[{"quality_controlled":"1","publication_identifier":{"eisbn":["9781957171395"]},"day":"01","doi":"10.1364/cleo_fs.2024.fw3k.3","language":[{"iso":"eng"}],"year":"2024","_id":"21603","date_published":"2024-06-01T00:00:00Z","publication_status":"published","extern":"1","status":"public","conference":{"location":"Charlotte, NC, United States","end_date":"2024-05-10","name":"CLEO: Conference on Lasers and Electro-Optics","start_date":"2024-05-05"},"citation":{"chicago":"Karnieli, Aviv, Nicholas Rivera, Charles Roques-Carmes, and Shanhui Fan. “Free-Electron Ponderomotive Guiding for Strong Coupling and Single-Photon Nonlinearity.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/cleo_fs.2024.fw3k.3\">https://doi.org/10.1364/cleo_fs.2024.fw3k.3</a>.","short":"A. Karnieli, N. Rivera, C. Roques-Carmes, S. Fan, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2024.","mla":"Karnieli, Aviv, et al. “Free-Electron Ponderomotive Guiding for Strong Coupling and Single-Photon Nonlinearity.” <i>Conference on Lasers and Electro-Optics</i>, FW3K.3, Optica Publishing Group, 2024, doi:<a href=\"https://doi.org/10.1364/cleo_fs.2024.fw3k.3\">10.1364/cleo_fs.2024.fw3k.3</a>.","ama":"Karnieli A, Rivera N, Roques-Carmes C, Fan S. Free-electron ponderomotive guiding for strong coupling and single-photon nonlinearity. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2024. doi:<a href=\"https://doi.org/10.1364/cleo_fs.2024.fw3k.3\">10.1364/cleo_fs.2024.fw3k.3</a>","apa":"Karnieli, A., Rivera, N., Roques-Carmes, C., &#38; Fan, S. (2024). Free-electron ponderomotive guiding for strong coupling and single-photon nonlinearity. In <i>Conference on Lasers and Electro-Optics</i>. Charlotte, NC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_fs.2024.fw3k.3\">https://doi.org/10.1364/cleo_fs.2024.fw3k.3</a>","ieee":"A. Karnieli, N. Rivera, C. Roques-Carmes, and S. Fan, “Free-electron ponderomotive guiding for strong coupling and single-photon nonlinearity,” in <i>Conference on Lasers and Electro-Optics</i>, Charlotte, NC, United States, 2024.","ista":"Karnieli A, Rivera N, Roques-Carmes C, Fan S. 2024. Free-electron ponderomotive guiding for strong coupling and single-photon nonlinearity. Conference on Lasers and Electro-Optics. CLEO: Conference on Lasers and Electro-Optics, FW3K.3."},"OA_type":"closed access","article_number":"FW3K.3","author":[{"last_name":"Karnieli","full_name":"Karnieli, Aviv","first_name":"Aviv"},{"last_name":"Rivera","first_name":"Nicholas","full_name":"Rivera, Nicholas"},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"We show how ponderomotive guiding of free electrons inside hollow optical fibers enables strong electron-photon coupling, together with exceptionally high single photon nonlinearities."}],"article_processing_charge":"No","publisher":"Optica Publishing Group","oa_version":"None","date_created":"2026-03-30T12:22:48Z","title":"Free-electron ponderomotive guiding for strong coupling and single-photon nonlinearity","type":"conference","publication":"Conference on Lasers and Electro-Optics","month":"06","date_updated":"2026-05-05T06:29:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"01","doi":"10.1364/cleo_si.2024.sf3j.5","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eisbn":["9781957171395"]},"conference":{"start_date":"2024-05-05","location":"Charlotte, NC, United States","end_date":"2024-05-10","name":"CLEO: Conference on Lasers and Electro-Optics"},"citation":{"short":"S. Choi, Y. Salamin, C. Roques-Carmes, R. Dangovski, D. Luo, Z. Chen, M. Horodynski, J. Sloan, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2024.","chicago":"Choi, Seou, Yannick Salamin, Charles Roques-Carmes, Rumen Dangovski, Di Luo, Zhuo Chen, Michael Horodynski, Jamison Sloan, and Marin Soljačić. “Photonic Probabilistic Computing Leveraging Quantum Vacuum Noise.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/cleo_si.2024.sf3j.5\">https://doi.org/10.1364/cleo_si.2024.sf3j.5</a>.","apa":"Choi, S., Salamin, Y., Roques-Carmes, C., Dangovski, R., Luo, D., Chen, Z., … Soljačić, M. (2024). Photonic probabilistic computing leveraging quantum vacuum noise. In <i>Conference on Lasers and Electro-Optics</i>. Charlotte, NC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_si.2024.sf3j.5\">https://doi.org/10.1364/cleo_si.2024.sf3j.5</a>","ama":"Choi S, Salamin Y, Roques-Carmes C, et al. Photonic probabilistic computing leveraging quantum vacuum noise. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2024. doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sf3j.5\">10.1364/cleo_si.2024.sf3j.5</a>","ieee":"S. Choi <i>et al.</i>, “Photonic probabilistic computing leveraging quantum vacuum noise,” in <i>Conference on Lasers and Electro-Optics</i>, Charlotte, NC, United States, 2024.","ista":"Choi S, Salamin Y, Roques-Carmes C, Dangovski R, Luo D, Chen Z, Horodynski M, Sloan J, Soljačić M. 2024. Photonic probabilistic computing leveraging quantum vacuum noise. Conference on Lasers and Electro-Optics. CLEO: Conference on Lasers and Electro-Optics, SF3J.5.","mla":"Choi, Seou, et al. “Photonic Probabilistic Computing Leveraging Quantum Vacuum Noise.” <i>Conference on Lasers and Electro-Optics</i>, SF3J.5, Optica Publishing Group, 2024, doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sf3j.5\">10.1364/cleo_si.2024.sf3j.5</a>."},"OA_type":"closed access","_id":"21633","year":"2024","date_published":"2024-06-01T00:00:00Z","extern":"1","status":"public","publication_status":"published","author":[{"first_name":"Seou","full_name":"Choi, Seou","last_name":"Choi"},{"first_name":"Yannick","full_name":"Salamin, Yannick","last_name":"Salamin"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes"},{"first_name":"Rumen","full_name":"Dangovski, Rumen","last_name":"Dangovski"},{"last_name":"Luo","first_name":"Di","full_name":"Luo, Di"},{"last_name":"Chen","full_name":"Chen, Zhuo","first_name":"Zhuo"},{"full_name":"Horodynski, Michael","first_name":"Michael","last_name":"Horodynski"},{"last_name":"Sloan","full_name":"Sloan, Jamison","first_name":"Jamison"},{"last_name":"Soljačić","first_name":"Marin","full_name":"Soljačić, Marin"}],"article_number":"SF3J.5","abstract":[{"text":"We present a photonic probabilistic computing platform with a measurement-feedback scheme in a biased optical parametric oscillator. Probabilistic inference and generation of MNIST handwritten-digits are experimentally demonstrated.","lang":"eng"}],"scopus_import":"1","publisher":"Optica Publishing Group","article_processing_charge":"No","type":"conference","title":"Photonic probabilistic computing leveraging quantum vacuum noise","publication":"Conference on Lasers and Electro-Optics","month":"06","oa_version":"None","date_created":"2026-03-30T12:22:48Z","date_updated":"2026-05-05T06:41:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"OA_type":"closed access","citation":{"chicago":"Karnieli, Aviv, Offek Tziperman, Charles Roques-Carmes, and Shanhui Fan. “Coherent Generation of Decoherence-Free States in Nonlinear Waveguide Quantum Electrodynamics.” In <i>Frontiers in Optics + Laser Science 2024 </i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/fio.2024.fw1c.2\">https://doi.org/10.1364/fio.2024.fw1c.2</a>.","short":"A. Karnieli, O. Tziperman, C. Roques-Carmes, S. Fan, in:, Frontiers in Optics + Laser Science 2024 , Optica Publishing Group, 2024.","mla":"Karnieli, Aviv, et al. “Coherent Generation of Decoherence-Free States in Nonlinear Waveguide Quantum Electrodynamics.” <i>Frontiers in Optics + Laser Science 2024 </i>, FW1C.2, Optica Publishing Group, 2024, doi:<a href=\"https://doi.org/10.1364/fio.2024.fw1c.2\">10.1364/fio.2024.fw1c.2</a>.","ista":"Karnieli A, Tziperman O, Roques-Carmes C, Fan S. 2024. Coherent generation of decoherence-free states in nonlinear waveguide quantum electrodynamics. Frontiers in Optics + Laser Science 2024 . FiO, LS: Fronitiers in Optics + Laser Science, FW1C.2.","ama":"Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Coherent generation of decoherence-free states in nonlinear waveguide quantum electrodynamics. In: <i>Frontiers in Optics + Laser Science 2024 </i>. Optica Publishing Group; 2024. doi:<a href=\"https://doi.org/10.1364/fio.2024.fw1c.2\">10.1364/fio.2024.fw1c.2</a>","ieee":"A. Karnieli, O. Tziperman, C. Roques-Carmes, and S. Fan, “Coherent generation of decoherence-free states in nonlinear waveguide quantum electrodynamics,” in <i>Frontiers in Optics + Laser Science 2024 </i>, Denver, CO, United States, 2024.","apa":"Karnieli, A., Tziperman, O., Roques-Carmes, C., &#38; Fan, S. (2024). Coherent generation of decoherence-free states in nonlinear waveguide quantum electrodynamics. In <i>Frontiers in Optics + Laser Science 2024 </i>. Denver, CO, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/fio.2024.fw1c.2\">https://doi.org/10.1364/fio.2024.fw1c.2</a>"},"conference":{"start_date":"2024-09-23","end_date":"2024-09-26","name":"FiO, LS: Fronitiers in Optics + Laser Science","location":"Denver, CO, United States"},"publication_status":"published","status":"public","extern":"1","_id":"21636","year":"2024","date_published":"2024-10-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","doi":"10.1364/fio.2024.fw1c.2","publication_identifier":{"eisbn":["9781957171951"]},"quality_controlled":"1","author":[{"full_name":"Karnieli, Aviv","first_name":"Aviv","last_name":"Karnieli"},{"full_name":"Tziperman, Offek","first_name":"Offek","last_name":"Tziperman"},{"first_name":"Charles","full_name":"Roques-Carmes, Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","last_name":"Roques-Carmes"},{"last_name":"Fan","full_name":"Fan, Shanhui","first_name":"Shanhui"}],"article_number":"FW1C.2","publisher":"Optica Publishing Group","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We show that emitter arrays coupled to nonlinear parametric-amplifier waveguides support a unique, coherent inter-atomic interaction. This allows for unitary adiabatic evolution and coherent generation of decoherence-free excited states in waveguide quantum electrodynamics."}],"date_updated":"2026-05-05T06:40:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","publication":"Frontiers in Optics + Laser Science 2024 ","type":"conference","title":"Coherent generation of decoherence-free states in nonlinear waveguide quantum electrodynamics","date_created":"2026-03-30T12:22:48Z","oa_version":"None"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"We present a three-component multilayer scintillator that can achieve greater x-ray energy resolution than conventional single or dual-component systems, from 10 to 100 keV. Our approach relies on spectral multiplexing of different x-ray energy bins."}],"article_processing_charge":"No","publisher":"Optica Publishing Group","oa_version":"None","date_created":"2026-03-30T12:22:48Z","type":"conference","title":"Multilayer scintillators for enhanced energy resolution in X-ray imaging","publication":"Conference on Lasers and Electro-Optics","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-05T10:42:12Z","quality_controlled":"1","publication_identifier":{"eisbn":["9781957171395"]},"doi":"10.1364/cleo_si.2024.sf3b.4","day":"01","language":[{"iso":"eng"}],"date_published":"2024-06-01T00:00:00Z","_id":"21632","year":"2024","publication_status":"published","status":"public","extern":"1","conference":{"start_date":"2024-05-05","name":"CLEO: Science and Innovations","end_date":"2024-05-10","location":"Charlotte, CA, United States"},"OA_type":"closed access","citation":{"chicago":"Min, Seokhwan, Charles Roques-Carmes, Seou Choi, Simo Pajovic, Sachin Vaidya, and Marin Soljačić. “Multilayer Scintillators for Enhanced Energy Resolution in X-Ray Imaging.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/cleo_si.2024.sf3b.4\">https://doi.org/10.1364/cleo_si.2024.sf3b.4</a>.","short":"S. Min, C. Roques-Carmes, S. Choi, S. Pajovic, S. Vaidya, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2024.","mla":"Min, Seokhwan, et al. “Multilayer Scintillators for Enhanced Energy Resolution in X-Ray Imaging.” <i>Conference on Lasers and Electro-Optics</i>, SF3B.4, Optica Publishing Group, 2024, doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sf3b.4\">10.1364/cleo_si.2024.sf3b.4</a>.","ama":"Min S, Roques-Carmes C, Choi S, Pajovic S, Vaidya S, Soljačić M. Multilayer scintillators for enhanced energy resolution in X-ray imaging. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2024. doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sf3b.4\">10.1364/cleo_si.2024.sf3b.4</a>","ieee":"S. Min, C. Roques-Carmes, S. Choi, S. Pajovic, S. Vaidya, and M. Soljačić, “Multilayer scintillators for enhanced energy resolution in X-ray imaging,” in <i>Conference on Lasers and Electro-Optics</i>, Charlotte, CA, United States, 2024.","apa":"Min, S., Roques-Carmes, C., Choi, S., Pajovic, S., Vaidya, S., &#38; Soljačić, M. (2024). Multilayer scintillators for enhanced energy resolution in X-ray imaging. In <i>Conference on Lasers and Electro-Optics</i>. Charlotte, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_si.2024.sf3b.4\">https://doi.org/10.1364/cleo_si.2024.sf3b.4</a>","ista":"Min S, Roques-Carmes C, Choi S, Pajovic S, Vaidya S, Soljačić M. 2024. Multilayer scintillators for enhanced energy resolution in X-ray imaging. Conference on Lasers and Electro-Optics. CLEO: Science and Innovations, SF3B.4."},"article_number":"SF3B.4","author":[{"first_name":"Seokhwan","full_name":"Min, Seokhwan","last_name":"Min"},{"first_name":"Charles","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes"},{"last_name":"Choi","first_name":"Seou","full_name":"Choi, Seou"},{"last_name":"Pajovic","first_name":"Simo","full_name":"Pajovic, Simo"},{"last_name":"Vaidya","full_name":"Vaidya, Sachin","first_name":"Sachin"},{"last_name":"Soljačić","full_name":"Soljačić, Marin","first_name":"Marin"}]},{"external_id":{"arxiv":["2402.00704"],"pmid":["39300058"]},"language":[{"iso":"eng"}],"quality_controlled":"1","OA_type":"gold","citation":{"mla":"Roques-Carmes, Charles, et al. “Measuring, Processing, and Generating Partially Coherent Light with Self-Configuring Optics.” <i>Light: Science &#38; Applications</i>, vol. 13, 260, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41377-024-01622-y\">10.1038/s41377-024-01622-y</a>.","ama":"Roques-Carmes C, Fan S, Miller DAB. Measuring, processing, and generating partially coherent light with self-configuring optics. <i>Light: Science &#38; Applications</i>. 2024;13. doi:<a href=\"https://doi.org/10.1038/s41377-024-01622-y\">10.1038/s41377-024-01622-y</a>","ieee":"C. Roques-Carmes, S. Fan, and D. A. B. Miller, “Measuring, processing, and generating partially coherent light with self-configuring optics,” <i>Light: Science &#38; Applications</i>, vol. 13. Springer Nature, 2024.","apa":"Roques-Carmes, C., Fan, S., &#38; Miller, D. A. B. (2024). Measuring, processing, and generating partially coherent light with self-configuring optics. <i>Light: Science &#38; Applications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41377-024-01622-y\">https://doi.org/10.1038/s41377-024-01622-y</a>","ista":"Roques-Carmes C, Fan S, Miller DAB. 2024. Measuring, processing, and generating partially coherent light with self-configuring optics. Light: Science &#38; Applications. 13, 260.","chicago":"Roques-Carmes, Charles, Shanhui Fan, and David A. B. Miller. “Measuring, Processing, and Generating Partially Coherent Light with Self-Configuring Optics.” <i>Light: Science &#38; Applications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41377-024-01622-y\">https://doi.org/10.1038/s41377-024-01622-y</a>.","short":"C. Roques-Carmes, S. Fan, D.A.B. Miller, Light: Science &#38; Applications 13 (2024)."},"year":"2024","date_published":"2024-09-20T00:00:00Z","publication_status":"published","status":"public","extern":"1","author":[{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"last_name":"Fan","full_name":"Fan, Shanhui","first_name":"Shanhui"},{"last_name":"Miller","first_name":"David A. B.","full_name":"Miller, David A. B."}],"intvolume":"        13","OA_place":"publisher","abstract":[{"lang":"eng","text":"Optical phenomena always display some degree of partial coherence between their respective degrees of freedom. Partial coherence is of particular interest in multimodal systems, where classical and quantum correlations between spatial, polarization, and spectral degrees of freedom can lead to fascinating phenomena (e.g., entanglement) and be leveraged for advanced imaging and sensing modalities (e.g., in hyperspectral, polarization, and ghost imaging). Here, we present a universal method to analyze, process, and generate spatially partially coherent light in multimode systems by using self-configuring optical networks. Our method relies on cascaded self-configuring layers whose average power outputs are sequentially optimized. Once optimized, the network separates the input light into its mutually incoherent components, which is formally equivalent to a diagonalization of the input density matrix. We illustrate our method with numerical simulations of Mach-Zehnder interferometer arrays and show how this method can be used to perform partially coherent environmental light sensing, generation of multimode partially coherent light with arbitrary coherency matrices, and unscrambling of quantum optical mixtures. We provide guidelines for the experimental realization of this method, including the influence of losses, paving the way for self-configuring photonic devices that can automatically learn optimal modal representations of partially coherent light fields."}],"oa":1,"publisher":"Springer Nature","title":"Measuring, processing, and generating partially coherent light with self-configuring optics","publication":"Light: Science & Applications","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"21634"}]},"date_created":"2026-03-30T12:22:47Z","date_updated":"2026-05-05T10:45:37Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41377-024-01622-y","open_access":"1"}],"pmid":1,"doi":"10.1038/s41377-024-01622-y","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"20","publication_identifier":{"eissn":["2047-7538"]},"_id":"21535","volume":13,"article_type":"original","article_number":"260","scopus_import":"1","ddc":["530"],"article_processing_charge":"No","type":"journal_article","month":"09","oa_version":"Published Version","DOAJ_listed":"1"},{"publication_identifier":{"eisbn":["9781957171395"]},"doi":"10.1364/cleo_si.2024.sth4q.5","day":"01","_id":"21634","conference":{"location":"Charlotte, CA, United States","end_date":"2024-05-10","name":"CLEO: Science and Innovations","start_date":"2024-05-05"},"article_number":"STh4Q.5","scopus_import":"1","article_processing_charge":"No","oa_version":"Preprint","month":"06","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["2402.00704"]},"extern":"1","publication_status":"published","status":"public","date_published":"2024-06-01T00:00:00Z","year":"2024","OA_type":"green","citation":{"chicago":"Roques-Carmes, Charles, Shanhui Fan, and David A. B. Miller. “Measuring and Processing Partially Coherent Light with Self-Configuring Optics.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2024. <a href=\"https://doi.org/10.1364/cleo_si.2024.sth4q.5\">https://doi.org/10.1364/cleo_si.2024.sth4q.5</a>.","short":"C. Roques-Carmes, S. Fan, D.A.B. Miller, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2024.","mla":"Roques-Carmes, Charles, et al. “Measuring and Processing Partially Coherent Light with Self-Configuring Optics.” <i>Conference on Lasers and Electro-Optics</i>, STh4Q.5, Optica Publishing Group, 2024, doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sth4q.5\">10.1364/cleo_si.2024.sth4q.5</a>.","ama":"Roques-Carmes C, Fan S, Miller DAB. Measuring and processing partially coherent light with self-configuring optics. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2024. doi:<a href=\"https://doi.org/10.1364/cleo_si.2024.sth4q.5\">10.1364/cleo_si.2024.sth4q.5</a>","ieee":"C. Roques-Carmes, S. Fan, and D. A. B. Miller, “Measuring and processing partially coherent light with self-configuring optics,” in <i>Conference on Lasers and Electro-Optics</i>, Charlotte, CA, United States, 2024.","apa":"Roques-Carmes, C., Fan, S., &#38; Miller, D. A. B. (2024). Measuring and processing partially coherent light with self-configuring optics. In <i>Conference on Lasers and Electro-Optics</i>. Charlotte, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_si.2024.sth4q.5\">https://doi.org/10.1364/cleo_si.2024.sth4q.5</a>","ista":"Roques-Carmes C, Fan S, Miller DAB. 2024. Measuring and processing partially coherent light with self-configuring optics. Conference on Lasers and Electro-Optics. CLEO: Science and Innovations, STh4Q.5."},"author":[{"id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles","last_name":"Roques-Carmes"},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"},{"full_name":"Miller, David A. B.","first_name":"David A. B.","last_name":"Miller"}],"oa":1,"abstract":[{"text":"We show that self-configuring optical networks can analyze partially incoherent light. We consider the case of N spatial input channels and present a power-optimization method to measure their coherency matrix.","lang":"eng"}],"OA_place":"repository","publisher":"Optica Publishing Group","date_created":"2026-03-30T12:22:48Z","publication":"Conference on Lasers and Electro-Optics","related_material":{"record":[{"id":"21535","relation":"later_version","status":"public"}]},"title":"Measuring and processing partially coherent light with self-configuring optics","date_updated":"2026-05-05T10:45:38Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2402.00704","open_access":"1"}],"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","month":"07","oa_version":"None","article_processing_charge":"No","page":"11976-11981","scopus_import":"1","ddc":["540"],"article_type":"original","_id":"21806","volume":12,"doi":"10.1039/d4tc01281j","day":"10","publication_identifier":{"eissn":["2050-7534"],"issnl":["2050-7526"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-05-12T06:50:12Z","title":"Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks","publication":"Journal of Materials Chemistry C","date_created":"2026-05-06T10:43:33Z","publisher":"Royal Society of Chemistry","abstract":[{"lang":"eng","text":"Light-responsive liquid crystal elastomer networks (LCNs) have received significant interest due to their potential application in soft robotics and shape-morphing devices. Here, we present a systematic examination of light-responsive LCNs prepared using a catalyst-free Diels–Alder cycloaddition and a new azobenzene functionalized monomer for main-chain incorporation. The networks have robust mechanical stiffness that can be reversibly modulated by 1 GPa by turning the UV light on and off. This study highlights the contribution of photothermal softening to reversibly control rheological properties of the newly developed LCNs and demonstrates the ability to tune the modulus on demand. We believe this work will guide future developments of light-responsive LCNs based on the newly developed Diels–Alder cycloaddition."}],"author":[{"full_name":"Park, Minwook","first_name":"Minwook","last_name":"Park"},{"last_name":"Guillen Campos","full_name":"Guillen Campos, Jesus","first_name":"Jesus"},{"full_name":"Stricker, Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","first_name":"Friedrich J","last_name":"Stricker"},{"last_name":"Read de Alaniz","first_name":"Javier","full_name":"Read de Alaniz, Javier"}],"intvolume":"        12","issue":"31","OA_type":"closed access","citation":{"chicago":"Park, Minwook, Jesus Guillen Campos, Friedrich J Stricker, and Javier Read de Alaniz. “Photo-Responsive Diels-Alder Based Azobenzene-Functionalized Main-Chain Liquid Crystal Networks.” <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4tc01281j\">https://doi.org/10.1039/d4tc01281j</a>.","short":"M. Park, J. Guillen Campos, F.J. Stricker, J. Read de Alaniz, Journal of Materials Chemistry C 12 (2024) 11976–11981.","mla":"Park, Minwook, et al. “Photo-Responsive Diels-Alder Based Azobenzene-Functionalized Main-Chain Liquid Crystal Networks.” <i>Journal of Materials Chemistry C</i>, vol. 12, no. 31, Royal Society of Chemistry, 2024, pp. 11976–81, doi:<a href=\"https://doi.org/10.1039/d4tc01281j\">10.1039/d4tc01281j</a>.","apa":"Park, M., Guillen Campos, J., Stricker, F. J., &#38; Read de Alaniz, J. (2024). Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4tc01281j\">https://doi.org/10.1039/d4tc01281j</a>","ieee":"M. Park, J. Guillen Campos, F. J. Stricker, and J. Read de Alaniz, “Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks,” <i>Journal of Materials Chemistry C</i>, vol. 12, no. 31. Royal Society of Chemistry, pp. 11976–11981, 2024.","ama":"Park M, Guillen Campos J, Stricker FJ, Read de Alaniz J. Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. <i>Journal of Materials Chemistry C</i>. 2024;12(31):11976-11981. doi:<a href=\"https://doi.org/10.1039/d4tc01281j\">10.1039/d4tc01281j</a>","ista":"Park M, Guillen Campos J, Stricker FJ, Read de Alaniz J. 2024. Photo-responsive Diels-Alder based azobenzene-functionalized main-chain liquid crystal networks. Journal of Materials Chemistry C. 12(31), 11976–11981."},"date_published":"2024-07-10T00:00:00Z","year":"2024","publication_status":"published","extern":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1"},{"author":[{"first_name":"Yuxing","full_name":"Yao, Yuxing","last_name":"Yao"},{"last_name":"Wilborn","first_name":"Atalaya Milan","full_name":"Wilborn, Atalaya Milan"},{"full_name":"Lemaire, Baptiste","first_name":"Baptiste","last_name":"Lemaire"},{"last_name":"Trigka","full_name":"Trigka, Foteini","first_name":"Foteini"},{"last_name":"Stricker","first_name":"Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","full_name":"Stricker, Friedrich J"},{"full_name":"Weible, Alan H.","first_name":"Alan H.","last_name":"Weible"},{"full_name":"Li, Shucong","first_name":"Shucong","last_name":"Li"},{"last_name":"Bennett","first_name":"Robert K. A.","full_name":"Bennett, Robert K. A."},{"last_name":"Cheung","full_name":"Cheung, Tung Chun","first_name":"Tung Chun"},{"last_name":"Grinthal","full_name":"Grinthal, Alison","first_name":"Alison"},{"last_name":"Zhernenkov","first_name":"Mikhail","full_name":"Zhernenkov, Mikhail"},{"first_name":"Guillaume","full_name":"Freychet, Guillaume","last_name":"Freychet"},{"first_name":"Patryk","full_name":"Wąsik, Patryk","last_name":"Wąsik"},{"first_name":"Boris","full_name":"Kozinsky, Boris","last_name":"Kozinsky"},{"last_name":"Lerch","full_name":"Lerch, Michael M.","first_name":"Michael M."},{"full_name":"Wang, Xiaoguang","first_name":"Xiaoguang","last_name":"Wang"},{"first_name":"Joanna","full_name":"Aizenberg, Joanna","last_name":"Aizenberg"}],"intvolume":"       386","issue":"6726","citation":{"mla":"Yao, Yuxing, et al. “Programming Liquid Crystal Elastomers for Multistep Ambidirectional Deformability.” <i>Science</i>, vol. 386, no. 6726, American Association for the Advancement of Science, 2024, pp. 1161–68, doi:<a href=\"https://doi.org/10.1126/science.adq6434\">10.1126/science.adq6434</a>.","ista":"Yao Y, Wilborn AM, Lemaire B, Trigka F, Stricker FJ, Weible AH, Li S, Bennett RKA, Cheung TC, Grinthal A, Zhernenkov M, Freychet G, Wąsik P, Kozinsky B, Lerch MM, Wang X, Aizenberg J. 2024. Programming liquid crystal elastomers for multistep ambidirectional deformability. Science. 386(6726), 1161–1168.","apa":"Yao, Y., Wilborn, A. M., Lemaire, B., Trigka, F., Stricker, F. J., Weible, A. H., … Aizenberg, J. (2024). Programming liquid crystal elastomers for multistep ambidirectional deformability. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adq6434\">https://doi.org/10.1126/science.adq6434</a>","ieee":"Y. Yao <i>et al.</i>, “Programming liquid crystal elastomers for multistep ambidirectional deformability,” <i>Science</i>, vol. 386, no. 6726. American Association for the Advancement of Science, pp. 1161–1168, 2024.","ama":"Yao Y, Wilborn AM, Lemaire B, et al. Programming liquid crystal elastomers for multistep ambidirectional deformability. <i>Science</i>. 2024;386(6726):1161-1168. doi:<a href=\"https://doi.org/10.1126/science.adq6434\">10.1126/science.adq6434</a>","chicago":"Yao, Yuxing, Atalaya Milan Wilborn, Baptiste Lemaire, Foteini Trigka, Friedrich J Stricker, Alan H. Weible, Shucong Li, et al. “Programming Liquid Crystal Elastomers for Multistep Ambidirectional Deformability.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adq6434\">https://doi.org/10.1126/science.adq6434</a>.","short":"Y. Yao, A.M. Wilborn, B. Lemaire, F. Trigka, F.J. Stricker, A.H. Weible, S. Li, R.K.A. Bennett, T.C. Cheung, A. Grinthal, M. Zhernenkov, G. Freychet, P. Wąsik, B. Kozinsky, M.M. Lerch, X. Wang, J. Aizenberg, Science 386 (2024) 1161–1168."},"OA_type":"closed access","date_published":"2024-12-06T00:00:00Z","year":"2024","publication_status":"published","extern":"1","status":"public","external_id":{"pmid":["39636998"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2026-05-12T09:48:12Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pmid":1,"title":"Programming liquid crystal elastomers for multistep ambidirectional deformability","publication":"Science","date_created":"2026-05-06T10:54:51Z","publisher":"American Association for the Advancement of Science","abstract":[{"text":"Ambidirectionality, which is the ability of structural elements to move beyond a reference state in two opposite directions, is common in nature. However, conventional soft materials are typically limited to a single, unidirectional deformation unless complex hybrid constructs are used. We exploited the combination of mesogen self-assembly, polymer chain elasticity, and polymerization-induced stress to design liquid crystalline elastomers that exhibit two mesophases: chevron smectic C (cSmC) and smectic A (SmA). Inducing the cSmC-SmA–isotropic phase transition led to an unusual inversion of the strain field in the microstructure, resulting in opposite deformation modes (e.g., consecutive shrinkage or expansion and right-handed or left-handed twisting and tilting in opposite directions) and high-frequency nonmonotonic oscillations. This ambidirectional movement is scalable and can be used to generate Gaussian transformations at the macroscale.","lang":"eng"}],"article_type":"original","_id":"21817","volume":386,"day":"06","doi":"10.1126/science.adq6434","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"type":"journal_article","month":"12","oa_version":"None","article_processing_charge":"No","page":"1161-1168","scopus_import":"1","ddc":["540"]},{"oa_version":"Preprint","month":"09","type":"conference","scopus_import":"1","page":"45955-45987","department":[{"_id":"DaAl"}],"article_processing_charge":"No","publication_identifier":{"eissn":["2640-3498"]},"day":"01","volume":235,"project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35"}],"_id":"18121","conference":{"location":"Vienna, Austria","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","start_date":"2024-07-21"},"acknowledgement":"The authors would like to thank Stephen Casper and Tony Wang for their feedback on this work, and Eldar Kurtic for his advice on aspects of the project. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.","date_created":"2024-09-22T22:01:46Z","publication":"Proceedings of the 41st International Conference on Machine Learning","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/SPADE"}],"record":[{"id":"21854","relation":"dissertation_contains","status":"public"}]},"title":"SPADE: Sparsity-guided debugging for deep neural networks","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-05-19T11:20:27Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.04519"}],"oa":1,"abstract":[{"lang":"eng","text":"It is known that sparsity can improve interpretability for deep neural networks. However, existing methods in the area either require networks that are pre-trained with sparsity constraints, or impose sparsity after the fact, altering the network’s general behavior. In this paper, we demonstrate, for the first time, that sparsity can instead be incorporated into the interpretation process itself, as a sample-specific preprocessing step. Unlike previous work, this approach, which we call SPADE, does not place constraints on the trained model and does not affect its behavior during inference on the sample. Given a trained model and a target sample, SPADE uses sample-targeted pruning to provide a \"trace\" of the network’s execution on the sample, reducing the network to the most important connections prior to computing an interpretation. We demonstrate that preprocessing with SPADE significantly increases the accuracy of image saliency maps across several interpretability methods. Additionally, SPADE improves the usefulness of neuron visualizations, aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE."}],"publisher":"ML Research Press","intvolume":"       235","author":[{"full_name":"Moakhar, Arshia Soltani","first_name":"Arshia Soltani","last_name":"Moakhar"},{"first_name":"Eugenia B","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova"},{"last_name":"Frantar","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2310.04519"]},"status":"public","publication_status":"published","date_published":"2024-09-01T00:00:00Z","year":"2024","alternative_title":["PMLR"],"corr_author":"1","citation":{"chicago":"Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:45955–87. ML Research Press, 2024.","short":"A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 45955–45987.","mla":"Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 45955–87.","ama":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging for deep neural networks. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:45955-45987.","apa":"Moakhar, A. S., Iofinova, E. B., Frantar, E., &#38; Alistarh, D.-A. (2024). SPADE: Sparsity-guided debugging for deep neural networks. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 45955–45987). Vienna, Austria: ML Research Press.","ieee":"A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided debugging for deep neural networks,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.","ista":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided debugging for deep neural networks. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 45955–45987."}},{"has_accepted_license":"1","author":[{"first_name":"Borzoo","full_name":"Bonakdarpour, Borzoo","last_name":"Bonakdarpour"},{"last_name":"Momtaz","full_name":"Momtaz, Anik","first_name":"Anik"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}],"intvolume":"     15191","language":[{"iso":"eng"}],"external_id":{"arxiv":["2408.05033"],"isi":["001420093700018"]},"quality_controlled":"1","corr_author":"1","file_date_updated":"2024-11-11T09:42:28Z","alternative_title":["LNCS"],"OA_type":"hybrid","citation":{"ista":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. 2024. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. 24th International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 15191, 282–301.","ama":"Bonakdarpour B, Momtaz A, Nickovic D, Sarac NE. Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In: <i>24th International Conference on Runtime Verification</i>. Vol 15191. Springer Nature; 2024:282-301. doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>","ieee":"B. Bonakdarpour, A. Momtaz, D. Nickovic, and N. E. Sarac, “Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy,” in <i>24th International Conference on Runtime Verification</i>, Istanbul, Turkey, 2024, vol. 15191, pp. 282–301.","apa":"Bonakdarpour, B., Momtaz, A., Nickovic, D., &#38; Sarac, N. E. (2024). Approximate distributed monitoring under partial synchrony: Balancing speed &#38; accuracy. In <i>24th International Conference on Runtime Verification</i> (Vol. 15191, pp. 282–301). Istanbul, Turkey: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>","mla":"Bonakdarpour, Borzoo, et al. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” <i>24th International Conference on Runtime Verification</i>, vol. 15191, Springer Nature, 2024, pp. 282–301, doi:<a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">10.1007/978-3-031-74234-7_18</a>.","short":"B. Bonakdarpour, A. Momtaz, D. Nickovic, N.E. Sarac, in:, 24th International Conference on Runtime Verification, Springer Nature, 2024, pp. 282–301.","chicago":"Bonakdarpour, Borzoo, Anik Momtaz, Dejan Nickovic, and Naci E Sarac. “Approximate Distributed Monitoring under Partial Synchrony: Balancing Speed &#38; Accuracy.” In <i>24th International Conference on Runtime Verification</i>, 15191:282–301. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-74234-7_18\">https://doi.org/10.1007/978-3-031-74234-7_18</a>."},"status":"public","publication_status":"published","year":"2024","date_published":"2024-10-12T00:00:00Z","publication":"24th International Conference on Runtime Verification","title":"Approximate distributed monitoring under partial synchrony: Balancing speed & accuracy","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. This work is sponsored in part by the United States NSF CCF-2118356 award. This research was partially funded by A-IQ Ready (Chips JU, grant agreement No. 101096658).","date_created":"2024-11-10T23:01:58Z","arxiv":1,"date_updated":"2026-05-20T08:43:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","date_updated":"2024-11-11T09:42:28Z","success":1,"file_id":"18539","date_created":"2024-11-11T09:42:28Z","file_size":1897101,"file_name":"2024_LNCS_Bonakdarpour.pdf","creator":"dernst","checksum":"7b8ca21b8c19ab796fa445b0e54003ca","content_type":"application/pdf","relation":"main_file"}],"OA_place":"publisher","abstract":[{"lang":"eng","text":"In distributed systems with processes that do not share a global clock, partial synchrony is achieved by clock synchronization that guarantees bounded clock skew among all applications. Existing solutions for distributed runtime verification under partial synchrony against temporal logic specifications are exact but suffer from significant computational overhead. In this paper, we propose an approximate distributed monitoring algorithm for Signal Temporal Logic (STL) that mitigates this issue by abstracting away potential interleaving behaviors. This conservative abstraction enables a significant speedup of the distributed monitors, albeit with a tradeoff in accuracy. We address this tradeoff with a methodology that combines our approximate monitor with its exact counterpart, resulting in enhanced efficiency without sacrificing precision. We evaluate our approach with multiple experiments, showcasing its efficacy in both real-world applications and synthetic examples."}],"oa":1,"publisher":"Springer Nature","ec_funded":1,"day":"12","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1007/978-3-031-74234-7_18","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031742330"],"issn":["0302-9743"]},"conference":{"start_date":"2024-10-15","location":"Istanbul, Turkey","end_date":"2024-10-17","name":"RV: Conference on Runtime Verification"},"volume":15191,"_id":"18521","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"month":"10","type":"conference","oa_version":"Published Version","APC_amount":"2748 EUR","page":"282-301","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"isi":1,"ddc":["000"],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)"},{"intvolume":"       300","issue":"9","author":[{"full_name":"Vogt, Austin","first_name":"Austin","last_name":"Vogt"},{"last_name":"Szurgot","full_name":"Szurgot, Mary","first_name":"Mary"},{"last_name":"Gardner","first_name":"Lauren","id":"f9dedd98-6d15-11f0-88a5-a7b4143fdec5","orcid":"0009-0000-5733-1546","full_name":"Gardner, Lauren"},{"last_name":"Schultz","full_name":"Schultz, David C.","first_name":"David C."},{"last_name":"Marmorstein","first_name":"Ronen","full_name":"Marmorstein, Ronen"}],"has_accepted_license":"1","year":"2024","date_published":"2024-09-01T00:00:00Z","status":"public","extern":"1","publication_status":"published","OA_type":"gold","citation":{"ista":"Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. 2024. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. Journal of Biological Chemistry. 300(9), 107604.","ama":"Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. <i>Journal of Biological Chemistry</i>. 2024;300(9). doi:<a href=\"https://doi.org/10.1016/j.jbc.2024.107604\">10.1016/j.jbc.2024.107604</a>","ieee":"A. Vogt, M. Szurgot, L. Gardner, D. C. Schultz, and R. Marmorstein, “HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding,” <i>Journal of Biological Chemistry</i>, vol. 300, no. 9. Elsevier, 2024.","apa":"Vogt, A., Szurgot, M., Gardner, L., Schultz, D. C., &#38; Marmorstein, R. (2024). HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbc.2024.107604\">https://doi.org/10.1016/j.jbc.2024.107604</a>","mla":"Vogt, Austin, et al. “HIRA Complex Deposition of Histone H3.3 Is Driven by Histone Tetramerization and Histone-DNA Binding.” <i>Journal of Biological Chemistry</i>, vol. 300, no. 9, 107604, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jbc.2024.107604\">10.1016/j.jbc.2024.107604</a>.","short":"A. Vogt, M. Szurgot, L. Gardner, D.C. Schultz, R. Marmorstein, Journal of Biological Chemistry 300 (2024).","chicago":"Vogt, Austin, Mary Szurgot, Lauren Gardner, David C. Schultz, and Ronen Marmorstein. “HIRA Complex Deposition of Histone H3.3 Is Driven by Histone Tetramerization and Histone-DNA Binding.” <i>Journal of Biological Chemistry</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jbc.2024.107604\">https://doi.org/10.1016/j.jbc.2024.107604</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["39059488"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1016/j.jbc.2024.107604","open_access":"1"}],"date_updated":"2026-06-02T14:52:50Z","date_created":"2026-05-24T08:25:45Z","acknowledgement":"We would like to acknowledge Elliot Dean and Christina Freeman for technical assistance with recombinant protein expression in insect cells and members of the Marmorstein laboratory for many discussions related to this work. Schematic Figures were created with BioRender.com.","title":"HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding","publication":"Journal of Biological Chemistry","publisher":"Elsevier","oa":1,"abstract":[{"lang":"eng","text":"The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in the deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition."}],"OA_place":"publisher","PlanS_conform":"1","article_number":"107604","article_type":"original","_id":"21913","volume":300,"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1016/j.jbc.2024.107604","day":"01","oa_version":"Published Version","DOAJ_listed":"1","type":"journal_article","month":"09","article_processing_charge":"Yes","ddc":["572"]},{"author":[{"orcid":"0009-0003-7382-8036","full_name":"Babkin, Serafim","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","first_name":"Serafim","last_name":"Babkin"},{"last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"issue":"5","intvolume":"        16","has_accepted_license":"1","file_date_updated":"2024-05-07T12:58:47Z","corr_author":"1","citation":{"chicago":"Babkin, Serafim, Andrew P Higginbotham, and Maksym Serbyn. “Proximity-Induced Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic Field.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">https://doi.org/10.21468/scipostphys.16.5.115</a>.","short":"S. Babkin, A.P. Higginbotham, M. Serbyn, SciPost Physics 16 (2024).","mla":"Babkin, Serafim, et al. “Proximity-Induced Gapless Superconductivity in Two-Dimensional Rashba Semiconductor in Magnetic Field.” <i>SciPost Physics</i>, vol. 16, no. 5, 115, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">10.21468/scipostphys.16.5.115</a>.","ieee":"S. Babkin, A. P. Higginbotham, and M. Serbyn, “Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field,” <i>SciPost Physics</i>, vol. 16, no. 5. SciPost Foundation, 2024.","apa":"Babkin, S., Higginbotham, A. P., &#38; Serbyn, M. (2024). Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">https://doi.org/10.21468/scipostphys.16.5.115</a>","ama":"Babkin S, Higginbotham AP, Serbyn M. Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. <i>SciPost Physics</i>. 2024;16(5). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.5.115\">10.21468/scipostphys.16.5.115</a>","ista":"Babkin S, Higginbotham AP, Serbyn M. 2024. Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field. SciPost Physics. 16(5), 115."},"publication_status":"published","status":"public","year":"2024","date_published":"2024-05-01T00:00:00Z","external_id":{"arxiv":["2311.09347"],"isi":["001215855200002"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2026-06-03T07:16:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"SciPost Physics","title":"Proximity-induced gapless superconductivity in two-dimensional Rashba semiconductor in magnetic field","acknowledgement":"We acknowledge useful discussions with M. Geier, A. Levchenko, B. Ramshaw, T. Scaffidi, and\r\nJ. Shabani. This research was funded by the Austrian Science Fund (FWF) F 86.\r\nFor the purpose of open access, authors have applied a CC BY public copyright licence to any\r\nAuthor Accepted Manuscript version arising from this submission. MS acknowledges hospitality of KITP supported in part by the National Science Foundation under Grants No. NSF\r\nPHY-1748958 and PHY-2309135. APH acknowledges the support of the NOMIS foundation.","date_created":"2024-05-06T09:02:18Z","publisher":"SciPost Foundation","abstract":[{"lang":"eng","text":"Two-dimensional semiconductor-superconductor heterostructures form the foundation of numerous nanoscale physical systems. However, measuring the properties of such heterostructures, and characterizing the semiconductor in-situ is challenging. A recent experimental study by [Phys. Rev. Lett. 128, 107701 (2022)] was able to probe the semiconductor within the heterostructure using microwave measurements of the superfluid density. This work revealed a rapid depletion of superfluid density in semiconductor, caused by the in-plane magnetic field which in presence of spin-orbit coupling creates so-called Bogoliubov Fermi surfaces. The experimental work used a simplified theoretical model that neglected the presence of non-magnetic disorder in the semiconductor, hence describing the data only qualitatively. Motivated by experiments, we introduce a theoretical model describing a disordered semiconductor with strong spin-orbit coupling that is proximitized by a superconductor. Our model provides specific predictions for the density of states and superfluid density. Presence of disorder leads to the emergence of a gapless superconducting phase, that may be viewed as a manifestation of Bogoliubov Fermi surface. When applied to real experimental data, our model showcases excellent quantitative agreement, enabling the extraction of material parameters such as mean free path and mobility, and estimating g-tensor after taking into account the orbital contribution of magnetic field. Our model can be used to probe in-situ parameters of other superconductor-semiconductor heterostructures and can be further extended to give access to transport properties."}],"file":[{"creator":"dernst","file_name":"2024_SciPostPhys_Babkin.pdf","file_size":2733685,"content_type":"application/pdf","relation":"main_file","checksum":"f999204856417dcf5a736ac8df432b96","date_updated":"2024-05-07T12:58:47Z","access_level":"open_access","success":1,"file_id":"15369","date_created":"2024-05-07T12:58:47Z"}],"oa":1,"article_number":"115","article_type":"original","volume":16,"project":[{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"},{"_id":"34a7f947-11ca-11ed-8bc3-c5dc2bbaae25","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems:  Probing topology in circuits and quantum materials","grant_number":"F8609"}],"_id":"15367","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"01","doi":"10.21468/scipostphys.16.5.115","publication_identifier":{"issn":["2542-4653"]},"month":"05","type":"journal_article","oa_version":"Published Version","article_processing_charge":"Yes","department":[{"_id":"MaSe"},{"_id":"AnHi"}],"ddc":["530"],"isi":1,"scopus_import":"1"},{"date_updated":"2026-06-03T07:16:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"date_created":"2024-09-01T22:01:09Z","acknowledgement":"We thank M. Möttönen, D. Subero, V. Vadimov, A. Alizadeh, C. Strunk, N. Roch, S. Kafanov, S. Kubatkin, A. Kerman and J. Peltonen for scientific discussions and Z.-Y. Chen for technical assistance. B.K. and J.P.P. acknowledge funding from the Research Council of Finland Centre of Excellence programme grant 336810 and grant 349601 (THEPOW), G.O.S. and A.L.Y. financial support from the Spanish Ministry of Science through grant TED2021-130292B-C43 funded by MCIN/AEI/10.13039/501100011033, ‘ERDF A way of making Europe’ and the EU through FET-Open project AndQC, A.P.H. support from the NOMIS Foundation, and C.M.M. support from the Danish National Research Foundation and a research grant (Project 43951) from VILLUM FONDEN. We thank the facilities and technical support of Otaniemi Research Infrastructure for Micro and Nanotechnologies (OtaNano). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the paper.","title":"Bolometric detection of Josephson radiation","publication":"Nature Nanotechnology","publisher":"Springer Nature","oa":1,"abstract":[{"text":"One of the most promising approaches towards large-scale quantum computation uses devices based on many Josephson junctions. Yet, even today, open questions regarding the single junction remain unsolved, such as the detailed understanding of the quantum phase transitions, the coupling of the Josephson junction to the environment or how to improve the coherence of a superconducting qubit. Here we design and build an engineered on-chip reservoir connected to a Josephson junction that acts as an efficient bolometer for detecting the Josephson radiation under non-equilibrium, that is, biased conditions. The bolometer converts the a.c. Josephson current at microwave frequencies up to about 100 GHz into a temperature rise measured by d.c. thermometry. A circuit model based on realistic parameter values captures both the current–voltage characteristics and the measured power quantitatively. The present experiment demonstrates an efficient, wide-band, thermal detection scheme of microwave photons and provides a sensitive detector of Josephson dynamics beyond the standard conductance measurements.","lang":"eng"}],"OA_place":"publisher","file":[{"file_name":"2024_NatureNanotechnology_Karimi.pdf","file_size":3047567,"creator":"dernst","checksum":"8b067ef217ddef63c539ecdfe705ab95","relation":"main_file","content_type":"application/pdf","date_updated":"2025-01-09T13:51:12Z","access_level":"open_access","file_id":"18818","success":1,"date_created":"2025-01-09T13:51:12Z"}],"intvolume":"        19","author":[{"last_name":"Karimi","full_name":"Karimi, Bayan","first_name":"Bayan"},{"full_name":"Steffensen, Gorm Ole","first_name":"Gorm Ole","last_name":"Steffensen"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham"},{"last_name":"Marcus","first_name":"Charles M.","full_name":"Marcus, Charles M."},{"last_name":"Levy Yeyati","first_name":"Alfredo","full_name":"Levy Yeyati, Alfredo"},{"first_name":"Jukka P.","full_name":"Pekola, Jukka P.","last_name":"Pekola"}],"has_accepted_license":"1","date_published":"2024-11-01T00:00:00Z","year":"2024","publication_status":"published","status":"public","citation":{"chicago":"Karimi, Bayan, Gorm Ole Steffensen, Andrew P Higginbotham, Charles M. Marcus, Alfredo Levy Yeyati, and Jukka P. Pekola. “Bolometric Detection of Josephson Radiation.” <i>Nature Nanotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41565-024-01770-7\">https://doi.org/10.1038/s41565-024-01770-7</a>.","short":"B. Karimi, G.O. Steffensen, A.P. Higginbotham, C.M. Marcus, A. Levy Yeyati, J.P. Pekola, Nature Nanotechnology 19 (2024) 1613–1618.","mla":"Karimi, Bayan, et al. “Bolometric Detection of Josephson Radiation.” <i>Nature Nanotechnology</i>, vol. 19, Springer Nature, 2024, pp. 1613–18, doi:<a href=\"https://doi.org/10.1038/s41565-024-01770-7\">10.1038/s41565-024-01770-7</a>.","ista":"Karimi B, Steffensen GO, Higginbotham AP, Marcus CM, Levy Yeyati A, Pekola JP. 2024. Bolometric detection of Josephson radiation. Nature Nanotechnology. 19, 1613–1618.","apa":"Karimi, B., Steffensen, G. O., Higginbotham, A. P., Marcus, C. M., Levy Yeyati, A., &#38; Pekola, J. P. (2024). Bolometric detection of Josephson radiation. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-024-01770-7\">https://doi.org/10.1038/s41565-024-01770-7</a>","ieee":"B. Karimi, G. O. Steffensen, A. P. Higginbotham, C. M. Marcus, A. Levy Yeyati, and J. P. Pekola, “Bolometric detection of Josephson radiation,” <i>Nature Nanotechnology</i>, vol. 19. Springer Nature, pp. 1613–1618, 2024.","ama":"Karimi B, Steffensen GO, Higginbotham AP, Marcus CM, Levy Yeyati A, Pekola JP. Bolometric detection of Josephson radiation. <i>Nature Nanotechnology</i>. 2024;19:1613-1618. doi:<a href=\"https://doi.org/10.1038/s41565-024-01770-7\">10.1038/s41565-024-01770-7</a>"},"file_date_updated":"2025-01-09T13:51:12Z","OA_type":"hybrid","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001296522000002"],"arxiv":["2402.09314"]},"oa_version":"Published Version","type":"journal_article","month":"11","article_processing_charge":"No","scopus_import":"1","ddc":["530"],"isi":1,"department":[{"_id":"AnHi"}],"page":"1613-1618","article_type":"original","project":[{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"_id":"17480","volume":19,"publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/s41565-024-01770-7","day":"01"},{"article_type":"original","article_number":"8830","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/s41467-024-53173-w","day":"12","volume":15,"project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera"}],"_id":"18444","DOAJ_listed":"1","oa_version":"Published Version","APC_amount":"6828 EUR","month":"10","type":"journal_article","isi":1,"ddc":["570"],"scopus_import":"1","department":[{"_id":"MaJö"}],"article_processing_charge":"Yes","has_accepted_license":"1","intvolume":"        15","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva"},{"last_name":"Satapathy","first_name":"Roshan K","full_name":"Satapathy, Roshan K","orcid":"0009-0006-2974-5075","id":"46046B7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Symonova","first_name":"Olga","orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"external_id":{"isi":["001336422500001"],"pmid":["39396050"]},"language":[{"iso":"eng"}],"status":"public","publication_status":"published","year":"2024","date_published":"2024-10-12T00:00:00Z","OA_type":"gold","corr_author":"1","citation":{"mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>, vol. 15, 8830, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>.","ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., &#38; Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-53173-w\">10.1038/s41467-024-53173-w</a>","chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-53173-w\">https://doi.org/10.1038/s41467-024-53173-w</a>.","short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024)."},"file_date_updated":"2024-10-21T12:11:10Z","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","date_created":"2024-10-20T22:02:05Z","publication":"Nature Communications","related_material":{"record":[{"relation":"dissertation_contains","id":"18568","status":"public"},{"id":"17488","relation":"research_data","status":"public"}]},"title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"date_updated":"2026-06-10T07:58:34Z","oa":1,"abstract":[{"lang":"eng","text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations."}],"file":[{"access_level":"open_access","date_updated":"2024-10-21T12:11:10Z","file_id":"18459","date_created":"2024-10-21T12:11:10Z","success":1,"file_name":"2024_NatureComm_Pokusaeva.pdf","file_size":8276667,"creator":"dernst","checksum":"2af4d6e7364329107aa94d072d594ce0","content_type":"application/pdf","relation":"main_file"}],"OA_place":"publisher","publisher":"Springer Nature"},{"quality_controlled":"1","external_id":{"isi":["001369697800005"],"arxiv":["2403.02395"],"pmid":["39642519"]},"language":[{"iso":"eng"}],"status":"public","publication_status":"published","date_published":"2024-11-22T00:00:00Z","year":"2024","OA_type":"green","citation":{"mla":"Shen, Ruizhe, et al. “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.” <i>Physical Review Letters</i>, vol. 133, no. 21, 216601, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.133.216601\">10.1103/PhysRevLett.133.216601</a>.","ista":"Shen R, Qin F, Desaules J-YM, Papić Z, Lee CH. 2024. Enhanced many-body quantum scars from the non-hermitian fock skin effect. Physical Review Letters. 133(21), 216601.","ama":"Shen R, Qin F, Desaules J-YM, Papić Z, Lee CH. Enhanced many-body quantum scars from the non-hermitian fock skin effect. <i>Physical Review Letters</i>. 2024;133(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.133.216601\">10.1103/PhysRevLett.133.216601</a>","ieee":"R. Shen, F. Qin, J.-Y. M. Desaules, Z. Papić, and C. H. Lee, “Enhanced many-body quantum scars from the non-hermitian fock skin effect,” <i>Physical Review Letters</i>, vol. 133, no. 21. American Physical Society, 2024.","apa":"Shen, R., Qin, F., Desaules, J.-Y. M., Papić, Z., &#38; Lee, C. H. (2024). Enhanced many-body quantum scars from the non-hermitian fock skin effect. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.133.216601\">https://doi.org/10.1103/PhysRevLett.133.216601</a>","chicago":"Shen, Ruizhe, Fang Qin, Jean-Yves Marc Desaules, Zlatko Papić, and Ching Hua Lee. “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.” <i>Physical Review Letters</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevLett.133.216601\">https://doi.org/10.1103/PhysRevLett.133.216601</a>.","short":"R. Shen, F. Qin, J.-Y.M. Desaules, Z. Papić, C.H. Lee, Physical Review Letters 133 (2024)."},"issue":"21","intvolume":"       133","author":[{"last_name":"Shen","full_name":"Shen, Ruizhe","first_name":"Ruizhe"},{"first_name":"Fang","full_name":"Qin, Fang","last_name":"Qin"},{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375","full_name":"Desaules, Jean-Yves Marc","first_name":"Jean-Yves Marc","last_name":"Desaules"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"},{"last_name":"Lee","first_name":"Ching Hua","full_name":"Lee, Ching Hua"}],"oa":1,"OA_place":"repository","abstract":[{"lang":"eng","text":"In contrast with extended Bloch waves, a single particle can become spatially localized due to the so-called skin effect originating from non-Hermitian pumping. Here we show that in kinetically constrained many-body systems, the skin effect can instead manifest as dynamical amplification within the Fock space, beyond the intuitively expected and previously studied particle localization and clustering. We exemplify this non-Hermitian Fock skin effect in an asymmetric version of the PXP model and show that it gives rise to ergodicity-breaking eigenstates—the non-Hermitian analogs of quantum many-body scars. A distinguishing feature of these non-Hermitian scars is their enhanced robustness against external disorders. We propose an experimental realization of the non-Hermitian scar enhancement in a tilted Bose-Hubbard optical lattice with laser-induced loss. Additionally, we implement digital simulations of such scar enhancement on the IBM quantum processor. Our results show that the Fock skin effect provides a powerful tool for creating robust nonergodic states in generic open quantum systems."}],"ec_funded":1,"publisher":"American Physical Society","acknowledgement":"F. Q. and C. H. L. acknowledge support from the QEP2.0 Grant from the Singapore National Research Foundation (Grant No. NRF2021-QEP2-02-P09) and the Singapore MOE Tier-II Grant (Grant No. MOE-T2EP50222-0003). J.-Y. D. and Z. P. acknowledge support by the Leverhulme Trust Research Leadership Award RL-2019-015. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. This research was supported in part by Grant No. NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP). We acknowledge the use of IBM Quantum services for this work. The views expressed are those of the authors and do not reflect the official policy or position of IBM or the IBM Quantum team.","date_created":"2024-12-08T23:01:55Z","related_material":{"record":[{"id":"17471","relation":"research_data","status":"public"}]},"publication":"Physical Review Letters","title":"Enhanced many-body quantum scars from the non-hermitian fock skin effect","arxiv":1,"pmid":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2403.02395","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-06-10T07:52:52Z","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/PhysRevLett.133.216601","day":"22","volume":133,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"_id":"18627","article_type":"original","article_number":"216601","isi":1,"scopus_import":"1","department":[{"_id":"MaSe"}],"article_processing_charge":"No","oa_version":"Preprint","month":"11","type":"journal_article"},{"day":"30","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.15479/AT:ISTA:17471","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020"}],"_id":"17471","year":"2024","date_published":"2024-08-30T00:00:00Z","status":"public","file_date_updated":"2024-08-30T13:19:57Z","citation":{"ama":"Desaules J-YM. Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>","ieee":"J.-Y. M. Desaules, “Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.’” Institute of Science and Technology Austria, 2024.","apa":"Desaules, J.-Y. M. (2024). Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>","ista":"Desaules J-YM. 2024. Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>.","mla":"Desaules, Jean-Yves Marc. <i>Data for “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>.","short":"J.-Y.M. Desaules, (2024).","chicago":"Desaules, Jean-Yves Marc. “Data for ‘Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>."},"contributor":[{"last_name":"Shen","first_name":"Ruizhe","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Qin","first_name":"Fang"},{"last_name":"Desaules","first_name":"Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","orcid":"0000-0002-3749-6375","contributor_type":"researcher"},{"last_name":"Papić","first_name":"Zlatko","contributor_type":"researcher"},{"first_name":"Ching Hua","last_name":"Lee","contributor_type":"researcher"}],"has_accepted_license":"1","author":[{"orcid":"0000-0002-3749-6375","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","full_name":"Desaules, Jean-Yves Marc","first_name":"Jean-Yves Marc","last_name":"Desaules"}],"oa":1,"ddc":["530"],"file":[{"content_type":"application/zip","relation":"main_file","checksum":"2bd49ce5a63f1951c1ed3d89cce4fe27","creator":"jdesaule","file_name":"FiguresData.zip","file_size":322400,"file_id":"17472","date_created":"2024-08-30T12:55:37Z","success":1,"access_level":"open_access","date_updated":"2024-08-30T12:55:37Z"},{"success":1,"file_id":"17473","date_created":"2024-08-30T13:19:57Z","date_updated":"2024-08-30T13:19:57Z","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"c2ba113a241e98c394cc3ca21f3fa126","creator":"jdesaule","file_size":1368,"file_name":"readme.txt"}],"abstract":[{"text":"Mechanisms for suppressing thermalization in disorder-free many-body systems, such as Hilbert space fragmentation and quantum many-body scars, have recently attracted much interest in foundations of quantum statistical physics and potential quantum information processing applications. However,  their sensitivity to realistic effects such as finite temperature remains largely unexplored. Here, we have utilized IBM's Kolkata quantum processor to demonstrate an unexpected robustness of quantum many-body scars at finite temperatures when the system is prepared in a thermal Gibbs ensemble. We identify such robustness in the PXP model, which describes quantum many-body scars in experimental systems of Rydberg atom arrays and ultracold atoms in tilted Bose--Hubbard optical lattices. By contrast, other theoretical models which host exact quantum many-body scars are found to lack such robustness, and their scarring properties quickly decay with temperature. Our study sheds light on the important differences between scarred models in terms of their algebraic structures, which impacts their resilience to finite temperature.","lang":"eng"}],"department":[{"_id":"MaSe"}],"ec_funded":1,"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","date_created":"2024-08-30T12:59:43Z","oa_version":"Published Version","title":"Data for \"Enhanced many-body quantum scars from the non-Hermitian Fock skin effect\"","type":"research_data","related_material":{"record":[{"id":"18627","relation":"used_in_publication","status":"public"}]},"keyword":["quantum many-body scars","non-equilibrium physics","non-Hermitian physics"],"month":"08","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","date_updated":"2026-06-10T07:52:53Z"},{"file":[{"creator":"rsatapat","file_name":"BehaviouralData.zip","file_size":965778072,"relation":"main_file","content_type":"application/x-zip-compressed","checksum":"df9d6c8ddffa046c3b1639281f83cfcf","date_updated":"2024-09-03T17:39:32Z","access_level":"open_access","file_id":"17489","date_created":"2024-09-03T17:39:32Z","success":1}],"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"abstract":[{"lang":"eng","text":"Behavioural data for Pokusaeva, Satapathy et al. Relevant information can be found in the 'README.txt' file."}],"oa":1,"ddc":["570"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","type":"research_data","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"18444"}]},"month":"09","keyword":["drosophila","behaviour","locomotion","gap junctions"],"date_created":"2024-09-03T17:42:46Z","oa_version":"Published Version","date_updated":"2026-06-10T07:58:35Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:17488","acknowledged_ssus":[{"_id":"M-Shop"}],"corr_author":"1","file_date_updated":"2024-09-03T17:39:32Z","citation":{"short":"R.K. Satapathy, M.A. Jösch, O. Symonova, V. Pokusaeva, (2024).","chicago":"Satapathy, Roshan K, Maximilian A Jösch, Olga Symonova, and Victoria Pokusaeva. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>.","ista":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>.","apa":"Satapathy, R. K., Jösch, M. A., Symonova, O., &#38; Pokusaeva, V. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>","ieee":"R. K. Satapathy, M. A. Jösch, O. Symonova, and V. Pokusaeva, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies.” Institute of Science and Technology Austria, 2024.","ama":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>","mla":"Satapathy, Roshan K., et al. <i>Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>."},"_id":"17488","project":[{"_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera"}],"year":"2024","date_published":"2024-09-01T00:00:00Z","status":"public","has_accepted_license":"1","author":[{"id":"46046B7A-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0006-2974-5075","full_name":"Satapathy, Roshan K","first_name":"Roshan K","last_name":"Satapathy"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch"},{"first_name":"Olga","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2012-9947","last_name":"Symonova"},{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","last_name":"Pokusaeva"}]},{"publication_status":"draft","status":"public","_id":"21967","year":"2024","date_published":"2024-10-18T00:00:00Z","project":[{"name":"The impact of deleterious mutations on small populations","grant_number":"26293","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"OA_type":"green","corr_author":"1","citation":{"short":"K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.).","chicago":"Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>.","apa":"Khudiakova, K., Boenkost, F., &#38; Tourniaire, J. N. (n.d.). Genealogies under purifying selection. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.10.15.618444\">https://doi.org/10.1101/2024.10.15.618444</a>","ama":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>","ieee":"K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying selection,” <i>bioRxiv</i>. .","ista":"Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection. bioRxiv, <a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>.","mla":"Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.10.15.618444\">10.1101/2024.10.15.618444</a>."},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"18","doi":"10.1101/2024.10.15.618444","author":[{"last_name":"Khudiakova","first_name":"Kseniia","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"last_name":"Boenkost","first_name":"Florin","full_name":"Boenkost, Florin"},{"first_name":"Julie N","full_name":"Tourniaire, Julie N","id":"5dc06dd8-8e51-11ec-9170-8d9c450cc216","last_name":"Tourniaire"}],"article_processing_charge":"No","ec_funded":1,"oa":1,"department":[{"_id":"NiBa"},{"_id":"JaMa"}],"abstract":[{"lang":"eng","text":"Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://doi.org/10.1101/2024.10.15.618444","open_access":"1"}],"date_updated":"2026-06-12T12:43:34Z","acknowledgement":"This work was supported by the Austrian Academy of Science, DOC fellowship No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations were performed on the ISTA High-performance Computing Cluster.","date_created":"2026-06-09T12:14:08Z","oa_version":"Preprint","publication":"bioRxiv","related_material":{"record":[{"status":"public","id":"21918","relation":"dissertation_contains"}]},"month":"10","type":"preprint","title":"Genealogies under purifying selection"},{"alternative_title":["ISTA Thesis"],"corr_author":"1","file_date_updated":"2025-01-11T23:30:04Z","citation":{"short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>."},"status":"public","publication_status":"published","date_published":"2024-07-05T00:00:00Z","year":"2024","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"author":[{"full_name":"Raices, Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Raices"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","ec_funded":1,"abstract":[{"text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. ","lang":"eng"}],"OA_place":"publisher","file":[{"date_updated":"2025-01-11T23:30:04Z","access_level":"closed","date_created":"2024-07-11T07:18:01Z","file_id":"17223","file_name":"ThesisRaices2024_postDefense.docx","file_size":13788479,"creator":"cchlebak","embargo_to":"open_access","checksum":"d5e9234bde8667b005a8cfe18bb467d3","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file"},{"creator":"cchlebak","file_name":"ThesisRaices2024_nosignature.pdf","file_size":5580296,"content_type":"application/pdf","relation":"main_file","checksum":"f5ed0139aa3e11ce58369f0915647c5c","embargo":"2025-01-11","access_level":"open_access","date_updated":"2025-01-11T23:30:04Z","date_created":"2024-07-11T07:22:32Z","file_id":"17224"}],"oa":1,"date_updated":"2026-04-07T13:03:22Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","date_created":"2024-07-05T14:15:29Z","supervisor":[{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"_id":"17206","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"doi":"10.15479/at:ista:17206","day":"05","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","article_processing_charge":"No","page":"82","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"ddc":["570"],"month":"07","type":"dissertation","oa_version":"Published Version"},{"degree_awarded":"PhD","day":"26","doi":"10.15479/at:ista:18101","publication_identifier":{"isbn":["978-3-99078-041-1"],"issn":["2663-337X"]},"supervisor":[{"first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"_id":"18101","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"25762","name":"Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms","_id":"9B9C98E0-BA93-11EA-9121-9846C619BF3A"}],"month":"09","type":"dissertation","oa_version":"Published Version","page":"131","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"ddc":["570"],"article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Porley, Dario J","id":"2FD6EA6C-F248-11E8-B48F-1D18A9856A87","first_name":"Dario J","last_name":"Porley"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"citation":{"mla":"Porley Esteves, Darío. <i>Structural Characterization of Spumavirus Capsid Assemblies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>.","ista":"Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria.","ieee":"D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024.","ama":"Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18101\">10.15479/at:ista:18101</a>","apa":"Porley Esteves, D. (2024). <i>Structural characterization of spumavirus capsid assemblies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>","chicago":"Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18101\">https://doi.org/10.15479/at:ista:18101</a>.","short":"D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024."},"corr_author":"1","file_date_updated":"2025-03-25T23:30:03Z","alternative_title":["ISTA Thesis"],"status":"public","publication_status":"published","date_published":"2024-09-26T00:00:00Z","year":"2024","title":"Structural characterization of spumavirus capsid assemblies","date_created":"2024-09-20T10:21:03Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-07T13:21:01Z","file":[{"embargo_to":"open_access","checksum":"3b8b0bacfe61112f3852744f3170e468","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_thesis_DPorley_final_20240919.docx","file_size":14213128,"creator":"dporley","date_created":"2024-09-26T13:40:33Z","file_id":"18149","date_updated":"2025-03-25T23:30:03Z","access_level":"closed"},{"creator":"dporley","file_size":18583031,"file_name":"PhD_thesis_DPorley_final_20240926_pdfa1.pdf","relation":"main_file","content_type":"application/pdf","checksum":"6c3a652a8eede874118e11d66a63652f","embargo":"2025-03-25","date_updated":"2025-03-25T23:30:03Z","access_level":"open_access","file_id":"18150","date_created":"2024-09-26T13:41:39Z"}],"abstract":[{"lang":"eng","text":"The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies."}],"OA_place":"publisher","oa":1,"publisher":"Institute of Science and Technology Austria","ec_funded":1}]