[{"ddc":["540"],"year":"2023","doi":"10.1021/acs.nanolett.3c00375","language":[{"iso":"eng"}],"month":"05","intvolume":"        23","publication_status":"published","date_updated":"2023-08-01T14:51:25Z","type":"journal_article","issue":"10","ec_funded":1,"abstract":[{"lang":"eng","text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states."}],"author":[{"first_name":"Ali","last_name":"Azadbakht","full_name":"Azadbakht, Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","first_name":"Billie"},{"last_name":"Varkevisser","first_name":"Thijs","full_name":"Varkevisser, Thijs"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"pmid":1,"scopus_import":"1","date_published":"2023-05-04T00:00:00Z","_id":"13094","date_created":"2023-05-28T22:01:03Z","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"article_processing_charge":"No","publication":"Nano Letters","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-05-30T07:55:31Z","title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","department":[{"_id":"AnSa"}],"status":"public","has_accepted_license":"1","publisher":"American Chemical Society","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"quality_controlled":"1","isi":1,"citation":{"chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” <i>Nano Letters</i>, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. 2023;23(10):4267–4273. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., &#38; Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>"},"oa":1,"day":"04","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_type":"letter_note","oa_version":"Published Version","volume":23,"page":"4267–4273","file":[{"checksum":"9734d4c617bab3578ef62916b764547a","access_level":"open_access","date_updated":"2023-05-30T07:55:31Z","date_created":"2023-05-30T07:55:31Z","creator":"dernst","file_id":"13100","success":1,"file_name":"2023_NanoLetters_Azadbakht.pdf","content_type":"application/pdf","relation":"main_file","file_size":3654910}]},{"type":"journal_article","date_updated":"2023-08-01T14:48:09Z","publication_status":"published","intvolume":"       145","month":"05","language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c01200","year":"2023","ddc":["540"],"date_created":"2023-05-28T22:01:04Z","_id":"13095","date_published":"2023-05-04T00:00:00Z","scopus_import":"1","pmid":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12820"}]},"abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.","lang":"eng"}],"author":[{"last_name":"Troussicot","first_name":"Laura","full_name":"Troussicot, Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"full_name":"Molin, Mikael","last_name":"Molin","first_name":"Mikael"},{"full_name":"Burmann, Björn M.","last_name":"Burmann","first_name":"Björn M."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"issue":"19","publisher":"American Chemical Society","title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","has_accepted_license":"1","department":[{"_id":"PaSc"}],"status":"public","file_date_updated":"2023-05-30T07:05:28Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Journal of the American Chemical Society","article_processing_charge":"No","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","file":[{"date_created":"2023-05-30T07:05:28Z","date_updated":"2023-05-30T07:05:28Z","checksum":"0758a930ef21c62fc91b14e657479f83","access_level":"open_access","file_size":6719299,"file_name":"2023_JACS_Troussicot.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"13098","success":1}],"volume":145,"page":"10700–10711","oa_version":"Published Version","article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"04","oa":1,"citation":{"ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. <i>Journal of the American Chemical Society</i>. 2023;145(19):10700–10711. doi:<a href=\"https://doi.org/10.1021/jacs.3c01200\">10.1021/jacs.3c01200</a>","mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:<a href=\"https://doi.org/10.1021/jacs.3c01200\">10.1021/jacs.3c01200</a>.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., &#38; Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c01200\">https://doi.org/10.1021/jacs.3c01200</a>","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c01200\">https://doi.org/10.1021/jacs.3c01200</a>.","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023."},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]}},{"article_type":"original","oa_version":"Published Version","volume":618,"page":"1065-1071","file":[{"file_size":12292188,"content_type":"application/pdf","relation":"main_file","file_name":"2023_Nature_Degen.pdf","success":1,"creator":"dernst","file_id":"14533","date_created":"2023-11-14T11:48:18Z","date_updated":"2023-11-14T11:48:18Z","access_level":"open_access","checksum":"0fab69252453bff1de7f0e2eceb76d34"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"citation":{"chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>.","ieee":"M. Degen <i>et al.</i>, “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” <i>Nature</i>, vol. 618. Springer Nature, pp. 1065–1071, 2023.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>.","ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. 2023;618:1065-1071. doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>"},"oa":1,"day":"29","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"quality_controlled":"1","isi":1,"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-11-14T11:48:18Z","department":[{"_id":"PaSc"}],"has_accepted_license":"1","status":"public","title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","article_processing_charge":"Yes (via OA deal)","publication":"Nature","external_id":{"isi":["000991386800011"]},"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","_id":"13096","date_created":"2023-05-28T22:01:04Z","scopus_import":"1","date_published":"2023-06-29T00:00:00Z","abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"author":[{"first_name":"Morris","last_name":"Degen","full_name":"Degen, Morris"},{"full_name":"Santos, José Carlos","last_name":"Santos","first_name":"José Carlos"},{"full_name":"Pluhackova, Kristyna","last_name":"Pluhackova","first_name":"Kristyna"},{"first_name":"Gonzalo","last_name":"Cebrero","full_name":"Cebrero, Gonzalo"},{"last_name":"Ramos","first_name":"Saray","full_name":"Ramos, Saray"},{"last_name":"Jankevicius","first_name":"Gytis","full_name":"Jankevicius, Gytis"},{"last_name":"Hartenian","first_name":"Ella","full_name":"Hartenian, Ella"},{"id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","first_name":"Undina","last_name":"Guillerm","full_name":"Guillerm, Undina"},{"full_name":"Mari, Stefania A.","last_name":"Mari","first_name":"Stefania A."},{"full_name":"Kohl, Bastian","first_name":"Bastian","last_name":"Kohl"},{"last_name":"Müller","first_name":"Daniel J.","full_name":"Müller, Daniel J."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"},{"last_name":"Maier","first_name":"Timm","full_name":"Maier, Timm"},{"first_name":"Camilo","last_name":"Perez","full_name":"Perez, Camilo"},{"last_name":"Sieben","first_name":"Christian","full_name":"Sieben, Christian"},{"full_name":"Broz, Petr","first_name":"Petr","last_name":"Broz"},{"full_name":"Hiller, Sebastian","first_name":"Sebastian","last_name":"Hiller"}],"date_updated":"2023-11-14T11:49:21Z","type":"journal_article","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"intvolume":"       618","publication_status":"published","language":[{"iso":"eng"}],"month":"06","ddc":["570"],"year":"2023","doi":"10.1038/s41586-023-05991-z"},{"oa":1,"citation":{"mla":"Wilson, Alexia C., and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons across Species.” <i>Frontiers in Neural Circuits</i>, vol. 17, 1146449, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fncir.2023.1146449\">10.3389/fncir.2023.1146449</a>.","ama":"Wilson AC, Sweeney LB. Spinal cords: Symphonies of interneurons across species. <i>Frontiers in Neural Circuits</i>. 2023;17. doi:<a href=\"https://doi.org/10.3389/fncir.2023.1146449\">10.3389/fncir.2023.1146449</a>","apa":"Wilson, A. C., &#38; Sweeney, L. B. (2023). Spinal cords: Symphonies of interneurons across species. <i>Frontiers in Neural Circuits</i>. Frontiers. <a href=\"https://doi.org/10.3389/fncir.2023.1146449\">https://doi.org/10.3389/fncir.2023.1146449</a>","ista":"Wilson AC, Sweeney LB. 2023. Spinal cords: Symphonies of interneurons across species. Frontiers in Neural Circuits. 17, 1146449.","short":"A.C. Wilson, L.B. Sweeney, Frontiers in Neural Circuits 17 (2023).","chicago":"Wilson, Alexia C, and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons across Species.” <i>Frontiers in Neural Circuits</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fncir.2023.1146449\">https://doi.org/10.3389/fncir.2023.1146449</a>.","ieee":"A. C. Wilson and L. B. Sweeney, “Spinal cords: Symphonies of interneurons across species,” <i>Frontiers in Neural Circuits</i>, vol. 17. Frontiers, 2023."},"article_number":"1146449","day":"26","publication_identifier":{"issn":["1662-5110"]},"isi":1,"quality_controlled":"1","volume":17,"oa_version":"Published Version","article_type":"original","file":[{"file_size":6667157,"success":1,"creator":"dernst","file_id":"14729","relation":"main_file","content_type":"application/pdf","file_name":"2023_FrontiersNeuralCircuits_Wilson.pdf","date_updated":"2024-01-03T13:33:21Z","date_created":"2024-01-03T13:33:21Z","access_level":"open_access","checksum":"7efd06de284a28e91e97127611a9c3fd"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_processing_charge":"Yes","publication":"Frontiers in Neural Circuits","project":[{"_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae","grant_number":"101041551","name":"Development and Evolution of Tetrapod Motor Circuits"}],"acknowledgement":"This work was supported by the ERC Starting grant, ERC-2021-STG #101041551.","external_id":{"isi":["000984606200001"],"pmid":["37180760"]},"publisher":"Frontiers","file_date_updated":"2024-01-03T13:33:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","department":[{"_id":"LoSw"}],"title":"Spinal cords: Symphonies of interneurons across species","has_accepted_license":"1","author":[{"last_name":"Wilson","first_name":"Alexia C","full_name":"Wilson, Alexia C","id":"5230e794-15b2-11ec-abd3-e2d5335ebd1d"},{"orcid":"0000-0001-9242-5601","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"abstract":[{"text":"Vertebrate movement is orchestrated by spinal inter- and motor neurons that, together with sensory and cognitive input, produce dynamic motor behaviors. These behaviors vary from the simple undulatory swimming of fish and larval aquatic species to the highly coordinated running, reaching and grasping of mice, humans and other mammals. This variation raises the fundamental question of how spinal circuits have changed in register with motor behavior. In simple, undulatory fish, exemplified by the lamprey, two broad classes of interneurons shape motor neuron output: ipsilateral-projecting excitatory neurons, and commissural-projecting inhibitory neurons. An additional class of ipsilateral inhibitory neurons is required to generate escape swim behavior in larval zebrafish and tadpoles. In limbed vertebrates, a more complex spinal neuron composition is observed. In this review, we provide evidence that movement elaboration correlates with an increase and specialization of these three basic interneuron types into molecularly, anatomically, and functionally distinct subpopulations. We summarize recent work linking neuron types to movement-pattern generation across fish, amphibians, reptiles, birds and mammals.","lang":"eng"}],"_id":"13097","date_created":"2023-05-28T22:01:04Z","pmid":1,"date_published":"2023-04-26T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"month":"04","ddc":["570"],"doi":"10.3389/fncir.2023.1146449","year":"2023","type":"journal_article","date_updated":"2024-01-31T10:15:53Z","publication_status":"published","intvolume":"        17"},{"publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","department":[{"_id":"JoFi"}],"title":"Entangling microwaves with light","article_processing_charge":"No","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"grant_number":"899354","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F07105"},{"grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000996515200004"],"arxiv":["2301.03315"]},"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","page":"718-721","oa_version":"Preprint","volume":380,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.03315","open_access":"1"}],"oa":1,"citation":{"apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &#38; Fink, J. M. (2023). <i>Entangling microwaves with light</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. 2023;380:718-721. doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>","mla":"Sahu, Rishabh, et al. <i>Entangling Microwaves with Light</i>. Vol. 380, American Association for the Advancement of Science, 2023, pp. 718–21, doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>.","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. American Association for the Advancement of Science.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Entangling Microwaves with Light, American Association for the Advancement of Science, 2023.","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>.","ieee":"R. Sahu <i>et al.</i>, “Entangling microwaves with light,” American Association for the Advancement of Science, 2023."},"day":"18","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"isi":1,"arxiv":1,"type":"dissertation","date_updated":"2025-07-15T09:17:40Z","publication_status":"published","keyword":["Multidisciplinary"],"intvolume":"       380","language":[{"iso":"eng"}],"month":"05","doi":"10.1126/science.adg3812","year":"2023","_id":"13106","date_created":"2023-05-31T11:39:24Z","degree_awarded":"PhD","date_published":"2023-05-18T00:00:00Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","description":"News on ISTA Website","relation":"press_release"}],"record":[{"id":"13122","status":"public","relation":"research_data"}]},"author":[{"first_name":"Rishabh","orcid":"0000-0001-6264-2162","last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267","first_name":"Liu"},{"full_name":"Hease, William J","last_name":"Hease","orcid":"0000-0001-9868-2166","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M"},{"full_name":"Minoguchi, Y.","last_name":"Minoguchi","first_name":"Y."},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"},{"full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification."}],"ec_funded":1},{"day":"31","citation":{"apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>."},"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"file":[{"checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","access_level":"closed","date_created":"2023-06-01T13:48:41Z","date_updated":"2023-06-01T13:48:41Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Lisa Knaus_approved_final.docx","file_id":"13112","creator":"lknaus","file_size":12991551},{"date_updated":"2023-06-07T08:41:49Z","date_created":"2023-06-02T09:47:29Z","access_level":"open_access","checksum":"6903d152aa01181d87a696085af31c83","file_size":9309015,"file_id":"13114","creator":"lknaus","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","content_type":"application/pdf","relation":"main_file"}],"oa_version":"Published Version","page":"147","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2023-06-07T08:41:49Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"12802"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans."}],"author":[{"last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"full_name":"Novarino, 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Version","date_published":"2023-07-26T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"26","citation":{"short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>","mla":"Dunajova, Zuzana, et al. <i>Chiral and Nematic Phases of Flexible Active Filaments</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>."},"oa":1,"related_material":{"record":[{"id":"13314","relation":"used_in_publication","status":"public"}]},"abstract":[{"text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. ","lang":"eng"}],"author":[{"full_name":"Dunajova, Zuzana","first_name":"Zuzana","last_name":"Dunajova","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Batirtze","last_name":"Prats Mateu","full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9198-2182 ","last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lim, Keesiang","last_name":"Lim","first_name":"Keesiang"},{"last_name":"Brandis","first_name":"Dörte","full_name":"Brandis, Dörte"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","last_name":"Velicky","first_name":"Philipp"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973"},{"first_name":"Richard W.","last_name":"Wong","full_name":"Wong, Richard W."},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T12:19:09Z","type":"research_data","has_accepted_license":"1","title":"Chiral and nematic phases of flexible active filaments","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-08-08T11:17:28Z","month":"07","article_processing_charge":"No","year":"2023","doi":"10.15479/AT:ISTA:13116","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M.  was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ","project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Motile active matter models of migrating cells and chiral filaments","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","grant_number":"26360"}],"ddc":["539"]},{"_id":"13117","date_created":"2023-06-04T22:01:02Z","date_published":"2023-05-24T00:00:00Z","scopus_import":"1","related_material":{"record":[{"id":"13124","status":"public","relation":"research_data"}]},"ec_funded":1,"author":[{"first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V.","last_name":"Poshakinskiy"},{"full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"full_name":"Poddubny, Alexander N.","first_name":"Alexander N.","last_name":"Poddubny"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"}],"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"type":"journal_article","arxiv":1,"date_updated":"2024-08-07T07:11:50Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_status":"published","intvolume":"        14","language":[{"iso":"eng"}],"month":"05","ddc":["530"],"doi":"10.1038/s41467-023-38761-6","year":"2023","volume":14,"oa_version":"Published Version","article_type":"original","file":[{"file_size":1654389,"creator":"dernst","file_id":"13123","success":1,"file_name":"2023_NaturePhysics_Redchenko.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2023-06-06T07:31:20Z","date_created":"2023-06-06T07:31:20Z","access_level":"open_access","checksum":"a857df40f0882859c48a1ff1e2001ec2"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa":1,"citation":{"ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” <i>Nature Communications</i>, vol. 14, 2998, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>.","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38761-6\">10.1038/s41467-023-38761-6</a>","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38761-6\">https://doi.org/10.1038/s41467-023-38761-6</a>"},"article_number":"2998","day":"24","publication_identifier":{"eissn":["2041-1723"]},"isi":1,"quality_controlled":"1","publisher":"Springer Nature","file_date_updated":"2023-06-06T07:31:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","department":[{"_id":"JoFi"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","article_processing_charge":"No","publication":"Nature Communications","project":[{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"]}},{"author":[{"first_name":"J.-A.","last_name":"Hernandez","full_name":"Hernandez, J.-A."},{"last_name":"Bethkenhagen","orcid":"0000-0002-1838-2129","first_name":"Mandy","full_name":"Bethkenhagen, Mandy","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"},{"full_name":"Ninet, S.","last_name":"Ninet","first_name":"S."},{"first_name":"M.","last_name":"French","full_name":"French, M."},{"full_name":"Benuzzi-Mounaix, A.","first_name":"A.","last_name":"Benuzzi-Mounaix"},{"first_name":"F.","last_name":"Datchi","full_name":"Datchi, F."},{"full_name":"Guarguaglini, M.","last_name":"Guarguaglini","first_name":"M."},{"last_name":"Lefevre","first_name":"F.","full_name":"Lefevre, F."},{"first_name":"F.","last_name":"Occelli","full_name":"Occelli, F."},{"full_name":"Redmer, R.","first_name":"R.","last_name":"Redmer"},{"full_name":"Vinci, T.","first_name":"T.","last_name":"Vinci"},{"last_name":"Ravasio","first_name":"A.","full_name":"Ravasio, A."}],"abstract":[{"text":"Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers.","lang":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"10.1038/s41567-023-02130-3"}]},"date_published":"2023-09-01T00:00:00Z","scopus_import":"1","date_created":"2023-06-04T22:01:02Z","_id":"13118","doi":"10.1038/s41567-023-02074-8","year":"2023","month":"09","language":[{"iso":"eng"}],"publication_status":"published","intvolume":"        19","type":"journal_article","date_updated":"2023-11-14T12:58:31Z","isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"day":"01","citation":{"short":"J.-A. Hernandez, M. Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, F. Lefevre, F. Occelli, R. Redmer, T. Vinci, A. Ravasio, Nature Physics 19 (2023) 1280–1285.","ieee":"J.-A. Hernandez <i>et al.</i>, “Melting curve of superionic ammonia at planetary interior conditions,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1280–1285, 2023.","chicago":"Hernandez, J.-A., Mandy Bethkenhagen, S. Ninet, M. French, A. Benuzzi-Mounaix, F. Datchi, M. Guarguaglini, et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02074-8\">https://doi.org/10.1038/s41567-023-02074-8</a>.","apa":"Hernandez, J.-A., Bethkenhagen, M., Ninet, S., French, M., Benuzzi-Mounaix, A., Datchi, F., … Ravasio, A. (2023). Melting curve of superionic ammonia at planetary interior conditions. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02074-8\">https://doi.org/10.1038/s41567-023-02074-8</a>","ama":"Hernandez J-A, Bethkenhagen M, Ninet S, et al. Melting curve of superionic ammonia at planetary interior conditions. <i>Nature Physics</i>. 2023;19:1280-1285. doi:<a href=\"https://doi.org/10.1038/s41567-023-02074-8\">10.1038/s41567-023-02074-8</a>","mla":"Hernandez, J. A., et al. “Melting Curve of Superionic Ammonia at Planetary Interior Conditions.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1280–85, doi:<a href=\"https://doi.org/10.1038/s41567-023-02074-8\">10.1038/s41567-023-02074-8</a>.","ista":"Hernandez J-A, Bethkenhagen M, Ninet S, French M, Benuzzi-Mounaix A, Datchi F, Guarguaglini M, Lefevre F, Occelli F, Redmer R, Vinci T, Ravasio A. 2023. Melting curve of superionic ammonia at planetary interior conditions. Nature Physics. 19, 1280–1285."},"oa_version":"None","page":"1280-1285","volume":19,"article_type":"original","external_id":{"isi":["000996921200001"]},"acknowledgement":"We acknowledge the crucial contribution of the LULI2000 laser and support teams to the success of the experiments. We also thank S. Brygoo and P. Loubeyre for useful discussions. This research was supported by the French National Research Agency (ANR) through the projects POMPEI (grant no. ANR-16-CE31-0008) and SUPER-ICES (grant ANR-15-CE30-008-01), and by the PLAS@PAR Federation. M.F. and R.R. gratefully acknowledge support by the DFG within the Research Unit FOR 2440. M.B. was supported by the European Union within the Marie Skłodowska-Curie actions (xICE grant 894725) and the NOMIS foundation. The DFT-MD calculations were performed at the North-German Supercomputing Alliance facilities.","publication":"Nature Physics","article_processing_charge":"No","status":"public","department":[{"_id":"BiCh"}],"title":"Melting curve of superionic ammonia at planetary interior conditions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature"},{"has_accepted_license":"1","status":"public","title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions","department":[{"_id":"GeKa"}],"file_date_updated":"2023-11-14T13:00:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","acknowledgement":"Open access funding provided by EPFL Lausanne.We acknowledge discussions with T. Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","external_id":{"isi":["001001139300008"]},"publication":"Nature","article_processing_charge":"Yes (via OA deal)","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"file":[{"checksum":"4887a296e3b6f54e8c0b946cbfd24f49","access_level":"open_access","date_created":"2023-11-14T13:00:19Z","date_updated":"2023-11-14T13:00:19Z","file_name":"2023_Nature_Helson.pdf","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"14534","success":1,"file_size":8156497}],"oa_version":"Published Version","page":"716-720","volume":618,"article_type":"original","isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"day":"22","oa":1,"citation":{"short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.","chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>.","ieee":"V. Helson <i>et al.</i>, “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” <i>Nature</i>, vol. 618. Springer Nature, pp. 716–720, 2023.","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 716–20, doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>.","ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. 2023;618:716-720. doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>","ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720."},"publication_status":"published","intvolume":"       618","type":"journal_article","date_updated":"2023-11-14T13:02:50Z","doi":"10.1038/s41586-023-06018-3","year":"2023","ddc":["530"],"month":"06","language":[{"iso":"eng"}],"date_published":"2023-06-22T00:00:00Z","scopus_import":"1","date_created":"2023-06-04T22:01:03Z","_id":"13119","abstract":[{"text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.","lang":"eng"}],"author":[{"full_name":"Helson, Victor","last_name":"Helson","first_name":"Victor"},{"full_name":"Zwettler, Timo","last_name":"Zwettler","first_name":"Timo"},{"first_name":"Farokh","last_name":"Mivehvar","full_name":"Mivehvar, Farokh"},{"full_name":"Colella, Elvia","last_name":"Colella","first_name":"Elvia"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert","first_name":"Kevin Etienne Robert","last_name":"Roux"},{"first_name":"Hideki","last_name":"Konishi","full_name":"Konishi, Hideki"},{"full_name":"Ritsch, Helmut","last_name":"Ritsch","first_name":"Helmut"},{"full_name":"Brantut, Jean Philippe","first_name":"Jean Philippe","last_name":"Brantut"}]},{"file_date_updated":"2023-08-07T11:55:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"status":"public","title":"Closure properties of general grammars - formally verified","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Jasmin Blanchette: This research has received funding from the Netherlands Organization\r\nfor Scientific Research (NWO) under the Vidi program (project No. 016.Vidi.189.037, Lean Forward).\r\n__\r\nWe thank Vladimir Kolmogorov for making this collaboration possible. We\r\nthank Václav Končický for discussing ideas about the Kleene star construction. We thank Patrick Johnson, Floris van Doorn, and Damiano Testa for their small yet very valuable contributions to our code. We thank Eric Wieser for simplifying one of our proofs. We thank Mark Summerfield for suggesting textual improvements. We thank the anonymous reviewers for very helpful comments. Finally, we thank the Lean community for helping us with various technical issues and answering many questions. ","external_id":{"arxiv":["2302.06420"]},"article_processing_charge":"No","publication":"14th International Conference on Interactive Theorem Proving","alternative_title":["LIPIcs"],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"oa_version":"Published Version","volume":268,"file":[{"date_created":"2023-08-07T11:55:43Z","date_updated":"2023-08-07T11:55:43Z","checksum":"773a0197f05b67feaa6cb1e17ec3642d","access_level":"open_access","file_size":715976,"content_type":"application/pdf","relation":"main_file","file_name":"2023_LIPIcS_Dvorak.pdf","success":1,"file_id":"13982","creator":"dernst"}],"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772846"]},"quality_controlled":"1","oa":1,"citation":{"short":"M. Dvorak, J. Blanchette, in:, 14th International Conference on Interactive Theorem Proving, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. Dvorak and J. Blanchette, “Closure properties of general grammars - formally verified,” in <i>14th International Conference on Interactive Theorem Proving</i>, Bialystok, Poland, 2023, vol. 268.","chicago":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” In <i>14th International Conference on Interactive Theorem Proving</i>, Vol. 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>.","ama":"Dvorak M, Blanchette J. Closure properties of general grammars - formally verified. In: <i>14th International Conference on Interactive Theorem Proving</i>. Vol 268. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>","mla":"Dvorak, Martin, and Jasmin Blanchette. “Closure Properties of General Grammars - Formally Verified.” <i>14th International Conference on Interactive Theorem Proving</i>, vol. 268, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">10.4230/LIPIcs.ITP.2023.15</a>.","apa":"Dvorak, M., &#38; Blanchette, J. (2023). Closure properties of general grammars - formally verified. In <i>14th International Conference on Interactive Theorem Proving</i> (Vol. 268). Bialystok, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ITP.2023.15\">https://doi.org/10.4230/LIPIcs.ITP.2023.15</a>","ista":"Dvorak M, Blanchette J. 2023. Closure properties of general grammars - formally verified. 14th International Conference on Interactive Theorem Proving. ITP: International Conference on Interactive Theorem Proving, LIPIcs, vol. 268, 15."},"article_number":"15","day":"27","publication_status":"published","intvolume":"       268","type":"conference","arxiv":1,"date_updated":"2023-09-25T11:04:29Z","ddc":["000"],"doi":"10.4230/LIPIcs.ITP.2023.15","year":"2023","language":[{"iso":"eng"}],"month":"07","date_published":"2023-07-27T00:00:00Z","scopus_import":"1","_id":"13120","conference":{"name":"ITP: International Conference on Interactive Theorem Proving","end_date":"2023-08-04","start_date":"2023-07-31","location":"Bialystok, Poland"},"date_created":"2023-06-05T07:29:05Z","abstract":[{"text":"We formalized general (i.e., type-0) grammars using the Lean 3 proof assistant. We defined basic notions of rewrite rules and of words derived by a grammar, and used grammars to show closure of the class of type-0 languages under four operations: union, reversal, concatenation, and the Kleene star. The literature mostly focuses on Turing machine arguments, which are possibly more difficult to formalize. For the Kleene star, we could not follow the literature and came up with our own grammar-based construction.","lang":"eng"}],"author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","orcid":"0000-0001-5293-214X","first_name":"Martin","full_name":"Dvorak, Martin"},{"full_name":"Blanchette, Jasmin","last_name":"Blanchette","first_name":"Jasmin"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/madvorak/grammars/tree/publish"}]}},{"publisher":"Zenodo","date_updated":"2025-07-15T09:17:40Z","type":"research_data_reference","department":[{"_id":"JoFi"}],"title":"Entangling microwaves with light","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","article_processing_charge":"No","year":"2023","doi":"10.5281/ZENODO.7789417","date_created":"2023-06-06T06:46:16Z","_id":"13122","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2023-03-31T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"day":"31","citation":{"ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>.","short":"R. Sahu, (2023).","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>"},"oa":1,"related_material":{"record":[{"id":"13106","relation":"used_in_publication","status":"public"}]},"abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"author":[{"full_name":"Sahu, Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}]},{"department":[{"_id":"JoFi"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","date_updated":"2024-09-10T12:23:51Z","type":"research_data_reference","year":"2023","doi":"10.5281/ZENODO.7858567","ddc":["530"],"month":"04","article_processing_charge":"No","date_published":"2023-04-28T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7858567","open_access":"1"}],"date_created":"2023-06-06T07:36:50Z","_id":"13124","oa_version":"Published Version","author":[{"first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander"},{"full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poddubny, Alexander","last_name":"Poddubny","first_name":"Alexander"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"day":"28","citation":{"chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>","mla":"Redchenko, Elena, et al. <i>Tunable Directional Photon Scattering from a Pair of Superconducting Qubits</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>"},"oa":1,"related_material":{"record":[{"id":"13117","status":"public","relation":"used_in_publication"}]}},{"publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-06-13T07:28:36Z","status":"public","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","department":[{"_id":"MaSe"}],"has_accepted_license":"1","article_processing_charge":"No","publication":"Physical Review A","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899"}],"acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]},"article_type":"original","oa_version":"Published Version","volume":107,"file":[{"file_name":"2023_PhysRevA_Sack.pdf","content_type":"application/pdf","relation":"main_file","file_id":"13131","creator":"dernst","success":1,"file_size":2524611,"checksum":"0d71423888eeccaa60d8f41197f26306","access_level":"open_access","date_created":"2023-06-13T07:28:36Z","date_updated":"2023-06-13T07:28:36Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"citation":{"ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. 2023;107(6). doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physreva.107.062404\">10.1103/physreva.107.062404</a>.","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., &#38; Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” <i>Physical Review A</i>, vol. 107, no. 6. American Physical Society, 2023.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physreva.107.062404\">https://doi.org/10.1103/physreva.107.062404</a>."},"oa":1,"day":"02","article_number":"062404","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"quality_controlled":"1","isi":1,"date_updated":"2023-12-13T14:47:25Z","arxiv":1,"type":"journal_article","intvolume":"       107","publication_status":"published","language":[{"iso":"eng"}],"month":"06","ddc":["530"],"year":"2023","doi":"10.1103/physreva.107.062404","_id":"13125","date_created":"2023-06-07T06:57:32Z","scopus_import":"1","date_published":"2023-06-02T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14622"}]},"issue":"6","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"ec_funded":1,"author":[{"full_name":"Sack, Stefan","first_name":"Stefan","last_name":"Sack","orcid":"0000-0001-5400-8508","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5"},{"first_name":"Raimel A","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"full_name":"Kueng, Richard","first_name":"Richard","last_name":"Kueng"},{"orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}]},{"month":"08","doi":"10.15479/AT:ISTA:13126","year":"2023","ddc":["610"],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"type":"research_data","date_updated":"2024-02-21T12:18:19Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14257"}],"link":[{"description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ","relation":"research_data","url":"https://pub.ista.ac.at/group_danzl/data/CATS/"}]},"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"ec_funded":1,"author":[{"full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-06-07T07:15:12Z","_id":"13126","date_published":"2023-08-04T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","article_processing_charge":"No","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","project":[{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"status":"public","file_date_updated":"2023-08-04T13:19:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"04","oa":1,"citation":{"short":"J.G. Danzl, (2023).","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a 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M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino"},{"first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","last_name":"Czech"},{"first_name":"Romana","last_name":"Höftberger"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}]},{"article_processing_charge":"Yes","publication":"Nature Communications","project":[{"grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-06-13T08:05:46Z","has_accepted_license":"1","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"status":"public","citation":{"short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>.","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232."},"oa":1,"day":"03","article_number":"3232","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","isi":1,"article_type":"original","oa_version":"Published Version","volume":14,"file":[{"file_name":"2023_NatureComm_CasillasPerez.pdf","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"13132","success":1,"file_size":2358167,"access_level":"open_access","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","date_created":"2023-06-13T08:05:46Z","date_updated":"2023-06-13T08:05:46Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"month":"06","ddc":["570"],"year":"2023","doi":"10.1038/s41467-023-38947-y","date_updated":"2023-08-07T13:09:09Z","type":"journal_article","acknowledged_ssus":[{"_id":"LifeSc"}],"intvolume":"        14","publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"12945"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense."}],"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E"},{"first_name":"Katarína","last_name":"Bod'Ová","orcid":"0000-0002-7214-0171","full_name":"Bod'Ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V","full_name":"Grasse, Anna V"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"_id":"13127","date_created":"2023-06-11T22:00:40Z","pmid":1,"scopus_import":"1","date_published":"2023-06-03T00:00:00Z"},{"volume":66,"page":"1280-1295","oa_version":"Preprint","article_type":"original","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"day":"01","oa":1,"citation":{"ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>.","apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023."},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"publisher":"Cambridge University Press","status":"public","department":[{"_id":"GradSch"}],"title":"An energy decomposition theorem for matrices and related questions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Canadian Mathematical Bulletin","article_processing_charge":"No","external_id":{"isi":["001011963000001"],"arxiv":["2106.07328"]},"date_created":"2023-06-11T22:00:40Z","_id":"13128","date_published":"2023-12-01T00:00:00Z","scopus_import":"1","author":[{"full_name":"Mohammadi, Ali","first_name":"Ali","last_name":"Mohammadi"},{"full_name":"Pham, Thang","last_name":"Pham","first_name":"Thang"},{"full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X","last_name":"Wang","first_name":"Yiting","id":"1917d194-076e-11ed-97cd-837255f88785"}],"abstract":[{"text":"Given  A⊆GL2(Fq), we prove that there exist disjoint subsets  B,C⊆A such that  A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We also study some related questions on moderate expanders over matrix rings, namely, for  A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever  |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings,  ForumMath., 31, 951–970).\r\n","lang":"eng"}],"issue":"4","arxiv":1,"type":"journal_article","date_updated":"2024-01-29T11:00:46Z","publication_status":"published","intvolume":"        66","month":"12","language":[{"iso":"eng"}],"doi":"10.4153/S000843952300036X","year":"2023"},{"publisher":"Springer Nature","has_accepted_license":"1","status":"public","department":[{"_id":"JuFi"}],"title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Foundations of Computational Mathematics","article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","external_id":{"isi":["000999623100001"]},"oa_version":"Published Version","article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"main_file_link":[{"url":"https://doi.org/10.1007/s10208-023-09613-y","open_access":"1"}],"day":"30","oa":1,"citation":{"mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” <i>Foundations of Computational Mathematics</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s10208-023-09613-y\">10.1007/s10208-023-09613-y</a>.","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. <i>Foundations of Computational Mathematics</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s10208-023-09613-y\">10.1007/s10208-023-09613-y</a>","apa":"Clozeau, N., Josien, M., Otto, F., &#38; Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. <i>Foundations of Computational Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10208-023-09613-y\">https://doi.org/10.1007/s10208-023-09613-y</a>","ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023).","chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” <i>Foundations of Computational Mathematics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10208-023-09613-y\">https://doi.org/10.1007/s10208-023-09613-y</a>.","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” <i>Foundations of Computational Mathematics</i>. Springer Nature, 2023."},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"type":"journal_article","date_updated":"2023-08-02T06:12:39Z","publication_status":"epub_ahead","month":"05","language":[{"iso":"eng"}],"doi":"10.1007/s10208-023-09613-y","year":"2023","ddc":["510"],"date_created":"2023-06-11T22:00:40Z","_id":"13129","date_published":"2023-05-30T00:00:00Z","scopus_import":"1","author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","first_name":"Nicolas","last_name":"Clozeau"},{"full_name":"Josien, Marc","last_name":"Josien","first_name":"Marc"},{"full_name":"Otto, Felix","first_name":"Felix","last_name":"Otto"},{"first_name":"Qiang","last_name":"Xu","full_name":"Xu, Qiang"}],"abstract":[{"text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.","lang":"eng"}]},{"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Discrete analytical objects in the body-centered cubic grid","status":"public","department":[{"_id":"HeEd"}],"article_processing_charge":"No","publication":"Pattern Recognition","project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"}],"external_id":{"isi":["001013526000001"]},"acknowledgement":"The first author has been partially supported by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia through the project no. 451-03-47/2023-01/200156. The fourth author is funded by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","article_type":"original","oa_version":"None","volume":142,"citation":{"short":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, E. Andres, Pattern Recognition 142 (2023).","ieee":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, and E. Andres, “Discrete analytical objects in the body-centered cubic grid,” <i>Pattern Recognition</i>, vol. 142, no. 10. Elsevier, 2023.","chicago":"Čomić, Lidija, Gaëlle Largeteau-Skapin, Rita Zrour, Ranita Biswas, and Eric Andres. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>.","apa":"Čomić, L., Largeteau-Skapin, G., Zrour, R., Biswas, R., &#38; Andres, E. (2023). Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>","ama":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. 2023;142(10). doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>","mla":"Čomić, Lidija, et al. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>, vol. 142, no. 10, 109693, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>.","ista":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. 2023. Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. 142(10), 109693."},"day":"01","article_number":"109693","publication_identifier":{"issn":["0031-3203"]},"quality_controlled":"1","isi":1,"date_updated":"2023-10-10T07:37:16Z","type":"journal_article","intvolume":"       142","publication_status":"published","language":[{"iso":"eng"}],"month":"10","year":"2023","doi":"10.1016/j.patcog.2023.109693","_id":"13134","date_created":"2023-06-18T22:00:45Z","scopus_import":"1","date_published":"2023-10-01T00:00:00Z","issue":"10","abstract":[{"lang":"eng","text":"We propose a characterization of discrete analytical spheres, planes and lines in the body-centered cubic (BCC) grid, both in the Cartesian and in the recently proposed alternative compact coordinate system, in which each integer triplet addresses some voxel in the grid. We define spheres and planes through double Diophantine inequalities and investigate their relevant topological features, such as functionality or the interrelation between the thickness of the objects and their connectivity and separation properties. We define lines as the intersection of planes. The number of the planes (up to six) is equal to the number of the pairs of faces of a BCC voxel that are parallel to the line."}],"author":[{"full_name":"Čomić, Lidija","first_name":"Lidija","last_name":"Čomić"},{"full_name":"Largeteau-Skapin, Gaëlle","first_name":"Gaëlle","last_name":"Largeteau-Skapin"},{"full_name":"Zrour, Rita","first_name":"Rita","last_name":"Zrour"},{"full_name":"Biswas, Ranita","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"}]},{"author":[{"last_name":"Agresti","orcid":"0000-0002-9573-2962","first_name":"Antonio","full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"ec_funded":1,"abstract":[{"text":"In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model.","lang":"eng"}],"issue":"9","date_created":"2023-06-18T22:00:45Z","_id":"13135","date_published":"2023-09-25T00:00:00Z","scopus_import":"1","month":"09","language":[{"iso":"eng"}],"doi":"10.1016/j.jde.2023.05.038","year":"2023","ddc":["510"],"type":"journal_article","date_updated":"2024-01-29T11:04:41Z","publication_status":"published","intvolume":"       368","day":"25","oa":1,"citation":{"chicago":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>.","ieee":"A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity,” <i>Journal of Differential Equations</i>, vol. 368, no. 9. Elsevier, pp. 247–300, 2023.","short":"A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300.","ista":"Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 368(9), 247–300.","apa":"Agresti, A., &#38; Veraar, M. (2023). Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>","ama":"Agresti A, Veraar M. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. 2023;368(9):247-300. doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>","mla":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>, vol. 368, no. 9, Elsevier, 2023, pp. 247–300, doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>."},"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"file":[{"success":1,"file_id":"14895","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2023_JourDifferentialEquations_Agresti.pdf","file_size":834638,"checksum":"246b703b091dfe047bfc79abf0891a63","access_level":"open_access","date_updated":"2024-01-29T11:03:09Z","date_created":"2024-01-29T11:03:09Z"}],"oa_version":"Published Version","page":"247-300","volume":368,"article_type":"original","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication":"Journal of Differential Equations","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 948819) Image 1. The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","external_id":{"isi":["001019018700001"]},"project":[{"name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","grant_number":"948819"}],"publisher":"Elsevier","has_accepted_license":"1","title":"Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity","department":[{"_id":"JuFi"}],"status":"public","file_date_updated":"2024-01-29T11:03:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]