[{"department":[{"_id":"JoCs"},{"_id":"GaTk"}],"publication_status":"published","external_id":{"pmid":["37758476"],"isi":["001148071000005"]},"fulldoi":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","date_updated":"2026-07-06T12:47:25Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society for Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156."},"month":"11","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","day":"29","type":"journal_article","file_date_updated":"2024-06-02T22:30:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"48","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"doi":"10.1523/JNEUROSCI.0194-23.2023","publication_identifier":{"eissn":["1529-2401"]},"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","status":"public","year":"2023","quality_controlled":"1","pmid":1,"volume":43,"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","author":[{"full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"date_published":"2023-11-29T00:00:00Z","file":[{"date_updated":"2024-06-02T22:30:03Z","date_created":"2023-12-11T11:30:37Z","content_type":"application/pdf","creator":"dernst","file_name":"2023_JourNeuroscience_Nardin.pdf","checksum":"e2503c8f84be1050e28f64320f1d5bd2","access_level":"open_access","relation":"main_file","file_id":"14674","embargo":"2024-06-01","file_size":2280632}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10077"}]},"publisher":"Society for Neuroscience","isi":1,"has_accepted_license":"1","article_type":"original","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"date_created":"2023-12-10T23:00:58Z","oa":1,"publication":"The Journal of Neuroscience","scopus_import":"1","intvolume":" 43","page":"8140-8156","ddc":["570"],"_id":"14656"},{"volume":62,"quality_controlled":"1","author":[{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald","orcid":"0000-0002-5869-1604","full_name":"Wald, Sebastian"},{"first_name":"Fritz R","last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924"},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","arxiv":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20798"}]},"corr_author":"1","date_published":"2023-01-01T00:00:00Z","publisher":"Optica Publishing Group","isi":1,"date_created":"2024-01-08T13:19:14Z","oa":1,"article_type":"original","_id":"14759","das_tickbox":"1","page":"1-7","scopus_import":"1","intvolume":" 62","publication":"Applied Optics","publication_status":"published","researchdata_availability":"upon request","department":[{"_id":"OnHo"}],"fulldoi":"https://doi.org/10.1364/ao.474118","external_id":{"arxiv":["2208.11591"],"isi":["000906607900001"]},"date_updated":"2026-11-01T23:30:26Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","article_processing_charge":"No","oa_version":"Preprint","month":"01","supplementarymaterial":"yes","citation":{"short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:10.1364/ao.474118.","chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics. Optica Publishing Group, 2023. https://doi.org/10.1364/ao.474118.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 2023;62(1):1-7. doi:10.1364/ao.474118","apa":"Wald, S., Diorico, F. R., & Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. Optica Publishing Group. https://doi.org/10.1364/ao.474118","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” Applied Optics, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023."},"type":"journal_article","day":"01","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.11591","open_access":"1"}],"dataavailabilitystatement":"Data underlying the results presented in this paper are not publicly available at this time but may be obtained from the authors upon reasonable request.","abstract":[{"text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.","lang":"eng"}],"issue":"1","year":"2023","status":"public","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","doi":"10.1364/ao.474118","publication_identifier":{"eissn":["2155-3165"],"issn":["1559-128X"]}},{"abstract":[{"lang":"eng","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."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","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.","year":"2023","publication_identifier":{"eissn":["2041-1723"]},"APC_amount":"6228 EUR","doi":"10.1038/s41467-023-39493-3","month":"06","citation":{"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. Nature Communications. 2023;14. doi:10.1038/s41467-023-39493-3","apa":"Qiu, L., Sahu, R., Hease, W. J., Arnold, G. M., & Fink, J. M. (2023). Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action. Nature Communications. Nature Research. https://doi.org/10.1038/s41467-023-39493-3","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.","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,” Nature Communications, vol. 14. Nature Research, 2023.","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.” Nature Communications. Nature Research, 2023. https://doi.org/10.1038/s41467-023-39493-3.","mla":"Qiu, Liu, et al. “Coherent Optical Control of a Superconducting Microwave Cavity via Electro-Optical Dynamical Back-Action.” Nature Communications, vol. 14, 3784, Nature Research, 2023, doi:10.1038/s41467-023-39493-3.","short":"L. Qiu, R. Sahu, W.J. Hease, G.M. Arnold, J.M. Fink, Nature Communications 14 (2023)."},"type":"journal_article","day":"24","file_date_updated":"2023-07-10T10:10:54Z","ec_funded":1,"date_updated":"2026-11-01T23:30:29Z","article_number":"3784","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"published","department":[{"_id":"JoFi"}],"fulldoi":"https://doi.org/10.1038/s41467-023-39493-3","external_id":{"arxiv":["2210.12443"],"pmid":["37355691"],"isi":["001018100800002"]},"date_created":"2023-07-09T22:01:11Z","oa":1,"has_accepted_license":"1","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"article_type":"original","ddc":["000"],"_id":"13200","publication":"Nature Communications","scopus_import":"1","intvolume":" 14","DOAJ_listed":"1","isi":1,"publisher":"Nature Research","language":[{"iso":"eng"}],"arxiv":1,"related_material":{"record":[{"id":"18871","relation":"dissertation_contains","status":"public"}]},"corr_author":"1","date_published":"2023-06-24T00:00:00Z","file":[{"content_type":"application/pdf","file_name":"2023_NatureComms_Qiu.pdf","creator":"alisjak","date_created":"2023-07-10T10:10:54Z","date_updated":"2023-07-10T10:10:54Z","file_id":"13206","relation":"main_file","success":1,"file_size":1349134,"access_level":"open_access","checksum":"ec7ccd2c08f90d59cab302fd0d7776a4"}],"pmid":1,"quality_controlled":"1","volume":14,"OA_type":"gold","OA_place":"publisher","author":[{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","first_name":"Liu","last_name":"Qiu","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu"},{"first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162"},{"first_name":"William J","last_name":"Hease","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","last_name":"Arnold"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"title":"Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action"},{"_id":"18953","publication":"arXiv","oa":1,"date_created":"2025-01-29T11:11:34Z","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"grant_number":"101089099","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"related_material":{"record":[{"id":"19073","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"18871"}]},"corr_author":"1","date_published":"2023-10-25T00:00:00Z","arxiv":1,"language":[{"iso":"eng"}],"title":"All-optical single-shot readout of a superconducting qubit","author":[{"first_name":"Georg M","last_name":"Arnold","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"full_name":"Werner, Thomas","orcid":"0009-0001-2346-5236","last_name":"Werner","first_name":"Thomas","id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7"},{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky"},{"last_name":"Qiu","first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"}],"OA_place":"repository","year":"2023","acknowledgement":"We thank F. Hassani and M. Zemlicka for assistance\r\nwith qubit design and high power readout respectively,\r\nand P. Winkel and I. Pop at KIT for providing the JPA.\r\nThis work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG\r\nQUNNECT) and no. 101089099 (ERC CoG cQEO), the\r\nEuropean Union’s Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN) and the Austrian Science Fund (FWF)\r\nthrough BeyondC (grant no. F7105). L.Q. acknowledges\r\ngenerous support from the ISTFELLOW programme\r\nand G.A. is the recipient of a DOC fellowship of the\r\nAustrian Academy of Sciences at IST Austria.","status":"public","doi":"10.48550/ARXIV.2310.16817","abstract":[{"lang":"eng","text":"The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"day":"25","type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.16817","open_access":"1"}],"ec_funded":1,"month":"10","citation":{"ama":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv. doi:10.48550/ARXIV.2310.16817","apa":"Arnold, G. M., Werner, T., Sahu, R., Kapoor, L., Qiu, L., & Fink, J. M. (n.d.). All-optical single-shot readout of a superconducting qubit. arXiv. https://doi.org/10.48550/ARXIV.2310.16817","ieee":"G. M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, and J. M. Fink, “All-optical single-shot readout of a superconducting qubit,” arXiv. .","ista":"Arnold GM, Werner T, Sahu R, Kapoor L, Qiu L, Fink JM. All-optical single-shot readout of a superconducting qubit. arXiv, 10.48550/ARXIV.2310.16817.","short":"G.M. Arnold, T. Werner, R. Sahu, L. Kapoor, L. Qiu, J.M. Fink, ArXiv (n.d.).","chicago":"Arnold, Georg M, Thomas Werner, Rishabh Sahu, Lucky Kapoor, Liu Qiu, and Johannes M Fink. “All-Optical Single-Shot Readout of a Superconducting Qubit.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2310.16817.","mla":"Arnold, Georg M., et al. “All-Optical Single-Shot Readout of a Superconducting Qubit.” ArXiv, doi:10.48550/ARXIV.2310.16817."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","date_updated":"2026-11-01T23:30:29Z","fulldoi":"https://doi.org/10.48550/ARXIV.2310.16817","external_id":{"arxiv":["2310.16817"]},"publication_status":"draft","department":[{"_id":"JoFi"}]},{"year":"2023","status":"public","acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","publication_identifier":{"issn":["2470-9468"]},"doi":"10.1126/sciimmunol.adc9584","abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"issue":"87","type":"journal_article","keyword":["General Medicine","Immunology"],"day":"01","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"month":"09","citation":{"apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Published Version","article_number":"adc9584","date_updated":"2026-11-01T23:30:31Z","fulldoi":"https://doi.org/10.1126/sciimmunol.adc9584","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"_id":"14274","ddc":["570"],"scopus_import":"1","intvolume":" 8","publication":"Science Immunology","oa":1,"date_created":"2023-09-06T08:07:51Z","article_type":"original","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"publisher":"American Association for the Advancement of Science","isi":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"14279"},{"id":"14697","status":"public","relation":"dissertation_contains"},{"id":"19745","status":"public","relation":"dissertation_contains"}]},"corr_author":"1","date_published":"2023-09-01T00:00:00Z","language":[{"iso":"eng"}],"author":[{"last_name":"Alanko","first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","last_name":"Canigova","first_name":"Nikola"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","volume":8,"quality_controlled":"1","pmid":1},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","article_processing_charge":"No","date_updated":"2026-04-07T14:02:30Z","fulldoi":"https://doi.org/10.15479/at:ista:14226","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"year":"2023","status":"public","publication_identifier":{"issn":["2791-4585"]},"doi":"10.15479/at:ista:14226","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"file_date_updated":"2024-02-26T23:30:03Z","day":"24","type":"dissertation","month":"08","citation":{"apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226."},"file":[{"relation":"source_file","embargo_to":"open_access","file_id":"14227","file_size":15501411,"access_level":"closed","checksum":"453caf851d75c3478c10ed09bd242a91","content_type":"application/x-zip-compressed","file_name":"documents-export-2023-08-24.zip","creator":"cchlebak","date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:02:49Z"},{"checksum":"7349d29963d6695e555e171748648d9a","access_level":"open_access","embargo":"2024-02-25","relation":"main_file","file_id":"14228","file_size":6854783,"date_created":"2023-08-24T13:03:42Z","date_updated":"2024-02-26T23:30:03Z","content_type":"application/pdf","file_name":"thesis_pdf_a.pdf","creator":"cchlebak"}],"corr_author":"1","date_published":"2023-08-24T00:00:00Z","language":[{"iso":"eng"}],"author":[{"last_name":"Stephenson","first_name":"Elizabeth R","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X"}],"title":"Generalizing medial axes with homology switches","supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","_id":"14226","page":"43","ddc":["500"],"oa":1,"date_created":"2023-08-24T13:01:18Z","degree_awarded":"MS","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Master's Thesis"]},{"date_updated":"2026-11-01T23:30:42Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"fulldoi":"https://doi.org/10.15479/at:ista:14510","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2023","status":"public","doi":"10.15479/at:ista:14510","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"month":"11","citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2024-11-23T23:30:38Z","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"type":"dissertation","day":"10","ec_funded":1,"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14591"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8139"}]},"file":[{"date_created":"2023-11-20T09:18:51Z","date_updated":"2024-11-23T23:30:38Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","creator":"ngnyliuk","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","access_level":"closed","relation":"source_file","embargo_to":"open_access","file_id":"14567","file_size":20824903},{"embargo":"2024-11-23","file_id":"14568","relation":"main_file","file_size":24871844,"checksum":"bfc96d47fc4e7e857dd71656097214a4","access_level":"open_access","content_type":"application/pdf","creator":"ngnyliuk","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","date_updated":"2024-11-23T23:30:38Z","date_created":"2023-11-20T09:23:11Z"}],"date_published":"2023-11-10T00:00:00Z","corr_author":"1","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"OA_place":"publisher","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","first_name":"Nataliia","last_name":"Gnyliukh","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"date_created":"2023-11-10T09:10:06Z","degree_awarded":"PhD","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"has_accepted_license":"1","_id":"14510","page":"180","ddc":["570"],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria"},{"citation":{"short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523"},"month":"10","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"type":"preprint","day":"10","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"date_created":"2023-11-22T10:17:49Z","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"publication":"bioRxiv","doi":"10.1101/2023.10.09.561523","status":"public","_id":"14591","year":"2023","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"OA_place":"repository","publication_status":"draft","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"fulldoi":"https://doi.org/10.1101/2023.10.09.561523","author":[{"last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","first_name":"Aline","last_name":"Monzer"},{"first_name":"Annamaria","last_name":"Hlavata","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria"},{"full_name":"Isono, Erika","first_name":"Erika","last_name":"Isono"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","language":[{"iso":"eng"}],"date_updated":"2026-11-01T23:30:42Z","date_published":"2023-10-10T00:00:00Z","corr_author":"1","article_processing_charge":"No","oa_version":"Preprint","related_material":{"record":[{"status":"public","relation":"later_version","id":"15330"},{"id":"14510","relation":"dissertation_contains","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-07-06T12:50:45Z","fulldoi":"https://doi.org/10.15479/at:ista:12470","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-99078-026-8"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:12470","status":"public","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"ec_funded":1,"day":"09","type":"dissertation","file_date_updated":"2023-07-27T22:30:54Z","citation":{"ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470."},"month":"01","corr_author":"1","date_published":"2023-01-09T00:00:00Z","file":[{"access_level":"open_access","checksum":"1a2306e5f59f52df598e7ecfadf921ac","relation":"main_file","file_id":"12471","embargo":"2023-07-09","file_size":41771714,"date_created":"2023-01-31T15:11:42Z","date_updated":"2023-07-27T22:30:54Z","content_type":"application/pdf","creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.pdf"},{"file_size":66983464,"embargo_to":"open_access","file_id":"12472","relation":"source_file","checksum":"0bebbdee0773443959e1f6ab8caf281f","access_level":"closed","creator":"cchlebak","file_name":"20230109_PhD_thesis_JM_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11943"},{"id":"11950","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"author":[{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","OA_place":"publisher","supervisor":[{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"ddc":["610"],"page":"201","_id":"12470","has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"degree_awarded":"PhD","date_created":"2023-01-31T15:10:53Z","oa":1,"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"]},{"fulldoi":"https://doi.org/10.15479/at:ista:14622","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2026-09-14T08:36:32Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2024-11-30T23:30:03Z","day":"30","type":"dissertation","citation":{"ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622."},"month":"11","doi":"10.15479/at:ista:14622","publication_identifier":{"issn":["2663-337X"]},"year":"2023","status":"public","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"abstract":[{"text":"This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms\r\n(VQAs), a promising class of quantum algorithms that are well suited for near-term quantum\r\ncomputation due to their moderate hardware requirements and resilience to noise. Our\r\nprimary focus lies on two particular types of VQAs: the Quantum Approximate Optimization\r\nAlgorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum\r\nEigensolver (VQE), utilized for finding ground states of quantum many-body systems.\r\nIn the first part of the thesis, we examine the issue of effective parameter initialization for\r\nthe QAOA. The work demonstrates that random initialization of the QAOA often leads to\r\nconvergence in local minima with sub-optimal performance. To mitigate this issue, we propose\r\nan initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA).\r\nWe show that TQA initialization leads to the same performance as the best of an exponentially\r\nscaling number of random initializations.\r\nThe second study introduces Transition States (TS), stationary points with a single direction\r\nof descent, as a tool for systematically exploring the QAOA optimization landscape. This\r\nleads us to propose a novel greedy parameter initialization strategy that guarantees for the\r\nenergy to decrease with increasing number of circuit layers.\r\nIn the third section, we extend the QAOA to qudit systems, which are higher-dimensional\r\ngeneralizations of qubits. This chapter provides theoretical insights and practical strategies for\r\nleveraging the increased computational power of qudits in the context of quantum optimization\r\nalgorithms and suggests a quantum circuit for implementing the algorithm on an ion trap\r\nquantum computer.\r\nFinally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with\r\nvanishing gradients that obstruct efficient parameter optimization. This novel approach relies\r\non defining a notion of weak barren plateaus based on the entropies of local reduced density\r\nmatrices and showcases how these can be efficiently quantified using shadow tomography.\r\nTo illustrate the approach we employ the strategy in the VQE and show that it allows to\r\nsuccessfully avoid barren plateaus in the initialization and throughout the optimization.\r\nTaken together, this thesis greatly enhances our understanding of parameter initialization and\r\noptimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems,\r\nand presents a method to address the challenge of barren plateaus using the VQE. These\r\ninsights are instrumental in advancing the field of near-term quantum computation.","lang":"eng"}],"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","author":[{"last_name":"Sack","first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508"}],"OA_place":"publisher","supervisor":[{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"file":[{"embargo":"2024-11-30","file_id":"14635","relation":"main_file","file_size":11947523,"access_level":"open_access","checksum":"068fd3570506ec42b2faa390de784bc4","content_type":"application/pdf","creator":"ssack","file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z","date_updated":"2024-11-30T23:30:03Z"},{"creator":"ssack","file_name":"PhD Thesis (1).zip","content_type":"application/zip","date_created":"2023-11-30T15:54:11Z","date_updated":"2024-11-30T23:30:03Z","file_size":18422964,"file_id":"14636","embargo_to":"open_access","relation":"source_file","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a","access_level":"closed"}],"date_published":"2023-11-30T00:00:00Z","corr_author":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"13125"},{"relation":"part_of_dissertation","status":"public","id":"11471"},{"id":"9760","relation":"part_of_dissertation","status":"public"}]},"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","doi_confirm":"1","alternative_title":["ISTA Thesis"],"_id":"14622","ddc":["530"],"page":"142","degree_awarded":"PhD","project":[{"name":"IBM PhD Nomination Fellowship - Stefan Sack","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"},{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"has_accepted_license":"1","oa":1,"date_created":"2023-11-28T10:58:13Z"},{"date_created":"2023-06-07T06:57:32Z","oa":1,"has_accepted_license":"1","article_type":"original","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"ddc":["530"],"_id":"13125","publication":"Physical Review A","scopus_import":"1","intvolume":" 107","publisher":"American Physical Society","isi":1,"language":[{"iso":"eng"}],"arxiv":1,"related_material":{"record":[{"id":"17208","status":"public","relation":"dissertation_contains"},{"id":"14622","relation":"dissertation_contains","status":"public"}]},"corr_author":"1","date_published":"2023-06-02T00:00:00Z","file":[{"success":1,"file_size":2524611,"file_id":"13131","relation":"main_file","checksum":"0d71423888eeccaa60d8f41197f26306","access_level":"open_access","file_name":"2023_PhysRevA_Sack.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2023-06-13T07:28:36Z","date_updated":"2023-06-13T07:28:36Z"}],"quality_controlled":"1","volume":107,"author":[{"orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan","last_name":"Sack"},{"last_name":"Medina Ramos","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"},{"full_name":"Kueng, Richard","last_name":"Kueng","first_name":"Richard"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","issue":"6","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. "}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","year":"2023","doi":"10.1103/physreva.107.062404","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"month":"06","citation":{"apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404."},"day":"02","type":"journal_article","file_date_updated":"2023-06-13T07:28:36Z","ec_funded":1,"date_updated":"2026-11-01T23:31:00Z","article_number":"062404","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","oa_version":"Published Version","publication_status":"published","department":[{"_id":"MaSe"}],"fulldoi":"https://doi.org/10.1103/physreva.107.062404","external_id":{"isi":["001016927100012"],"arxiv":["2209.01159"]}},{"fulldoi":"https://doi.org/10.1093/molbev/msad245","external_id":{"isi":["001122489000003"],"pmid":["37988296"]},"publication_status":"published","department":[{"_id":"BeVi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","oa_version":"Published Version","date_updated":"2026-11-01T23:31:02Z","article_number":"msad245","day":"01","type":"journal_article","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"file_date_updated":"2024-01-02T11:39:38Z","month":"12","citation":{"apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., & Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution, vol. 40, no. 12. Oxford University Press, 2023.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:10.1093/molbev/msad245.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245."},"status":"public","acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","year":"2023","doi":"10.1093/molbev/msad245","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"issue":"12","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","author":[{"full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne","first_name":"Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Lorena Alexandra","last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f","full_name":"Layana Franco, Lorena Alexandra","orcid":"0000-0002-1253-6297"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"quality_controlled":"1","volume":40,"related_material":{"link":[{"relation":"press_release","description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/"}],"record":[{"id":"14614","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"19386"}]},"date_published":"2023-12-01T00:00:00Z","corr_author":"1","file":[{"checksum":"47c1c72fb499f26ea52d216b242208c8","access_level":"open_access","file_size":8623505,"success":1,"relation":"main_file","file_id":"14727","date_created":"2024-01-02T11:39:38Z","date_updated":"2024-01-02T11:39:38Z","file_name":"2023_MolecularBioEvo_Lasne.pdf","creator":"dernst","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","isi":1,"ddc":["570"],"_id":"14613","publication":"Molecular Biology and Evolution","scopus_import":"1","intvolume":" 40","oa":1,"date_created":"2023-11-27T16:14:37Z","has_accepted_license":"1","article_type":"original","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3"}]},{"volume":19,"quality_controlled":"1","title":"Superconductivity from a melted insulator in Josephson junction arrays","author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","last_name":"Mukhopadhyay","first_name":"Soham","orcid":"0000-0001-5263-5559","full_name":"Mukhopadhyay, Soham"},{"first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","orcid":"0000-0002-0672-9295"},{"id":"e0390f72-f6e0-11ea-865d-862393336714","last_name":"Saez Mollejo","first_name":"Jaime","full_name":"Saez Mollejo, Jaime"},{"id":"4D495994-AE37-11E9-AC72-31CAE5697425","last_name":"Puglia","first_name":"Denise","orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise"},{"full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032","first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17881"}]},"file":[{"file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","creator":"dernst","content_type":"application/pdf","date_updated":"2024-01-29T11:25:38Z","date_created":"2024-01-29T11:25:38Z","success":1,"file_size":1977706,"file_id":"14899","relation":"main_file","checksum":"1fc86d71bfbf836e221c1e925343adc5","access_level":"open_access"}],"corr_author":"1","date_published":"2023-11-01T00:00:00Z","publisher":"Springer Nature","isi":1,"oa":1,"date_created":"2023-08-11T07:41:17Z","article_type":"original","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"has_accepted_license":"1","_id":"14032","page":"1630-1635","ddc":["530"],"scopus_import":"1","intvolume":" 19","publication":"Nature Physics","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"fulldoi":"https://doi.org/10.1038/s41567-023-02161-w","external_id":{"isi":["001054563800006"]},"date_updated":"2026-11-01T23:31:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","month":"11","citation":{"short":"S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w.","chicago":"Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w.","ieee":"S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w","ista":"Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635.","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w"},"file_date_updated":"2024-01-29T11:25:38Z","keyword":["General Physics and Astronomy"],"type":"journal_article","day":"01","ec_funded":1,"abstract":[{"text":"Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2023","status":"public","acknowledgement":"We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.).","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-023-02161-w"},{"publisher":"Oxford University Press","isi":1,"ddc":["570"],"_id":"12521","publication":"Evolution Letters","intvolume":" 7","scopus_import":"1","oa":1,"date_created":"2023-02-06T13:59:12Z","has_accepted_license":"1","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"article_type":"original","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","author":[{"first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","last_name":"Khudiakova","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"quality_controlled":"1","pmid":1,"volume":7,"related_material":{"record":[{"id":"18531","status":"public","relation":"dissertation_contains"}]},"date_published":"2023-02-01T00:00:00Z","corr_author":"1","file":[{"creator":"dernst","file_name":"2023_EvLetters_Mrnjavac.pdf","content_type":"application/pdf","date_created":"2023-08-16T11:43:33Z","date_updated":"2023-08-16T11:43:33Z","success":1,"file_size":2592189,"relation":"main_file","file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","access_level":"open_access"}],"language":[{"iso":"eng"}],"day":"01","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"type":"journal_article","file_date_updated":"2023-08-16T11:43:33Z","ec_funded":1,"month":"02","citation":{"ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023)."},"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","status":"public","year":"2023","doi":"10.1093/evlett/qrac004","publication_identifier":{"issn":["2056-3744"]},"issue":"1","abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"fulldoi":"https://doi.org/10.1093/evlett/qrac004","external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-11-01T23:31:06Z","article_number":"qrac004"},{"author":[{"full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425"},{"full_name":"Kögler, Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b","last_name":"Kögler","first_name":"Kevin"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","volume":202,"quality_controlled":"1","date_published":"2023-07-30T00:00:00Z","corr_author":"1","related_material":{"record":[{"id":"23072","relation":"dissertation_contains","status":"public"},{"id":"17465","status":"public","relation":"dissertation_contains"}]},"arxiv":1,"language":[{"iso":"eng"}],"publisher":"ML Research Press","alternative_title":["PMLR"],"conference":{"start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States","name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29"},"intvolume":" 202","scopus_import":"1","publication":"Proceedings of the 40th International Conference on Machine Learning","_id":"14459","page":"31151-31209","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"date_created":"2023-10-29T23:01:17Z","external_id":{"arxiv":["2212.13468"]},"department":[{"_id":"MaMo"},{"_id":"DaAl"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-11-01T23:31:07Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.13468"}],"day":"30","type":"conference","citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:31151-31209.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","apa":"Shevchenko, A., Kögler, K., Hassani, H., & Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ista":"Shevchenko A, Kögler K, Hassani H, Mondelli M. 2023. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 31151–31209.","short":"A. Shevchenko, K. Kögler, H. Hassani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 31151–31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In Proceedings of the 40th International Conference on Machine Learning, 202:31151–209. ML Research Press, 2023.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 31151–209."},"month":"07","publication_identifier":{"eissn":["2640-3498"]},"year":"2023","acknowledgement":"Aleksandr Shevchenko, Kevin Kogler and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed Hassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","status":"public","abstract":[{"lang":"eng","text":"Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions."}]},{"related_material":{"record":[{"id":"13124","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"19533"}]},"corr_author":"1","date_published":"2023-05-24T00:00:00Z","file":[{"content_type":"application/pdf","creator":"dernst","file_name":"2023_NaturePhysics_Redchenko.pdf","date_updated":"2023-06-06T07:31:20Z","date_created":"2023-06-06T07:31:20Z","file_id":"13123","relation":"main_file","success":1,"file_size":1654389,"access_level":"open_access","checksum":"a857df40f0882859c48a1ff1e2001ec2"}],"language":[{"iso":"eng"}],"arxiv":1,"author":[{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"full_name":"Poshakinskiy, Alexander V.","last_name":"Poshakinskiy","first_name":"Alexander V."},{"last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348"},{"first_name":"Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032"},{"full_name":"Poddubny, Alexander N.","last_name":"Poddubny","first_name":"Alexander N."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"pmid":1,"quality_controlled":"1","volume":14,"ddc":["530"],"_id":"13117","publication":"Nature Communications","scopus_import":"1","intvolume":" 14","date_created":"2023-06-04T22:01:02Z","oa":1,"has_accepted_license":"1","article_type":"original","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"26B354CA-B435-11E9-9278-68D0E5697425","name":"Controllable Collective States of Superconducting Qubit Ensembles"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"publisher":"Springer Nature","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2026-11-01T23:31:11Z","article_number":"2998","fulldoi":"https://doi.org/10.1038/s41467-023-38761-6","external_id":{"isi":["001001099700002"],"arxiv":["2205.03293"],"pmid":["37225689"]},"publication_status":"published","department":[{"_id":"JoFi"}],"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.","status":"public","year":"2023","doi":"10.1038/s41467-023-38761-6","publication_identifier":{"eissn":["2041-1723"]},"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"type":"journal_article","day":"24","file_date_updated":"2023-06-06T07:31:20Z","ec_funded":1,"month":"05","citation":{"apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","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.","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","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,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6.","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.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023)."}},{"fulldoi":"https://doi.org/10.1038/s41593-023-01280-0","external_id":{"pmid":["36959418"],"isi":["000955258300002"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","date_updated":"2026-11-01T23:31:12Z","day":"01","type":"journal_article","file_date_updated":"2023-10-04T11:40:51Z","ec_funded":1,"month":"04","citation":{"short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience, vol. 26, Springer Nature, 2023, pp. 606–14, doi:10.1038/s41593-023-01280-0.","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Nature Neuroscience. Springer Nature, 2023. https://doi.org/10.1038/s41593-023-01280-0.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 2023;26:606-614. doi:10.1038/s41593-023-01280-0","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” Nature Neuroscience, vol. 26. Springer Nature, pp. 606–614, 2023.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., & Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01280-0","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614."},"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","status":"public","year":"2023","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"doi":"10.1038/s41593-023-01280-0","abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"orcid":"0000-0001-7400-6665","full_name":"Gupta, Divyansh","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Divyansh"},{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"first_name":"Anton L","last_name":"Sumser","id":"3320A096-F248-11E8-B48F-1D18A9856A87","full_name":"Sumser, Anton L","orcid":"0000-0002-4792-1881"},{"orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova"},{"last_name":"Svaton","first_name":"Jan","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","full_name":"Svaton, Jan","orcid":"0000-0002-6198-2939"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"title":"Panoramic visual statistics shape retina-wide organization of receptive fields","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"Bio"}],"quality_controlled":"1","pmid":1,"volume":26,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12370"},{"status":"public","relation":"dissertation_contains","id":"18574"}]},"corr_author":"1","date_published":"2023-04-01T00:00:00Z","file":[{"checksum":"a33d91e398e548f34003170e10988368","access_level":"open_access","file_size":6144866,"success":1,"file_id":"14395","relation":"main_file","date_updated":"2023-10-04T11:40:51Z","date_created":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf","creator":"dernst","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"isi":1,"publisher":"Springer Nature","page":"606-614","ddc":["570"],"_id":"12349","publication":"Nature Neuroscience","intvolume":" 26","scopus_import":"1","date_created":"2023-01-23T14:14:19Z","oa":1,"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425"}],"article_type":"original"},{"doi":"10.15479/AT:ISTA:12370","year":"2023","status":"public","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"abstract":[{"text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. ","lang":"eng"}],"ec_funded":1,"file_date_updated":"2023-01-26T10:51:34Z","type":"research_data","day":"26","citation":{"short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","mla":"Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.","apa":"Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370","ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370."},"month":"01","oa_version":"Published Version","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-11-01T23:31:12Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:12370","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"_id":"12370","ddc":["571"],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"},{"name":"Circuits of Visual Attention","call_identifier":"H2020","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1098-2017","name":"Connecting sensory with motor processing in the superior colliculus"}],"contributor":[{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Olga","last_name":"Symonova"},{"contributor_type":"researcher","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","first_name":"Wiktor F"},{"contributor_type":"researcher","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","last_name":"Svaton","first_name":"Jan"}],"has_accepted_license":"1","oa":1,"date_created":"2023-01-25T12:45:18Z","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"text/plain","creator":"dgupta","file_name":"readme_exvivo.txt","date_updated":"2023-01-26T10:51:34Z","date_created":"2023-01-26T10:51:34Z","relation":"main_file","file_id":"12396","file_size":1917,"success":1,"checksum":"172cd1c315cbf063c122298396bc17a7","access_level":"open_access"},{"checksum":"d3cecda51cad86b1182195731c01a14f","access_level":"open_access","file_id":"12397","relation":"main_file","success":1,"file_size":1585,"date_created":"2023-01-26T10:50:50Z","date_updated":"2023-01-26T10:50:50Z","content_type":"text/plain","file_name":"readme_invivo.txt","creator":"dgupta"},{"content_type":"application/octet-stream","creator":"dgupta","file_name":"exvivo_RFs.mat","date_created":"2023-01-26T10:43:30Z","date_updated":"2023-01-26T10:43:30Z","file_id":"12398","relation":"main_file","file_size":5019459775,"success":1,"access_level":"open_access","checksum":"b85018b27f2c43a6d94ee0e8b841220d"},{"file_size":94999721,"success":1,"relation":"main_file","file_id":"12399","checksum":"f75dccd96a3f837cdeed65b5134e697e","access_level":"open_access","file_name":"RGC_in_vivo_RFs_selected.mat","creator":"dgupta","content_type":"application/octet-stream","date_created":"2023-01-26T10:40:35Z","date_updated":"2023-01-26T10:40:35Z"},{"content_type":"application/octet-stream","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-3_210924_1534_Result.mat","date_created":"2023-01-25T16:03:49Z","date_updated":"2023-01-25T16:03:49Z","file_id":"12382","relation":"main_file","success":1,"file_size":720893739,"access_level":"open_access","checksum":"d41836ffe03ea0efb677de31287c8d2e"},{"checksum":"0a0cba5208241a95f9bb7684d0a43afa","access_level":"open_access","relation":"main_file","file_id":"12383","success":1,"file_size":248122209,"date_created":"2023-01-25T16:03:30Z","date_updated":"2023-01-25T16:03:30Z","content_type":"application/octet-stream","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-3_211026_1235_Result.mat"},{"access_level":"open_access","checksum":"cf72c1f325631212f305ff1a6d342bc3","relation":"main_file","file_id":"12384","success":1,"file_size":1757729346,"date_updated":"2023-01-25T16:04:54Z","date_created":"2023-01-25T16:04:54Z","content_type":"application/octet-stream","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-3_211202_1505_Result.mat"},{"date_created":"2023-01-25T16:04:41Z","date_updated":"2023-01-25T16:04:41Z","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-3_211208_1738_Result.mat","content_type":"application/octet-stream","access_level":"open_access","checksum":"f4cd25f37d433a7dced3aa8cc326c755","file_size":1177344595,"success":1,"file_id":"12385","relation":"main_file"},{"checksum":"8c31637d447f2088fdb5ba1c6775f243","access_level":"open_access","file_size":2246592895,"success":1,"file_id":"12386","relation":"main_file","date_created":"2023-01-25T16:06:22Z","date_updated":"2023-01-25T16:06:22Z","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-3_220111_1735_Result.mat","content_type":"application/octet-stream"},{"content_type":"application/octet-stream","file_name":"invivo_BL6-eyeGC8m-dC-4_220216_0950_Result.mat","creator":"dgupta","date_updated":"2023-01-25T16:07:41Z","date_created":"2023-01-25T16:07:41Z","file_id":"12387","relation":"main_file","success":1,"file_size":2151341770,"access_level":"open_access","checksum":"246d660ef06a9151c59b74490d991460"},{"checksum":"b32987dd4589d05b9dfadb93d4178c0d","access_level":"open_access","file_size":3719145736,"success":1,"relation":"main_file","file_id":"12393","date_created":"2023-01-26T10:19:02Z","date_updated":"2023-01-26T10:19:02Z","file_name":"invivo_BL6-eyeGC8m-dC-4_220428_1351_Result.mat","creator":"dgupta","content_type":"application/octet-stream"},{"file_size":5818789752,"success":1,"file_id":"12395","relation":"main_file","checksum":"6c88ca7d1df405f04002146d251dc22e","access_level":"open_access","creator":"dgupta","file_name":"invivo_BL6-eyeGC8m-dC-4_220502_1357_Result.mat","content_type":"application/octet-stream","date_created":"2023-01-26T10:34:46Z","date_updated":"2023-01-26T10:34:46Z"},{"file_size":2614677996,"success":1,"file_id":"12394","relation":"main_file","access_level":"open_access","checksum":"494057076bb0b0a28e4b7146bb50113c","file_name":"invivo_BL6-eyeGC8m-dC-4_220524_1726_Result.mat","creator":"dgupta","content_type":"application/octet-stream","date_updated":"2023-01-26T10:23:19Z","date_created":"2023-01-26T10:23:19Z"},{"date_created":"2023-01-25T16:20:51Z","date_updated":"2023-01-25T16:20:51Z","content_type":"application/octet-stream","file_name":"invivo_BL6-eyeGC8m-dC-5_220613_1750_Result.mat","creator":"dgupta","access_level":"open_access","checksum":"e51015d43ede6b1628803c58e424f99f","file_id":"12388","relation":"main_file","success":1,"file_size":1840481462},{"file_name":"invivo_BL6-eyeGC8m-dC-5_220630_1518_Result.mat","creator":"dgupta","content_type":"application/octet-stream","date_created":"2023-01-25T16:23:02Z","date_updated":"2023-01-25T16:23:02Z","success":1,"file_size":1617777136,"file_id":"12389","relation":"main_file","checksum":"9483686a44e69eadea428b705c33a9a2","access_level":"open_access"}],"corr_author":"1","date_published":"2023-01-26T00:00:00Z","related_material":{"record":[{"id":"12349","relation":"used_in_publication","status":"public"},{"id":"18574","relation":"used_in_publication","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"author":[{"first_name":"Divyansh","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Divyansh","orcid":"0000-0001-7400-6665"},{"id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L","last_name":"Sumser","orcid":"0000-0002-4792-1881","full_name":"Sumser, Anton L"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A"}],"title":"Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields"},{"publisher":"Institute of Science and Technology Austria","_id":"13116","ddc":["539"],"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"has_accepted_license":"1","oa":1,"date_created":"2023-06-02T12:30:40Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"title":"Chiral and nematic phases of flexible active filaments","author":[{"full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Dunajova"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","last_name":"Prats Mateu"},{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp"},{"full_name":"Lim, Keesiang","first_name":"Keesiang","last_name":"Lim"},{"last_name":"Brandis","first_name":"Dörte","full_name":"Brandis, Dörte"},{"full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Wong","first_name":"Richard W.","full_name":"Wong, Richard W."},{"full_name":"Elgeti, Jens","last_name":"Elgeti","first_name":"Jens"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2023-08-08T11:17:28Z","date_updated":"2023-08-08T11:17:28Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"ReadMe File.docx","creator":"pradler","access_level":"open_access","checksum":"4b4ec5d4df7672b3af5ba23b126b171b","file_id":"13983","relation":"main_file","file_size":13111,"success":1},{"success":1,"file_size":1499504777,"relation":"main_file","file_id":"13298","access_level":"open_access","checksum":"6f1673d6ae4f547cd49cfe7f87d9ab7e","file_name":"TIRF_FtsZ WT 0.625µM.7z.001","creator":"pradler","content_type":"application/octet-stream","date_updated":"2023-07-25T06:55:43Z","date_created":"2023-07-25T06:55:43Z"},{"date_created":"2023-07-25T08:31:07Z","date_updated":"2023-07-25T08:31:07Z","creator":"pradler","file_name":"TIRF_FtsZ WT 0.900µM.7z.001","content_type":"application/octet-stream","access_level":"open_access","checksum":"bc0dea871af164f7419ac838a34a4162","file_size":3986437211,"success":1,"file_id":"13306","relation":"main_file"},{"checksum":"dde91b799364a8456ac463dcba7bf37d","access_level":"open_access","file_size":1292391225,"success":1,"file_id":"13299","relation":"main_file","date_updated":"2023-07-25T06:56:54Z","date_created":"2023-07-25T06:56:54Z","file_name":"TIRF_FtsZ WT 1.15µM.7z.001","creator":"pradler","content_type":"application/octet-stream"},{"date_created":"2023-07-25T08:25:07Z","date_updated":"2023-07-25T08:25:07Z","creator":"pradler","file_name":"TIRF_FtsZ WT 1.25µM.7z.001","content_type":"application/octet-stream","access_level":"open_access","checksum":"ba59f4e3f062b378f45e579ec28898ce","success":1,"file_size":4494279051,"relation":"main_file","file_id":"13305"},{"checksum":"906e1fe2aaacd1a746c49ffe39bcca66","access_level":"open_access","success":1,"file_size":4697620480,"file_id":"13303","relation":"main_file","date_updated":"2023-07-25T08:12:32Z","date_created":"2023-07-25T08:12:32Z","creator":"pradler","file_name":"TIRF_FtsZ WT 1.50µM.7z.001","content_type":"application/octet-stream"},{"file_name":"TIRF_FtsZ WT 1.50µM.7z.002","creator":"pradler","content_type":"application/octet-stream","date_updated":"2023-07-25T08:18:54Z","date_created":"2023-07-25T08:18:54Z","success":1,"file_size":3548897162,"file_id":"13304","relation":"main_file","access_level":"open_access","checksum":"96e416494b129cb0139c8250246bfaff"},{"checksum":"f1dfdee3d833cf8d2c6b3ecbbee566f3","access_level":"open_access","success":1,"file_size":1472947913,"file_id":"13300","relation":"main_file","date_created":"2023-07-25T06:59:59Z","date_updated":"2023-07-25T06:59:59Z","file_name":"TIRF_FtsZ WT 2.0µM.7z.001","creator":"pradler","content_type":"application/octet-stream"},{"date_created":"2023-07-25T07:05:40Z","date_updated":"2023-07-25T07:05:40Z","content_type":"application/octet-stream","creator":"pradler","file_name":"TIRF_FtsZ WT 3.0µM.7z.001","access_level":"open_access","checksum":"fe77296c7bfce8b95a67ecbbb07ced81","relation":"main_file","file_id":"13301","success":1,"file_size":1993549431},{"checksum":"6bc6edb807f38b00528875b4e7070bbf","access_level":"open_access","file_size":1336984015,"success":1,"file_id":"13302","relation":"main_file","date_updated":"2023-07-25T07:06:07Z","date_created":"2023-07-25T07:06:07Z","file_name":"TIRF_FtsZ WT 5.0µM.7z.001","creator":"pradler","content_type":"application/octet-stream"},{"file_name":"STED experiments.7z.001","creator":"pradler","content_type":"application/octet-stream","date_updated":"2023-07-24T12:10:55Z","date_created":"2023-07-24T12:10:55Z","success":1,"file_size":227620212,"relation":"main_file","file_id":"13281","checksum":"e46bbe73e90dc56e245ecda464930009","access_level":"open_access"},{"success":1,"file_size":3433349230,"file_id":"13307","relation":"main_file","access_level":"open_access","checksum":"473aa9f1c097b8b03294b1f6d4f4aa04","creator":"pradler","file_name":"AFM_FtsZ WT.7z.001","content_type":"application/octet-stream","date_updated":"2023-07-25T09:16:06Z","date_created":"2023-07-25T09:16:06Z"},{"date_created":"2023-07-24T12:11:54Z","date_updated":"2023-07-24T12:11:54Z","creator":"pradler","file_name":"TIRF_FtsZ WT and L169R intensity calibration.7z.001","content_type":"application/octet-stream","checksum":"bc685a414d95bcd5bba4dcad0187e928","access_level":"open_access","file_size":1416013335,"success":1,"relation":"main_file","file_id":"13282"},{"checksum":"e6cac262a3cf5a6a45bf28edf1dac8cd","access_level":"open_access","success":1,"file_size":2711456292,"file_id":"13285","relation":"main_file","date_updated":"2023-07-24T12:26:12Z","date_created":"2023-07-24T12:26:12Z","creator":"pradler","file_name":"TIRF_FtsZ L169R below 0.6µM.7z","content_type":"application/octet-stream"},{"success":1,"file_size":2272169467,"file_id":"13296","relation":"main_file","checksum":"755179b242a7a4ee03133a15c5eab4ce","access_level":"open_access","creator":"pradler","file_name":"TIRF_FtsZ L169R 0.625µM.7z","content_type":"application/octet-stream","date_created":"2023-07-24T19:19:25Z","date_updated":"2023-07-24T19:19:25Z"},{"success":1,"file_size":2915542985,"file_id":"13287","relation":"main_file","checksum":"7179ce242938a688381d7126b9a7ec45","access_level":"open_access","creator":"pradler","file_name":"TIRF_FtsZ L169R 0.900µM.7z","content_type":"application/octet-stream","date_created":"2023-07-24T13:02:04Z","date_updated":"2023-07-24T13:02:04Z"},{"access_level":"open_access","checksum":"a808996cbca0f795e00de85f1922b497","file_id":"13294","relation":"main_file","file_size":2769959727,"success":1,"date_created":"2023-07-24T15:27:17Z","date_updated":"2023-07-24T15:27:17Z","content_type":"application/octet-stream","creator":"pradler","file_name":"TIRF_FtsZ L169R 1.15µM.7z"},{"content_type":"application/octet-stream","file_name":"TIRF_FtsZ L169R 1.25uM.7z","creator":"pradler","date_created":"2023-07-24T19:22:29Z","date_updated":"2023-07-24T19:22:29Z","relation":"main_file","file_id":"13297","success":1,"file_size":4440142247,"checksum":"9a42594d749e648a099fefd3e24108a8","access_level":"open_access"},{"relation":"main_file","file_id":"13295","file_size":2727119370,"success":1,"checksum":"d8df3e458dbdb83622ab4dd6c9313a4e","access_level":"open_access","content_type":"application/octet-stream","file_name":"TIRF_FtsZ L169R 1.50µM.7z","creator":"pradler","date_created":"2023-07-24T15:27:09Z","date_updated":"2023-07-24T15:27:09Z"},{"content_type":"application/octet-stream","creator":"pradler","file_name":"TIRF_FtsZ L169R 2.0µM.7z","date_created":"2023-07-24T12:12:41Z","date_updated":"2023-07-24T12:12:41Z","file_id":"13283","relation":"main_file","success":1,"file_size":1479677783,"access_level":"open_access","checksum":"020db3ef1d1cbfb3cbe5bf49d6669849"},{"checksum":"22f2aa112442fb767c0a58876d974ab0","access_level":"open_access","relation":"main_file","file_id":"13284","file_size":1560846342,"success":1,"date_created":"2023-07-24T12:13:51Z","date_updated":"2023-07-24T12:13:51Z","content_type":"application/octet-stream","file_name":"TIRF_FtsZ L169R 3.0µM.7z","creator":"pradler"},{"creator":"pradler","file_name":"AFM_FtsZ L169R.7z.001","content_type":"application/octet-stream","date_created":"2023-07-25T09:12:45Z","date_updated":"2023-07-25T09:12:45Z","success":1,"file_size":2918160653,"file_id":"13308","relation":"main_file","checksum":"6fac58e020d7b30092945cb210100670","access_level":"open_access"},{"success":1,"file_size":77476061,"relation":"main_file","file_id":"13947","checksum":"3cdbf4a61857cb940439473c999bdfa6","access_level":"open_access","file_name":"EDFig4p_F5.csv","creator":"mloose","content_type":"text/csv","date_created":"2023-08-03T19:50:52Z","date_updated":"2023-08-03T19:50:52Z"},{"checksum":"a59d5b825b4fe830cdb8833b4851508d","access_level":"open_access","file_id":"13948","relation":"main_file","file_size":74938608,"success":1,"date_updated":"2023-08-03T19:50:50Z","date_created":"2023-08-03T19:50:50Z","content_type":"text/csv","file_name":"EDFig4p_F40.csv","creator":"mloose"},{"creator":"mloose","file_name":"EDFig4p_F200.csv","content_type":"text/csv","date_updated":"2023-08-03T19:51:14Z","date_created":"2023-08-03T19:51:14Z","file_size":81680327,"success":1,"relation":"main_file","file_id":"13949","access_level":"open_access","checksum":"fe40a48ed7708260557faa1e7e8687d4"},{"relation":"main_file","file_id":"13950","file_size":169151538,"success":1,"access_level":"open_access","checksum":"30bebf102f03445445f3dd3c19209497","content_type":"text/csv","file_name":"Fig3a_4b_F40.csv","creator":"mloose","date_created":"2023-08-03T19:51:45Z","date_updated":"2023-08-03T19:51:45Z"},{"date_updated":"2023-08-03T19:51:45Z","date_created":"2023-08-03T19:51:45Z","file_name":"Fig3a_F5.csv","creator":"mloose","content_type":"text/csv","access_level":"open_access","checksum":"29db5611c9e622710fbf7b1c83c621ec","success":1,"file_size":94791496,"relation":"main_file","file_id":"13951"},{"content_type":"text/csv","creator":"mloose","file_name":"Fig3a_F200.csv","date_updated":"2023-08-03T19:51:54Z","date_created":"2023-08-03T19:51:54Z","file_id":"13952","relation":"main_file","file_size":59166206,"success":1,"access_level":"open_access","checksum":"848456b4230c086e8999f57d57dba7f1"}],"date_published":"2023-07-26T00:00:00Z","corr_author":"1","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13314"},{"relation":"used_in_publication","status":"public","id":"21423"}]},"ec_funded":1,"file_date_updated":"2023-08-08T11:17:28Z","day":"26","type":"research_data","citation":{"short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116.","mla":"Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116.","ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023."},"month":"07","doi":"10.15479/AT:ISTA:13116","year":"2023","status":"public","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. ","lang":"eng"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:13116","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"article_processing_charge":"No","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-11-01T23:31:14Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-11-01T23:31:14Z","fulldoi":"https://doi.org/10.1038/s41567-023-02218-w","external_id":{"pmid":["38075437"],"isi":["001178645300041"]},"publication_status":"published","department":[{"_id":"JoDa"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"GradSch"}],"year":"2023","status":"public","acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).","doi":"10.1038/s41567-023-02218-w","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2024-01-30T14:28:30Z","type":"journal_article","day":"01","ec_funded":1,"month":"12","citation":{"ieee":"Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926.","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w.","mla":"Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926."},"related_material":{"record":[{"relation":"research_data","status":"public","id":"13116"},{"id":"21439","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"21423"}]},"file":[{"content_type":"application/pdf","creator":"dernst","file_name":"2023_NaturePhysics_Dunajova.pdf","date_created":"2024-01-30T14:28:30Z","date_updated":"2024-01-30T14:28:30Z","relation":"main_file","file_id":"14916","file_size":22471673,"success":1,"checksum":"bc7673ca07d37309013a86166577b2f7","access_level":"open_access"}],"date_published":"2023-12-01T00:00:00Z","corr_author":"1","language":[{"iso":"eng"}],"title":"Chiral and nematic phases of flexible active filaments","author":[{"full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87","last_name":"Dunajova","first_name":"Zuzana"},{"full_name":"Prats Mateu, Batirtze","id":"299FE892-F248-11E8-B48F-1D18A9856A87","first_name":"Batirtze","last_name":"Prats Mateu"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp"},{"full_name":"Lim, Keesiang","last_name":"Lim","first_name":"Keesiang"},{"id":"21d64d35-f128-11eb-9611-b8bcca7a12fd","last_name":"Brandis","first_name":"Dörte","full_name":"Brandis, Dörte"},{"last_name":"Velicky","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431"},{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Wong, Richard W.","last_name":"Wong","first_name":"Richard W."},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"volume":19,"quality_controlled":"1","pmid":1,"_id":"13314","ddc":["530"],"page":"1916-1926","intvolume":" 19","scopus_import":"1","publication":"Nature Physics","oa":1,"date_created":"2023-07-27T14:44:45Z","article_type":"original","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"has_accepted_license":"1","publisher":"Springer Nature","isi":1}]