[{"file":[{"checksum":"a5b4d8dba83f96e955a3625c0eebee98","content_type":"application/pdf","file_id":"21879","date_updated":"2026-05-15T15:53:57Z","file_name":"2026_Werner_Thomas_Thesis.pdf","creator":"twerner","file_size":9330516,"access_level":"open_access","date_created":"2026-05-15T15:53:57Z","relation":"main_file"},{"file_id":"21880","checksum":"b41282beaacfb32472769b9e3b1758d8","content_type":"application/x-zip-compressed","date_updated":"2026-05-15T15:54:06Z","file_name":"2026_Werner_Thomas_Thesis.zip","access_level":"closed","creator":"twerner","file_size":9370704,"relation":"source_file","date_created":"2026-05-15T15:54:06Z"}],"title":"Interfacing superconducting qubits with optical photons","abstract":[{"lang":"eng","text":"Atoms and photons, two things so different but yet so alike. The former, the building block of matter, something we learn about in school and imagine it as some tiny marbles encircled by other tinier marbles. The latter, an electromagnetic wave, a light particle or an excitation of the electromagnetic field. Quantum mechanics tells us about the properties of these two entities. And even if it sounds, looks and writes counter-intuitive, it has proven right for over a century now.\r\n\r\nIn this work, I elaborate on how we tested the laws of quantum mechanics and how we used them learn more about the tiny building blocks of nature and the fields they use to talk to each other. The atoms we use, are artificial. Superconducting qubits, small electrical circuits with quantized energy levels behave like electrons that transition between different orbitals in an atom. One of the qubits' advantages, is also a big disadvantage. We design the circuits' energy levels and fabricate them in a cleanroom. This allows for arbitrary spaced energy levels but in contrast to real atoms, prevents two superconducting qubits from being alike. Still, this qubit platform is one of the frontrunners for future quantum computing technology and testing fundamental physics due to their scalability.\r\n\r\nWe interface superconducting qubits, which operate in the GHz regime, with microwave photons. We use 3D aluminum cavities as mediators between qubits and photons. The cavities allow for non-destructive readout of the qubit state, they shield the qubits from noise at the qubit frequency and they give us an easy way to frequency-tune these joint systems.\r\n\r\nWe need to operate superconducting qubits and their cavities at millikelvin temperatures in dilution refrigerators. At higher temperatures, superconductivity suffers and even worse, the environment is filled with thermal noise photons. This poses a fundamental limitation on the scalability of superconducting qubit devices. Also connecting multiple devices in different fridges does not work over room temperature links because the microwave photons used for this purpose will be covered in noise and the quantum information they carry, will be unusable.\r\n\r\nInfrared photons do not suffer from this noise problem since there are close to zero thermal noise photons at their frequencies at room temperature. We cannot simply interface superconducting devices with optical photons due their frequency mismatch and the destructive effect of optical photons on superconductors. Therefore, we use microwave-to-optics transducers that allow to convert microwave photons into optical ones and vice-versa. The transducers that we use are macroscopic electro-optic transducers using the Pockels effect in a disk-shaped Lithium Niobate whispering gallery mode resonator. By using a strong optical pump, photons from the two frequency domains experience a beam-splitter interaction and get converted from one to the other.\r\n\r\nWe measure the generated optical photons using elaborate optical setups, optical heterodyning and single photon detectors to gain knowledge about the qubit state or the converted microwave photons. Bridging the microwave and the optical world allows us to take advantage of both of their strengths but it also requires deep knowledge about both of their working principles.\r\n\r\nIn this work, we describe two experiments that our group conducted to showcase the opportunities that arise from interfacing superconducting qubits with optical photons but also the pitfalls, one may encounter on the way.\r\n\r\nIn the first experiment, we managed to all-optically read out a superconducting qubit. We show that the assignment fidelity, the probability that a measurement of the qubit state matches the prepared state, is close to equal for all-optical, microwave-to-optics and conventional microwave readout. We show T1 and T2 measurements for all three readout types and give an analysis of the noise caused by the optics. Finally, we show that the infrared light does not affect the qubit performance in a negative way but that the heating it causes does. This is an important insight that we used in the next experiment.\r\n\r\nThe second experiment is the upconversion of itinerant single microwave photons to the optical domain. We show that we can generate single microwave photons from a qubit-cavity system. We upconvert these single photons, measure them with a single photon detector and reconstruct their shape. By conducting a single photon Rabi measurement, we show correlations between the microwave and the optical domain. And by thorough signal-to-noise measurements and noise analysis, we find that we can generate single infrared photons with high signal-to-noise ratio 5.1 and low transducer added noise (<0.012 quanta). We show that this measurement creates a path towards entanglement of a superconducting qubit and an optical photon and what parameters need to be improved to achieve it. Additionally, this experiment is a proof of principle for an on-demand infrared single photon source. More generally, it allows to link microwave quantum technology in general to the optical domain."}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-05-20T13:35:43Z","keyword":["Superconducting qubits","Quantum optics","Single photons and quantum effects","Nonlinear optics"],"doi":"10.15479/AT-ISTA-21863","status":"public","project":[{"name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states","grant_number":"101089099","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"call_identifier":"H2020","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"5b807754-ab3d-11f0-914f-ff8c34502cc9","name":"Integrated optical coupling for low loss electro-optic interconnects","grant_number":"101248662"},{"grant_number":"101187231","name":"Cavity-Integrated Electro-Optics: Measuring, Converting and Manipulating Microwaves with Light","_id":"91aaf765-16d5-11f0-9cad-a8e7e44cccb7"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"},{"_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738","name":"Open Superconducting Quantum Computers (OpenSuperQPlus)","grant_number":"101080139"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"LifeSc"},{"_id":"SSU"}],"_id":"21863","date_published":"2026-05-12T00:00:00Z","date_created":"2026-05-12T09:04:02Z","file_date_updated":"2026-05-15T15:54:06Z","year":"2026","day":"12","article_processing_charge":"No","type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","related_material":{"record":[{"id":"19073","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"21870","status":"public"}]},"ec_funded":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","citation":{"chicago":"Werner, Thomas. “Interfacing Superconducting Qubits with Optical Photons.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21863\">https://doi.org/10.15479/AT-ISTA-21863</a>.","ieee":"T. Werner, “Interfacing superconducting qubits with optical photons,” Institute of Science and Technology Austria, 2026.","mla":"Werner, Thomas. <i>Interfacing Superconducting Qubits with Optical Photons</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21863\">10.15479/AT-ISTA-21863</a>.","ista":"Werner T. 2026. Interfacing superconducting qubits with optical photons. Institute of Science and Technology Austria.","ama":"Werner T. Interfacing superconducting qubits with optical photons. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21863\">10.15479/AT-ISTA-21863</a>","apa":"Werner, T. (2026). <i>Interfacing superconducting qubits with optical photons</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21863\">https://doi.org/10.15479/AT-ISTA-21863</a>","short":"T. Werner, Interfacing Superconducting Qubits with Optical Photons, Institute of Science and Technology Austria, 2026."},"corr_author":"1","supervisor":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M"}],"OA_place":"publisher","oa_version":"Published Version","page":"97","language":[{"iso":"eng"}],"acknowledgement":"The author of this work was supported by the European Research Council under grant no.\r\n101089099 (ERC CoG cQEO) and the European Union’s Horizon 2020 research and innovation\r\nprogram under grant no. 899354 (FETopen SuperQuLAN).\r\nThis work was also supported by the European Research Council under grant nos. 758053\r\n(ERC StG QUNNECT), 101248662 (ERC POC CoupledEOT), and the European Innovation\r\nCouncil no. 101187231 (PathfinderOpen CIELO). This research was funded in whole or in part\r\nby the Austrian Science Fund (FWF) [10.55776/F71]. For open access purposes, the author\r\nhas applied a CC BY public copyright license to any author accepted manuscript version arising\r\nfrom this submission.\r\niii\r\nMy co-authors in the works mentioned later acknowledge generous support from the ISTFELLOW program, the NOMIS-ISTA fellowship, the Horizon Europe Program HORIZONCL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and a DOC fellowship of the Austrian Academy of Sciences at IST Austria.\r\n","ddc":["530","537","539"],"month":"05","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"author":[{"id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","first_name":"Thomas","orcid":"0009-0001-2346-5236","last_name":"Werner","full_name":"Werner, Thomas"}],"publication_status":"published"},{"scopus_import":"1","acknowledgement":"We thank Fritz Diorico and Onur Hosten who suggested the filter cavity design, and gave important insights about the assembly and the testing of the FabryPerot filter cavities. Ekatrina Fedotova and Diego A.\r\nLancheros Naranjo worked on the filter cavity setup in\r\nthe early stages of this work. Gustavo Wiederhecker and\r\nYiewen Chu provided insights as to the origins of the\r\nobserved optical noise and Nicola Carlon Zambon suggested using telecom filters to mitigate it further. This\r\nwork was supported by the European Research Council under grant agreement no. 101089099 (ERC CoG\r\ncQEO), and 101248662 (ERC POC CoupledEOT), the\r\nEuropean Unions Horizon 2020 research and innovation\r\nprogram under grant agreement no. 899354 (FETopen\r\nSuperQuLAN), the European Innovation Council no.\r\n101187231 (PathfinderOpen CIELO), and the Austrian\r\nScience Fund (FWF) no. F7105 (SFB BeyondC). J.F.\r\nand L.K. acknowledge support from the Horizon Europe\r\nProgram HORIZON-CL4-2022-QUANTUM-01-SGA via\r\nProject No. 101113946 OpenSuperQPlus100. A.M. acknowledges support from the NOMIS-ISTA fellowship.","publication_status":"draft","department":[{"_id":"JoFi"},{"_id":"GradSch"}],"author":[{"orcid":"0009-0001-2346-5236","last_name":"Werner","full_name":"Werner, Thomas","id":"1fcd8497-dba3-11ea-a45e-c6fbd715f7c7","first_name":"Thomas"},{"full_name":"Riyazi, Erfan","last_name":"Riyazi","id":"53322f94-5355-11ee-ae5a-ff6f81c87d51","first_name":"Erfan"},{"id":"221708e1-1ff6-11ee-9fa6-85146607433e","first_name":"Samarth","orcid":"0000-0002-1965-4309","last_name":"Hawaldar","full_name":"Hawaldar, Samarth"},{"first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","first_name":"Georg M","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","last_name":"Arnold"},{"first_name":"Paul Falthansl-Scheinecker","full_name":"Paul Falthansl-Scheinecker, Paul Falthansl-Scheinecker","last_name":"Paul Falthansl-Scheinecker"},{"full_name":"Naranjo, Jennifer A. Sánchez","last_name":"Naranjo","first_name":"Jennifer A. Sánchez"},{"last_name":"Loi","full_name":"Loi, Dante","first_name":"Dante"},{"last_name":"Kapoor","full_name":"Kapoor, Lucky N.","first_name":"Lucky N."},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"first_name":"Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","full_name":"Qiu, Liu","orcid":"0000-0003-4345-4267"},{"last_name":"Militaru","full_name":"Militaru, Andrei","first_name":"Andrei","id":"d67706f8-8eb1-11ee-ad1b-9c30dfa19e0b"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"month":"01","language":[{"iso":"eng"}],"oa_version":"Preprint","OA_place":"repository","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"21863"}]},"corr_author":"1","citation":{"apa":"Werner, T., Riyazi, E., Hawaldar, S., Sahu, R., Arnold, G. M., Paul Falthansl-Scheinecker, P. F.-S., … Fink, J. M. (n.d.). Electro-optic conversion of itinerant Fock states. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2602.00928\">https://doi.org/10.48550/arXiv.2602.00928</a>","ama":"Werner T, Riyazi E, Hawaldar S, et al. Electro-optic conversion of itinerant Fock states. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2602.00928\">10.48550/arXiv.2602.00928</a>","short":"T. Werner, E. Riyazi, S. Hawaldar, R. Sahu, G.M. Arnold, P.F.-S. Paul Falthansl-Scheinecker, J.A.S. Naranjo, D. Loi, L.N. Kapoor, M. Zemlicka, L. Qiu, A. Militaru, J.M. Fink, ArXiv (n.d.).","mla":"Werner, Thomas, et al. “Electro-Optic Conversion of Itinerant Fock States.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2602.00928\">10.48550/arXiv.2602.00928</a>.","ieee":"T. Werner <i>et al.</i>, “Electro-optic conversion of itinerant Fock states,” <i>arXiv</i>. .","chicago":"Werner, Thomas, Erfan Riyazi, Samarth Hawaldar, Rishabh Sahu, Georg M Arnold, Paul Falthansl-Scheinecker Paul Falthansl-Scheinecker, Jennifer A. Sánchez Naranjo, et al. “Electro-Optic Conversion of Itinerant Fock States.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2602.00928\">https://doi.org/10.48550/arXiv.2602.00928</a>.","ista":"Werner T, Riyazi E, Hawaldar S, Sahu R, Arnold GM, Paul Falthansl-Scheinecker PF-S, Naranjo JAS, Loi D, Kapoor LN, Zemlicka M, Qiu L, Militaru A, Fink JM. Electro-optic conversion of itinerant Fock states. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2602.00928\">10.48550/arXiv.2602.00928</a>."},"OA_type":"green","article_processing_charge":"No","day":"31","type":"preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"arXiv","date_created":"2026-05-12T13:58:18Z","date_published":"2026-01-31T00:00:00Z","_id":"21870","external_id":{"arxiv":["2602.00928"]},"year":"2026","arxiv":1,"project":[{"_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a","grant_number":"101089099","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states"},{"_id":"5b807754-ab3d-11f0-914f-ff8c34502cc9","name":"Integrated optical coupling for low loss electro-optic interconnects","grant_number":"101248662"},{"name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020"},{"grant_number":"101187231","name":"Cavity-Integrated Electro-Optics: Measuring, Converting and Manipulating Microwaves with Light","_id":"91aaf765-16d5-11f0-9cad-a8e7e44cccb7"},{"name":"Integrating superconducting quantum circuits","grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"status":"public","date_updated":"2026-05-20T13:35:42Z","doi":"10.48550/arXiv.2602.00928","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"abstract":[{"text":"Superconducting qubits are a leading candidate for utility-scale quantum computing due to their fast gate speeds and steadily decreasing error rates. The requirement for millikelvin operating temperatures, however, creates a significant scaling bottleneck. Modular architectures using optical fiber links could bridge separate cryogenic nodes, but superconducting circuits do not have coherent optical transitions and microwave-to-optical conversion has not been shown for any non-classical photon state. In this work, we demonstrate the on-demand generation and tomographic reconstruction of itinerant single microwave photons at 8.9 GHz from a superconducting qubit. We upconvert this non-Gaussian state with a transducer added noise below 0.012 quanta and count the converted telecom photons at 193.4 THz with a signal-to-noise ratio of up to 5.1$\\pm$1.1. We characterize the trade-offs between throughput and noise, and establish a viable path toward heralded entanglement distribution and gate teleportation. Looking ahead, these results empower existing superconducting devices to take a key role in distributed quantum technologies and heterogeneous quantum systems.","lang":"eng"}],"title":"Electro-optic conversion of itinerant Fock states","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2602.00928","open_access":"1"}]},{"acknowledgement":"We thank Karl Rössler and Sebastian Brandner for the human SEEG implantations; Katja Kobow for providing the histopathological findings of the patients; Jay Jeschke for help with human electrode localization; Esha Brahmbhatt and Deren Aykan for help with animal habituation; Mursel Karadas for the rodent treadmill design; Nicholas Paleologos, Noam Nitzan, Michael D Hadler and Samuel McKenzie for rating events in a human ripple survey included in a previous version of the manuscript; Nicholas Paleologos for sharing NYU iEEG data for validating UMAP parameters; Julio Esparza for help on the topological analysis through discussions; Thomas Hainmüller, Yiyao Zhang and Mursel Karadas for feedback on the manuscript. We would like to acknowledge Corticale SRL (Genoa, Italy) for providing the SiNAPS probes, and NeuroNexus (Ann Arbor, MI) for their contribution of the data acquisition system and Radiens software. We further acknowledge both Corticale and NeuroNexus for training and support making this research possible. This work was supported by the German Research Foundation (DFG; Walter Benjamin Fellowship MA 10301/1-1, A.M.), NYU Langone Health Finding a Cure for Epilepsy and Seizures (FACES, A.M.), the NOMIS Fellowship (A.N.-O.), the National Institutes of Health (R01NS127954, K23NS104252, A.L.; MH122391, U19NS107616, R01MH139216 G.B.,), and the NYU Department of Neurology (A.L.).","intvolume":"        16","ddc":["570"],"scopus_import":"1","month":"12","volume":16,"publication_status":"published","department":[{"_id":"PeJo"}],"author":[{"first_name":"Anna","last_name":"Maslarova","full_name":"Maslarova, Anna"},{"last_name":"Shin","full_name":"Shin, Jiyun N.","first_name":"Jiyun N."},{"id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","first_name":"Andrea C","orcid":"0000-0002-9280-8597","full_name":"Navas Olivé, Andrea C","last_name":"Navas Olivé"},{"last_name":"Vöröslakos","full_name":"Vöröslakos, Mihály","first_name":"Mihály"},{"full_name":"Hamer, Hajo","last_name":"Hamer","first_name":"Hajo"},{"last_name":"Doerfler","full_name":"Doerfler, Arnd","first_name":"Arnd"},{"first_name":"Simon","last_name":"Henin","full_name":"Henin, Simon"},{"first_name":"György","last_name":"Buzsáki","full_name":"Buzsáki, György"},{"full_name":"Liu, Anli","last_name":"Liu","first_name":"Anli"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"OA_place":"publisher","has_accepted_license":"1","OA_type":"gold","article_number":"11636","citation":{"ista":"Maslarova A, Shin JN, Navas Olivé AC, Vöröslakos M, Hamer H, Doerfler A, Henin S, Buzsáki G, Liu A. 2025. Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. Nature Communications. 16, 11636.","mla":"Maslarova, Anna, et al. “Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.” <i>Nature Communications</i>, vol. 16, 11636, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-66562-6\">10.1038/s41467-025-66562-6</a>.","chicago":"Maslarova, Anna, Jiyun N. Shin, Andrea C Navas Olivé, Mihály Vöröslakos, Hajo Hamer, Arnd Doerfler, Simon Henin, György Buzsáki, and Anli Liu. “Spatiotemporal Patterns Differentiate Hippocampal Sharp-Wave Ripples from Interictal Epileptiform Discharges in Mice and Humans.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-66562-6\">https://doi.org/10.1038/s41467-025-66562-6</a>.","ieee":"A. Maslarova <i>et al.</i>, “Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"A. Maslarova, J.N. Shin, A.C. Navas Olivé, M. Vöröslakos, H. Hamer, A. Doerfler, S. Henin, G. Buzsáki, A. Liu, Nature Communications 16 (2025).","apa":"Maslarova, A., Shin, J. N., Navas Olivé, A. C., Vöröslakos, M., Hamer, H., Doerfler, A., … Liu, A. (2025). Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-66562-6\">https://doi.org/10.1038/s41467-025-66562-6</a>","ama":"Maslarova A, Shin JN, Navas Olivé AC, et al. Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-66562-6\">10.1038/s41467-025-66562-6</a>"},"article_processing_charge":"Yes","day":"30","publication":"Nature Communications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_published":"2025-12-30T00:00:00Z","_id":"20977","external_id":{"pmid":["39975118"]},"pmid":1,"date_created":"2026-01-11T23:01:35Z","file_date_updated":"2026-01-12T09:30:15Z","year":"2025","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"DOAJ_listed":"1","date_updated":"2026-01-12T09:31:56Z","doi":"10.1038/s41467-025-66562-6","status":"public","oa":1,"article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"success":1,"checksum":"a8a1670e197484382e087be60f643945","content_type":"application/pdf","file_id":"20978","date_updated":"2026-01-12T09:30:15Z","file_name":"2025_NatureComm_Maslarova.pdf","date_created":"2026-01-12T09:30:15Z","relation":"main_file","file_size":7629997,"access_level":"open_access","creator":"dernst"}],"publisher":"Springer Nature","quality_controlled":"1","abstract":[{"text":"Hippocampal sharp-wave ripples (SPW-Rs) are high-frequency oscillations critical for memory consolidation. Despite extensive characterization in rodents, their detection in humans is limited by coarse spatial sampling, interictal epileptiform discharges (IEDs), and a lack of consensus on human ripple localization and morphology. Here, we demonstrate that mouse and human hippocampal ripples share spatial, spectral and temporal features, which are clearly distinct from IEDs. In recordings from male APP/PS1 mice, SPW-Rs were distinguishable from IEDs by multiple criteria. Hippocampal ripples recorded during NREM sleep in female and male surgical epilepsy patients exhibited similar narrowband frequency peaks and multiple ripple cycles in the CA1 and subiculum regions. Conversely, IEDs showed a broad spatial extent and wide-band frequency power. We developed a semi-automated, ripple curation toolbox (ripmap) to separate event waveforms by low-dimensional embedding to reduce false-positive rate in selected ripple channels. Our approach improves ripple detection and provides a firm foundation for future human memory research.","lang":"eng"}],"title":"Spatiotemporal patterns differentiate hippocampal sharp-wave ripples from interictal epileptiform discharges in mice and humans","publication_identifier":{"eissn":["2041-1723"]}},{"oa":1,"article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","call_identifier":"H2020"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"name":"Molecular Drug Targets","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Synaptic networks of human brain","grant_number":"PAT 4178023","_id":"8d9195e9-16d5-11f0-9cad-d075be887a1e"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"status":"public","doi":"10.1016/j.cell.2024.11.022","date_updated":"2026-04-14T08:34:32Z","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"file":[{"success":1,"content_type":"application/pdf","checksum":"d5a818edc32d249cdf75e1bb5b70a4b7","file_id":"18884","date_updated":"2025-01-27T08:46:33Z","file_name":"2025_Cell_Watson.pdf","date_created":"2025-01-27T08:46:33Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":14082343}],"publisher":"Elsevier","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","abstract":[{"text":"Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. ","lang":"eng"}],"quality_controlled":"1","publication":"Cell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_processing_charge":"Yes (via OA deal)","day":"23","file_date_updated":"2025-01-27T08:46:33Z","year":"2025","date_published":"2025-01-23T00:00:00Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"_id":"18879","external_id":{"pmid":["39667938"],"isi":["001408395600001"]},"date_created":"2025-01-26T23:01:49Z","pmid":1,"OA_place":"publisher","OA_type":"hybrid","issue":"2","corr_author":"1","citation":{"ista":"Watson J, Vargas Barroso VM, Morse R, Navas Olivé AC, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. 2025. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell. 188(2), 501–514.e18.","chicago":"Watson, Jake, Victor M Vargas Barroso, Rebecca Morse, Andrea C Navas Olivé, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>.","ieee":"J. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>Cell</i>, vol. 188, no. 2. Elsevier, p. 501–514.e18, 2025.","mla":"Watson, Jake, et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>Cell</i>, vol. 188, no. 2, Elsevier, 2025, p. 501–514.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>.","short":"J. Watson, V.M. Vargas Barroso, R. Morse, A.C. Navas Olivé, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, Cell 188 (2025) 501–514.e18.","ama":"Watson J, Vargas Barroso VM, Morse R, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. 2025;188(2):501-514.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">10.1016/j.cell.2024.11.022</a>","apa":"Watson, J., Vargas Barroso, V. M., Morse, R., Navas Olivé, A. C., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (2025). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2024.11.022\">https://doi.org/10.1016/j.cell.2024.11.022</a>"},"ec_funded":1,"related_material":{"record":[{"id":"18688","status":"public","relation":"earlier_version"}]},"has_accepted_license":"1","volume":188,"month":"01","isi":1,"publication_status":"published","author":[{"orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake"},{"first_name":"Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","full_name":"Vargas Barroso, Victor M"},{"id":"ceb89ae7-dc8d-11ea-abe3-da3301d0eab4","first_name":"Rebecca","full_name":"Morse, Rebecca","last_name":"Morse"},{"full_name":"Navas Olivé, Andrea C","last_name":"Navas Olivé","orcid":"0000-0002-9280-8597","id":"739d26c9-52e8-11ee-8d72-f14d3893b4ce","first_name":"Andrea C"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","first_name":"Mojtaba","last_name":"Tavakoli","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973"},{"first_name":"Matthias","last_name":"Tomschik","full_name":"Tomschik, Matthias"},{"first_name":"Karl","last_name":"Rössler","full_name":"Rössler, Karl"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JoDa"},{"_id":"PeJo"},{"_id":"GradSch"}],"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, Walter Kaufmann for assistance with handling frozen tissue, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Lab Support Facility, Miba Machine Shop, and Scientific Computing. We are particularly grateful to the patient donors for their support of this project and also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff; Romana Hoeftberger and the Division of Neuropathology and Neurochemistry; Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology; and Christoph Baumgartner, Martha Feucht, and Ekaterina Pataraia for their clinical care of the patients included in this study. We thank Laura Jonkman, the NABCA biobank, and postmortem brain sample donors for their support of this research. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (advanced grant no. 692692 to P.J. and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J. and grant DK W1232 to M.R.T. and J.G.D.), the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.), and a NOMIS-ISTA fellowship (to A.N.-O.).","intvolume":"       188","ddc":["570"],"scopus_import":"1","page":"501-514.e18","oa_version":"Published Version","language":[{"iso":"eng"}]},{"page":"7736-7756","oa_version":"Published Version","language":[{"iso":"eng"}],"acknowledgement":"We thank Oded Farago, Angelo Cacciuto, Jeriann Beiter and Pietro Sillano for helpful discussions and a critical reading of the manuscript. MMB and AP acknowledge funding by the European Unions Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. FF acknowledges financial support by the NOMIS foundation. BM and AŠ acknowledge funding by ERC Starting Grant “NEPA” 802960. MA and AŠ acknowledge funding by the Volkswagen Foundation Grant Az 96727.","ddc":["540"],"intvolume":"        21","scopus_import":"1","month":"07","volume":21,"isi":1,"publication_status":"published","author":[{"full_name":"Muñoz Basagoiti, Maitane","last_name":"Muñoz Basagoiti","orcid":"0000-0003-1483-1457","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","first_name":"Maitane"},{"orcid":"0000-0001-8501-6017","last_name":"Frey","full_name":"Frey, Felix F","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337"},{"last_name":"Santana de Freitas Amaral","full_name":"Santana de Freitas Amaral, Miguel","first_name":"Miguel","id":"4f2d02dd-47a9-11ec-ad10-82820ed3f501"},{"id":"a43ed60a-dd22-11ed-9bf7-b34133792ea9","first_name":"Adam","full_name":"Prada, Adam","last_name":"Prada"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}],"department":[{"_id":"AnSa"}],"ec_funded":1,"has_accepted_license":"1","issue":"40","OA_type":"hybrid","corr_author":"1","citation":{"ieee":"M. Muñoz Basagoiti, F. F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, and A. Šarić, “A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations,” <i>Soft Matter</i>, vol. 21, no. 40. Royal Society of Chemistry, pp. 7736–7756, 2025.","chicago":"Muñoz Basagoiti, Maitane, Felix F Frey, Billie Meadowcroft, Miguel Santana de Freitas Amaral, Adam Prada, and Anđela Šarić. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>.","mla":"Muñoz Basagoiti, Maitane, et al. “A Tutorial for Mesoscale Computer Simulations of Lipid Membranes: Tether Pulling, Tubulation and Fluctuations.” <i>Soft Matter</i>, vol. 21, no. 40, Royal Society of Chemistry, 2025, pp. 7736–56, doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>.","ista":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. 2025. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. Soft Matter. 21(40), 7736–7756.","ama":"Muñoz Basagoiti M, Frey FF, Meadowcroft B, Santana de Freitas Amaral M, Prada A, Šarić A. A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. 2025;21(40):7736-7756. doi:<a href=\"https://doi.org/10.1039/d5sm00148j\">10.1039/d5sm00148j</a>","apa":"Muñoz Basagoiti, M., Frey, F. F., Meadowcroft, B., Santana de Freitas Amaral, M., Prada, A., &#38; Šarić, A. (2025). A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d5sm00148j\">https://doi.org/10.1039/d5sm00148j</a>","short":"M. Muñoz Basagoiti, F.F. Frey, B. Meadowcroft, M. Santana de Freitas Amaral, A. Prada, A. Šarić, Soft Matter 21 (2025) 7736–7756."},"OA_place":"publisher","date_published":"2025-07-28T00:00:00Z","external_id":{"arxiv":["2502.09798"],"isi":["001562846800001"]},"_id":"20318","date_created":"2025-09-10T05:34:36Z","file_date_updated":"2025-12-30T10:16:40Z","year":"2025","article_processing_charge":"Yes (via OA deal)","day":"28","publication":"Soft Matter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","file":[{"date_created":"2025-12-30T10:16:40Z","relation":"main_file","access_level":"open_access","file_size":4841140,"creator":"dernst","file_name":"2025_SoftMatter_MunozBasagoiti.pdf","date_updated":"2025-12-30T10:16:40Z","success":1,"content_type":"application/pdf","checksum":"590bedad19b6f6d40a7ee036a056a6d9","file_id":"20912"}],"publisher":"Royal Society of Chemistry","title":"A tutorial for mesoscale computer simulations of lipid membranes: Tether pulling, tubulation and fluctuations","abstract":[{"text":"Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations. Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations, by providing a pedagogical examination of membrane tether pulling, shape and mechanics of membrane tubes, and membrane fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"},{"name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"doi":"10.1039/d5sm00148j","status":"public","date_updated":"2025-12-30T10:16:52Z","arxiv":1,"oa":1,"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"}},{"date_created":"2025-10-26T23:01:34Z","pmid":1,"_id":"20531","external_id":{"isi":["001547542300001"],"pmid":["40668071"]},"date_published":"2025-10-17T00:00:00Z","year":"2025","day":"17","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Evolution","title":"Deleterious mutations and selection for sex in spatially structured, diploid populations","quality_controlled":"1","abstract":[{"text":"Genetic drift is potentially an important component of selection for sex, as it is a source of statistical associations between alleles at selected loci. By increasing local drift, population structure may thus amplify the evolutionary advantage of sex. However, most previous models have focused either on haploid populations or on diploid populations without spatial structure. In this article, we use two- and three-locus analytical models and multilocus simulations to explore selection for sex in a diploid population structured according to the island model, in the presence of recurrent deleterious mutations. Our results show that selection generally favors an intermediate rate of sex that decreases as the direct cost of sex increases and increases moderately as the degree of population structure increases. Selection for sex is generated by multiple effects involving genetic associations within and between loci. When selection occurs at many loci, it is generally dominated by interference effects involving deleterious alleles at different loci, captured by our three-locus model. In our multilocus simulations, we observed an irreversible spread of asexual mutants under strong costs of sex, and when deleterious mutations are partially recessive. However, population structure may prevent this spread of asexual mutants when dispersal rates are sufficiently small.","lang":"eng"}],"publisher":"Oxford University Press","publication_identifier":{"eissn":["1558-5646"]},"main_file_link":[{"url":"https://doi.org/10.1101/2025.01.22.634382","open_access":"1"}],"status":"public","doi":"10.1093/evolut/qpaf143","date_updated":"2025-12-01T15:03:54Z","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"article_type":"original","oa":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","page":"2167-2180","scopus_import":"1","intvolume":"        79","acknowledgement":"L.F. is funded by the NOMIS-ISTA Fellowship Program. We thank Colin Olito and two anonymous reviewers for helpful comments, and the bioinformatics and computing services at Roscoff’s Biological Station (Abims platform) and at Institute of Science and Technology Austria for computing time.","author":[{"id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise","orcid":"0000-0003-0371-9339","last_name":"Fouqueau","full_name":"Fouqueau, Louise"},{"full_name":"Roze, Denis","last_name":"Roze","first_name":"Denis"}],"department":[{"_id":"NiBa"}],"publication_status":"published","isi":1,"volume":79,"month":"10","citation":{"mla":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>, vol. 79, no. 10, Oxford University Press, 2025, pp. 2167–80, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>.","ieee":"L. Fouqueau and D. Roze, “Deleterious mutations and selection for sex in spatially structured, diploid populations,” <i>Evolution</i>, vol. 79, no. 10. Oxford University Press, pp. 2167–2180, 2025.","chicago":"Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for Sex in Spatially Structured, Diploid Populations.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>.","ista":"Fouqueau L, Roze D. 2025. Deleterious mutations and selection for sex in spatially structured, diploid populations. Evolution. 79(10), 2167–2180.","apa":"Fouqueau, L., &#38; Roze, D. (2025). Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf143\">https://doi.org/10.1093/evolut/qpaf143</a>","ama":"Fouqueau L, Roze D. Deleterious mutations and selection for sex in spatially structured, diploid populations. <i>Evolution</i>. 2025;79(10):2167-2180. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf143\">10.1093/evolut/qpaf143</a>","short":"L. Fouqueau, D. Roze, Evolution 79 (2025) 2167–2180."},"issue":"10","OA_type":"green","OA_place":"repository"},{"file":[{"relation":"main_file","date_created":"2024-06-12T07:53:19Z","file_size":28370759,"creator":"fhassani","access_level":"open_access","file_name":"Thesis_main_final.pdf","date_updated":"2024-06-20T11:52:22Z","checksum":"258c353d47fa37ea63ea43b1e10a34a0","content_type":"application/pdf","file_id":"17137"},{"creator":"fhassani","file_size":445735,"access_level":"closed","relation":"source_file","date_created":"2024-06-12T07:54:27Z","file_name":"Thesis_main.tex","date_updated":"2024-06-12T07:54:27Z","content_type":"text/x-tex","checksum":"deffa5d0db88093f74812fa71520d5e1","file_id":"17138"}],"abstract":[{"text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing.","lang":"eng"}],"title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-040-4"]},"keyword":["Quantum information","Qubits","Superconducting devices"],"status":"public","doi":"10.15479/at:ista:17133","date_updated":"2026-04-15T06:43:02Z","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"oa":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"_id":"17133","date_published":"2024-06-11T00:00:00Z","date_created":"2024-06-11T18:20:05Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2024-06-20T11:52:22Z","year":"2024","day":"11","article_processing_charge":"No","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","degree_awarded":"PhD","related_material":{"record":[{"id":"13227","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"9928","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8755"}]},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","citation":{"ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>.","short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>"},"corr_author":"1","supervisor":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"OA_place":"publisher","oa_version":"Published Version","page":"161","language":[{"iso":"eng"}],"ddc":["530"],"month":"06","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"author":[{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid"}],"publication_status":"published"},{"title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","quality_controlled":"1","publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/jeb/voae067","open_access":"1"}],"publication_identifier":{"eissn":["1420-9101"]},"status":"public","date_updated":"2026-06-18T17:53:35Z","doi":"10.1093/jeb/voae067","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"oa":1,"article_type":"letter_note","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"17207","external_id":{"isi":["001258359900001"],"pmid":["38941551"]},"date_published":"2024-06-28T00:00:00Z","date_created":"2024-07-07T22:01:04Z","pmid":1,"year":"2024","day":"28","article_processing_charge":"No","publication":"Journal of evolutionary biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"6","citation":{"mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>.","ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” <i>Journal of evolutionary biology</i>, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.","chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>.","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.","apa":"Fouqueau, L., &#38; Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>","ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of evolutionary biology</i>. 2024;37(6):579-587. doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587."},"oa_version":"Published Version","page":"579-587","language":[{"iso":"eng"}],"acknowledgement":"This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","scopus_import":"1","intvolume":"        37","ddc":["570"],"month":"06","volume":37,"author":[{"first_name":"Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise","last_name":"Fouqueau"},{"orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"}],"department":[{"_id":"NiBa"}],"isi":1,"publication_status":"published"},{"corr_author":"1","article_number":"1104","citation":{"apa":"Cheng, B., Hamel, S., &#38; Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>, vol. 14, 1104, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-36841-1\">10.1038/s41467-023-36841-1</a>.","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-36841-1\">https://doi.org/10.1038/s41467-023-36841-1</a>.","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104."},"has_accepted_license":"1","das_tickbox":"1","supplementarymaterial":"no","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":14,"month":"02","publication_status":"published","isi":1,"author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"first_name":"Sebastien","full_name":"Hamel, Sebastien","last_name":"Hamel"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","first_name":"Mandy","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy","orcid":"0000-0002-1838-2129"}],"department":[{"_id":"BiCh"}],"acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","ddc":["540"],"intvolume":"        14","scopus_import":"1","publication_identifier":{"eissn":["2041-1723"]},"file":[{"file_name":"2023_NatComm_Cheng.pdf","date_created":"2023-03-07T10:58:00Z","relation":"main_file","file_size":1946443,"creator":"cchlebak","access_level":"open_access","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","file_id":"12713","content_type":"application/pdf","date_updated":"2023-03-07T10:58:00Z"}],"researchdata_availability":"yes","publisher":"Springer Nature","quality_controlled":"1","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","abstract":[{"lang":"eng","text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution."}],"oa":1,"dataavailabilitystatement":"All original data generated for the study, including the MLP, the training set, simulation input files, intermediate data, PYTHON notebook, are in the SI repository https://github.com/BingqingCheng/highp-ch\r\nhttps://doi.org/10.5281/ZENODO.7578498","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"status":"public","doi":"10.1038/s41467-023-36841-1","date_updated":"2026-08-07T10:50:07Z","file_date_updated":"2023-03-07T10:58:00Z","year":"2023","date_published":"2023-02-27T00:00:00Z","_id":"12702","external_id":{"pmid":["36843123"],"isi":["000939678300002"]},"pmid":1,"date_created":"2023-03-05T23:01:04Z","publication":"Nature Communications","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","article_processing_charge":"No","day":"27"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology."}],"title":"Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome","publisher":"Elsevier","file":[{"file_name":"2022_CellReports_Kaneko.pdf","date_created":"2022-04-15T11:00:58Z","relation":"main_file","access_level":"open_access","file_size":4774216,"creator":"dernst","success":1,"checksum":"49105c6c27c9af0f37f50a8bbb4d380d","content_type":"application/pdf","file_id":"11172","date_updated":"2022-04-15T11:00:58Z"}],"publication_identifier":{"eissn":["2211-1247"]},"doi":"10.1016/j.celrep.2022.110580","status":"public","date_updated":"2025-06-11T14:00:11Z","project":[{"call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa":1,"pmid":1,"date_created":"2022-04-10T22:01:39Z","external_id":{"isi":["000779794000001"],"pmid":["35354025"]},"_id":"11143","date_published":"2022-03-29T00:00:00Z","year":"2022","file_date_updated":"2022-04-15T11:00:58Z","day":"29","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Cell Reports","has_accepted_license":"1","ec_funded":1,"citation":{"apa":"Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., &#38; Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>","ama":"Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. <i>Cell Reports</i>. 2022;38(13). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>","short":"K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022).","mla":"Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>, vol. 38, no. 13, 110580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">10.1016/j.celrep.2022.110580</a>.","chicago":"Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110580\">https://doi.org/10.1016/j.celrep.2022.110580</a>.","ieee":"K. Kaneko <i>et al.</i>, “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” <i>Cell Reports</i>, vol. 38, no. 13. Elsevier, 2022.","ista":"Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580."},"article_number":"110580","issue":"13","language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","ddc":["570"],"intvolume":"        38","acknowledgement":"We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com).","author":[{"full_name":"Kaneko, Keisuke","last_name":"Kaneko","first_name":"Keisuke"},{"id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher","orcid":"0000-0002-4809-5059","last_name":"Currin","full_name":"Currin, Christopher"},{"first_name":"Kevin M.","last_name":"Goff","full_name":"Goff, Kevin M."},{"first_name":"Eric R.","last_name":"Wengert","full_name":"Wengert, Eric R."},{"first_name":"Ala","full_name":"Somarowthu, Ala","last_name":"Somarowthu"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P"},{"last_name":"Goldberg","full_name":"Goldberg, Ethan M.","first_name":"Ethan M."}],"department":[{"_id":"TiVo"}],"isi":1,"publication_status":"published","volume":38,"month":"03"},{"issue":"1","citation":{"ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60."},"has_accepted_license":"1","oa_version":"Published Version","page":"P44-60","language":[{"iso":"eng"}],"volume":121,"month":"01","author":[{"last_name":"Zisis","full_name":"Zisis, Themistoklis","first_name":"Themistoklis"},{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"last_name":"Brandstätter","full_name":"Brandstätter, Tom","first_name":"Tom"},{"first_name":"Wei Xiong","full_name":"Siow, Wei Xiong","last_name":"Siow"},{"first_name":"Joseph","last_name":"d’Alessandro","full_name":"d’Alessandro, Joseph"},{"full_name":"Vollmar, Angelika M.","last_name":"Vollmar","first_name":"Angelika M."},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."},{"first_name":"Stefan","last_name":"Zahler","full_name":"Zahler, Stefan"}],"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"isi":1,"publication_status":"published","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","scopus_import":"1","ddc":["570"],"intvolume":"       121","publication_identifier":{"issn":["0006-3495"]},"file":[{"file_name":"2022_BiophysicalJour_Zisis.pdf","access_level":"open_access","file_size":4475504,"creator":"dernst","date_created":"2022-07-29T10:17:10Z","relation":"main_file","content_type":"application/pdf","file_id":"11697","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","success":1,"date_updated":"2022-07-29T10:17:10Z"}],"abstract":[{"lang":"eng","text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n"}],"quality_controlled":"1","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","publisher":"Elsevier","oa":1,"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","date_updated":"2025-06-11T13:59:29Z","doi":"10.1016/j.bpj.2021.12.006","status":"public","keyword":["Biophysics"],"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"file_date_updated":"2022-07-29T10:17:10Z","year":"2022","external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"_id":"10530","date_published":"2022-01-04T00:00:00Z","pmid":1,"date_created":"2021-12-10T09:48:19Z","publication":"Biophysical Journal","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"04","article_processing_charge":"No"}]