[{"status":"public","intvolume":"        15","type":"journal_article","dataavailabilitystatement":"All experimental data included in this work are available at https://zenodo.org/records/10119346.","day":"02","file_date_updated":"2024-01-17T11:03:00Z","publication":"Nature Communications","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","date_published":"2024-01-02T00:00:00Z","article_type":"original","oaworkID":1,"month":"01","file":[{"access_level":"open_access","date_updated":"2024-01-17T11:03:00Z","file_size":2336595,"file_name":"2024_NatureComm_Valentini.pdf","checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","date_created":"2024-01-17T11:03:00Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"14825","success":1}],"date_created":"2024-01-14T23:00:56Z","department":[{"_id":"GeKa"}],"has_accepted_license":"1","author":[{"first_name":"Marco","full_name":"Valentini, Marco","last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","last_name":"Sagi","first_name":"Oliver"},{"id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","last_name":"Baghumyan","full_name":"Baghumyan, Levon","first_name":"Levon"},{"first_name":"Thijs","last_name":"de Gijsel","full_name":"de Gijsel, Thijs","id":"a0ece13c-b527-11ee-929d-bad130106eee"},{"first_name":"Jason","last_name":"Jung","full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Andrea","full_name":"Ballabio, Andrea","last_name":"Ballabio"},{"id":"2A67C376-F248-11E8-B48F-1D18A9856A87","full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin","orcid":"0000-0002-2862-8372","first_name":"Juan L"},{"id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra","last_name":"Aggarwal","full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","last_name":"Janik","full_name":"Janik, Marian"},{"last_name":"Adletzberger","full_name":"Adletzberger, Thomas","first_name":"Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rubén","full_name":"Seoane Souto, Rubén","last_name":"Seoane Souto"},{"first_name":"Martin","last_name":"Leijnse","full_name":"Leijnse, Martin"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"first_name":"Constantin","full_name":"Schrade, Constantin","last_name":"Schrade"},{"last_name":"Bakkers","full_name":"Bakkers, Erik","first_name":"Erik"},{"first_name":"Daniel","full_name":"Chrastina, Daniel","last_name":"Chrastina"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios","first_name":"Georgios"}],"abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform.","lang":"eng"}],"publication_status":"published","citation":{"mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","quality_controlled":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"},{"grant_number":"101069515","name":"Integrated GermaNIum quanTum tEchnology","_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452"},{"grant_number":"101115315","name":"Quantum bits with Kitaev Transmons","_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811"},{"grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","name":"Towards scalable hut wire quantum devices"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"name":"Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"}],"_id":"14793","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"volume":15,"date_updated":"2026-02-26T11:39:00Z","oa":1,"article_processing_charge":"Yes","researchdata_availability":"yes","title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","external_id":{"oaworkID":["w4390499170"],"pmid":["38167818"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-023-44114-0","year":"2024","APC_amount":"12345","supplementarymaterial":"yes","ddc":["530"],"article_number":"169","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"file_date_updated":"2023-09-25T08:22:58Z","publication":"Nature Communications","type":"journal_article","day":"13","status":"public","intvolume":"        14","department":[{"_id":"MiSi"}],"has_accepted_license":"1","file":[{"creator":"dernst","file_id":"14365","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2023-09-25T08:22:58Z","checksum":"ad670e3b3c64fc585675948370f6b149","date_created":"2023-09-25T08:22:58Z","file_size":2725421,"file_name":"2023_NatureComm_Sitarska.pdf"}],"date_created":"2023-09-24T22:01:10Z","date_published":"2023-09-13T00:00:00Z","article_type":"original","month":"09","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","date_updated":"2023-12-21T14:30:01Z","volume":14,"oa":1,"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","_id":"14360","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","citation":{"mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>."},"author":[{"first_name":"Ewa","full_name":"Sitarska, Ewa","last_name":"Sitarska"},{"first_name":"Silvia Dias","last_name":"Almeida","full_name":"Almeida, Silvia Dias"},{"first_name":"Marianne Sandvold","last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold"},{"full_name":"Stopp, Julian A","last_name":"Stopp","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Czuchnowski, Jakub","last_name":"Czuchnowski","first_name":"Jakub"},{"first_name":"Marc","full_name":"Siggel, Marc","last_name":"Siggel"},{"full_name":"Roessner, Rita","last_name":"Roessner","first_name":"Rita"},{"last_name":"Tschanz","full_name":"Tschanz, Aline","first_name":"Aline"},{"first_name":"Christer","last_name":"Ejsing","full_name":"Ejsing, Christer"},{"full_name":"Schwab, Yannick","last_name":"Schwab","first_name":"Yannick"},{"first_name":"Jan","last_name":"Kosinski","full_name":"Kosinski, Jan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"last_name":"Erzberger","full_name":"Erzberger, Anna","first_name":"Anna"},{"first_name":"Alba","full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz"}],"abstract":[{"text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.","lang":"eng"}],"article_number":"5644","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"}]},"year":"2023","doi":"10.1038/s41467-023-41173-1","external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles"},{"article_type":"original","date_published":"2023-09-13T00:00:00Z","month":"09","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"has_accepted_license":"1","date_created":"2023-09-24T22:01:10Z","file":[{"access_level":"open_access","date_updated":"2023-09-25T08:32:37Z","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","date_created":"2023-09-25T08:32:37Z","file_size":2317272,"file_name":"2023_NatureComm_Riedl.pdf","file_id":"14366","creator":"dernst","relation":"main_file","content_type":"application/pdf","success":1}],"type":"journal_article","day":"13","status":"public","intvolume":"        14","file_date_updated":"2023-09-25T08:32:37Z","publication":"Nature Communications","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"year":"2023","doi":"10.1038/s41467-023-41432-1","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"title":"Synchronization in collectively moving inanimate and living active matter","isi":1,"article_number":"5633","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530","570"],"publication_status":"published","citation":{"ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl","first_name":"Michael"},{"id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","first_name":"Isabelle D","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"}],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"oa":1,"volume":14,"date_updated":"2023-12-13T12:29:41Z","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","project":[{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"quality_controlled":"1","oa_version":"Published Version","_id":"14361","pmid":1,"publication_identifier":{"eissn":["2041-1723"]}},{"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","external_id":{"isi":["001075884500007"],"pmid":["37735168"]},"ec_funded":1,"doi":"10.1038/s41467-023-41456-7","year":"2023","ddc":["570"],"isi":1,"article_number":"5878","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi","first_name":"Emmi"},{"first_name":"Inam","last_name":"Liaqat","full_name":"Liaqat, Inam"},{"first_name":"Emma","last_name":"Jakobsson","full_name":"Jakobsson, Emma"},{"full_name":"Nurmi, Harri","last_name":"Nurmi","first_name":"Harri"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518","first_name":"Kari"}],"abstract":[{"lang":"eng","text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization."}],"citation":{"short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>","mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>, vol. 14, 5878, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>.","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>.","ieee":"M. C. Ucar <i>et al.</i>, “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., &#38; Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","publication_identifier":{"eissn":["2041-1723"]},"_id":"14378","pmid":1,"article_processing_charge":"Yes","oa":1,"volume":14,"date_updated":"2023-12-13T12:31:05Z","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","article_type":"original","date_published":"2023-09-21T00:00:00Z","month":"09","file":[{"success":1,"file_id":"14384","creator":"dernst","relation":"main_file","content_type":"application/pdf","checksum":"4fe5423403f2531753bcd9e0fea48e05","date_created":"2023-10-03T07:46:36Z","file_size":8143264,"file_name":"2023_NatureComm_Ucar.pdf","access_level":"open_access","date_updated":"2023-10-03T07:46:36Z"}],"date_created":"2023-10-01T22:01:13Z","department":[{"_id":"EdHa"}],"has_accepted_license":"1","status":"public","intvolume":"        14","type":"journal_article","day":"21","file_date_updated":"2023-10-03T07:46:36Z","publication":"Nature Communications"},{"type":"journal_article","day":"02","status":"public","intvolume":"        14","file_date_updated":"2023-10-16T07:34:49Z","publication":"Nature Communications","article_type":"original","date_published":"2023-10-02T00:00:00Z","month":"10","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"has_accepted_license":"1","file":[{"date_created":"2023-10-16T07:34:49Z","checksum":"7d1dffd36b672ec679f08f70ce79da87","file_name":"2023_NatureComm_Zeng.pdf","file_size":3194116,"date_updated":"2023-10-16T07:34:49Z","access_level":"open_access","success":1,"file_id":"14432","creator":"dernst","content_type":"application/pdf","relation":"main_file"}],"date_created":"2023-10-15T22:01:10Z","publication_status":"published","citation":{"ieee":"Z. Zeng <i>et al.</i>, “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., &#38; Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41865-8\">https://doi.org/10.1038/s41467-023-41865-8</a>.","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” <i>Nature Communications</i>, vol. 14, 6131, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41865-8\">10.1038/s41467-023-41865-8</a>.","short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023).","ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131."},"author":[{"first_name":"Zezhu","full_name":"Zeng, Zezhu","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","first_name":"Felix","orcid":"0009-0000-1457-795X","full_name":"Wodaczek, Felix","last_name":"Wodaczek"},{"full_name":"Liu, Keyang","last_name":"Liu","first_name":"Keyang"},{"full_name":"Stein, Frederick","last_name":"Stein","first_name":"Frederick"},{"first_name":"Jürg","full_name":"Hutter, Jürg","last_name":"Hutter"},{"first_name":"Ji","full_name":"Chen, Ji","last_name":"Chen"},{"first_name":"Bingqing","last_name":"Cheng","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"abstract":[{"text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.","lang":"eng"}],"date_updated":"2023-12-13T13:02:07Z","volume":14,"oa":1,"article_processing_charge":"Yes","arxiv":1,"acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"pmid":1,"_id":"14425","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"doi":"10.1038/s41467-023-41865-8","year":"2023","external_id":{"pmid":["37783698"],"isi":["001084354900008"],"arxiv":["2303.07433"]},"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","isi":1,"article_number":"6131","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["540","000"],"related_material":{"link":[{"url":"https://github.com/BingqingCheng/TiO2-water","relation":"software"}]}},{"article_number":"2998","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"related_material":{"record":[{"id":"13124","relation":"research_data","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-023-38761-6","year":"2023","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"]},"title":"Tunable directional photon scattering from a pair of superconducting qubits","volume":14,"oa":1,"date_updated":"2024-08-07T07:11:50Z","article_processing_charge":"No","arxiv":1,"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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","project":[{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","call_identifier":"FWF"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"quality_controlled":"1","_id":"13117","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","citation":{"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>.","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.","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>","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.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","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>"},"author":[{"first_name":"Elena","full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poshakinskiy, Alexander V.","last_name":"Poshakinskiy","first_name":"Alexander V."},{"full_name":"Sett, Riya","last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"JoFi"}],"has_accepted_license":"1","file":[{"success":1,"creator":"dernst","file_id":"13123","relation":"main_file","content_type":"application/pdf","checksum":"a857df40f0882859c48a1ff1e2001ec2","date_created":"2023-06-06T07:31:20Z","file_size":1654389,"file_name":"2023_NaturePhysics_Redchenko.pdf","access_level":"open_access","date_updated":"2023-06-06T07:31:20Z"}],"date_created":"2023-06-04T22:01:02Z","article_type":"original","date_published":"2023-05-24T00:00:00Z","month":"05","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","file_date_updated":"2023-06-06T07:31:20Z","publication":"Nature Communications","type":"journal_article","day":"24","status":"public","intvolume":"        14"},{"language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","article_type":"original","date_published":"2023-06-03T00:00:00Z","month":"06","file":[{"date_updated":"2023-06-13T08:05:46Z","access_level":"open_access","file_name":"2023_NatureComm_CasillasPerez.pdf","file_size":2358167,"date_created":"2023-06-13T08:05:46Z","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","content_type":"application/pdf","relation":"main_file","file_id":"13132","creator":"dernst","success":1}],"date_created":"2023-06-11T22:00:40Z","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"has_accepted_license":"1","status":"public","intvolume":"        14","type":"journal_article","day":"03","file_date_updated":"2023-06-13T08:05:46Z","publication":"Nature Communications","external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","ec_funded":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"year":"2023","doi":"10.1038/s41467-023-38947-y","ddc":["570"],"related_material":{"record":[{"relation":"research_data","id":"12945","status":"public"}]},"isi":1,"article_number":"3232","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'Ová","full_name":"Bod'Ová, Katarína","orcid":"0000-0002-7214-0171"},{"first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","citation":{"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>","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>.","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>","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","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."},"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","grant_number":"771402"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"oa_version":"Published Version","quality_controlled":"1","pmid":1,"_id":"13127","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2023-08-07T13:09:09Z","oa":1,"volume":14,"article_processing_charge":"Yes"},{"year":"2023","doi":"10.1038/s41467-023-39317-4","title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","external_id":{"isi":["001048208600023"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"3506","ddc":["570"],"citation":{"mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>, vol. 14, 3506, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>.","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>","short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","ieee":"K. R. B. Gert <i>et al.</i>, “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>","chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>."},"publication_status":"published","abstract":[{"lang":"eng","text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization."}],"author":[{"first_name":"Krista R.B.","last_name":"Gert","full_name":"Gert, Krista R.B."},{"full_name":"Panser, Karin","last_name":"Panser","first_name":"Karin"},{"full_name":"Surm, Joachim","last_name":"Surm","first_name":"Joachim"},{"last_name":"Steinmetz","full_name":"Steinmetz, Benjamin S.","first_name":"Benjamin S."},{"full_name":"Schleiffer, Alexander","last_name":"Schleiffer","first_name":"Alexander"},{"full_name":"Jovine, Luca","last_name":"Jovine","first_name":"Luca"},{"first_name":"Yehu","last_name":"Moran","full_name":"Moran, Yehu"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauli, Andrea","last_name":"Pauli","first_name":"Andrea"}],"article_processing_charge":"No","volume":14,"date_updated":"2023-12-13T11:26:34Z","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"_id":"13164","quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","month":"06","date_published":"2023-06-14T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"FyKo"}],"date_created":"2023-06-25T22:00:45Z","file":[{"success":1,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"13172","file_size":1555006,"file_name":"2023_NatureComm_Gert.pdf","checksum":"d6165f41c7f1c2c04b04256ec9f003fb","date_created":"2023-06-26T10:26:04Z","access_level":"open_access","date_updated":"2023-06-26T10:26:04Z"}],"day":"14","type":"journal_article","intvolume":"        14","status":"public","publication":"Nature Communications","file_date_updated":"2023-06-26T10:26:04Z"},{"type":"journal_article","day":"24","status":"public","intvolume":"        14","file_date_updated":"2023-07-10T10:10:54Z","publication":"Nature Communications","date_published":"2023-06-24T00:00:00Z","article_type":"original","month":"06","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Nature Research","department":[{"_id":"JoFi"}],"has_accepted_license":"1","date_created":"2023-07-09T22:01:11Z","file":[{"file_id":"13206","creator":"alisjak","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2023-07-10T10:10:54Z","checksum":"ec7ccd2c08f90d59cab302fd0d7776a4","date_created":"2023-07-10T10:10:54Z","file_size":1349134,"file_name":"2023_NatureComms_Qiu.pdf"}],"citation":{"short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023).","ista":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. 2023. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. 14, 3784.","ama":"Qiu L, Sahu R, Hease WJ, Arnold GM, Fink JM. Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>, vol. 14, 3784, Nature Research, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39493-3\">10.1038/s41467-023-39493-3</a>.","chicago":"Qiu, Liu, Rishabh Sahu, William J Hease, Georg M Arnold, and Johannes M Fink. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” <i>Nature Communications</i>. Nature Research, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>.","ieee":"L. Qiu, R. Sahu, W. J. Hease, G. M. Arnold, and J. M. Fink, “Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action,” <i>Nature Communications</i>, vol. 14. Nature Research, 2023.","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., &#38; Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-023-39493-3\">https://doi.org/10.1038/s41467-023-39493-3</a>"},"publication_status":"published","author":[{"first_name":"Liu","full_name":"Qiu, Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","full_name":"Sahu, Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J","last_name":"Hease","first_name":"William J"},{"first_name":"Georg M","full_name":"Arnold, Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks.","lang":"eng"}],"article_processing_charge":"No","date_updated":"2024-08-07T07:11:55Z","volume":14,"oa":1,"arxiv":1,"quality_controlled":"1","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053"},{"call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"oa_version":"Published Version","acknowledgement":"This work was supported by the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 899354 (FETopen SuperQuLAN), and the Austrian Science Fund (FWF) through BeyondC (F7105). L.Q. acknowledges generous support from the ISTFELLOW programme. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"_id":"13200","ec_funded":1,"year":"2023","doi":"10.1038/s41467-023-39493-3","external_id":{"pmid":["37355691"],"arxiv":["2210.12443"],"isi":["001018100800002"]},"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action","article_number":"3784","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"]},{"citation":{"ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., &#38; Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>","chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>.","ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>, vol. 14, 3968, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>.","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968.","short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023)."},"publication_status":"published","abstract":[{"text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.","lang":"eng"}],"author":[{"full_name":"Hassani, Farid","last_name":"Hassani","orcid":"0000-0001-6937-5773","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","last_name":"Peruzzo","full_name":"Peruzzo, Matilda","first_name":"Matilda"},{"first_name":"Lucky","full_name":"Kapoor, Lucky","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"first_name":"Andrea","full_name":"Trioni, Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M"}],"article_processing_charge":"No","volume":14,"date_updated":"2023-12-13T11:32:25Z","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"_id":"13227","pmid":1,"project":[{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","name":"Integrating superconducting quantum circuits","call_identifier":"FWF"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","year":"2023","doi":"10.1038/s41467-023-39656-2","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"isi":["001024729900009"],"pmid":["37407570"]},"title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"3968","ddc":["530"],"day":"05","type":"journal_article","intvolume":"        14","status":"public","publication":"Nature Communications","file_date_updated":"2023-07-18T08:43:07Z","month":"07","date_published":"2023-07-05T00:00:00Z","article_type":"original","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"JoFi"}],"date_created":"2023-07-16T22:01:08Z","file":[{"checksum":"a85773b5fe23516f60f7d5d31b55c200","date_created":"2023-07-18T08:43:07Z","file_size":2899592,"file_name":"2023_NatureComm_Hassani.pdf","access_level":"open_access","date_updated":"2023-07-18T08:43:07Z","success":1,"file_id":"13248","creator":"dernst","relation":"main_file","content_type":"application/pdf"}]},{"doi":"10.1038/s41467-023-39625-9","year":"2023","ec_funded":1,"title":"The effect of environmental information on evolution of cooperation in stochastic games","external_id":{"isi":["001029450400031"],"pmid":["37438341"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"4153","related_material":{"record":[{"id":"13336","relation":"research_data","status":"public"}]},"ddc":["000"],"publication_status":"published","citation":{"apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>.","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023)."},"abstract":[{"lang":"eng","text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation."}],"author":[{"last_name":"Kleshnina","full_name":"Kleshnina, Maria","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Simsa","full_name":"Simsa, Stepan","orcid":"0000-0001-6687-1210","first_name":"Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"volume":14,"date_updated":"2025-07-14T09:09:53Z","oa":1,"article_processing_charge":"Yes","pmid":1,"_id":"13258","publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","oa_version":"Published Version","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"quality_controlled":"1","month":"07","date_published":"2023-07-12T00:00:00Z","article_type":"original","publisher":"Springer Nature","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"KrCh"}],"file":[{"date_created":"2023-07-31T11:32:36Z","checksum":"5aceefdfe76686267b93ae4fe81899f1","file_name":"2023_NatureComm_Kleshnina.pdf","file_size":1601682,"date_updated":"2023-07-31T11:32:36Z","access_level":"open_access","success":1,"file_id":"13337","creator":"dernst","content_type":"application/pdf","relation":"main_file"}],"date_created":"2023-07-23T22:01:11Z","day":"12","type":"journal_article","intvolume":"        14","status":"public","publication":"Nature Communications","file_date_updated":"2023-07-31T11:32:36Z"},{"title":"Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering","external_id":{"pmid":["37316515"],"arxiv":["2209.02283"]},"year":"2023","doi":"10.1038/s41467-023-38540-3","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-023-38540-3"}],"article_number":"3512","author":[{"first_name":"Jordyn","full_name":"Hales, Jordyn","last_name":"Hales"},{"last_name":"Bajpai","full_name":"Bajpai, Utkarsh","first_name":"Utkarsh"},{"last_name":"Liu","full_name":"Liu, Tongtong","first_name":"Tongtong"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Li","full_name":"Li, Mingda","first_name":"Mingda"},{"last_name":"Mitrano","full_name":"Mitrano, Matteo","first_name":"Matteo"},{"first_name":"Yao","last_name":"Wang","full_name":"Wang, Yao"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"abstract":[{"text":"Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements.","lang":"eng"}],"citation":{"chicago":"Hales, Jordyn, Utkarsh Bajpai, Tongtong Liu, Denitsa Rangelova Baykusheva, Mingda Li, Matteo Mitrano, and Yao Wang. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>.","ieee":"J. Hales <i>et al.</i>, “Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Hales, J., Bajpai, U., Liu, T., Baykusheva, D. R., Li, M., Mitrano, M., &#38; Wang, Y. (2023). Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38540-3\">https://doi.org/10.1038/s41467-023-38540-3</a>","ista":"Hales J, Bajpai U, Liu T, Baykusheva DR, Li M, Mitrano M, Wang Y. 2023. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. Nature Communications. 14, 3512.","short":"J. Hales, U. Bajpai, T. Liu, D.R. Baykusheva, M. Li, M. Mitrano, Y. Wang, Nature Communications 14 (2023).","mla":"Hales, Jordyn, et al. “Witnessing Light-Driven Entanglement Using Time-Resolved Resonant Inelastic X-Ray Scattering.” <i>Nature Communications</i>, vol. 14, 3512, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>.","ama":"Hales J, Bajpai U, Liu T, et al. Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38540-3\">10.1038/s41467-023-38540-3</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publication_identifier":{"eissn":["2041-1723"]},"_id":"13989","pmid":1,"article_processing_charge":"No","date_updated":"2023-08-22T06:50:04Z","volume":14,"oa":1,"arxiv":1,"language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","article_type":"original","date_published":"2023-06-14T00:00:00Z","month":"06","date_created":"2023-08-09T13:06:59Z","status":"public","intvolume":"        14","type":"journal_article","day":"14","publication":"Nature Communications"},{"type":"journal_article","day":"04","status":"public","intvolume":"        14","file_date_updated":"2023-08-14T07:01:12Z","publication":"Nature Communications","article_type":"original","date_published":"2023-08-04T00:00:00Z","month":"08","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"has_accepted_license":"1","date_created":"2023-08-13T22:01:13Z","file":[{"access_level":"open_access","date_updated":"2023-08-14T07:01:12Z","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","date_created":"2023-08-14T07:01:12Z","file_size":2315325,"file_name":"2023_NatureComm_Zhao.pdf","creator":"dernst","file_id":"14044","relation":"main_file","content_type":"application/pdf","success":1}],"citation":{"chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>.","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40388-6\">https://doi.org/10.1038/s41467-023-40388-6</a>","ieee":"Z. Zhao <i>et al.</i>, “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” <i>Nature Communications</i>, vol. 14, 4681, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>.","ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40388-6\">10.1038/s41467-023-40388-6</a>"},"publication_status":"published","author":[{"first_name":"Ziyu","last_name":"Zhao","full_name":"Zhao, Ziyu"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene","last_name":"Vercellino","full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449"},{"first_name":"Jana","last_name":"Knoppová","full_name":"Knoppová, Jana"},{"first_name":"Roman","full_name":"Sobotka, Roman","last_name":"Sobotka"},{"first_name":"James W.","full_name":"Murray, James W.","last_name":"Murray"},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Komenda","full_name":"Komenda, Josef","first_name":"Josef"}],"abstract":[{"lang":"eng","text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster."}],"article_processing_charge":"Yes","volume":14,"oa":1,"date_updated":"2023-12-13T12:06:56Z","oa_version":"Published Version","quality_controlled":"1","acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"_id":"14040","doi":"10.1038/s41467-023-40388-6","year":"2023","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"external_id":{"isi":["001042606700004"]},"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","isi":1,"article_number":"4681","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"]},{"doi":"10.1038/s41467-023-40930-6","year":"2023","external_id":{"pmid":["37633939"]},"title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"5231","ddc":["570"],"publication_status":"published","citation":{"ieee":"N. C. Vierra <i>et al.</i>, “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>, vol. 14, 5231, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231."},"abstract":[{"text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.","lang":"eng"}],"author":[{"first_name":"Nicholas C.","full_name":"Vierra, Nicholas C.","last_name":"Vierra"},{"first_name":"Luisa","last_name":"Ribeiro-Silva","full_name":"Ribeiro-Silva, Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"first_name":"Deborah","last_name":"Van Der List","full_name":"Van Der List, Deborah"},{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","full_name":"Bhandari, Pradeep","orcid":"0000-0003-0863-4481","first_name":"Pradeep"},{"first_name":"Olivia A.","full_name":"Mack, Olivia A.","last_name":"Mack"},{"last_name":"Carroll","full_name":"Carroll, James","first_name":"James"},{"full_name":"Le Monnier, Elodie","last_name":"Le Monnier","first_name":"Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sue A.","last_name":"Aicher","full_name":"Aicher, Sue A."},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"James S.","last_name":"Trimmer","full_name":"Trimmer, James S."}],"oa":1,"date_updated":"2023-09-06T06:53:32Z","volume":14,"article_processing_charge":"Yes","pmid":1,"_id":"14253","publication_identifier":{"eissn":["2041-1723"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","oa_version":"Published Version","quality_controlled":"1","month":"08","article_type":"original","date_published":"2023-08-26T00:00:00Z","publisher":"Springer Nature","scopus_import":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"RySh"}],"date_created":"2023-09-03T22:01:14Z","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"14270","creator":"dernst","success":1,"access_level":"open_access","date_updated":"2023-09-06T06:50:07Z","file_size":9412549,"file_name":"2023_NatureComm_Vierra.pdf","checksum":"6ab8aab4e957f626a09a1c73db3388fb","date_created":"2023-09-06T06:50:07Z"}],"day":"26","type":"journal_article","intvolume":"        14","status":"public","publication":"Nature Communications","file_date_updated":"2023-09-06T06:50:07Z"},{"publication":"Nature Communications","file_date_updated":"2023-03-07T10:58:00Z","intvolume":"        14","status":"public","day":"27","type":"journal_article","date_created":"2023-03-05T23:01:04Z","file":[{"access_level":"open_access","date_updated":"2023-03-07T10:58:00Z","checksum":"5ff61ad21511950c15abb73b18613883","date_created":"2023-03-07T10:58:00Z","file_size":1946443,"file_name":"2023_NatComm_Cheng.pdf","file_id":"12713","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","success":1}],"has_accepted_license":"1","department":[{"_id":"BiCh"}],"scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"02","date_published":"2023-02-27T00:00:00Z","article_type":"original","publication_identifier":{"eissn":["2041-1723"]},"_id":"12702","pmid":1,"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","oa_version":"Published Version","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","date_updated":"2023-08-01T13:36:11Z","volume":14,"oa":1,"abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing"},{"first_name":"Sebastien","full_name":"Hamel, Sebastien","last_name":"Hamel"},{"first_name":"Mandy","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f"}],"citation":{"chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>.","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., &#38; Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>, vol. 14, 1104, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>."},"publication_status":"published","ddc":["540"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"1104","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","external_id":{"pmid":["36843123"],"isi":["000939678300002"]},"doi":"10.1038/s41467-023-36841-1","year":"2023"},{"date_created":"2023-04-02T22:01:09Z","file":[{"checksum":"0a97b31191432dae5853bbb5ccb7698d","date_created":"2023-04-03T06:38:56Z","file_size":2613996,"file_name":"2023_NatureComm_Zhang.pdf","access_level":"open_access","date_updated":"2023-04-03T06:38:56Z","success":1,"creator":"dernst","file_id":"12797","relation":"main_file","content_type":"application/pdf"}],"department":[{"_id":"PeJo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","article_type":"original","date_published":"2023-03-25T00:00:00Z","month":"03","file_date_updated":"2023-04-03T06:38:56Z","publication":"Nature Communications","status":"public","intvolume":"        14","type":"journal_article","day":"25","ddc":["570"],"article_number":"1659","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"external_id":{"isi":["001066658700003"]},"title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","doi":"10.1038/s41467-023-37259-5","year":"2023","quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","publication_identifier":{"eissn":["2041-1723"]},"_id":"12786","article_processing_charge":"No","date_updated":"2023-12-13T11:15:58Z","volume":14,"oa":1,"author":[{"first_name":"Danyang","last_name":"Zhang","full_name":"Zhang, Danyang"},{"first_name":"Remigijus","last_name":"Lape","full_name":"Lape, Remigijus"},{"first_name":"Saher A.","full_name":"Shaikh, Saher A.","last_name":"Shaikh"},{"first_name":"Bianka K.","full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","full_name":"Watson, Jake","last_name":"Watson","orcid":"0000-0002-8698-3823"},{"first_name":"Ondrej","last_name":"Cais","full_name":"Cais, Ondrej"},{"first_name":"Terunaga","last_name":"Nakagawa","full_name":"Nakagawa, Terunaga"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}],"abstract":[{"lang":"eng","text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators."}],"citation":{"ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>, vol. 14, 1659, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37259-5\">10.1038/s41467-023-37259-5</a>.","short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>","ieee":"D. Zhang <i>et al.</i>, “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37259-5\">https://doi.org/10.1038/s41467-023-37259-5</a>."},"publication_status":"published"},{"article_type":"original","date_published":"2023-03-24T00:00:00Z","month":"03","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"has_accepted_license":"1","date_created":"2023-04-09T22:01:00Z","file":[{"checksum":"54f06f9eee11d43bab253f3492c983ba","date_created":"2023-04-11T06:27:00Z","file_size":4146777,"file_name":"2023_NatureComm_Brandstaetter.pdf","access_level":"open_access","date_updated":"2023-04-11T06:27:00Z","success":1,"file_id":"12821","creator":"dernst","relation":"main_file","content_type":"application/pdf"}],"type":"journal_article","day":"24","status":"public","intvolume":"        14","file_date_updated":"2023-04-11T06:27:00Z","publication":"Nature Communications","year":"2023","doi":"10.1038/s41467-023-37054-2","external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"title":"Curvature induces active velocity waves in rotating spherical tissues","isi":1,"article_number":"1643","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"citation":{"short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>, vol. 14, 1643, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>.","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>.","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., &#38; Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>"},"publication_status":"published","author":[{"first_name":"Tom","full_name":"Brandstätter, Tom","last_name":"Brandstätter"},{"orcid":"0000-0001-7205-2975","full_name":"Brückner, David","last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Han, Yu Long","last_name":"Han","first_name":"Yu Long"},{"full_name":"Alert, Ricard","last_name":"Alert","first_name":"Ricard"},{"first_name":"Ming","last_name":"Guo","full_name":"Guo, Ming"},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."}],"abstract":[{"lang":"eng","text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues."}],"article_processing_charge":"No","volume":14,"oa":1,"date_updated":"2023-08-01T14:05:30Z","quality_controlled":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"eissn":["2041-1723"]},"pmid":1,"_id":"12818"},{"department":[{"_id":"KrCh"}],"has_accepted_license":"1","file":[{"checksum":"a4b3b7b36fbef068cabf4fb99501fef6","date_created":"2023-04-25T09:13:53Z","file_size":1786475,"file_name":"2023_NatureComm_Schmid.pdf","access_level":"open_access","date_updated":"2023-04-25T09:13:53Z","success":1,"file_id":"12868","creator":"dernst","relation":"main_file","content_type":"application/pdf"}],"date_created":"2023-04-23T22:01:03Z","date_published":"2023-04-12T00:00:00Z","article_type":"original","month":"04","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","file_date_updated":"2023-04-25T09:13:53Z","publication":"Nature Communications","type":"journal_article","day":"12","status":"public","intvolume":"        14","article_number":"2086","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"ec_funded":1,"doi":"10.1038/s41467-023-37817-x","year":"2023","external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","oa":1,"volume":14,"date_updated":"2025-07-14T09:09:52Z","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","_id":"12861","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","citation":{"mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>, vol. 14, 2086, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>.","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","apa":"Schmid, L., Ekbatani, F., Hilbe, C., &#38; Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>."},"author":[{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid","full_name":"Schmid, Laura","orcid":"0000-0002-6978-7329","first_name":"Laura"},{"first_name":"Farbod","last_name":"Ekbatani","full_name":"Ekbatani, Farbod"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"abstract":[{"text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations.","lang":"eng"}]},{"doi":"10.1038/s41467-023-38005-7","year":"2023","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"article_number":"2396","isi":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"publication_status":"published","citation":{"ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>","mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>, vol. 14, 2396, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>.","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>","ieee":"J. Díez-Mérida <i>et al.</i>, “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>."},"author":[{"first_name":"J.","last_name":"Díez-Mérida","full_name":"Díez-Mérida, J."},{"full_name":"Díez-Carlón, A.","last_name":"Díez-Carlón","first_name":"A."},{"full_name":"Yang, S. Y.","last_name":"Yang","first_name":"S. Y."},{"first_name":"Y. M.","full_name":"Xie, Y. M.","last_name":"Xie"},{"full_name":"Gao, X. J.","last_name":"Gao","first_name":"X. J."},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","full_name":"Senior, Jorden L","last_name":"Senior"},{"last_name":"Watanabe","full_name":"Watanabe, K.","first_name":"K."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"X.","last_name":"Lu","full_name":"Lu, X."},{"first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K. T.","full_name":"Law, K. T.","last_name":"Law"},{"first_name":"Dmitri K.","last_name":"Efetov","full_name":"Efetov, Dmitri K."}],"abstract":[{"lang":"eng","text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices."}],"volume":14,"oa":1,"date_updated":"2023-08-01T14:34:00Z","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","quality_controlled":"1","oa_version":"Published Version","_id":"12913","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"date_published":"2023-04-26T00:00:00Z","article_type":"original","month":"04","language":[{"iso":"eng"}],"publisher":"Springer Nature","scopus_import":"1","department":[{"_id":"AnHi"}],"has_accepted_license":"1","file":[{"success":1,"content_type":"application/pdf","relation":"main_file","file_id":"12917","creator":"dernst","file_name":"2023_NatureComm_DiezMerida.pdf","file_size":1405588,"date_created":"2023-05-08T07:26:40Z","checksum":"a778105665c10beb2354c92d2b295115","date_updated":"2023-05-08T07:26:40Z","access_level":"open_access"}],"date_created":"2023-05-07T22:01:03Z","type":"journal_article","day":"26","status":"public","intvolume":"        14","file_date_updated":"2023-05-08T07:26:40Z","publication":"Nature Communications"},{"abstract":[{"lang":"eng","text":"Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution."}],"author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"last_name":"Malinverni","full_name":"Malinverni, Duccio","first_name":"Duccio"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"full_name":"Paloni, Matteo","last_name":"Paloni","first_name":"Matteo"},{"first_name":"Iva","full_name":"Sučec, Iva","last_name":"Sučec"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"first_name":"Juan Pablo","last_name":"Bustamante","full_name":"Bustamante, Juan Pablo"},{"last_name":"Barducci","full_name":"Barducci, Alessandro","first_name":"Alessandro"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"citation":{"mla":"Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>, vol. 13, 1927, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>.","ama":"Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-29423-0\">10.1038/s41467-022-29423-0</a>","ista":"Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.","short":"D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).","apa":"Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>","ieee":"D. F. Gauto <i>et al.</i>, “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","chicago":"Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-29423-0\">https://doi.org/10.1038/s41467-022-29423-0</a>."},"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"_id":"11179","oa_version":"Published Version","quality_controlled":"1","acknowledgement":"We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.).","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","date_updated":"2023-08-03T06:54:56Z","oa":1,"volume":13,"external_id":{"isi":["000781498700009"]},"title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","year":"2022","doi":"10.1038/s41467-022-29423-0","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-31243-1"}]},"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"1927","intvolume":"        13","status":"public","day":"08","type":"journal_article","publication":"Nature Communications","file_date_updated":"2022-05-02T08:48:00Z","scopus_import":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"04","date_published":"2022-04-08T00:00:00Z","article_type":"original","file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_id":"11348","success":1,"access_level":"open_access","date_updated":"2022-05-02T08:48:00Z","file_size":2637590,"file_name":"2022_NatureCommunications_Gauto.pdf","checksum":"db61d5534e988743d6266d3675d77b08","date_created":"2022-05-02T08:48:00Z"}],"date_created":"2022-04-17T22:01:45Z","has_accepted_license":"1","department":[{"_id":"PaSc"}]}]