., &#38; Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0277148\">https://doi.org/10.1371/journal.pone.0277148</a>"},"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"},"scopus_import":"1","isi":1,"status":"public"},{"status":"public","scopus_import":"1","isi":1,"publication":"40th International Symposium on Theoretical Aspects of Computer Science","citation":{"short":"M. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Henzinger, Monika, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>.","mla":"Henzinger, Monika, et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>.","ista":"Henzinger M, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","ama":"Henzinger M, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: <i>40th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">10.4230/LIPIcs.STACS.2023.36</a>","apa":"Henzinger, M., Neumann, S., Räcke, H., &#38; Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In <i>40th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2023.36\">https://doi.org/10.4230/LIPIcs.STACS.2023.36</a>","ieee":"M. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in <i>40th International Symposium on Theoretical Aspects of Computer Science</i>, Hamburg, Germany, 2023, vol. 254."},"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"},"corr_author":"1","ddc":["000"],"department":[{"_id":"MoHe"}],"publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"date_updated":"2025-09-09T12:22:44Z","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","title":"Dynamic maintenance of monotone dynamic programs and applications","article_number":"36","article_processing_charge":"No","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"conference":{"end_date":"2023-03-09","location":"Hamburg, Germany","name":"STACS: Symposium on Theoretical Aspects of Computer Science","start_date":"2023-03-07"},"year":"2023","oa":1,"volume":254,"date_published":"2023-03-01T00:00:00Z","arxiv":1,"alternative_title":["LIPIcs"],"publication_status":"published","abstract":[{"lang":"eng","text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack."}],"file_date_updated":"2023-03-27T06:37:22Z","day":"01","ec_funded":1,"external_id":{"isi":["001532693100036"],"arxiv":["2301.01744"]},"oa_version":"Published Version","month":"03","has_accepted_license":"1","doi":"10.4230/LIPIcs.STACS.2023.36","project":[{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775"}],"date_created":"2023-03-26T22:01:07Z","author":[{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Neumann, Stefan","last_name":"Neumann","first_name":"Stefan"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"intvolume":"       254","type":"conference","file":[{"file_id":"12769","success":1,"checksum":"22141ab8bc55188e2dfff665e5daecbd","relation":"main_file","file_size":872706,"access_level":"open_access","content_type":"application/pdf","file_name":"2023_LIPICS_HenzingerM.pdf","date_created":"2023-03-27T06:37:22Z","creator":"dernst","date_updated":"2023-03-27T06:37:22Z"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"12760"},{"abstract":[{"text":"We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine\r\nthe fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent\r\nmultiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"publication_status":"published","article_type":"original","arxiv":1,"volume":33,"date_published":"2023-02-01T00:00:00Z","oa":1,"year":"2023","month":"02","oa_version":"Preprint","external_id":{"isi":["000946432400015"],"arxiv":["2012.13218"]},"ec_funded":1,"day":"01","type":"journal_article","intvolume":"        33","author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856"}],"date_created":"2023-03-26T22:01:08Z","doi":"10.1214/22-AAP1820","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"_id":"12761","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.13218"}],"publisher":"Institute of Mathematical Statistics","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Functional central limit theorems for Wigner matrices. Annals of Applied Probability. 33(1), 447–489.","mla":"Cipolloni, Giorgio, et al. “Functional Central Limit Theorems for Wigner Matrices.” <i>Annals of Applied Probability</i>, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 447–89, doi:<a href=\"https://doi.org/10.1214/22-AAP1820\">10.1214/22-AAP1820</a>.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Functional Central Limit Theorems for Wigner Matrices.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/22-AAP1820\">https://doi.org/10.1214/22-AAP1820</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Applied Probability 33 (2023) 447–489.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Functional central limit theorems for Wigner matrices,” <i>Annals of Applied Probability</i>, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 447–489, 2023.","ama":"Cipolloni G, Erdös L, Schröder DJ. Functional central limit theorems for Wigner matrices. <i>Annals of Applied Probability</i>. 2023;33(1):447-489. doi:<a href=\"https://doi.org/10.1214/22-AAP1820\">10.1214/22-AAP1820</a>","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2023). Functional central limit theorems for Wigner matrices. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-AAP1820\">https://doi.org/10.1214/22-AAP1820</a>"},"page":"447-489","publication":"Annals of Applied Probability","isi":1,"scopus_import":"1","status":"public","department":[{"_id":"LaEr"}],"corr_author":"1","issue":"1","article_processing_charge":"No","title":"Functional central limit theorems for Wigner matrices","acknowledgement":"The second author is partially funded by the ERC Advanced Grant “RMTBEYOND” No. 101020331. The third author is supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation.","date_updated":"2025-04-14T07:57:19Z","publication_identifier":{"issn":["1050-5164"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1"},{"status":"public","scopus_import":"1","publication":"Journal of Applied and Computational Topology","page":"619-641","citation":{"apa":"Boissonnat, J. D., &#38; Wintraecken, M. (2023). The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>","ama":"Boissonnat JD, Wintraecken M. The reach of subsets of manifolds. <i>Journal of Applied and Computational Topology</i>. 2023;7:619-641. doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>","ieee":"J. D. Boissonnat and M. Wintraecken, “The reach of subsets of manifolds,” <i>Journal of Applied and Computational Topology</i>, vol. 7. Springer Nature, pp. 619–641, 2023.","short":"J.D. Boissonnat, M. Wintraecken, Journal of Applied and Computational Topology 7 (2023) 619–641.","chicago":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s41468-023-00116-x\">https://doi.org/10.1007/s41468-023-00116-x</a>.","mla":"Boissonnat, Jean Daniel, and Mathijs Wintraecken. “The Reach of Subsets of Manifolds.” <i>Journal of Applied and Computational Topology</i>, vol. 7, Springer Nature, 2023, pp. 619–41, doi:<a href=\"https://doi.org/10.1007/s41468-023-00116-x\">10.1007/s41468-023-00116-x</a>.","ista":"Boissonnat JD, Wintraecken M. 2023. The reach of subsets of manifolds. Journal of Applied and Computational Topology. 7, 619–641."},"corr_author":"1","department":[{"_id":"HeEd"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"acknowledgement":"We thank Eddie Aamari, David Cohen-Steiner, Isa Costantini, Fred Chazal, Ramsay Dyer, André Lieutier, and Alef Sterk for discussion and Pierre Pansu for encouragement. We further acknowledge the anonymous reviewers whose comments helped improve the exposition.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). The first author is further supported by the French government, through the 3IA Côte d’Azur Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-19-P3IA-0002. The second author is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Austrian science fund (FWF) M-3073.","date_updated":"2025-04-14T07:44:01Z","title":"The reach of subsets of manifolds","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"year":"2023","volume":7,"date_published":"2023-09-01T00:00:00Z","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality."}],"day":"01","ec_funded":1,"oa_version":"Submitted Version","month":"09","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"doi":"10.1007/s41468-023-00116-x","date_created":"2023-03-26T22:01:08Z","author":[{"full_name":"Boissonnat, Jean Daniel","first_name":"Jean Daniel","last_name":"Boissonnat"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         7","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://inserm.hal.science/INRIA-SACLAY/hal-04083524v1"}],"publisher":"Springer Nature","_id":"12763"},{"scopus_import":"1","isi":1,"publication":"Discrete and Computational Geometry","page":"123-153","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"},"citation":{"mla":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>, vol. 70, Springer Nature, 2023, pp. 123–53, doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>.","ista":"Kourimska H. 2023. Discrete yamabe problem for polyhedral surfaces. Discrete and Computational Geometry. 70, 123–153.","chicago":"Kourimska, Hana. “Discrete Yamabe Problem for Polyhedral Surfaces.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>.","short":"H. Kourimska, Discrete and Computational Geometry 70 (2023) 123–153.","ieee":"H. Kourimska, “Discrete yamabe problem for polyhedral surfaces,” <i>Discrete and Computational Geometry</i>, vol. 70. Springer Nature, pp. 123–153, 2023.","ama":"Kourimska H. Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. 2023;70:123-153. doi:<a href=\"https://doi.org/10.1007/s00454-023-00484-2\">10.1007/s00454-023-00484-2</a>","apa":"Kourimska, H. (2023). Discrete yamabe problem for polyhedral surfaces. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00484-2\">https://doi.org/10.1007/s00454-023-00484-2</a>"},"status":"public","pmid":1,"department":[{"_id":"HeEd"}],"corr_author":"1","ddc":["510"],"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"date_updated":"2025-04-23T08:59:15Z","acknowledgement":"Open access funding provided by the Austrian Science Fund (FWF). This research was supported by the FWF grant, Project number I4245-N35, and by the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) - Project-ID 195170736 - TRR109.","title":"Discrete yamabe problem for polyhedral surfaces","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique."}],"file_date_updated":"2023-10-04T11:46:24Z","oa":1,"year":"2023","volume":70,"date_published":"2023-07-01T00:00:00Z","month":"07","has_accepted_license":"1","day":"01","external_id":{"pmid":["37292248"],"isi":["000948148000001"]},"oa_version":"Published Version","intvolume":"        70","type":"journal_article","project":[{"grant_number":"I04245","_id":"26AD5D90-B435-11E9-9278-68D0E5697425","name":"Algebraic Footprints of Geometric Features in Homology","call_identifier":"FWF"}],"doi":"10.1007/s00454-023-00484-2","date_created":"2023-03-26T22:01:09Z","author":[{"orcid":"0000-0001-7841-0091","full_name":"Kourimska, Hana","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","last_name":"Kourimska","first_name":"Hana"}],"publisher":"Springer Nature","_id":"12764","file":[{"file_id":"14396","relation":"main_file","success":1,"checksum":"cdbf90ba4a7ddcb190d37b9e9d4cb9d3","file_size":1026683,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_created":"2023-10-04T11:46:24Z","file_name":"2023_DiscreteGeometry_Kourimska.pdf","date_updated":"2023-10-04T11:46:24Z"}]},{"OA_place":"repository","day":"01","external_id":{"isi":["000948940500001"]},"oa_version":"Submitted Version","month":"04","oa":1,"year":"2023","volume":37,"date_published":"2023-04-01T00:00:00Z","article_type":"review","publication_status":"published","abstract":[{"text":"Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection.\r\nBecause they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group.\r\nHere, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals.\r\nWe discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies.\r\nFinally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.","lang":"eng"}],"publisher":"British Ecological Society","main_file_link":[{"open_access":"1","url":"https://digitalcommons.chapman.edu/cgi/viewcontent.cgi?article=1585&context=sees_articles"}],"_id":"12765","doi":"10.1111/1365-2435.14310","author":[{"last_name":"Stockmaier","first_name":"Sebastian","full_name":"Stockmaier, Sebastian"},{"full_name":"Ulrich, Yuko","first_name":"Yuko","last_name":"Ulrich"},{"full_name":"Albery, Gregory F.","last_name":"Albery","first_name":"Gregory F."},{"first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"first_name":"Patricia C.","last_name":"Lopes","full_name":"Lopes, Patricia C."}],"date_created":"2023-03-26T22:01:09Z","type":"journal_article","intvolume":"        37","issue":"4","department":[{"_id":"SyCr"}],"status":"public","scopus_import":"1","isi":1,"publication":"Functional Ecology","page":"809-820","citation":{"short":"S. Stockmaier, Y. Ulrich, G.F. Albery, S. Cremer, P.C. Lopes, Functional Ecology 37 (2023) 809–820.","chicago":"Stockmaier, Sebastian, Yuko Ulrich, Gregory F. Albery, Sylvia Cremer, and Patricia C. Lopes. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>. British Ecological Society, 2023. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>.","ista":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. 2023. Behavioural defences against parasites across host social structures. Functional Ecology. 37(4), 809–820.","mla":"Stockmaier, Sebastian, et al. “Behavioural Defences against Parasites across Host Social Structures.” <i>Functional Ecology</i>, vol. 37, no. 4, British Ecological Society, 2023, pp. 809–20, doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>.","ama":"Stockmaier S, Ulrich Y, Albery GF, Cremer S, Lopes PC. Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. 2023;37(4):809-820. doi:<a href=\"https://doi.org/10.1111/1365-2435.14310\">10.1111/1365-2435.14310</a>","apa":"Stockmaier, S., Ulrich, Y., Albery, G. F., Cremer, S., &#38; Lopes, P. C. (2023). Behavioural defences against parasites across host social structures. <i>Functional Ecology</i>. British Ecological Society. <a href=\"https://doi.org/10.1111/1365-2435.14310\">https://doi.org/10.1111/1365-2435.14310</a>","ieee":"S. Stockmaier, Y. Ulrich, G. F. Albery, S. Cremer, and P. C. Lopes, “Behavioural defences against parasites across host social structures,” <i>Functional Ecology</i>, vol. 37, no. 4. British Ecological Society, pp. 809–820, 2023."},"quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","publication_identifier":{"eissn":["1365-2435"],"issn":["0269-8463"]},"date_updated":"2025-07-10T11:50:31Z","title":"Behavioural defences against parasites across host social structures","article_processing_charge":"No"},{"date_created":"2023-04-02T22:01:09Z","author":[{"full_name":"Zhang, Danyang","first_name":"Danyang","last_name":"Zhang"},{"full_name":"Lape, Remigijus","last_name":"Lape","first_name":"Remigijus"},{"first_name":"Saher A.","last_name":"Shaikh","full_name":"Shaikh, Saher A."},{"last_name":"Kohegyi","first_name":"Bianka K.","full_name":"Kohegyi, Bianka K."},{"last_name":"Watson","first_name":"Jake","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"full_name":"Cais, Ondrej","first_name":"Ondrej","last_name":"Cais"},{"first_name":"Terunaga","last_name":"Nakagawa","full_name":"Nakagawa, Terunaga"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"doi":"10.1038/s41467-023-37259-5","type":"journal_article","intvolume":"        14","file":[{"date_created":"2023-04-03T06:38:56Z","file_name":"2023_NatureComm_Zhang.pdf","creator":"dernst","date_updated":"2023-04-03T06:38:56Z","file_id":"12797","relation":"main_file","success":1,"checksum":"0a97b31191432dae5853bbb5ccb7698d","file_size":2613996,"access_level":"open_access","content_type":"application/pdf"}],"_id":"12786","publisher":"Springer Nature","volume":14,"date_published":"2023-03-25T00:00:00Z","oa":1,"year":"2023","file_date_updated":"2023-04-03T06:38:56Z","abstract":[{"lang":"eng","text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","external_id":{"isi":["001066658700003"]},"day":"25","has_accepted_license":"1","month":"03","title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","date_updated":"2023-12-13T11:15:58Z","publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","article_number":"1659","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","citation":{"apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>","ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>","ieee":"D. Zhang <i>et al.</i>, “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>.","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>, vol. 14, 1659, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>.","short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023)."},"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"},"publication":"Nature Communications","isi":1,"scopus_import":"1","ddc":["570"],"department":[{"_id":"PeJo"}]},{"oa_version":"Preprint","ec_funded":1,"external_id":{"isi":["000957635500003"],"pmid":["36962042"],"arxiv":["2206.07067"]},"day":"10","month":"03","arxiv":1,"date_published":"2023-03-10T00:00:00Z","volume":130,"year":"2023","oa":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/","relation":"press_release","description":"News on the ISTA website"}],"record":[{"relation":"dissertation_contains","status":"public","id":"19393"}]},"abstract":[{"text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants.","lang":"eng"}],"article_type":"original","publication_status":"published","_id":"12788","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2206.07067"}],"publisher":"American Physical Society","date_created":"2023-04-02T22:01:10Z","author":[{"first_name":"Volker","last_name":"Karle","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","orcid":"0000-0002-6963-0129"},{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevLett.130.103202","intvolume":"       130","type":"journal_article","corr_author":"1","issue":"10","department":[{"_id":"MiLe"}],"pmid":1,"status":"public","citation":{"ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>","apa":"Karle, V., Ghazaryan, A., &#38; Lemeshko, M. (2023). Topological charges of periodically kicked molecules. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">10.1103/PhysRevLett.130.103202</a>.","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.130.103202\">https://doi.org/10.1103/PhysRevLett.130.103202</a>."},"publication":"Physical Review Letters","isi":1,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","title":"Topological charges of periodically kicked molecules","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_updated":"2026-04-07T11:48:53Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"article_processing_charge":"No","article_number":"103202"},{"article_processing_charge":"No","article_number":"034901","title":"Accurate determination of the shapes of granular charge distributions","acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","date_updated":"2025-04-14T07:54:10Z","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>.","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>.","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” <i>Physical Review E</i>, vol. 107, no. 3. American Physical Society, 2023.","ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. 2023;107(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">10.1103/PhysRevE.107.034901</a>","apa":"Mujica, N., &#38; Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.034901\">https://doi.org/10.1103/PhysRevE.107.034901</a>"},"publication":"Physical Review E","isi":1,"scopus_import":"1","status":"public","pmid":1,"department":[{"_id":"ScWa"}],"corr_author":"1","ddc":["530"],"issue":"3","intvolume":"       107","type":"journal_article","date_created":"2023-04-02T22:01:10Z","author":[{"full_name":"Mujica, Nicolás","last_name":"Mujica","first_name":"Nicolás"},{"orcid":"0000-0002-2299-3176","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R"}],"doi":"10.1103/PhysRevE.107.034901","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"_id":"12789","publisher":"American Physical Society","file":[{"file_size":1428631,"access_level":"open_access","content_type":"application/pdf","file_id":"14612","relation":"main_file","success":1,"checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","date_created":"2023-11-27T09:51:48Z","file_name":"PhysRevE.107.034901 (1).pdf","creator":"swaituka","date_updated":"2023-11-27T09:51:48Z"}],"file_date_updated":"2023-11-27T09:51:48Z","abstract":[{"lang":"eng","text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior."}],"publication_status":"published","acknowledged_ssus":[{"_id":"M-Shop"}],"article_type":"original","volume":107,"date_published":"2023-03-01T00:00:00Z","year":"2023","oa":1,"has_accepted_license":"1","month":"03","oa_version":"Published Version","ec_funded":1,"external_id":{"pmid":["37072968"],"isi":["000992142700001"]},"day":"01"}]