[{"article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.14104"}],"abstract":[{"text":"State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with  100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors. ","lang":"eng"}],"ec_funded":1,"oa_version":"Preprint","volume":20,"day":"20","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"},{"grant_number":"707438","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425"},{"name":"Open Superconducting Quantum Computers (OpenSuperQPlus)","_id":"bdb7cfc1-d553-11ed-ba76-d2eaab167738","grant_number":"101080139"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"quality_controlled":"1","external_id":{"arxiv":["2206.14104"],"isi":["001095315600001"]},"department":[{"_id":"JoFi"}],"month":"10","date_updated":"2026-04-15T06:39:01Z","article_number":"044054","isi":1,"title":"Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses","citation":{"mla":"Zemlicka, Martin, et al. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>, vol. 20, no. 4, 044054, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses,” <i>Physical Review Applied</i>, vol. 20, no. 4. American Physical Society, 2023.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2023. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Physical Review Applied. 20(4), 044054.","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum-Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>.","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. 2023;20(4). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">10.1103/PhysRevApplied.20.044054</a>","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2023). Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.20.044054\">https://doi.org/10.1103/PhysRevApplied.20.044054</a>","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, Physical Review Applied 20 (2023)."},"year":"2023","date_published":"2023-10-20T00:00:00Z","doi":"10.1103/PhysRevApplied.20.044054","article_processing_charge":"No","publisher":"American Physical Society","publication_identifier":{"eissn":["2331-7019"]},"publication_status":"published","intvolume":"        20","scopus_import":"1","status":"public","date_created":"2023-11-12T23:00:55Z","language":[{"iso":"eng"}],"publication":"Physical Review Applied","acknowledged_ssus":[{"_id":"NanoFab"}],"issue":"4","corr_author":"1","type":"journal_article","author":[{"first_name":"Martin","orcid":"0009-0005-0878-3032","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda"},{"first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","first_name":"Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"}],"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105), the European Research Council under Grant Agreement No. 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. M.Z. was the recipient of a SAIA scholarship, E.R. of\r\na DOC fellowship of the Austrian Academy of Sciences, and M.P. of a Pöttinger scholarship at IST Austria. S.B. acknowledges support from Marie Skłodowska Curie Program No. 707438 (MSC-IF SUPEREOM). J.M.F. acknowledges support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100 and the ISTA Nanofabrication Facility.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"14520","relation":"research_data"}]},"oa":1,"arxiv":1,"_id":"14517"},{"day":"18","volume":380,"oa_version":"Preprint","ec_funded":1,"external_id":{"pmid":["37200415"],"arxiv":["2301.03315"],"isi":["000996515200004"]},"quality_controlled":"1","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"abstract":[{"lang":"eng","text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification."}],"article_type":"original","year":"2023","date_published":"2023-05-18T00:00:00Z","citation":{"ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721.","ieee":"R. Sahu <i>et al.</i>, “Entangling microwaves with light,” <i>Science</i>, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” <i>Science</i>, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &#38; Fink, J. M. (2023). Entangling microwaves with light. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. <i>Science</i>. 2023;380(6646):718-721. doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>."},"publication_status":"published","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"doi":"10.1126/science.adg3812","date_updated":"2026-04-15T06:39:33Z","month":"05","department":[{"_id":"JoFi"}],"title":"Entangling microwaves with light","isi":1,"status":"public","date_created":"2023-05-31T11:39:24Z","scopus_import":"1","keyword":["Multidisciplinary"],"publication":"Science","language":[{"iso":"eng"}],"pmid":1,"intvolume":"       380","page":"718-721","related_material":{"record":[{"id":"13122","status":"public","relation":"research_data"}],"link":[{"url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","description":"News on ISTA Website","relation":"press_release"}]},"oa":1,"_id":"13106","arxiv":1,"corr_author":"1","issue":"6646","author":[{"last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","orcid":"0000-0001-6264-2162"},{"full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","last_name":"Qiu","first_name":"Liu","orcid":"0000-0003-4345-4267"},{"orcid":"0000-0001-9868-2166","first_name":"William J","last_name":"Hease","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","last_name":"Arnold","orcid":"0000-0003-1397-7876","first_name":"Georg M"},{"last_name":"Minoguchi","full_name":"Minoguchi, Y.","first_name":"Y."},{"full_name":"Rabl, P.","last_name":"Rabl","first_name":"P."},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"_id":"13122","publisher":"Zenodo","article_processing_charge":"No","doi":"10.5281/ZENODO.7789417","related_material":{"record":[{"id":"13106","status":"public","relation":"used_in_publication"}]},"date_published":"2023-03-31T00:00:00Z","year":"2023","oa":1,"citation":{"chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","short":"R. Sahu, (2023).","mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>."},"title":"Entangling microwaves with light","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","orcid":"0000-0001-6264-2162"}],"type":"research_data_reference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","date_updated":"2026-04-15T06:39:32Z","department":[{"_id":"JoFi"}],"month":"03","day":"31","oa_version":"Published Version","status":"public","date_created":"2023-06-06T06:46:16Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7789418"}],"abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}]},{"intvolume":"        14","pmid":1,"file":[{"relation":"main_file","file_size":2899592,"success":1,"access_level":"open_access","checksum":"a85773b5fe23516f60f7d5d31b55c200","date_created":"2023-07-18T08:43:07Z","creator":"dernst","file_id":"13248","content_type":"application/pdf","file_name":"2023_NatureComm_Hassani.pdf","date_updated":"2023-07-18T08:43:07Z"}],"ddc":["530"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"publication":"Nature Communications","scopus_import":"1","status":"public","date_created":"2023-07-16T22:01:08Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","author":[{"first_name":"Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"},{"full_name":"Kapoor, Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky","orcid":"0000-0001-8319-2148"},{"first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea"},{"orcid":"0009-0005-0878-3032","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-07-18T08:43:07Z","corr_author":"1","_id":"13227","oa":1,"related_material":{"record":[{"status":"public","id":"17133","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis."}],"article_type":"original","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"}],"quality_controlled":"1","external_id":{"isi":["001024729900009"],"pmid":["37407570"]},"day":"05","oa_version":"Published Version","volume":14,"title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","article_number":"3968","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"07","department":[{"_id":"JoFi"}],"date_updated":"2026-04-15T06:39:57Z","publication_status":"published","doi":"10.1038/s41467-023-39656-2","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"citation":{"chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>.","ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., &#38; Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39656-2\">https://doi.org/10.1038/s41467-023-39656-2</a>","short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023).","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” <i>Nature Communications</i>, vol. 14, 3968, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39656-2\">10.1038/s41467-023-39656-2</a>.","ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968."},"date_published":"2023-07-05T00:00:00Z","year":"2023"},{"date_created":"2023-06-06T07:36:50Z","status":"public","day":"28","oa_version":"Published Version","ddc":["530"],"abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"citation":{"apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>.","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","mla":"Redchenko, Elena, et al. <i>Tunable Directional Photon Scattering from a Pair of Superconducting Qubits</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023."},"year":"2023","date_published":"2023-04-28T00:00:00Z","oa":1,"related_material":{"record":[{"relation":"used_in_publication","id":"13117","status":"public"}]},"doi":"10.5281/ZENODO.7858567","publisher":"Zenodo","article_processing_charge":"No","_id":"13124","department":[{"_id":"JoFi"}],"month":"04","corr_author":"1","date_updated":"2026-04-15T06:40:27Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","author":[{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander","first_name":"Alexander"},{"first_name":"Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","full_name":"Sett, Riya","last_name":"Sett"},{"orcid":"0009-0005-0878-3032","first_name":"Martin","last_name":"Zemlicka","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Poddubny","full_name":"Poddubny, Alexander"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tunable directional photon scattering from a pair of superconducting qubits"},{"tmp":{"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)","short":"CC BY-NC-SA (4.0)"},"date_updated":"2026-04-15T06:43:26Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"month":"05","title":"Cavity quantum electrooptics","date_published":"2023-05-05T00:00:00Z","year":"2023","citation":{"ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13175\">https://doi.org/10.15479/at:ista:13175</a>","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13175\">10.15479/at:ista:13175</a>.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria."},"degree_awarded":"PhD","publication_status":"published","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:13175","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"oa_version":"Published Version","day":"05","ec_funded":1,"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"alternative_title":["ISTA Thesis"],"file_date_updated":"2023-07-06T11:35:15Z","corr_author":"1","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162","first_name":"Rishabh"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","type":"dissertation","related_material":{"record":[{"status":"public","id":"12900","relation":"old_edition"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"id":"9114","status":"public","relation":"part_of_dissertation"}]},"oa":1,"_id":"13175","OA_place":"publisher","file":[{"file_id":"13176","creator":"cchlebak","file_name":"thesis_pdfa.pdf","date_updated":"2023-06-30T08:17:25Z","content_type":"application/pdf","access_level":"open_access","success":1,"file_size":18688376,"relation":"main_file","date_created":"2023-06-30T08:17:25Z","checksum":"7d03f1a5a5258ee43dfc3323dea4e08f"},{"creator":"cchlebak","file_id":"13196","date_updated":"2023-07-06T11:35:15Z","file_name":"thesis.zip","content_type":"application/x-zip-compressed","access_level":"closed","file_size":37847025,"relation":"source_file","date_created":"2023-07-06T11:35:15Z","checksum":"c3b45317ae58e0527533f98c202d81b7"}],"ddc":["537","535","539"],"page":"202","supervisor":[{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"status":"public","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"date_created":"2023-06-30T08:07:43Z","has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}]},{"oa_version":"Published Version","day":"05","ec_funded":1,"project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","grant_number":"899354"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. "}],"year":"2023","date_published":"2023-05-05T00:00:00Z","citation":{"mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023."},"publication_status":"published","degree_awarded":"PhD","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-030-5"]},"doi":"10.15479/at:ista:12900","tmp":{"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)","short":"CC BY-NC-SA (4.0)"},"date_updated":"2026-04-15T06:43:26Z","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"month":"05","title":"Cavity quantum electrooptics","supervisor":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"status":"public","date_created":"2023-05-05T11:08:50Z","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"source_file","file_size":36767177,"date_created":"2023-05-09T08:45:14Z","checksum":"8cbdab9c37ee55e591092a6f66b272c4","creator":"rsahu","embargo_to":"open_access","file_id":"12928","file_name":"thesis.zip","date_updated":"2023-06-06T22:30:03Z","content_type":"application/x-zip-compressed"},{"content_type":"application/pdf","file_name":"thesis_pdfa_final.pdf","date_updated":"2023-07-06T11:37:40Z","file_id":"12929","creator":"rsahu","checksum":"439659ead46618147309be39d9dd5a8c","date_created":"2023-05-09T08:51:17Z","relation":"main_file","file_size":17501990,"access_level":"closed"}],"ddc":["537","535","539"],"page":"190","related_material":{"record":[{"id":"13175","status":"public","relation":"new_edition"},{"relation":"part_of_dissertation","status":"public","id":"10924"},{"status":"public","id":"9114","relation":"part_of_dissertation"}]},"_id":"12900","OA_place":"publisher","file_date_updated":"2023-07-06T11:37:40Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0001-6264-2162","first_name":"Rishabh","last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation"},{"_id":"12897","related_material":{"record":[{"status":"public","id":"9817","relation":"part_of_dissertation"},{"relation":"dissertation_contains","status":"public","id":"13188"},{"status":"public","id":"7117","relation":"part_of_dissertation"}]},"oa":1,"author":[{"first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","type":"dissertation","corr_author":"1","file_date_updated":"2023-12-08T23:30:04Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","status":"public","date_created":"2023-05-05T10:40:14Z","supervisor":[{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385"}],"page":"180","ddc":["516","004","518","531"],"file":[{"embargo":"2023-12-07","content_type":"application/pdf","date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-hafner-2023may11-a2b.pdf","file_id":"12942","creator":"chafner","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","date_created":"2023-05-11T10:43:20Z","relation":"main_file","file_size":50714445,"access_level":"open_access"},{"file_size":265319,"relation":"source_file","access_level":"closed","checksum":"a6b51334be2b81672357b1549afab40c","date_created":"2023-05-11T10:43:44Z","embargo_to":"open_access","creator":"chafner","file_id":"12943","content_type":"application/pdf","file_name":"thesis-release-form.pdf","date_updated":"2023-12-08T23:30:04Z"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12897","degree_awarded":"PhD","publication_status":"published","date_published":"2023-05-05T00:00:00Z","year":"2023","citation":{"chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria."},"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","date_updated":"2025-04-15T07:16:15Z","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"month":"05","alternative_title":["ISTA Thesis"],"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"ec_funded":1,"day":"05","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will."}]},{"intvolume":"        42","ddc":["516"],"file":[{"success":1,"access_level":"open_access","file_size":19635168,"relation":"main_file","date_created":"2023-07-04T08:11:28Z","checksum":"4954c1cfa487725bc156dcfec872478a","file_id":"13194","creator":"chafner","date_updated":"2023-07-04T08:11:28Z","file_name":"kirchhoff-rods.pdf","content_type":"application/pdf"},{"date_updated":"2023-07-04T07:46:28Z","file_name":"supp-main.pdf","content_type":"application/pdf","title":"Supplemental Material with Proofs","creator":"chafner","file_id":"13190","date_created":"2023-07-04T07:46:28Z","checksum":"79c9975fbc82ff71f1767331d2204cca","access_level":"open_access","file_size":420909,"relation":"supplementary_material"},{"file_size":430086,"relation":"supplementary_material","access_level":"open_access","checksum":"4ab647e4f03c711e1e6a5fc1eb8684db","date_created":"2023-07-04T07:46:30Z","title":"Cheat Sheet for Notation","file_id":"13191","creator":"chafner","content_type":"application/pdf","file_name":"supp-cheat.pdf","date_updated":"2023-07-04T07:46:30Z"},{"title":"Supplemental Video","creator":"chafner","file_id":"13192","content_type":"video/mp4","file_name":"kirchhoff-video-final.mp4","date_updated":"2023-07-04T07:46:39Z","file_size":268088064,"relation":"supplementary_material","access_level":"open_access","checksum":"c0fd9a57d012046de90c185ffa904b76","date_created":"2023-07-04T07:46:39Z"},{"checksum":"71b00712b489ada2cd9815910ee180a9","date_created":"2023-07-04T07:47:10Z","file_size":25790,"relation":"supplementary_material","access_level":"open_access","content_type":"application/x-zip-compressed","date_updated":"2023-07-04T07:47:10Z","file_name":"matlab-submission.zip","title":"Matlab Source Code with Example","creator":"chafner","file_id":"13193"}],"publication":"ACM Transactions on Graphics","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"has_accepted_license":"1","keyword":["Computer Graphics","Computational Design","Computational Geometry","Shape Modeling"],"status":"public","scopus_import":"1","date_created":"2023-07-04T07:41:30Z","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Julian Fischer for his help in proving Proposition 1. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 715767).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"type":"journal_article","corr_author":"1","issue":"5","file_date_updated":"2023-07-04T08:11:28Z","_id":"13188","related_material":{"record":[{"status":"public","id":"12897","relation":"part_of_dissertation"}]},"oa":1,"article_type":"original","abstract":[{"text":"The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.\r\nWe also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics.","lang":"eng"}],"quality_controlled":"1","external_id":{"isi":["001086833300010"]},"project":[{"grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"ec_funded":1,"day":"20","oa_version":"Submitted Version","volume":42,"article_number":"171","isi":1,"title":"The design space of Kirchhoff rods","date_updated":"2026-04-22T22:30:04Z","department":[{"_id":"BeBi"}],"month":"09","publisher":"Association for Computing Machinery","article_processing_charge":"No","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"doi":"10.1145/3606033","publication_status":"published","year":"2023","date_published":"2023-09-20T00:00:00Z","citation":{"ista":"Hafner C, Bickel B. 2023. The design space of Kirchhoff rods. ACM Transactions on Graphics. 42(5), 171.","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5, 171, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>.","ieee":"C. Hafner and B. Bickel, “The design space of Kirchhoff rods,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 5. Association for Computing Machinery, 2023.","apa":"Hafner, C., &#38; Bickel, B. (2023). The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 42 (2023).","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Kirchhoff Rods.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3606033\">https://doi.org/10.1145/3606033</a>.","ama":"Hafner C, Bickel B. The design space of Kirchhoff rods. <i>ACM Transactions on Graphics</i>. 2023;42(5). doi:<a href=\"https://doi.org/10.1145/3606033\">10.1145/3606033</a>"}},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"7888","status":"public"},{"status":"public","id":"8966","relation":"part_of_dissertation"}]},"oa":1,"_id":"12891","corr_author":"1","file_date_updated":"2024-05-06T22:30:03Z","author":[{"first_name":"Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","last_name":"Schauer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","date_created":"2023-05-05T08:48:20Z","status":"public","supervisor":[{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","ddc":["570"],"file":[{"relation":"main_file","file_size":31434230,"access_level":"open_access","checksum":"59b0303dc483f40a96a610a90aab7ee9","date_created":"2023-05-05T13:01:14Z","creator":"aschauer","file_id":"12907","embargo":"2024-05-05","content_type":"application/pdf","date_updated":"2024-05-06T22:30:03Z","file_name":"Thesis_Schauer_final.pdf"},{"access_level":"closed","relation":"source_file","file_size":43809109,"date_created":"2023-05-05T13:04:15Z","checksum":"25f54e12479b6adaabd129a20568e6c1","file_id":"12908","embargo_to":"open_access","creator":"aschauer","date_updated":"2024-05-06T22:30:03Z","file_name":"Thesis_Schauer_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"page":"190","date_published":"2023-05-05T00:00:00Z","year":"2023","citation":{"apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023."},"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:12891","degree_awarded":"PhD","publication_status":"published","date_updated":"2025-06-12T06:56:58Z","month":"05","department":[{"_id":"GradSch"},{"_id":"CaHe"}],"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","ec_funded":1,"day":"05","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}]},{"ddc":["570"],"file":[{"date_updated":"2024-06-02T22:30:03Z","file_name":"2023_JourNeuroscience_Nardin.pdf","content_type":"application/pdf","embargo":"2024-06-01","file_id":"14674","creator":"dernst","date_created":"2023-12-11T11:30:37Z","checksum":"e2503c8f84be1050e28f64320f1d5bd2","access_level":"open_access","file_size":2280632,"relation":"main_file"}],"intvolume":"        43","pmid":1,"page":"8140-8156","date_created":"2023-12-10T23:00:58Z","status":"public","scopus_import":"1","publication":"The Journal of Neuroscience","language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"48","file_date_updated":"2024-06-02T22:30:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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.","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"},{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina"}],"type":"journal_article","related_material":{"record":[{"id":"10077","status":"public","relation":"earlier_version"}]},"oa":1,"_id":"14656","article_type":"original","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"}],"ec_funded":1,"oa_version":"Published Version","volume":43,"day":"29","external_id":{"pmid":["37758476"],"isi":["001148071000005"]},"quality_controlled":"1","project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"date_updated":"2025-09-09T13:37:51Z","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"month":"11","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","date_published":"2023-11-29T00:00:00Z","year":"2023","citation":{"apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023."},"publisher":"Society for Neuroscience","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1529-2401"]},"doi":"10.1523/JNEUROSCI.0194-23.2023","publication_status":"published"},{"department":[{"_id":"MaMo"},{"_id":"DaAl"}],"month":"07","date_updated":"2026-04-22T22:30:08Z","title":"Fundamental limits of two-layer autoencoders, and achieving them with gradient methods","citation":{"ama":"Shevchenko A, Kögler K, Hassani H, Mondelli M. Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:31151-31209.","chicago":"Shevchenko, Alexander, Kevin Kögler, Hamed Hassani, and Marco Mondelli. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:31151–209. ML Research Press, 2023.","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.","apa":"Shevchenko, A., Kögler, K., Hassani, H., &#38; Mondelli, M. (2023). Fundamental limits of two-layer autoencoders, and achieving them with gradient methods. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 31151–31209). Honolulu, Hawaii, HI, United States: ML Research Press.","ieee":"A. Shevchenko, K. Kögler, H. Hassani, and M. Mondelli, “Fundamental limits of two-layer autoencoders, and achieving them with gradient methods,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, HI, United States, 2023, vol. 202, pp. 31151–31209.","mla":"Shevchenko, Alexander, et al. “Fundamental Limits of Two-Layer Autoencoders, and Achieving Them with Gradient Methods.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 31151–209.","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."},"year":"2023","date_published":"2023-07-30T00:00:00Z","publication_status":"published","publisher":"ML Research Press","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","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."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.13468","open_access":"1"}],"conference":{"end_date":"2023-07-29","name":"ICML: International Conference on Machine Learning","start_date":"2023-07-23","location":"Honolulu, Hawaii, HI, United States"},"volume":202,"oa_version":"Preprint","day":"30","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","external_id":{"arxiv":["2212.13468"]},"alternative_title":["PMLR"],"corr_author":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","author":[{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr","first_name":"Aleksandr"},{"first_name":"Kevin","last_name":"Kögler","full_name":"Kögler, Kevin","id":"94ec913c-dc85-11ea-9058-e5051ab2428b"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco"}],"related_material":{"record":[{"status":"public","id":"17465","relation":"dissertation_contains"}]},"oa":1,"_id":"14459","arxiv":1,"intvolume":"       202","page":"31151-31209","status":"public","scopus_import":"1","date_created":"2023-10-29T23:01:17Z","language":[{"iso":"eng"}],"publication":"Proceedings of the 40th International Conference on Machine Learning"},{"external_id":{"isi":["001030689600003"],"pmid":["37307446"]},"quality_controlled":"1","oa_version":"Published Version","volume":120,"day":"12","abstract":[{"text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.","lang":"eng"}],"article_type":"original","publication_status":"published","doi":"10.1073/pnas.2221313120","publisher":"National Academy of Sciences","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(25). doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2221313120\">https://doi.org/10.1073/pnas.2221313120</a>.","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","ieee":"Y. Wang <i>et al.</i>, “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25. National Academy of Sciences, 2023.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2221313120\">10.1073/pnas.2221313120</a>."},"year":"2023","date_published":"2023-06-12T00:00:00Z","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","article_number":"e2221313120","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"month":"06","department":[{"_id":"JiFr"}],"date_updated":"2023-12-13T23:30:04Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","status":"public","scopus_import":"1","date_created":"2023-07-09T22:01:12Z","pmid":1,"intvolume":"       120","file":[{"date_created":"2023-07-10T08:48:40Z","checksum":"d800e06252eaefba28531fa9440f23f0","access_level":"open_access","relation":"main_file","file_size":5244581,"date_updated":"2023-12-13T23:30:03Z","file_name":"2023_PNAS_Wang.pdf","embargo":"2023-12-12","content_type":"application/pdf","file_id":"13204","creator":"alisjak"}],"ddc":["570"],"_id":"13201","oa":1,"type":"journal_article","author":[{"last_name":"Wang","full_name":"Wang, Yalu","first_name":"Yalu"},{"full_name":"Yuan, Zhi","last_name":"Yuan","first_name":"Zhi"},{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"last_name":"Xiao","full_name":"Xiao, Huixin","first_name":"Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"full_name":"Guo, Yan","last_name":"Guo","first_name":"Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the  National  Natural  Science  Foundation  of  China  (32170265  and  32022007),  Hainan  Provincial  Natural  Science  Foundation  of  China  (323CXTD379),  Chinese  Universities  Scientific  Fund  (2023TC019),  Beijing  Municipal  Natural  Science  Foundation  (5192011),  Beijing  Outstanding  University  Discipline  Program,  and  China Postdoctoral Science Foundation (BH2020259460).","file_date_updated":"2023-12-13T23:30:03Z","issue":"25"},{"has_accepted_license":"1","publication":"Molecular Ecology","language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"date_created":"2023-01-12T12:09:17Z","status":"public","scopus_import":"1","pmid":1,"page":"1441-1457","intvolume":"        32","file":[{"date_updated":"2023-08-16T08:15:41Z","file_name":"2023_MolecularEcology_Shipilina.pdf","content_type":"application/pdf","file_id":"14062","creator":"dernst","date_created":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","access_level":"open_access","success":1,"file_size":7144607,"relation":"main_file"}],"ddc":["570"],"_id":"12159","related_material":{"record":[{"id":"20694","status":"public","relation":"dissertation_contains"}]},"oa":1,"acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daria","orcid":"0000-0002-1145-9226","last_name":"Shipilina","full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arka","orcid":"0000-0002-4530-8469","last_name":"Pal","full_name":"Pal, Arka","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Chan","full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank"},{"last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"type":"journal_article","file_date_updated":"2023-08-16T08:15:41Z","corr_author":"1","issue":"6","external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"quality_controlled":"1","project":[{"grant_number":"P32166","name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"volume":32,"oa_version":"Published Version","day":"01","abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"article_type":"original","publication_status":"published","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/mec.16793","year":"2023","date_published":"2023-03-01T00:00:00Z","citation":{"mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457."},"title":"On the origin and structure of haplotype blocks","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2026-04-22T22:30:14Z","month":"03","department":[{"_id":"NiBa"}]},{"file":[{"checksum":"069d87f025e0799bf9e3c375664264f2","date_created":"2023-02-07T13:07:38Z","file_size":23082464,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2024-02-07","file_name":"PhDThesis_BettinaZens_2023_final.pdf","date_updated":"2024-02-08T23:30:04Z","file_id":"12527","creator":"bzens"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhDThesis_BettinaZens_2023_final.docx","date_updated":"2024-02-08T23:30:04Z","file_id":"12528","creator":"bzens","embargo_to":"open_access","checksum":"8c66ed203495d6e078ed1002a866520c","date_created":"2023-02-07T13:09:05Z","file_size":106169509,"relation":"source_file","access_level":"closed"}],"ddc":["570"],"page":"187","supervisor":[{"first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur"}],"keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"date_created":"2023-02-02T14:50:20Z","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"file_date_updated":"2024-02-08T23:30:04Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0002-9561-1239","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","last_name":"Zens"}],"related_material":{"record":[{"status":"public","id":"8586","relation":"part_of_dissertation"}]},"oa":1,"OA_place":"publisher","_id":"12491","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"day":"02","oa_version":"Published Version","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"alternative_title":["ISTA Thesis"],"month":"02","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"date_updated":"2026-04-07T13:49:23Z","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","citation":{"mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023."},"year":"2023","date_published":"2023-02-02T00:00:00Z","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/at:ista:12491","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria"},{"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"date_created":"2023-08-08T15:33:29Z","status":"public","acknowledged_ssus":[{"_id":"LifeSc"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":10416761,"access_level":"open_access","checksum":"55c876b73d49db15228a7f571592ec77","date_created":"2024-03-01T08:56:06Z","creator":"cchlebak","embargo_to":"open_access","file_id":"15044","title":"Combined Version of original Thesis and Addendum","content_type":"application/pdf","date_updated":"2024-10-29T23:31:04Z","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf"},{"date_updated":"2024-08-09T22:30:03Z","file_name":"Thesis_AnnaFranschitz_202308.pdf","embargo":"2024-08-08","content_type":"application/pdf","file_id":"13986","creator":"afransch","date_created":"2023-08-08T18:01:28Z","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","access_level":"open_access","relation":"main_file","file_size":10797612},{"embargo_to":"open_access","file_id":"13987","creator":"afransch","file_name":"Thesis_AnnaFranschitz_202308.docx","date_updated":"2024-08-09T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":2619085,"relation":"source_file","date_created":"2023-08-08T18:02:25Z","checksum":"40abf7ccca14a3893f72dc7fb88585d6"},{"date_created":"2024-03-01T08:37:15Z","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","access_level":"open_access","relation":"main_file","file_size":85956,"file_name":"Addendum_AnnaFranschitz202402.pdf","date_updated":"2024-10-29T23:31:04Z","embargo":"2024-08-08","description":"Minor modifications and clarifications - Feb 2024","content_type":"application/pdf","file_id":"15042","creator":"cchlebak","title":"Addendum"},{"embargo_to":"open_access","creator":"cchlebak","file_id":"15043","title":"Addendum - source file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-08-09T22:30:03Z","file_name":"Addendum_AnnaFranschitz202402.docx","relation":"source_file","file_size":11818,"access_level":"closed","checksum":"66745aa01f960f17472c024875c049ed","date_created":"2024-03-01T08:39:20Z"}],"ddc":["570","577"],"page":"89","oa":1,"OA_place":"publisher","_id":"13984","file_date_updated":"2024-10-29T23:31:04Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Franschitz, Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87","last_name":"Franschitz","first_name":"Anna"}],"oa_version":"Published Version","day":"08","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection.","lang":"eng"}],"citation":{"ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>","chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","apa":"Franschitz, A. (2023). <i>Individual and social immunity against viral infections in ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13984\">https://doi.org/10.15479/at:ista:13984</a>","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","mla":"Franschitz, Anna. <i>Individual and Social Immunity against Viral Infections in Ants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13984\">10.15479/at:ista:13984</a>.","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria."},"date_published":"2023-08-08T00:00:00Z","year":"2023","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/at:ista:13984","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-034-3"],"issn":["2663-337X"]},"month":"08","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"date_updated":"2026-04-07T13:51:29Z","title":"Individual and social immunity against viral infections in ants"},{"article_type":"original","abstract":[{"lang":"eng","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."}],"ec_funded":1,"day":"01","volume":19,"oa_version":"Published Version","quality_controlled":"1","external_id":{"isi":["001054563800006"]},"project":[{"grant_number":"P33692","name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"date_updated":"2026-04-22T22:30:21Z","month":"11","department":[{"_id":"GradSch"},{"_id":"AnHi"},{"_id":"JoFi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Superconductivity from a melted insulator in Josephson junction arrays","date_published":"2023-11-01T00:00:00Z","year":"2023","citation":{"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.","ieee":"S. Mukhopadhyay <i>et al.</i>, “Superconductivity from a melted insulator in Josephson junction arrays,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1630–1635, 2023.","mla":"Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>.","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.","apa":"Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., &#38; Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>","ama":"Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. <i>Nature Physics</i>. 2023;19:1630-1635. doi:<a href=\"https://doi.org/10.1038/s41567-023-02161-w\">10.1038/s41567-023-02161-w</a>","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.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02161-w\">https://doi.org/10.1038/s41567-023-02161-w</a>."},"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publisher":"Springer Nature","doi":"10.1038/s41567-023-02161-w","publication_status":"published","ddc":["530"],"file":[{"creator":"dernst","file_id":"14899","date_updated":"2024-01-29T11:25:38Z","file_name":"2023_NaturePhysics_Mukhopadhyay.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"file_size":1977706,"relation":"main_file","date_created":"2024-01-29T11:25:38Z","checksum":"1fc86d71bfbf836e221c1e925343adc5"}],"page":"1630-1635","intvolume":"        19","status":"public","scopus_import":"1","date_created":"2023-08-11T07:41:17Z","keyword":["General Physics and Astronomy"],"publication":"Nature Physics","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"has_accepted_license":"1","corr_author":"1","file_date_updated":"2024-01-29T11:25:38Z","author":[{"last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","full_name":"Mukhopadhyay, Soham","orcid":"0000-0001-5263-5559","first_name":"Soham"},{"last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","first_name":"Jorden L","orcid":"0000-0002-0672-9295"},{"first_name":"Jaime","last_name":"Saez Mollejo","full_name":"Saez Mollejo, Jaime","id":"e0390f72-f6e0-11ea-865d-862393336714"},{"first_name":"Denise","orcid":"0000-0003-1144-2763","id":"4D495994-AE37-11E9-AC72-31CAE5697425","full_name":"Puglia, Denise","last_name":"Puglia"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","orcid":"0009-0005-0878-3032"},{"last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"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.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa":1,"related_material":{"record":[{"id":"17881","status":"public","relation":"dissertation_contains"}]},"_id":"14032"},{"file_date_updated":"2024-05-18T22:30:03Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","full_name":"Boocock, Daniel R","orcid":"0000-0002-1585-2631","first_name":"Daniel R"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8602"}]},"oa":1,"OA_place":"publisher","_id":"12964","file":[{"date_created":"2023-05-17T13:39:54Z","checksum":"d51240675fc6dc0e3f5dc0c902695d3a","access_level":"open_access","relation":"main_file","file_size":40414730,"file_name":"thesis_boocock.pdf","date_updated":"2024-05-18T22:30:03Z","embargo":"2024-05-17","content_type":"application/pdf","creator":"dboocock","file_id":"12988"},{"checksum":"581a2313ffeb40fe77e8a122a25a7795","date_created":"2023-05-17T13:39:53Z","file_size":34338567,"relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"thesis_boocock.zip","date_updated":"2024-05-18T22:30:03Z","file_id":"12989","embargo_to":"open_access","creator":"dboocock"}],"ddc":["530"],"page":"146","supervisor":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"}],"status":"public","date_created":"2023-05-15T14:52:36Z","has_accepted_license":"1","language":[{"iso":"eng"}],"tmp":{"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)","short":"CC BY-NC-SA (4.0)"},"month":"05","department":[{"_id":"GradSch"},{"_id":"EdHa"}],"date_updated":"2026-04-07T13:52:57Z","title":"Mechanochemical pattern formation across biological scales","citation":{"ista":"Boocock DR. 2023. Mechanochemical pattern formation across biological scales. Institute of Science and Technology Austria.","mla":"Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>.","ieee":"D. R. Boocock, “Mechanochemical pattern formation across biological scales,” Institute of Science and Technology Austria, 2023.","apa":"Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological scales</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>","short":"D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales, Institute of Science and Technology Austria, 2023.","chicago":"Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological Scales.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12964\">https://doi.org/10.15479/at:ista:12964</a>.","ama":"Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12964\">10.15479/at:ista:12964</a>"},"year":"2023","date_published":"2023-05-17T00:00:00Z","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/at:ista:12964","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-032-9"]},"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are\r\nestablished to determine cell fate and complex tissue patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns are also seen in collectively migrating groups, for\r\ninstance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through\r\nthe local interaction of individual constituents or are dictated by higher level instructions is\r\nstill an open question however there is evidence for the involvement of both types of process.\r\nWhere patterns arise spontaneously there is a long standing interest in how far the interplay\r\nof mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling, contributes to the behaviour. This is because many systems are able to both\r\nchemically regulate mechanical force production and chemically sense mechanical deformation,\r\nforming mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio and/or temporal patterning.\r\nWe work with experimental collaborators to investigate the possibility that this type of\r\ninteraction drives pattern formation in biological systems at different scales. We focus first on\r\ntissue-level ERK-density waves observed during the wound healing response across different\r\nsystems where many previous studies have proposed that patterns depend on polarized cell\r\nmigration and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween ERK signaling and cell contraction. We perform further modeling and experiment\r\nto study how this instability couples with polar cell migration in order to produce a robust\r\nand efficient wound healing response. In a following chapter we implement ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate the interaction of\r\nERK-density patterning with different tissue rheologies and find that the spatio-temporal\r\ndynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter we move towards lower spatial scales in the context of subcellular\r\npatterning of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand its activator). Experimental evidence supports an intrinsic chemical oscillator which we\r\nencode in a reaction model and couple to a contractile active gel description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations and contractile spatial patterning which\r\nreproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological perturbations to inhibit myosin contractility leaves the role of\r\ncontractile instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof reaction-diffusion instability.","lang":"eng"}],"oa_version":"Published Version","day":"17","ec_funded":1,"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"alternative_title":["ISTA Thesis"]},{"tmp":{"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)","short":"CC BY-NC-SA (4.0)"},"department":[{"_id":"GradSch"},{"_id":"TiVo"}],"month":"10","date_updated":"2026-04-07T13:53:13Z","title":"Synapseek: Meta-learning synaptic plasticity rules","citation":{"ieee":"B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.","mla":"Confavreux, Basile J. <i>Synapseek: Meta-Learning Synaptic Plasticity Rules</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>.","ista":"Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.","ama":"Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14422\">10.15479/at:ista:14422</a>","chicago":"Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>.","short":"B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.","apa":"Confavreux, B. J. (2023). <i>Synapseek: Meta-learning synaptic plasticity rules</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14422\">https://doi.org/10.15479/at:ista:14422</a>"},"date_published":"2023-10-12T00:00:00Z","year":"2023","publication_status":"published","degree_awarded":"PhD","doi":"10.15479/at:ista:14422","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n","lang":"eng"}],"oa_version":"Published Version","day":"12","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"alternative_title":["ISTA Thesis"],"file_date_updated":"2024-10-13T22:30:04Z","corr_author":"1","type":"dissertation","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","full_name":"Confavreux, Basile J","last_name":"Confavreux"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9633"}]},"oa":1,"OA_place":"publisher","_id":"14422","file":[{"creator":"cchlebak","file_id":"14424","file_name":"Confavreux_Thesis_2A.pdf","date_updated":"2024-10-13T22:30:04Z","embargo":"2024-10-12","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":30599717,"date_created":"2023-10-12T14:53:50Z","checksum":"7f636555eae7803323df287672fd13ed"},{"file_id":"14440","creator":"cchlebak","embargo_to":"open_access","file_name":"Confavreux Thesis.zip","date_updated":"2024-10-13T22:30:04Z","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_size":68406739,"date_created":"2023-10-18T07:38:34Z","checksum":"725e85946db92290a4583a0de9779e1b"}],"ddc":["610"],"page":"148","supervisor":[{"orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels"}],"status":"public","date_created":"2023-10-12T14:13:25Z","has_accepted_license":"1","language":[{"iso":"eng"}]},{"type":"dissertation","author":[{"first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina","last_name":"Alcarva"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","file_date_updated":"2024-04-08T22:30:03Z","OA_place":"publisher","_id":"12809","oa":1,"page":"115","ddc":["570"],"file":[{"access_level":"open_access","file_size":9881969,"relation":"main_file","date_created":"2023-04-07T06:16:06Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","file_id":"12814","creator":"cchlebak","date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","content_type":"application/pdf","embargo":"2024-04-07"},{"date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","content_type":"application/pdf","creator":"cchlebak","embargo_to":"open_access","file_id":"12815","date_created":"2023-04-07T06:17:11Z","checksum":"81198f63c294890f6d58e8b29782efdc","access_level":"closed","file_size":44201583,"relation":"source_file"},{"relation":"source_file","file_size":84731244,"access_level":"closed","checksum":"0317bf7f457bb585f99d453ffa69eb53","date_created":"2023-04-07T06:18:05Z","creator":"cchlebak","embargo_to":"open_access","file_id":"12816","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-04-08T22:30:03Z","file_name":"Thesis_CatarinaAlcarva_final.docx"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"has_accepted_license":"1","date_created":"2023-04-06T07:54:09Z","status":"public","supervisor":[{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","department":[{"_id":"GradSch"},{"_id":"RySh"}],"month":"04","date_updated":"2026-04-07T13:53:28Z","doi":"10.15479/at:ista:12809","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","publication_status":"published","degree_awarded":"PhD","citation":{"ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","mla":"Alcarva, Catarina. <i>Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12809\">10.15479/at:ista:12809</a>","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). <i>Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12809\">https://doi.org/10.15479/at:ista:12809</a>"},"year":"2023","date_published":"2023-04-06T00:00:00Z","abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"oa_version":"Published Version","day":"06"}]