[{"publisher":"Institute of Science and Technology Austria","date_created":"2023-03-15T13:22:13Z","date_published":"2023-03-23T00:00:00Z","doi":"10.15479/at:ista:12726","page":"260","day":"23","year":"2023","has_accepted_license":"1","title":"Synchronization in collectively moving active matter","article_processing_charge":"No","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria."},"month":"03","alternative_title":["ISTA Thesis"],"oa_version":"None","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"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"id":"7932","status":"public","relation":"part_of_dissertation"},{"id":"461","status":"public","relation":"part_of_dissertation"},{"relation":"new_edition","id":"14530","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"checksum":"eba0e19fe57a8c15e7aeab55a845efb7","file_id":"12745","relation":"main_file","access_level":"closed","content_type":"application/pdf","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","file_size":63734746,"date_updated":"2023-11-24T11:57:46Z"},{"date_created":"2023-03-23T12:54:34Z","file_name":"Thesis_Riedl_2023_source.rar","creator":"cchlebak","date_updated":"2023-09-24T22:30:03Z","file_size":339473651,"checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","file_id":"12746","access_level":"closed","relation":"source_file","content_type":"application/octet-stream","embargo_to":"open_access"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"status":"public","type":"dissertation","_id":"12726","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"file_date_updated":"2023-11-24T11:57:46Z","ddc":["530"],"date_updated":"2023-11-30T10:55:13Z","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}]},{"oa_version":"Updated Version","abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"month":"11","alternative_title":["ISTA Thesis"],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","file_id":"14536","file_size":36743942,"date_updated":"2023-11-15T09:52:54Z","creator":"mriedl","file_name":"Thesis_Riedl_2023_corr.pdf","date_created":"2023-11-15T09:52:54Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"id":"10703","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10791","status":"public"},{"relation":"part_of_dissertation","id":"7932","status":"public"},{"status":"public","id":"461","relation":"part_of_dissertation"},{"relation":"old_edition","status":"public","id":"12726"}]},"_id":"14530","status":"public","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"type":"dissertation","ddc":["530","570"],"supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-30T10:55:13Z","file_date_updated":"2023-11-15T09:52:54Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","oa":1,"day":"16","has_accepted_license":"1","year":"2023","doi":"10.15479/14530","date_published":"2023-11-16T00:00:00Z","date_created":"2023-11-15T09:59:03Z","page":"260","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530."},"title":"Synchronization in collectively moving active matter","author":[{"orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael"}],"article_processing_charge":"No"},{"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_size":34828019,"date_updated":"2023-11-22T09:46:06Z","creator":"pduc","file_name":"Phan_Thesis_pdfa.pdf","date_created":"2023-11-17T13:36:44Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"db0c37d213bc002125bd59690e9db246","file_id":"14548"},{"file_id":"14549","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"dissertation_src.zip","date_created":"2023-11-17T13:44:53Z","file_size":279319709,"date_updated":"2023-11-17T13:47:54Z","creator":"pduc"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10851"},{"relation":"part_of_dissertation","status":"public","id":"13264"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"11","supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"date_updated":"2023-11-30T10:56:04Z","ddc":["530"],"file_date_updated":"2023-11-22T09:46:06Z","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"_id":"14547","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"has_accepted_license":"1","year":"2023","day":"16","page":"80","date_published":"2023-11-16T00:00:00Z","doi":"10.15479/14547","date_created":"2023-11-17T13:45:26Z","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547.","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547.","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T","last_name":"Phan","full_name":"Phan, Duc T"}],"article_processing_charge":"No","title":"Resonant microwave spectroscopy of Al-InAs"},{"publication_status":"published","publication_identifier":{"eissn":["2331-7019"]},"language":[{"iso":"eng"}],"issue":"6","volume":19,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14547"}]},"abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2206.05746","open_access":"1"}],"scopus_import":"1","intvolume":" 19","month":"06","date_updated":"2023-11-30T10:56:03Z","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"_id":"13264","type":"journal_article","article_type":"original","status":"public","year":"2023","isi":1,"publication":"Physical Review Applied","day":"09","date_created":"2023-07-23T22:01:12Z","doi":"10.1103/PhysRevApplied.19.064032","date_published":"2023-06-09T00:00:00Z","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","oa":1,"quality_controlled":"1","publisher":"American Physical Society","citation":{"ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.19.064032.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","ieee":"D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical Society, 2023.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.19.064032","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:10.1103/PhysRevApplied.19.064032."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["001012022600004"],"arxiv":["2206.05746"]},"author":[{"first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T","last_name":"Phan"},{"first_name":"Paul","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","full_name":"Falthansl-Scheinecker, Paul","last_name":"Falthansl-Scheinecker"},{"last_name":"Mishra","full_name":"Mishra, Umang","first_name":"Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51"},{"first_name":"W. M.","full_name":"Strickland, W. M.","last_name":"Strickland"},{"full_name":"Langone, D.","last_name":"Langone","first_name":"D."},{"last_name":"Shabani","full_name":"Shabani, J.","first_name":"J."},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"}],"title":"Gate-tunable superconductor-semiconductor parametric amplifier","article_number":"064032"},{"citation":{"chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. ."},"date_updated":"2023-12-01T13:51:06Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin","last_name":"Nagel"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer","full_name":"Monzer, Aline"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","full_name":"Hlavata, Annamaria","last_name":"Hlavata"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"_id":"14591","type":"preprint","status":"public","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"year":"2023","publication_status":"submitted","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"10","ec_funded":1,"date_created":"2023-11-22T10:17:49Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"date_published":"2023-10-10T00:00:00Z","doi":"10.1101/2023.10.09.561523","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2","open_access":"1"}],"month":"10"},{"file_date_updated":"2023-12-04T08:15:43Z","ddc":["570"],"extern":"1","date_updated":"2023-12-04T08:17:22Z","keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14639","license":"https://creativecommons.org/licenses/by/4.0/","volume":15,"language":[{"iso":"eng"}],"file":[{"file_size":14791081,"date_updated":"2023-12-04T08:15:43Z","creator":"dernst","file_name":"2023_GenomeMed_Lin.pdf","date_created":"2023-12-04T08:15:43Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14640","checksum":"279efd212005549aba817a487d56d363"}],"publication_status":"published","publication_identifier":{"issn":["1756-994X"]},"intvolume":" 15","month":"11","oa_version":"Published Version","abstract":[{"text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.","lang":"eng"}],"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","article_processing_charge":"Yes","author":[{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"last_name":"Vona","full_name":"Vona, Barbara","first_name":"Barbara"},{"first_name":"Tracy","full_name":"Lau, Tracy","last_name":"Lau"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","first_name":"Kevin","orcid":"0000-0002-2512-7812","full_name":"Huang, Kevin","last_name":"Huang"},{"full_name":"Zaki, Maha S.","last_name":"Zaki","first_name":"Maha S."},{"full_name":"Aldeen, Huda Shujaa","last_name":"Aldeen","first_name":"Huda Shujaa"},{"first_name":"Ehsan Ghayoor","last_name":"Karimiani","full_name":"Karimiani, Ehsan Ghayoor"},{"first_name":"Clarissa","last_name":"Rocca","full_name":"Rocca, Clarissa"},{"first_name":"Mahmoud M.","last_name":"Noureldeen","full_name":"Noureldeen, Mahmoud M."},{"first_name":"Ahmed K.","full_name":"Saad, Ahmed K.","last_name":"Saad"},{"first_name":"Cassidy","last_name":"Petree","full_name":"Petree, Cassidy"},{"first_name":"Tobias","last_name":"Bartolomaeus","full_name":"Bartolomaeus, Tobias"},{"first_name":"Rami","last_name":"Abou Jamra","full_name":"Abou Jamra, Rami"},{"first_name":"Giovanni","full_name":"Zifarelli, Giovanni","last_name":"Zifarelli"},{"last_name":"Gotkhindikar","full_name":"Gotkhindikar, Aditi","first_name":"Aditi"},{"last_name":"Wentzensen","full_name":"Wentzensen, Ingrid M.","first_name":"Ingrid M."},{"last_name":"Liao","full_name":"Liao, Mingjuan","first_name":"Mingjuan"},{"first_name":"Emalyn Elise","full_name":"Cork, Emalyn Elise","last_name":"Cork"},{"last_name":"Varshney","full_name":"Varshney, Pratishtha","first_name":"Pratishtha"},{"first_name":"Narges","full_name":"Hashemi, Narges","last_name":"Hashemi"},{"last_name":"Mohammadi","full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan"},{"full_name":"Rad, Aboulfazl","last_name":"Rad","first_name":"Aboulfazl"},{"first_name":"Juanita","last_name":"Neira","full_name":"Neira, Juanita"},{"last_name":"Toosi","full_name":"Toosi, Mehran Beiraghi","first_name":"Mehran Beiraghi"},{"first_name":"Cordula","last_name":"Knopp","full_name":"Knopp, Cordula"},{"first_name":"Ingo","full_name":"Kurth, Ingo","last_name":"Kurth"},{"last_name":"Challman","full_name":"Challman, Thomas D.","first_name":"Thomas D."},{"first_name":"Rebecca","full_name":"Smith, Rebecca","last_name":"Smith"},{"full_name":"Abdalla, Asmahan","last_name":"Abdalla","first_name":"Asmahan"},{"last_name":"Haaf","full_name":"Haaf, Thomas","first_name":"Thomas"},{"first_name":"Mohnish","full_name":"Suri, Mohnish","last_name":"Suri"},{"first_name":"Manali","full_name":"Joshi, Manali","last_name":"Joshi"},{"first_name":"Wendy K.","full_name":"Chung, Wendy K.","last_name":"Chung"},{"first_name":"Andres","full_name":"Moreno-De-Luca, Andres","last_name":"Moreno-De-Luca"},{"first_name":"Henry","last_name":"Houlden","full_name":"Houlden, Henry"},{"first_name":"Reza","full_name":"Maroofian, Reza","last_name":"Maroofian"},{"last_name":"Varshney","full_name":"Varshney, Gaurav K.","first_name":"Gaurav K."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102, Springer Nature, 2023, doi:10.1186/s13073-023-01258-4.","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4","ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01258-4","ieee":"S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer Nature, 2023.","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4.","ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102."},"article_number":"102","date_created":"2023-12-04T08:10:55Z","date_published":"2023-11-23T00:00:00Z","doi":"10.1186/s13073-023-01258-4","publication":"Genome Medicine","day":"23","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1"},{"file_date_updated":"2023-12-04T08:04:14Z","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"ddc":["531","006"],"date_updated":"2023-12-04T08:09:05Z","keyword":["Computer Graphics and Computer-Aided Design"],"status":"public","type":"journal_article","article_type":"original","_id":"14628","issue":"5","volume":42,"language":[{"iso":"eng"}],"file":[{"file_name":"tog-22-0089-File004.zip","date_created":"2023-11-29T15:16:01Z","file_size":95467870,"date_updated":"2023-11-29T15:16:01Z","creator":"yichen","success":1,"checksum":"0192f597d7a2ceaf89baddfd6190d4c8","file_id":"14630","content_type":"application/zip","relation":"main_file","access_level":"open_access"},{"success":1,"checksum":"7fb024963be81933494f38de191e4710","file_id":"14631","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"tog-22-0089-File005.zip","date_created":"2023-11-29T15:16:01Z","creator":"yichen","file_size":103731880,"date_updated":"2023-11-29T15:16:01Z"},{"file_name":"2023_ACMToG_Makatura.pdf","date_created":"2023-12-04T08:04:14Z","file_size":57067476,"date_updated":"2023-12-04T08:04:14Z","creator":"dernst","success":1,"checksum":"b7d6829ce396e21cac9fae0ec7130a6b","file_id":"14638","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301","1557-7368"]},"intvolume":" 42","month":"10","oa_version":"Published Version","abstract":[{"text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.","lang":"eng"}],"title":"Procedural metamaterials: A unified procedural graph for metamaterial design","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Liane","last_name":"Makatura","full_name":"Makatura, Liane"},{"first_name":"Bohan","full_name":"Wang, Bohan","last_name":"Wang"},{"first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","full_name":"Chen, Yi-Lu","last_name":"Chen"},{"first_name":"Bolei","full_name":"Deng, Bolei","last_name":"Deng"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.","ieee":"L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389"},"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"article_number":"168","date_created":"2023-11-29T15:02:03Z","date_published":"2023-10-01T00:00:00Z","doi":"10.1145/3605389","publication":"ACM Transactions on Graphics","day":"01","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program."},{"file_date_updated":"2023-12-05T10:37:02Z","department":[{"_id":"CaBe"}],"date_updated":"2023-12-05T10:37:28Z","ddc":["572"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"preprint","status":"public","_id":"14644","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_status":"submitted","language":[{"iso":"eng"}],"file":[{"file_name":"2023_Tluckova_etal_REx.pdf","date_created":"2023-12-05T10:37:02Z","file_size":4892920,"date_updated":"2023-12-05T10:37:02Z","creator":"dernst","success":1,"checksum":"c45608cb97ee36d7b50ba518db8e07b0","file_id":"14646","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"month":"12","abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"oa_version":"Submitted Version","article_processing_charge":"No","author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","full_name":"Tluckova, Katarina","last_name":"Tluckova"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"}],"title":"Mechanism of mammalian transcriptional repression by noncoding RNA","citation":{"apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA"}],"date_created":"2023-12-04T14:51:00Z","doi":"10.15479/AT:ISTA:14644","date_published":"2023-12-05T00:00:00Z","year":"2023","has_accepted_license":"1","day":"05","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF)."},{"department":[{"_id":"MiLe"}],"file_date_updated":"2023-12-11T10:49:07Z","date_updated":"2023-12-11T10:55:52Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14658","ec_funded":1,"issue":"4","volume":5,"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"ee31c0d0de5d1b65591990ae6705a601","file_id":"14672","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_PhysReviewResearch_Becker.pdf","date_created":"2023-12-11T10:49:07Z","creator":"dernst","file_size":2362158,"date_updated":"2023-12-11T10:49:07Z"}],"scopus_import":"1","intvolume":" 5","month":"10","abstract":[{"lang":"eng","text":"We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom."}],"oa_version":"Published Version","article_processing_charge":"Yes","external_id":{"arxiv":["2305.09529"]},"author":[{"first_name":"J. M.","last_name":"Becker","full_name":"Becker, J. M."},{"id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios","full_name":"Koutentakis, Georgios","last_name":"Koutentakis"},{"first_name":"P.","full_name":"Schmelcher, P.","last_name":"Schmelcher"}],"title":"Spin-charge correlations in finite one-dimensional multiband Fermi systems","citation":{"chicago":"Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043039.","ista":"Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4), 043039.","mla":"Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research, vol. 5, no. 4, 043039, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043039.","ama":"Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043039","apa":"Becker, J. M., Koutentakis, G., & Schmelcher, P. (2023). Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043039","ieee":"J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations in finite one-dimensional multiband Fermi systems,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023.","short":"J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"article_number":"043039","date_created":"2023-12-10T23:00:58Z","date_published":"2023-10-12T00:00:00Z","doi":"10.1103/PhysRevResearch.5.043039","year":"2023","has_accepted_license":"1","publication":"Physical Review Research","day":"12","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413."},{"status":"public","keyword":["General Physics and Astronomy"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14650","file_date_updated":"2023-12-11T07:42:04Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-12-11T07:44:08Z","month":"12","intvolume":" 15","oa_version":"Published Version","abstract":[{"text":"We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.","lang":"eng"}],"issue":"6","volume":15,"ec_funded":1,"file":[{"success":1,"checksum":"e664372a1fe9d628a9bb1d135ebab7d8","file_id":"14669","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_SciPostPhysics_Volosniev.pdf","date_created":"2023-12-11T07:42:04Z","file_size":3543541,"date_updated":"2023-12-11T07:42:04Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2542-4653"]},"publication_status":"published","project":[{"name":"A path-integral approach to composite impurities","grant_number":"M02641","call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"232","title":"Non-equilibrium dynamics of dipolar polarons","author":[{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"},{"orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Santos, Luis","last_name":"Santos","first_name":"Luis"},{"full_name":"Peña Ardila, Luisllu A.","last_name":"Peña Ardila","first_name":"Luisllu A."}],"external_id":{"arxiv":["2305.17969"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","chicago":"Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.6.232.","short":"A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023).","ieee":"A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” SciPost Physics, vol. 15, no. 6. SciPost Foundation, 2023.","apa":"Volosniev, A., Bighin, G., Santos, L., & Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.6.232","ama":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 2023;15(6). doi:10.21468/scipostphys.15.6.232","mla":"Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.6.232."},"publisher":"SciPost Foundation","quality_controlled":"1","oa":1,"acknowledgement":"We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247.","date_published":"2023-12-07T00:00:00Z","doi":"10.21468/scipostphys.15.6.232","date_created":"2023-12-10T13:03:07Z","day":"07","publication":"SciPost Physics","has_accepted_license":"1","year":"2023"},{"article_number":"117168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2023. https://doi.org/10.1016/j.ijms.2023.117168.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2023.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023).","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168."},"title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)","author":[{"first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl"},{"first_name":"Anna","full_name":"Ploner, Anna","last_name":"Ploner"},{"full_name":"Meisenbichler, Christina","last_name":"Meisenbichler","first_name":"Christina"},{"first_name":"Robert","last_name":"Konrat","full_name":"Konrat, Robert"},{"first_name":"Thomas","last_name":"Müller","full_name":"Müller, Thomas"}],"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"23","publication":"International Journal of Mass Spectrometry","year":"2023","date_published":"2023-11-23T00:00:00Z","doi":"10.1016/j.ijms.2023.117168","date_created":"2023-12-10T23:00:57Z","_id":"14653","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-12-11T08:16:35Z","department":[{"_id":"GradSch"}],"oa_version":"Published Version","abstract":[{"text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.","lang":"eng"}],"month":"11","intvolume":" 495","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ijms.2023.117168"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1387-3806"]},"publication_status":"epub_ahead","volume":495},{"date_created":"2023-12-06T13:07:01Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1101/2023.11.30.569337","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"01","publication_status":"submitted","year":"2023","month":"12","main_file_link":[{"url":"https://doi.org/10.1101/2023.11.30.569337","open_access":"1"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We thank Dr. Shital Suryavanshi and the animal house staff of the Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions. This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India (Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079).","oa_version":"Preprint","abstract":[{"text":"In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.","lang":"eng"}],"title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"last_name":"Bose","full_name":"Bose, Mahima","first_name":"Mahima"},{"first_name":"Varun","last_name":"Suresh","full_name":"Suresh, Varun"},{"last_name":"Mishra","full_name":"Mishra, Urvi","first_name":"Urvi"},{"first_name":"Ishita","full_name":"Talwar, Ishita","last_name":"Talwar"},{"last_name":"Yadav","full_name":"Yadav, Anuradha","first_name":"Anuradha"},{"full_name":"Biswas, Shiona","last_name":"Biswas","first_name":"Shiona"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"first_name":"Shubha","full_name":"Tole, Shubha","last_name":"Tole"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-11T07:37:17Z","citation":{"ista":"Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv, 10.1101/2023.11.30.569337.","chicago":"Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2023.11.30.569337.","apa":"Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.11.30.569337","ama":"Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. doi:10.1101/2023.11.30.569337","short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, BioRxiv (n.d.).","ieee":"M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2023.11.30.569337."},"status":"public","type":"preprint","_id":"14647"},{"abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"scopus_import":"1","intvolume":" 131","month":"12","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"volume":131,"issue":"22","_id":"14655","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-12-11T07:59:25Z","department":[{"_id":"AnSa"}],"acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","year":"2023","publication":"Physical Review Letters","day":"01","date_created":"2023-12-10T23:00:57Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1103/PhysRevLett.131.228401","article_number":"228401","citation":{"ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.","apa":"Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.228401","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American Physical Society, 2023.","short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2303.03088"]},"author":[{"first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","full_name":"Sorichetti, Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti"},{"full_name":"Lenz, Martin","last_name":"Lenz","first_name":"Martin"}],"title":"Transverse fluctuations control the assembly of semiflexible filaments"},{"abstract":[{"text":"The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set 𝑆⊂ℝ𝑑, then there are at most 2𝑑 points of 𝑆 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let 𝑄 be a convex polytope in ℝ𝑑 containing the standard Euclidean unit ball 𝐁𝑑. Then there exist at most 2𝑑 vertices of 𝑄 whose convex hull 𝑄′ satisfies 𝑟𝐁𝑑⊂𝑄′ with 𝑟⩾𝑑−2𝑑. They conjectured that 𝑟⩾𝑐𝑑−1∕2 holds with a universal constant 𝑐>0. We prove 𝑟⩾15𝑑2, the first polynomial lower bound on 𝑟. Furthermore, we show that 𝑟 is not greater than 2/√𝑑.","lang":"eng"}],"acknowledgement":"M.N. was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences aswell as the National Research, Development and Innovation Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovationand Technology from the source of the NRDI as well as the ELTE TKP 2021-NKTA-62 fundingscheme","oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1112/blms.12965"}],"publisher":"London Mathematical Society","scopus_import":"1","quality_controlled":"1","month":"12","publication_status":"epub_ahead","year":"2023","publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]},"language":[{"iso":"eng"}],"publication":"Bulletin of the London Mathematical Society","day":"04","date_created":"2023-12-10T23:00:58Z","date_published":"2023-12-04T00:00:00Z","doi":"10.1112/blms.12965","_id":"14660","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-12-11T10:03:54Z","citation":{"apa":"Ivanov, G., & Naszódi, M. (2023). Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12965","ama":"Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. 2023. doi:10.1112/blms.12965","short":"G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society (2023).","ieee":"G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,” Bulletin of the London Mathematical Society. London Mathematical Society, 2023.","mla":"Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society, London Mathematical Society, 2023, doi:10.1112/blms.12965.","ista":"Ivanov G, Naszódi M. 2023. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society.","chicago":"Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society. London Mathematical Society, 2023. https://doi.org/10.1112/blms.12965."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2212.04308"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"last_name":"Naszódi","full_name":"Naszódi, Márton","first_name":"Márton"}],"title":"Quantitative Steinitz theorem: A polynomial bound","department":[{"_id":"UlWa"}]},{"scopus_import":"1","month":"11","intvolume":" 120","abstract":[{"text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function.","lang":"eng"}],"oa_version":"None","pmid":1,"volume":120,"related_material":{"link":[{"url":"https://github.com/ccluri/metabolic_spiking","relation":"software"}]},"issue":"48","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"date_created":"2023-12-11T12:45:12Z","file_name":"2023_PNAS_Chintaluri.pdf","creator":"dernst","date_updated":"2023-12-11T12:45:12Z","file_size":16891602,"checksum":"bf4ec38602a70dae4338077a5a4d497f","file_id":"14678","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"14666","department":[{"_id":"TiVo"}],"file_date_updated":"2023-12-11T12:45:12Z","date_updated":"2023-12-11T12:47:41Z","ddc":["570"],"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1).","date_published":"2023-11-21T00:00:00Z","doi":"10.1073/pnas.2306525120","date_created":"2023-12-10T23:01:00Z","has_accepted_license":"1","year":"2023","day":"21","publication":"Proceedings of the National Academy of Sciences of the United States of America","project":[{"grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"article_number":"e2306525120","author":[{"full_name":"Chintaluri, Chaitanya","last_name":"Chintaluri","first_name":"Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181"}],"external_id":{"pmid":["37988463"]},"article_processing_charge":"Yes (in subscription journal)","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","citation":{"short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023.","apa":"Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120","ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.","ista":"Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120.","chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"JoCs"},{"_id":"GaTk"}],"file_date_updated":"2023-12-11T11:30:37Z","ddc":["570"],"date_updated":"2023-12-11T11:37:20Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14656","volume":43,"issue":"48","ec_funded":1,"file":[{"content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file","checksum":"e2503c8f84be1050e28f64320f1d5bd2","file_id":"14674","embargo":"2024-06-01","date_updated":"2023-12-11T11:30:37Z","file_size":2280632,"creator":"dernst","date_created":"2023-12-11T11:30:37Z","file_name":"2023_JourNeuroscience_Nardin.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1529-2401"]},"publication_status":"published","month":"11","intvolume":" 43","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele"},{"last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","full_name":"Savin, Cristina","last_name":"Savin"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37758476"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023"},"project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"doi":"10.1523/JNEUROSCI.0194-23.2023","date_published":"2023-11-29T00:00:00Z","date_created":"2023-12-10T23:00:58Z","page":"8140-8156","day":"29","publication":"The Journal of Neuroscience","has_accepted_license":"1","year":"2023","publisher":"Society of Neuroscience","quality_controlled":"1","oa":1,"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript."},{"date_updated":"2023-12-11T11:17:53Z","ddc":["000","570"],"department":[{"_id":"KrCh"}],"file_date_updated":"2023-12-11T11:10:32Z","_id":"14657","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1742-5662"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2eefab13127c7786dbd33303c482a004","file_id":"14673","success":1,"creator":"dernst","date_updated":"2023-12-11T11:10:32Z","file_size":1720243,"date_created":"2023-12-11T11:10:32Z","file_name":"2023_RoyalInterface_Tkadlec.pdf"}],"ec_funded":1,"volume":20,"issue":"208","abstract":[{"text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","intvolume":" 20","month":"11","citation":{"chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface. The Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355.","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 20(208), 20230355.","mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface, vol. 20, no. 208, 20230355, The Royal Society, 2023, doi:10.1098/rsif.2023.0355.","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” Journal of the Royal Society, Interface, vol. 20, no. 208. The Royal Society, 2023.","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society, Interface 20 (2023).","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. The Royal Society. https://doi.org/10.1098/rsif.2023.0355","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 2023;20(208). doi:10.1098/rsif.2023.0355"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38016637"]},"author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"last_name":"Kaveh","full_name":"Kaveh, Kamran","first_name":"Kamran"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"title":"Evolutionary dynamics of mutants that modify population structure","article_number":"20230355","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"year":"2023","has_accepted_license":"1","publication":"Journal of the Royal Society, Interface","day":"29","date_created":"2023-12-10T23:00:58Z","date_published":"2023-11-29T00:00:00Z","doi":"10.1098/rsif.2023.0355","acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","oa":1,"quality_controlled":"1","publisher":"The Royal Society"},{"intvolume":" 145","month":"11","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”.","lang":"eng"}],"issue":"45","volume":145,"language":[{"iso":"eng"}],"file":[{"file_size":4304472,"date_updated":"2023-12-11T11:44:54Z","creator":"dernst","file_name":"2023_JACS_Hema.pdf","date_created":"2023-12-11T11:44:54Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"a1f37df6b83f88f51ba64468ce0c1589","file_id":"14675"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14664","file_date_updated":"2023-12-11T11:44:54Z","department":[{"_id":"RaKl"}],"ddc":["540"],"date_updated":"2023-12-11T11:47:07Z","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program under the European Research Council (grant agreement 820008).We also thank the Deutsche Forschungsgemeinschaft (DFG) for support through priority program SPP1807(CL489/3-2) and RESOLV Cluster of Excellence EXC2033 (project number 390677874). A.B.G. acknowledges funding from the Zuckerman STEM Leadership Program. DFT calculations were carried out using resources provided by the Wrocław Center for Networking and Supercomputing, grant 329.","date_created":"2023-12-10T23:00:59Z","date_published":"2023-11-02T00:00:00Z","doi":"10.1021/jacs.3c08666","page":"24755-24764","publication":"Journal of the American Chemical Society","day":"02","year":"2023","has_accepted_license":"1","title":"Guest encapsulation alters the thermodynamic landscape of a coordination host","external_id":{"pmid":["37917939"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Kuntrapakam","full_name":"Hema, Kuntrapakam","last_name":"Hema"},{"first_name":"Angela B.","full_name":"Grommet, Angela B.","last_name":"Grommet"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"first_name":"Jinhua","last_name":"Wang","full_name":"Wang, Jinhua"},{"first_name":"Laura","full_name":"Schneider, Laura","last_name":"Schneider"},{"first_name":"Christoph","last_name":"Drechsler","full_name":"Drechsler, Christoph"},{"last_name":"Yanshyna","full_name":"Yanshyna, Oksana","first_name":"Oksana"},{"last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael","first_name":"Yael"},{"first_name":"Guido H.","last_name":"Clever","full_name":"Clever, Guido H."},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Hema K, Grommet AB, Białek MJ, et al. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 2023;145(45):24755-24764. doi:10.1021/jacs.3c08666","apa":"Hema, K., Grommet, A. B., Białek, M. J., Wang, J., Schneider, L., Drechsler, C., … Klajn, R. (2023). Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c08666","ieee":"K. Hema et al., “Guest encapsulation alters the thermodynamic landscape of a coordination host,” Journal of the American Chemical Society, vol. 145, no. 45. American Chemical Society, pp. 24755–24764, 2023.","short":"K. Hema, A.B. Grommet, M.J. Białek, J. Wang, L. Schneider, C. Drechsler, O. Yanshyna, Y. Diskin-Posner, G.H. Clever, R. Klajn, Journal of the American Chemical Society 145 (2023) 24755–24764.","mla":"Hema, Kuntrapakam, et al. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society, vol. 145, no. 45, American Chemical Society, 2023, pp. 24755–64, doi:10.1021/jacs.3c08666.","ista":"Hema K, Grommet AB, Białek MJ, Wang J, Schneider L, Drechsler C, Yanshyna O, Diskin-Posner Y, Clever GH, Klajn R. 2023. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 145(45), 24755–24764.","chicago":"Hema, Kuntrapakam, Angela B. Grommet, Michał J. Białek, Jinhua Wang, Laura Schneider, Christoph Drechsler, Oksana Yanshyna, Yael Diskin-Posner, Guido H. Clever, and Rafal Klajn. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c08666."}},{"publication_identifier":{"eissn":["2155-5435"]},"publication_status":"published","file":[{"checksum":"a97c771077af71ddfb2249e34530895c","file_id":"14676","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-12-11T11:55:09Z","file_name":"2023_ACSCatalysis_.pdf","date_updated":"2023-12-11T11:55:09Z","file_size":14813812,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":13,"issue":"22","abstract":[{"lang":"eng","text":"As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity."}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 13","date_updated":"2023-12-11T11:55:35Z","ddc":["540"],"file_date_updated":"2023-12-11T11:55:09Z","department":[{"_id":"MaIb"}],"_id":"14663","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","day":"06","publication":"ACS Catalysis","page":"15054-15073","doi":"10.1021/acscatal.3c03893","date_published":"2023-11-06T00:00:00Z","date_created":"2023-12-10T23:00:59Z","acknowledgement":"The authors acknowledge the financial support from the National Natural Science Foundation of China (22008211, 92045303, U21A20298), the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), and Zhejiang Innovation Team (2017R5203).","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"citation":{"chicago":"Zhao, Jinyan, Zihao Yao, Rhys Bunting, P. Hu, and Jianguo Wang. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis. American Chemical Society, 2023. https://doi.org/10.1021/acscatal.3c03893.","ista":"Zhao J, Yao Z, Bunting R, Hu P, Wang J. 2023. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 13(22), 15054–15073.","mla":"Zhao, Jinyan, et al. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis, vol. 13, no. 22, American Chemical Society, 2023, pp. 15054–73, doi:10.1021/acscatal.3c03893.","short":"J. Zhao, Z. Yao, R. Bunting, P. Hu, J. Wang, ACS Catalysis 13 (2023) 15054–15073.","ieee":"J. Zhao, Z. Yao, R. Bunting, P. Hu, and J. Wang, “Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles,” ACS Catalysis, vol. 13, no. 22. American Chemical Society, pp. 15054–15073, 2023.","apa":"Zhao, J., Yao, Z., Bunting, R., Hu, P., & Wang, J. (2023). Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.3c03893","ama":"Zhao J, Yao Z, Bunting R, Hu P, Wang J. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 2023;13(22):15054-15073. doi:10.1021/acscatal.3c03893"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jinyan","last_name":"Zhao","full_name":"Zhao, Jinyan"},{"first_name":"Zihao","last_name":"Yao","full_name":"Yao, Zihao"},{"id":"91deeae8-1207-11ec-b130-c194ad5b50c6","first_name":"Rhys","last_name":"Bunting","orcid":"0000-0001-6928-074X","full_name":"Bunting, Rhys"},{"full_name":"Hu, P.","last_name":"Hu","first_name":"P."},{"first_name":"Jianguo","last_name":"Wang","full_name":"Wang, Jianguo"}],"article_processing_charge":"Yes (in subscription journal)","title":"Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles"},{"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"acknowledgement":"The first author was partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors are grateful to the anonymous referees and associated editor for carefully reading this paper and providing helpful comments that improved the quality of the article. Also the authors would like to thank Peter Forrester for pointing out the reference [12] that was absent in the previous version of the manuscript.","page":"2083-2105","doi":"10.1214/22-AIHP1304","date_published":"2023-11-01T00:00:00Z","date_created":"2023-12-10T23:01:00Z","year":"2023","day":"01","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang","full_name":"Ji, Hong Chang","last_name":"Ji"}],"external_id":{"arxiv":["2112.11382"]},"article_processing_charge":"No","title":"Functional CLT for non-Hermitian random matrices","citation":{"chicago":"Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AIHP1304.","ista":"Erdös L, Ji HC. 2023. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 59(4), 2083–2105.","mla":"Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4, Institute of Mathematical Statistics, 2023, pp. 2083–105, doi:10.1214/22-AIHP1304.","short":"L. Erdös, H.C. Ji, Annales de l’institut Henri Poincare (B) Probability and Statistics 59 (2023) 2083–2105.","ieee":"L. Erdös and H. C. Ji, “Functional CLT for non-Hermitian random matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4. Institute of Mathematical Statistics, pp. 2083–2105, 2023.","apa":"Erdös, L., & Ji, H. C. (2023). Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1304","ama":"Erdös L, Ji HC. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2023;59(4):2083-2105. doi:10.1214/22-AIHP1304"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2112.11382","open_access":"1"}],"month":"11","intvolume":" 59","abstract":[{"lang":"eng","text":"For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. "},{"lang":"fre","text":"On étudie les fluctuations de f (X), où X est une matrice aléatoire non-hermitienne de grande taille à coefficients i.i.d. (réels ou complexes), et f une fonction analytique sur un domaine qui contient le spectre de X. On prouve que, pour une matrice carrée générique et bornée A, les fluctuations de la quantité tr f (X)A sont asymptotiquement gaussiennes et comportent deux modes indépendants, correspondant aux composantes traciale et de trace nulle de A. Une nouvelle formule est établie pour la variance de la composante de trace nulle, qui fait intervenir la norme de Frobenius de A et la norme L2 de f sur la frontière du spectre limite."}],"oa_version":"Preprint","issue":"4","volume":59,"ec_funded":1,"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"14667","department":[{"_id":"LaEr"}],"date_updated":"2023-12-11T12:36:56Z"}]