[{"OA_place":"repository","month":"12","author":[{"full_name":"Lê, Trung Kiên","first_name":"Trung Kiên","last_name":"Lê"},{"full_name":"Lukin, Daniil M.","first_name":"Daniil M.","last_name":"Lukin"},{"first_name":"Charles","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"full_name":"Karnieli, Aviv","first_name":"Aviv","last_name":"Karnieli"},{"full_name":"Lustig, Eran","first_name":"Eran","last_name":"Lustig"},{"last_name":"Guidry","full_name":"Guidry, Melissa A.","first_name":"Melissa A."},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"},{"full_name":"Vučković, Jelena","first_name":"Jelena","last_name":"Vučković"}],"date_published":"2024-12-19T00:00:00Z","date_updated":"2026-04-13T09:50:09Z","publication_status":"submitted","arxiv":1,"OA_type":"green","day":"19","title":"Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir","scopus_import":"1","status":"public","article_processing_charge":"No","extern":"1","language":[{"iso":"eng"}],"publication":"arXiv","citation":{"short":"T.K. Lê, D.M. Lukin, C. Roques-Carmes, A. Karnieli, E. Lustig, M.A. Guidry, S. Fan, J. Vučković, ArXiv (n.d.).","ama":"Lê TK, Lukin DM, Roques-Carmes C, et al. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2412.15068\">10.48550/arXiv.2412.15068</a>","ista":"Lê TK, Lukin DM, Roques-Carmes C, Karnieli A, Lustig E, Guidry MA, Fan S, Vučković J. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. arXiv, 2412.15068.","ieee":"T. K. Lê <i>et al.</i>, “Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir,” <i>arXiv</i>. .","chicago":"Lê, Trung Kiên, Daniil M. Lukin, Charles Roques-Carmes, Aviv Karnieli, Eran Lustig, Melissa A. Guidry, Shanhui Fan, and Jelena Vučković. “Cavity Quantum Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2412.15068\">https://doi.org/10.48550/arXiv.2412.15068</a>.","apa":"Lê, T. K., Lukin, D. M., Roques-Carmes, C., Karnieli, A., Lustig, E., Guidry, M. A., … Vučković, J. (n.d.). Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2412.15068\">https://doi.org/10.48550/arXiv.2412.15068</a>","mla":"Lê, Trung Kiên, et al. “Cavity Quantum Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” <i>ArXiv</i>, 2412.15068, doi:<a href=\"https://doi.org/10.48550/arXiv.2412.15068\">10.48550/arXiv.2412.15068</a>."},"_id":"21691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_number":"2412.15068","external_id":{"arxiv":["2412.15068"]},"date_created":"2026-04-09T09:10:41Z","doi":"10.48550/arXiv.2412.15068","oa":1,"year":"2024","type":"preprint","abstract":[{"lang":"eng","text":"Light-matter interaction with squeezed vacuum has received much interest for the ability to enhance the native interaction strength between an atom and a photon with a reservoir assumed to have an infinite bandwidth. Here, we study a model of parametrically driven cavity quantum electrodynamics (cavity QED) for enhancing light-matter interaction while subjected to a finite-bandwidth squeezed vacuum drive. Our method is capable of unveiling the effect of relative bandwidth as well as squeezing required to observe the anticipated anti-crossing spectrum and enhanced cooperativity without the ideal squeezed bath assumption. Furthermore, we analyze the practicality of said models when including intrinsic photon loss due to resonators imperfection. With these results, we outline the requirements for experimentally implementing an effectively squeezed bath in solid-state platforms such as InAs quantum dot cavity QED such that \\textit{in situ} control and enhancement of light-matter interaction could be realized."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2412.15068","open_access":"1"}]},{"extern":"1","status":"public","scopus_import":"1","article_processing_charge":"No","title":"Towards a second generation of metascintillators using the Purcell effect","_id":"21684","citation":{"short":"A. Shultzman, R. Schütz, Y. Kurman, N. Lahav, G. Dosovitskiy, C. Roques-Carmes, Y. Bekenstein, G. Konstantinou, R. Latella, L. Zhang, F.L.-H. Francis Loignon-Houle, A.J. Gonzalez, J.M. Benlloch, I. Kaminer, P. Lecoq, ArXiv (n.d.).","ama":"Shultzman A, Schütz R, Kurman Y, et al. Towards a second generation of metascintillators using the Purcell effect. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.15058\">10.48550/arXiv.2406.15058</a>","ista":"Shultzman A, Schütz R, Kurman Y, Lahav N, Dosovitskiy G, Roques-Carmes C, Bekenstein Y, Konstantinou G, Latella R, Zhang L, Francis Loignon-Houle FL-H, Gonzalez AJ, Benlloch JM, Kaminer I, Lecoq P. Towards a second generation of metascintillators using the Purcell effect. arXiv, 2406.15058.","ieee":"A. Shultzman <i>et al.</i>, “Towards a second generation of metascintillators using the Purcell effect,” <i>arXiv</i>. .","apa":"Shultzman, A., Schütz, R., Kurman, Y., Lahav, N., Dosovitskiy, G., Roques-Carmes, C., … Lecoq, P. (n.d.). Towards a second generation of metascintillators using the Purcell effect. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.15058\">https://doi.org/10.48550/arXiv.2406.15058</a>","chicago":"Shultzman, Avner, Roman Schütz, Yaniv Kurman, Neta Lahav, George Dosovitskiy, Charles Roques-Carmes, Yehonadav Bekenstein, et al. “Towards a Second Generation of Metascintillators Using the Purcell Effect.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.15058\">https://doi.org/10.48550/arXiv.2406.15058</a>.","mla":"Shultzman, Avner, et al. “Towards a Second Generation of Metascintillators Using the Purcell Effect.” <i>ArXiv</i>, 2406.15058, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.15058\">10.48550/arXiv.2406.15058</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","language":[{"iso":"eng"}],"date_published":"2024-06-21T00:00:00Z","author":[{"last_name":"Shultzman","full_name":"Shultzman, Avner","first_name":"Avner"},{"full_name":"Schütz, Roman","first_name":"Roman","last_name":"Schütz"},{"full_name":"Kurman, Yaniv","first_name":"Yaniv","last_name":"Kurman"},{"last_name":"Lahav","first_name":"Neta","full_name":"Lahav, Neta"},{"full_name":"Dosovitskiy, George","first_name":"George","last_name":"Dosovitskiy"},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"full_name":"Bekenstein, Yehonadav","first_name":"Yehonadav","last_name":"Bekenstein"},{"last_name":"Konstantinou","first_name":"Georgios","full_name":"Konstantinou, Georgios"},{"full_name":"Latella, Riccardo","first_name":"Riccardo","last_name":"Latella"},{"last_name":"Zhang","first_name":"Lei","full_name":"Zhang, Lei"},{"first_name":"Francis Loignon-Houle","full_name":"Francis Loignon-Houle, Francis Loignon-Houle","last_name":"Francis Loignon-Houle"},{"last_name":"Gonzalez","first_name":"Antonio J.","full_name":"Gonzalez, Antonio J."},{"full_name":"Benlloch, José María","first_name":"José María","last_name":"Benlloch"},{"full_name":"Kaminer, Ido","first_name":"Ido","last_name":"Kaminer"},{"last_name":"Lecoq","first_name":"Paul","full_name":"Lecoq, Paul"}],"month":"06","OA_place":"repository","arxiv":1,"day":"21","OA_type":"green","publication_status":"submitted","date_updated":"2026-04-13T10:50:23Z","year":"2024","oa":1,"doi":"10.48550/arXiv.2406.15058","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.15058"}],"abstract":[{"lang":"eng","text":"This study focuses on advancing metascintillators to break the 100 ps barrier and approach the 10 ps target. We exploit nanophotonic features, specifically the Purcell effect, to shape and enhance the scintillation properties of the first-generation metascintillator. We demonstrate that a faster emission is achievable along with a more efficient conversion efficiency. This results in a coincidence time resolution improved by a factor of 1.6, crucial for TOF-PET applications."}],"type":"preprint","oa_version":"Preprint","date_created":"2026-04-09T09:10:41Z","external_id":{"arxiv":["2406.15058"]},"article_number":"2406.15058"},{"extern":"1","title":"Multimode amplitude squeezing through cascaded nonlinear optical processes","scopus_import":"1","status":"public","article_processing_charge":"No","_id":"21680","citation":{"mla":"Pontula, Sahil, et al. “Multimode Amplitude Squeezing through Cascaded Nonlinear Optical Processes.” <i>ArXiv</i>, 2405.05201, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.05201\">10.48550/arXiv.2405.05201</a>.","ista":"Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing through cascaded nonlinear optical processes. arXiv, 2405.05201.","apa":"Pontula, S., Salamin, Y., Roques-Carmes, C., &#38; Soljacic, M. (n.d.). Multimode amplitude squeezing through cascaded nonlinear optical processes. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.05201\">https://doi.org/10.48550/arXiv.2405.05201</a>","ieee":"S. Pontula, Y. Salamin, C. Roques-Carmes, and M. Soljacic, “Multimode amplitude squeezing through cascaded nonlinear optical processes,” <i>arXiv</i>. .","chicago":"Pontula, Sahil, Yannick Salamin, Charles Roques-Carmes, and Marin Soljacic. “Multimode Amplitude Squeezing through Cascaded Nonlinear Optical Processes.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.05201\">https://doi.org/10.48550/arXiv.2405.05201</a>.","ama":"Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing through cascaded nonlinear optical processes. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.05201\">10.48550/arXiv.2405.05201</a>","short":"S. Pontula, Y. Salamin, C. Roques-Carmes, M. Soljacic, ArXiv (n.d.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","language":[{"iso":"eng"}],"date_published":"2024-05-08T00:00:00Z","OA_place":"repository","month":"05","author":[{"last_name":"Pontula","full_name":"Pontula, Sahil","first_name":"Sahil"},{"full_name":"Salamin, Yannick","first_name":"Yannick","last_name":"Salamin"},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","first_name":"Charles","full_name":"Roques-Carmes, Charles"},{"last_name":"Soljacic","full_name":"Soljacic, Marin","first_name":"Marin"}],"OA_type":"green","arxiv":1,"day":"08","date_updated":"2026-04-13T10:51:17Z","publication_status":"submitted","oa":1,"year":"2024","doi":"10.48550/arXiv.2405.05201","abstract":[{"lang":"eng","text":"Multimode squeezed light is enticing for several applications, from squeezed frequency combs for spectroscopy to signal multiplexing in optical computing. To generate squeezing in multiple frequency modes, optical parametric oscillators have been vital in realizing multimode squeezed vacuum states through second-order nonlinear processes. However, most work has focused on generating multimode squeezed vacua and squeezing in mode superpositions (supermodes). Bright squeezing in multiple discrete frequency modes, if realized, could unlock novel applications in quantum-enhanced spectroscopy and optical quantum computing. Here, we show how $Q$ factor engineering of a multimode nonlinear cavity with cascaded three wave mixing processes creates strong, spectrally tunable single mode output amplitude noise squeezing over 10 dB below the shot noise limit. In addition, we demonstrate squeezing for multiple discrete frequency modes above threshold. This bright squeezing arises from enhancement of the (noiseless) nonlinear rate relative to decay rates in the system due to the cascaded generation of photons in a single idler \"bath\" mode. A natural consequence of the strong nonlinear coupling in our system is the creation of an effective cavity in the synthetic frequency dimension that sustains Bloch oscillations in the modal energy distribution. Bloch mode engineering could provide an opportunity to better control nonlinear energy flow in the synthetic frequency dimension, with exciting applications in quantum random walks and topological photonics. Lastly, we show evidence of long-range correlations in amplitude noise between discrete frequency modes, pointing towards the potential of long-range entanglement in a synthetic frequency dimension."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.05201","open_access":"1"}],"type":"preprint","oa_version":"Preprint","date_created":"2026-04-09T09:10:41Z","external_id":{"arxiv":["2405.05201"]},"article_number":"2405.05201"},{"scopus_import":"1","article_processing_charge":"No","status":"public","title":"Strong coupling and single-photon nonlinearity in free-electron quantum optics","extern":"1","publication":"arXiv","language":[{"iso":"eng"}],"_id":"21679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” <i>ArXiv</i>, 2403.13071, doi:<a href=\"https://doi.org/10.48550/arXiv.2403.13071\">10.48550/arXiv.2403.13071</a>.","ista":"Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. arXiv, 2403.13071.","apa":"Karnieli, A., Roques-Carmes, C., Rivera, N., &#38; Fan, S. (n.d.). Strong coupling and single-photon nonlinearity in free-electron quantum optics. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2403.13071\">https://doi.org/10.48550/arXiv.2403.13071</a>","chicago":"Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2403.13071\">https://doi.org/10.48550/arXiv.2403.13071</a>.","ieee":"A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and single-photon nonlinearity in free-electron quantum optics,” <i>arXiv</i>. .","ama":"Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2403.13071\">10.48550/arXiv.2403.13071</a>","short":"A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ArXiv (n.d.)."},"author":[{"full_name":"Karnieli, Aviv","first_name":"Aviv","last_name":"Karnieli"},{"full_name":"Roques-Carmes, Charles","first_name":"Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"last_name":"Rivera","first_name":"Nicholas","full_name":"Rivera, Nicholas"},{"full_name":"Fan, Shanhui","first_name":"Shanhui","last_name":"Fan"}],"month":"03","OA_place":"repository","date_published":"2024-03-19T00:00:00Z","publication_status":"submitted","date_updated":"2026-04-13T10:57:33Z","arxiv":1,"OA_type":"green","day":"19","doi":"10.48550/arXiv.2403.13071","year":"2024","oa":1,"type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.13071"}],"abstract":[{"text":"The observation that free electrons can interact coherently with quantized electromagnetic fields and matter systems has led to a plethora of proposals leveraging the unique quantum properties of free electrons. At the heart of these proposals lies the assumption of a strong quantum interaction between a flying free electron and a photonic mode. However, existing schemes are intrinsically limited by electron diffraction, which puts an upper bound on the interaction length and therefore the quantum coupling strength. Here, we propose the use of \"free-electron fibers'': effectively one-dimensional photonic systems where free electrons co-propagate with two guided modes. The first mode applies a ponderomotive trap to the free electron, effectively lifting the limitations due to electron diffraction. The second mode strongly couples to the guided free electron, with an enhanced coupling that is orders of magnitude larger than previous designs. Moreover, the extended interaction lengths enabled by our scheme allows for strong single-photon nonlinearities mediated by free electrons. We predict a few interesting observable quantum effects in our system, such as deterministic single-photon emission and complex, nonlinear multimode dynamics. Our proposal paves the way towards the realization of many anticipated effects in free-electron quantum optics, such as non-Gaussian light generation, deterministic single photon emission, and quantum gates controlled by free-electron--photon interactions.","lang":"eng"}],"oa_version":"Preprint","article_number":"2403.13071","date_created":"2026-04-09T09:10:41Z","external_id":{"arxiv":["2403.13071"]}},{"oa_version":"Preprint","article_number":"2405.20241","external_id":{"arxiv":["2405.20241"]},"date_created":"2026-04-09T09:10:41Z","doi":"10.48550/arXiv.2405.20241","oa":1,"year":"2024","type":"preprint","abstract":[{"text":"Enhancing interactions in many-body quantum systems, while protecting them from environmental decoherence, is at the heart of many quantum technologies. Waveguide quantum electrodynamics is a promising platform for achieving this, as it hosts infinite-range interactions and decoherence-free subspaces of quantum emitters. However, as coherent interactions between emitters are typically washed out in the wavelength-spacing regime hosting decoherence-free states, coherent control over the latter becomes limited, and many-body Hamiltonians in this important regime remain out of reach. Here we show that by incorporating emitter arrays with nonlinear waveguides hosting parametric gain, we obtain a unique class of many-body interaction Hamiltonians with coupling strengths that increase with emitter spacing, and persist even for wavelength-spaced arrays. We then propose to use these Hamiltonians to coherently generate decoherence-free states directly from the ground state, using only global squeezing drives, without the need for local addressing of individual emitters. Interestingly, we find that the dynamics approaches a unitary evolution in the limit of weak intra-waveguide squeezing, and discuss potential experimental realizations of this effect. Our results pave the way towards coherent control protocols in waveguide quantum electrodynamics, with applications including quantum computing, simulation, memory and nonclassical light generation.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.20241"}],"OA_place":"repository","author":[{"full_name":"Karnieli, Aviv","first_name":"Aviv","last_name":"Karnieli"},{"first_name":"Offek","full_name":"Tziperman, Offek","last_name":"Tziperman"},{"last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles","first_name":"Charles"},{"first_name":"Shanhui","full_name":"Fan, Shanhui","last_name":"Fan"}],"month":"05","date_published":"2024-05-30T00:00:00Z","date_updated":"2026-04-13T10:53:32Z","publication_status":"submitted","day":"30","OA_type":"green","arxiv":1,"title":"Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics","status":"public","article_processing_charge":"No","scopus_import":"1","extern":"1","language":[{"iso":"eng"}],"publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"21681","citation":{"ama":"Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.20241\">10.48550/arXiv.2405.20241</a>","short":"A. Karnieli, O. Tziperman, C. Roques-Carmes, S. Fan, ArXiv (n.d.).","mla":"Karnieli, Aviv, et al. “Decoherence-Free Many-Body Hamiltonians in Nonlinear Waveguide Quantum Electrodynamics.” <i>ArXiv</i>, 2405.20241, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.20241\">10.48550/arXiv.2405.20241</a>.","ista":"Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv, 2405.20241.","apa":"Karnieli, A., Tziperman, O., Roques-Carmes, C., &#38; Fan, S. (n.d.). Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.20241\">https://doi.org/10.48550/arXiv.2405.20241</a>","chicago":"Karnieli, Aviv, Offek Tziperman, Charles Roques-Carmes, and Shanhui Fan. “Decoherence-Free Many-Body Hamiltonians in Nonlinear Waveguide Quantum Electrodynamics.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.20241\">https://doi.org/10.48550/arXiv.2405.20241</a>.","ieee":"A. Karnieli, O. Tziperman, C. Roques-Carmes, and S. Fan, “Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics,” <i>arXiv</i>. ."}},{"_id":"21683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Horodynski, Michael, et al. “Stochastic Logic in Biased Coupled Photonic Probabilistic Bits.” <i>ArXiv</i>, 2406.04000, doi:<a href=\"https://doi.org/10.48550/arXiv.2406.04000\">10.48550/arXiv.2406.04000</a>.","ieee":"M. Horodynski <i>et al.</i>, “Stochastic logic in biased coupled photonic probabilistic bits,” <i>arXiv</i>. .","apa":"Horodynski, M., Roques-Carmes, C., Salamin, Y., Choi, S., Sloan, J., Luo, D., &#38; Soljačić, M. (n.d.). Stochastic logic in biased coupled photonic probabilistic bits. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2406.04000\">https://doi.org/10.48550/arXiv.2406.04000</a>","chicago":"Horodynski, Michael, Charles Roques-Carmes, Yannick Salamin, Seou Choi, Jamison Sloan, Di Luo, and Marin Soljačić. “Stochastic Logic in Biased Coupled Photonic Probabilistic Bits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2406.04000\">https://doi.org/10.48550/arXiv.2406.04000</a>.","ista":"Horodynski M, Roques-Carmes C, Salamin Y, Choi S, Sloan J, Luo D, Soljačić M. Stochastic logic in biased coupled photonic probabilistic bits. arXiv, 2406.04000.","ama":"Horodynski M, Roques-Carmes C, Salamin Y, et al. Stochastic logic in biased coupled photonic probabilistic bits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2406.04000\">10.48550/arXiv.2406.04000</a>","short":"M. Horodynski, C. Roques-Carmes, Y. Salamin, S. Choi, J. Sloan, D. Luo, M. Soljačić, ArXiv (n.d.)."},"publication":"arXiv","language":[{"iso":"eng"}],"extern":"1","status":"public","scopus_import":"1","article_processing_charge":"No","title":"Stochastic logic in biased coupled photonic probabilistic bits","day":"06","arxiv":1,"OA_type":"green","publication_status":"submitted","date_updated":"2026-04-13T10:52:25Z","date_published":"2024-06-06T00:00:00Z","month":"06","author":[{"full_name":"Horodynski, Michael","first_name":"Michael","last_name":"Horodynski"},{"first_name":"Charles","full_name":"Roques-Carmes, Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82"},{"last_name":"Salamin","first_name":"Yannick","full_name":"Salamin, Yannick"},{"last_name":"Choi","full_name":"Choi, Seou","first_name":"Seou"},{"last_name":"Sloan","first_name":"Jamison","full_name":"Sloan, Jamison"},{"last_name":"Luo","first_name":"Di","full_name":"Luo, Di"},{"full_name":"Soljačić, Marin","first_name":"Marin","last_name":"Soljačić"}],"OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.04000"}],"abstract":[{"lang":"eng","text":"Optical computing often employs tailor-made hardware to implement specific algorithms, trading generality for improved performance in key aspects like speed and power efficiency. An important computing approach that is still missing its corresponding optical hardware is probabilistic computing, used e.g. for solving difficult combinatorial optimization problems. In this study, we propose an experimentally viable photonic approach to solve arbitrary probabilistic computing problems. Our method relies on the insight that coherent Ising machines composed of coupled and biased optical parametric oscillators can emulate stochastic logic. We demonstrate the feasibility of our approach by using numerical simulations equivalent to the full density matrix formulation of coupled optical parametric oscillators."}],"type":"preprint","oa":1,"year":"2024","doi":"10.48550/arXiv.2406.04000","date_created":"2026-04-09T09:10:41Z","external_id":{"arxiv":["2406.04000"]},"article_number":"2406.04000","oa_version":"Preprint"},{"year":"2024","project":[{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"volume":112,"isi":1,"page":"230-246.e11","abstract":[{"text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny.","lang":"eng"}],"oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","description":"News on ISTA Website"}]},"external_id":{"isi":["001163937900001"],"pmid":["38096816"]},"date_created":"2023-04-27T09:41:48Z","file":[{"file_id":"14944","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2024_Neuron_Cheung.pdf","checksum":"32b3788f7085cf44a84108d8faaff3ce","file_size":5942467,"date_created":"2024-02-06T13:56:15Z","success":1,"date_updated":"2024-02-06T13:56:15Z"}],"scopus_import":"1","status":"public","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","article_type":"original","publication":"Neuron","language":[{"iso":"eng"}],"_id":"12875","month":"01","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","first_name":"Florian"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","first_name":"Peter"},{"last_name":"Krausgruber","full_name":"Krausgruber, Thomas","first_name":"Thomas"},{"full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"full_name":"Schrammel, Martin","first_name":"Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","last_name":"Schrammel"},{"full_name":"Özgen, Natalie Y","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090","last_name":"Özgen"},{"first_name":"Alexis","full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","last_name":"Ivec"},{"first_name":"Christoph","full_name":"Bock, Christoph","last_name":"Bock"},{"first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"publication_status":"published","date_updated":"2025-12-30T10:54:12Z","ddc":["570"],"doi":"10.1016/j.neuron.2023.11.009","oa":1,"pmid":1,"type":"journal_article","file_date_updated":"2024-02-06T13:56:15Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0896-6273"]},"issue":"2","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"RySh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">https://doi.org/10.1016/j.neuron.2023.11.009</a>","ieee":"G. T. Cheung <i>et al.</i>, “Multipotent progenitors instruct ontogeny of the superior colliculus,” <i>Neuron</i>, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” <i>Neuron</i>, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. <i>Neuron</i>. 2024;112(2):230-246.e11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.11.009\">10.1016/j.neuron.2023.11.009</a>"},"intvolume":"       112","date_published":"2024-01-17T00:00:00Z","quality_controlled":"1","day":"17"},{"has_accepted_license":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"article_number":"102771","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"file_date_updated":"2024-07-16T11:50:03Z","pmid":1,"type":"journal_article","oa":1,"doi":"10.1016/j.xpro.2023.102771","day":"15","quality_controlled":"1","date_published":"2024-03-15T00:00:00Z","intvolume":"         5","department":[{"_id":"SiHi"}],"citation":{"short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024).","ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. 2024;5(1). doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” <i>STAR Protocols</i>, vol. 5, no. 1. Elsevier, 2024.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>.","apa":"Amberg, N., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">https://doi.org/10.1016/j.xpro.2023.102771</a>","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2024. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” <i>STAR Protocols</i>, vol. 5, no. 1, 102771, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2023.102771\">10.1016/j.xpro.2023.102771</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","publisher":"Elsevier","publication_identifier":{"issn":["2666-1667"]},"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38070137"]},"date_created":"2023-12-13T11:48:05Z","oa_version":"Published Version","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1","lang":"eng"}],"ec_funded":1,"project":[{"grant_number":"T01031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"volume":5,"year":"2024","ddc":["570"],"date_updated":"2025-04-15T08:23:06Z","publication_status":"published","author":[{"orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"month":"03","_id":"14683","language":[{"iso":"eng"}],"publication":"STAR Protocols","article_type":"review","title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","file":[{"file_name":"2024_STARProtoc_Amberg.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17260","creator":"dernst","date_updated":"2024-07-16T11:50:03Z","date_created":"2024-07-16T11:50:03Z","success":1,"file_size":8871807,"checksum":"3f0ee62e04bf5a44b45b035662826e95"}],"status":"public","scopus_import":"1"},{"month":"09","author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","first_name":"Carmen"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"ddc":["570"],"OA_type":"gold","date_updated":"2025-12-30T10:54:11Z","APC_amount":"804 EUR","publication_status":"published","article_type":"original","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","scopus_import":"1","status":"public","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_name":"2024_STARProtoc_Cheung.pdf","creator":"dernst","file_id":"18809","date_created":"2025-01-09T12:12:40Z","success":1,"date_updated":"2025-01-09T12:12:40Z","file_size":5186071,"checksum":"d8a8cdba82a394e731aa699ace1ae433"}],"_id":"17187","publication":"STAR Protocols","language":[{"iso":"eng"}],"oa_version":"Published Version","external_id":{"pmid":["38935508"]},"date_created":"2024-06-30T22:01:04Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"volume":5,"year":"2024","abstract":[{"text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1","lang":"eng"}],"ec_funded":1,"date_published":"2024-09-20T00:00:00Z","OA_place":"publisher","intvolume":"         5","day":"20","quality_controlled":"1","publication_identifier":{"eissn":["2666-1667"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"citation":{"mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>, vol. 5, no. 3, 103157, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>.","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., Streicher, C., &#38; Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">https://doi.org/10.1016/j.xpro.2024.103157</a>.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103157\">10.1016/j.xpro.2024.103157</a>","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024)."},"issue":"3","publisher":"Elsevier","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"corr_author":"1","has_accepted_license":"1","acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","article_number":"103157","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"doi":"10.1016/j.xpro.2024.103157","file_date_updated":"2025-01-09T12:12:40Z","pmid":1,"type":"journal_article"},{"file_date_updated":"2025-01-09T12:16:53Z","type":"journal_article","pmid":1,"doi":"10.1016/j.xpro.2024.103168","oa":1,"article_number":"103168","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024)."},"issue":"3","publisher":"Elsevier","article_processing_charge":"Yes","publication_identifier":{"eissn":["2666-1667"]},"quality_controlled":"1","day":"20","intvolume":"         5","OA_place":"publisher","date_published":"2024-09-20T00:00:00Z","abstract":[{"lang":"eng","text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1"}],"project":[{"grant_number":"F7805","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"volume":5,"year":"2024","external_id":{"pmid":["38968076"]},"date_created":"2024-07-14T22:01:10Z","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"STAR Protocols","_id":"17232","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","file":[{"creator":"dernst","file_id":"18810","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2024_STARProtoc_Cheung2.pdf","file_size":6445556,"checksum":"464f52ecc6ec92f509552823bb82bf79","date_created":"2025-01-09T12:16:53Z","success":1,"date_updated":"2025-01-09T12:16:53Z"}],"status":"public","scopus_import":"1","article_type":"original","date_updated":"2025-12-30T10:54:12Z","APC_amount":"804 EUR","publication_status":"published","ddc":["570"],"OA_type":"gold","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","full_name":"Cheung, Giselle T","first_name":"Giselle T","orcid":"0000-0001-8457-2572"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"}],"month":"09"},{"year":"2024","project":[{"name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","grant_number":"26253"},{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"volume":2831,"edition":"1","page":"283-299","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"oa_version":"None","date_created":"2024-08-13T12:16:41Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20212"}]},"external_id":{"pmid":["39134857"]},"status":"public","scopus_import":"1","title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","language":[{"iso":"eng"}],"publication":"Neuronal Morphogenesis","_id":"17425","author":[{"first_name":"Osvaldo","orcid":"0000-0001-6618-6889","full_name":"Miranda, Osvaldo","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","last_name":"Miranda"},{"orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"month":"08","publication_status":"published","series_title":"MIMB","editor":[{"last_name":"Toyooka","first_name":"Kazuhito","full_name":"Toyooka, Kazuhito"}],"date_updated":"2026-04-07T12:32:35Z","doi":"10.1007/978-1-0716-3969-6_19","place":"New York, NY","pmid":1,"type":"book_chapter","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","article_processing_charge":"No","publication_identifier":{"eissn":["1940-6029"],"isbn":["9781071639689"],"eisbn":["9781071639696"],"issn":["1064-3745"]},"publisher":"Springer Nature","citation":{"short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. <i>Neuronal Morphogenesis</i>. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>","ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in <i>Neuronal Morphogenesis</i>, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","apa":"Miranda, O., Cheung, G. T., &#38; Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), <i>Neuronal Morphogenesis</i> (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">https://doi.org/10.1007/978-1-0716-3969-6_19</a>.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” <i>Neuronal Morphogenesis</i>, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3969-6_19\">10.1007/978-1-0716-3969-6_19</a>."},"department":[{"_id":"GradSch"},{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Molecular Biology"],"intvolume":"      2831","date_published":"2024-08-13T00:00:00Z","quality_controlled":"1","day":"13"},{"related_material":{"record":[{"status":"public","id":"18681","relation":"dissertation_contains"},{"id":"18879","relation":"later_version","status":"public"}]},"date_created":"2024-12-19T11:35:08Z","acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"oa_version":"Preprint","ec_funded":1,"abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.05.02.592169","open_access":"1"}],"type":"preprint","project":[{"name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"}],"oa":1,"year":"2024","doi":"10.1101/2024.05.02.592169","day":"02","date_updated":"2026-04-14T08:34:32Z","publication_status":"draft","date_published":"2024-05-02T00:00:00Z","OA_place":"repository","author":[{"last_name":"Watson","full_name":"Watson, Jake F.","first_name":"Jake F."},{"first_name":"Victor","full_name":"Vargas-Barroso, Victor","last_name":"Vargas-Barroso"},{"full_name":"Morse-Mora, Rebecca J.","first_name":"Rebecca J.","last_name":"Morse-Mora"},{"last_name":"Navas-Olive","first_name":"Andrea","full_name":"Navas-Olive, Andrea"},{"last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba"},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"first_name":"Matthias","full_name":"Tomschik, Matthias","last_name":"Tomschik"},{"last_name":"Rössler","first_name":"Karl","full_name":"Rössler, Karl"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"month":"05","_id":"18688","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoDa"},{"_id":"PeJo"}],"citation":{"mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.)."},"publication":"bioRxiv","language":[{"iso":"eng"}],"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","article_processing_charge":"No","status":"public"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"pmid":1,"type":"journal_article","file_date_updated":"2025-01-09T07:48:01Z","doi":"10.1038/s41587-023-01911-8","oa":1,"quality_controlled":"1","day":"01","OA_place":"publisher","intvolume":"        42","date_published":"2024-07-01T00:00:00Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"citation":{"short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>."},"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"related_material":{"record":[{"id":"18660","relation":"dissertation_contains","status":"deleted"},{"relation":"research_data","id":"13126","status":"public"},{"relation":"dissertation_contains","id":"18674","status":"public"}],"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}]},"date_created":"2023-09-03T22:01:15Z","oa_version":"Published Version","page":"1051-1064","ec_funded":1,"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"year":"2024","project":[{"call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232"},{"grant_number":"Z00312","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"grant_number":"LS18-022","_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","grant_number":"101026635"}],"isi":1,"volume":42,"publication_status":"published","date_updated":"2026-04-14T08:34:35Z","OA_type":"hybrid","ddc":["570"],"author":[{"full_name":"Michalska, Julia M","first_name":"Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska"},{"full_name":"Lyudchik, Julia","first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"orcid":"0000-0002-2340-7431","first_name":"Philipp","full_name":"Velicky, Philipp","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana","first_name":"Hana"},{"last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","first_name":"Jake","full_name":"Watson, Jake"},{"first_name":"Alban","full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer"},{"first_name":"Nicole","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro"},{"full_name":"Roessler, Karl","first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","full_name":"Czech, Thomas","last_name":"Czech"},{"full_name":"Höftberger, Romana","first_name":"Romana","last_name":"Höftberger"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"}],"month":"07","language":[{"iso":"eng"}],"publication":"Nature Biotechnology","_id":"14257","scopus_import":"1","status":"public","file":[{"date_updated":"2025-01-09T07:48:01Z","date_created":"2025-01-09T07:48:01Z","success":1,"checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","file_size":26065165,"file_name":"2024_NatureBiotech_Michalska.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"18784"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","article_type":"original"},{"related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"id":"18677","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"13267","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14257"}]},"date_created":"2024-12-18T14:24:43Z","oa_version":"Published Version","page":"217","abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue requires volumetric imaging at nanoscale spatial resolution. While light microscopy excels at visualizing specific molecules and individual cells, achieving dense, synapse-level circuit reconstruction has not been possible with any light microscopy technique. Thus, the goal of my work was to develop image and data analysis pipelines for brain tissue visualization and reconstruction with light microscopy. To achieve dense circuit reconstruction with single-synapse resolution, I developed both conventional and deep-learning-based synapse detection algorithms, as well as connectivity analysis pipelines that integrate synapse detection with volumetric segmentation of brain tissue."}],"ec_funded":1,"year":"2024","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"publication_status":"published","date_updated":"2026-04-14T08:34:35Z","ddc":["004"],"author":[{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia","full_name":"Lyudchik, Julia"}],"month":"12","language":[{"iso":"eng"}],"_id":"18674","status":"public","file":[{"file_name":"18122024_PhDthesis_corrected_final_pdfa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"jlyudchi","file_id":"18675","date_updated":"2024-12-18T14:17:34Z","date_created":"2024-12-18T14:17:34Z","success":1,"file_size":160536833,"checksum":"1b42b8073e2bc09fc504da52372248c1"},{"date_updated":"2024-12-18T14:41:53Z","date_created":"2024-12-18T14:21:06Z","file_size":99172203,"checksum":"b4da84624060745519723698f7ddf54b","file_name":"18122024_PhDthesis_corrected_final_JL_markup.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"18676","creator":"jlyudchi"}],"title":"Image analysis for brain tissue reconstruction with super-resolution light microscopy","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"}],"corr_author":"1","type":"dissertation","file_date_updated":"2024-12-18T14:41:53Z","doi":"10.15479/at:ista:18674","oa":1,"day":"18","OA_place":"publisher","date_published":"2024-12-18T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Lyudchik J. Image analysis for brain tissue reconstruction with super-resolution light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>","short":"J. Lyudchik, Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy, Institute of Science and Technology Austria, 2024.","mla":"Lyudchik, Julia. <i>Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18674\">10.15479/at:ista:18674</a>.","ista":"Lyudchik J. 2024. Image analysis for brain tissue reconstruction with super-resolution light microscopy. Institute of Science and Technology Austria.","apa":"Lyudchik, J. (2024). <i>Image analysis for brain tissue reconstruction with super-resolution light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>","chicago":"Lyudchik, Julia. “Image Analysis for Brain Tissue Reconstruction with Super-Resolution Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18674\">https://doi.org/10.15479/at:ista:18674</a>.","ieee":"J. Lyudchik, “Image analysis for brain tissue reconstruction with super-resolution light microscopy,” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","supervisor":[{"orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":[" 978-3-99078-051-0"],"issn":["2663-337X"]}},{"oa_version":"Published Version","related_material":{"record":[{"id":"20393","relation":"dissertation_contains","status":"public"}]},"date_created":"2024-10-27T23:01:45Z","external_id":{"pmid":["39401260"],"isi":["001331700300003"]},"volume":20,"isi":1,"project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"year":"2024","abstract":[{"text":"A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.","lang":"eng"}],"author":[{"first_name":"Richard D.J.G.","full_name":"Ho, Richard D.J.G.","last_name":"Ho"},{"orcid":"0000-0001-6060-4795","first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Majka","first_name":"Maciej","full_name":"Majka, Maciej"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","first_name":"Marcin P"}],"month":"10","date_updated":"2026-04-07T12:31:58Z","APC_amount":"3197,23 EUR","publication_status":"published","ddc":["570"],"OA_type":"gold","title":"Dynamics of morphogen source formation in a growing tissue","scopus_import":"1","file":[{"file_size":3732443,"checksum":"42fa714459943cb3961b40fab8fd82c8","date_updated":"2024-10-29T11:59:09Z","date_created":"2024-10-29T11:59:09Z","success":1,"file_id":"18487","creator":"dernst","file_name":"2024_PloSComBio_Ho.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"status":"public","article_type":"original","language":[{"iso":"eng"}],"publication":"PLoS Computational Biology","_id":"18481","corr_author":"1","article_number":"e1012508","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"We thank Martina Greunz-Schindler for technical support, and Thomas Minchington and James Briscoe for comments on the manuscript.\r\nRDJGH, MM and MZ were supported by a grant from the Priority Research Area DigiWorld\r\nunder the Strategic Programme Excellence Initiative at Jagiellonian University. The research\r\nwas supported by the Polish National Agency for Academic Exchange, PN/PPO/2018/1/00011/U/00001 which paid the salary of MM and MZ up to Feb 2023. The research received support from National Science Center, Poland, 2021/42/E/NZ2/00188 which paid salary of MZ. Work in the AK labis supported by ISTA to KK and AK, the European\r\nResearch Council under Horizon Europe: grant 101044579 to AK, and Austrian Science Fund\r\n(FWF): Grant DOI 10.55776/F78 to AK. The salaries of AK and KK were paid by ISTA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","doi":"10.1371/journal.pcbi.1012508","oa":1,"file_date_updated":"2024-10-29T11:59:09Z","pmid":1,"type":"journal_article","intvolume":"        20","OA_place":"publisher","date_published":"2024-10-14T00:00:00Z","quality_controlled":"1","day":"14","DOAJ_listed":"1","article_processing_charge":"No","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. 2024. Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. 20, e1012508.","ieee":"R. D. J. G. Ho, K. Kishi, M. Majka, A. Kicheva, and M. P. Zagórski, “Dynamics of morphogen source formation in a growing tissue,” <i>PLoS Computational Biology</i>, vol. 20. Public Library of Science, 2024.","apa":"Ho, R. D. J. G., Kishi, K., Majka, M., Kicheva, A., &#38; Zagórski, M. P. (2024). Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>","chicago":"Ho, Richard D.J.G., Kasumi Kishi, Maciej Majka, Anna Kicheva, and Marcin P Zagórski. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">https://doi.org/10.1371/journal.pcbi.1012508</a>.","mla":"Ho, Richard D. J. G., et al. “Dynamics of Morphogen Source Formation in a Growing Tissue.” <i>PLoS Computational Biology</i>, vol. 20, e1012508, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>.","short":"R.D.J.G. Ho, K. Kishi, M. Majka, A. Kicheva, M.P. Zagórski, PLoS Computational Biology 20 (2024).","ama":"Ho RDJG, Kishi K, Majka M, Kicheva A, Zagórski MP. Dynamics of morphogen source formation in a growing tissue. <i>PLoS Computational Biology</i>. 2024;20. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012508\">10.1371/journal.pcbi.1012508</a>"},"department":[{"_id":"AnKi"}],"publisher":"Public Library of Science"},{"project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"}],"isi":1,"volume":15,"year":"2024","oa_version":"Published Version","external_id":{"isi":["001156218500022"],"pmid":["38302459"]},"date_created":"2025-01-27T13:01:01Z","title":"Assessing the precision of morphogen gradients in neural tube development","status":"public","file":[{"date_updated":"2025-01-27T13:04:03Z","success":1,"date_created":"2025-01-27T13:04:03Z","checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7","file_size":4723831,"file_name":"2024_NatureComm_Zagorski.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"18903","creator":"dernst"}],"scopus_import":"1","article_type":"letter_note","publication":"Nature Communications","language":[{"iso":"eng"}],"_id":"18902","author":[{"first_name":"Marcin","full_name":"Zagorski, Marcin","last_name":"Zagorski"},{"first_name":"Nathalie","full_name":"Brandenberg, Nathalie","last_name":"Brandenberg"},{"full_name":"Lutolf, Matthias","first_name":"Matthias","last_name":"Lutolf"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"}],"month":"02","date_updated":"2025-12-30T10:57:08Z","publication_status":"published","ddc":["570"],"OA_type":"gold","doi":"10.1038/s41467-024-45148-8","oa":1,"file_date_updated":"2025-01-27T13:04:03Z","type":"journal_article","pmid":1,"corr_author":"1","article_number":"929","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"citation":{"short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).","ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>","ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929.","chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>."},"department":[{"_id":"GaTk"},{"_id":"AnKi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer Nature","OA_place":"publisher","intvolume":"        15","date_published":"2024-02-01T00:00:00Z","quality_controlled":"1","DOAJ_listed":"1","day":"01"},{"status":"public","file":[{"date_updated":"2024-06-20T11:52:22Z","date_created":"2024-06-12T07:53:19Z","checksum":"258c353d47fa37ea63ea43b1e10a34a0","file_size":28370759,"file_name":"Thesis_main_final.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"17137","creator":"fhassani"},{"date_created":"2024-06-12T07:54:27Z","date_updated":"2024-06-12T07:54:27Z","checksum":"deffa5d0db88093f74812fa71520d5e1","file_size":445735,"content_type":"text/x-tex","access_level":"closed","relation":"source_file","file_name":"Thesis_main.tex","creator":"fhassani","file_id":"17138"}],"title":"Superconducting qubits capable of dynamic switching between protected and high-speed control regimes","_id":"17133","language":[{"iso":"eng"}],"author":[{"full_name":"Hassani, Farid","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"}],"month":"06","ddc":["530"],"publication_status":"published","date_updated":"2026-04-15T06:43:02Z","year":"2024","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"},{"grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"abstract":[{"lang":"eng","text":"An ideal quantum computer relies on qubits capable of performing fast gate operations and\r\nmaintaining strong interconnections while preserving their quantum coherence. Since the\r\ninception of experimental eforts toward building a quantum computer, the community has\r\nfaced challenges in engineering such a system. Among the various methods of implementing a\r\nquantum computer, superconducting qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith high coherence require isolation from the environment, while fast operation necessitates\r\nstrong coupling of the qubit. This thesis approaches this issue by proposing the idea of\r\nengineering superconducting qubits capable of transitioning between operating in a protected\r\nregime, where the qubit is completely isolated from the environment, and coupling to the\r\ncommunication channels as needed. In this direction, we use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices, searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis leads us to the inductively shunted transmon (IST) regime, characterized by EJ /EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well with a large barrier\r\nseparating the local ground states of each quantum well. In this regime, although it is\r\nanticipated that the two quantum wells would be isolated from each other, we observe single\r\nfuxon tunneling between them. The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical system, containing resonance conditions that allow the preparation of the\r\nfuxon ground or excited states. This enables us to study the relaxation rate of such transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling the barrier height\r\nbetween the two quantum wells allows for controllable coupling, which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe 0-π qubit is one of the very few known superconducting circuit types that ofers exponential\r\nprotection from both relaxation and dephasing simultaneously. However, this qubit is not\r\nexempt from the fact that such protection comes at the expense of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably break the circuit symmetry, the\r\nkey reason for the protection, to momentarily restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling of the protected state to the thermally occupied parasitic mode\r\nof the circuit. However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand show that this can be used as a tunable coupler between the protected states. In the\r\nfuture, this should allow to perform gate operations by dynamically controlling the asymmetry\r\ninstead of driving the protected transition with microwave pulses. Therefore, we believe that\r\nthe proposed method can make the use of protected qubits more practical in experimental\r\nrealizations of quantum computing."}],"page":"161","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"13227"},{"status":"public","relation":"part_of_dissertation","id":"9928"},{"status":"public","id":"8755","relation":"part_of_dissertation"}]},"date_created":"2024-06-11T18:20:05Z","publication_identifier":{"isbn":["978-3-99078-040-4"],"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"short":"F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.","ama":"Hassani F. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>","ista":"Hassani F. 2024. Superconducting qubits capable of dynamic switching between protected and high-speed control regimes. Institute of Science and Technology Austria.","chicago":"Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>.","apa":"Hassani, F. (2024). <i>Superconducting qubits capable of dynamic switching between protected and high-speed control regimes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17133\">https://doi.org/10.15479/at:ista:17133</a>","ieee":"F. Hassani, “Superconducting qubits capable of dynamic switching between protected and high-speed control regimes,” Institute of Science and Technology Austria, 2024.","mla":"Hassani, Farid. <i>Superconducting Qubits Capable of Dynamic Switching between Protected and High-Speed Control Regimes</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17133\">10.15479/at:ista:17133</a>."},"degree_awarded":"PhD","date_published":"2024-06-11T00:00:00Z","OA_place":"publisher","day":"11","oa":1,"doi":"10.15479/at:ista:17133","type":"dissertation","file_date_updated":"2024-06-20T11:52:22Z","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","has_accepted_license":"1","tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","keyword":["Quantum information","Qubits","Superconducting devices"]},{"publication":"European Journal of Human Genetics","language":[{"iso":"eng"}],"_id":"15362","title":"Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells","scopus_import":"1","status":"public","file":[{"creator":"dernst","file_id":"18799","file_name":"2024_EJHG_Andrianova.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":3060724,"checksum":"e45fc987f4e9ebafdd0ec4f0e9027de4","date_updated":"2025-01-09T09:21:25Z","success":1,"date_created":"2025-01-09T09:21:25Z"}],"article_type":"original","date_updated":"2026-04-15T08:51:09Z","publication_status":"published","ddc":["570"],"OA_type":"hybrid","month":"07","author":[{"last_name":"Andrianova","full_name":"Andrianova, Maria A.","first_name":"Maria A."},{"first_name":"Vladimir B.","full_name":"Seplyarskiy, Vladimir B.","last_name":"Seplyarskiy"},{"last_name":"Terradas","full_name":"Terradas, Mariona","first_name":"Mariona"},{"full_name":"Sánchez-Heras, Ana Beatriz","first_name":"Ana Beatriz","last_name":"Sánchez-Heras"},{"first_name":"Pilar","full_name":"Mur, Pilar","last_name":"Mur"},{"last_name":"Soto","first_name":"José Luis","full_name":"Soto, José Luis"},{"full_name":"Aiza, Gemma","first_name":"Gemma","last_name":"Aiza"},{"first_name":"Emma","full_name":"Borràs, Emma","last_name":"Borràs"},{"last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"last_name":"Kondrashov","first_name":"Alexey S.","full_name":"Kondrashov, Alexey S."},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"first_name":"Laura","full_name":"Valle, Laura","last_name":"Valle"}],"page":"837-845","ec_funded":1,"abstract":[{"lang":"eng","text":"Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate."}],"project":[{"grant_number":"429960716","name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"},{"name":"Evolutionary analysis of gene regulation","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","grant_number":"I05127"}],"isi":1,"volume":32,"year":"2024","date_created":"2024-05-05T22:01:04Z","external_id":{"pmid":["38658779"],"isi":["001207703200001"]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FyKo"}],"citation":{"mla":"Andrianova, Maria A., et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>, vol. 32, Springer Nature, 2024, pp. 837–45, doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>.","ista":"Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov F, Kondrashov AS, Bazykin GA, Valle L. 2024. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. European Journal of Human Genetics. 32, 837–845.","chicago":"Andrianova, Maria A., Vladimir B. Seplyarskiy, Mariona Terradas, Ana Beatriz Sánchez-Heras, Pilar Mur, José Luis Soto, Gemma Aiza, et al. “Discovery of Recessive Effect of Human Polymerase δ Proofreading Deficiency through Mutational Analysis of POLD1-Mutated Normal and Cancer Cells.” <i>European Journal of Human Genetics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>.","apa":"Andrianova, M. A., Seplyarskiy, V. B., Terradas, M., Sánchez-Heras, A. B., Mur, P., Soto, J. L., … Valle, L. (2024). Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-024-01598-8\">https://doi.org/10.1038/s41431-024-01598-8</a>","ieee":"M. A. Andrianova <i>et al.</i>, “Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells,” <i>European Journal of Human Genetics</i>, vol. 32. Springer Nature, pp. 837–845, 2024.","ama":"Andrianova MA, Seplyarskiy VB, Terradas M, et al. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. <i>European Journal of Human Genetics</i>. 2024;32:837-845. doi:<a href=\"https://doi.org/10.1038/s41431-024-01598-8\">10.1038/s41431-024-01598-8</a>","short":"M.A. Andrianova, V.B. Seplyarskiy, M. Terradas, A.B. Sánchez-Heras, P. Mur, J.L. Soto, G. Aiza, E. Borràs, F. Kondrashov, A.S. Kondrashov, G.A. Bazykin, L. Valle, European Journal of Human Genetics 32 (2024) 837–845."},"publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"quality_controlled":"1","day":"01","intvolume":"        32","OA_place":"publisher","date_published":"2024-07-01T00:00:00Z","file_date_updated":"2025-01-09T09:21:25Z","type":"journal_article","pmid":1,"doi":"10.1038/s41431-024-01598-8","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"This study was funded by the Spanish Ministry of Science and Innovation (Agencia Estatal de Investigación), co-funded by FEDER funds a way to build Europe [PID2020-112595RB-I00 (LV)], Instituto de Salud Carlos III [CIBERONC CB16/12/00234 (LV); ISCIII-AES-2017 PI17/01082 (JLS), PMP22/00064], Government of Catalonia [AGAUR 2021SGR01112, CERCA Program for institutional support (LV)], Scientific Foundation Asociación Española Contra el Cáncer [AECC Investigador (MT)], Austrian Science Fund FWF [Grant Agreement # I5127-B (FK)], German Research Foundation DFG [Grant Agreement # 429960716 (FK)], and ERC Consolidator [Grant Agreement # 771209 ChrFL (FK)]."},{"corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","doi":"10.15479/at:ista:18135","oa":1,"file_date_updated":"2024-09-26T13:12:55Z","type":"dissertation","OA_place":"publisher","date_published":"2024-09-23T00:00:00Z","day":"23","supervisor":[{"first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-042-8"]},"degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"ista":"Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria.","chicago":"Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>.","ieee":"A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024.","apa":"Lauritsen, A. B. (2024). <i>Energies of dilute Fermi gases and universalities in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18135\">https://doi.org/10.15479/at:ista:18135</a>","mla":"Lauritsen, Asbjørn Bækgaard. <i>Energies of Dilute Fermi Gases and Universalities in BCS Theory</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>.","short":"A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024.","ama":"Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18135\">10.15479/at:ista:18135</a>"},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","date_created":"2024-09-24T10:56:25Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11732"},{"relation":"part_of_dissertation","id":"14542","status":"public"},{"status":"public","id":"18107","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17240","status":"public"},{"status":"public","id":"14931","relation":"part_of_dissertation"}]},"project":[{"grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"year":"2024","page":"353","abstract":[{"text":"This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$  with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$.","lang":"eng"}],"ec_funded":1,"month":"09","author":[{"last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"}],"date_updated":"2026-04-16T08:17:55Z","publication_status":"published","ddc":["515","539"],"title":"Energies of dilute Fermi gases and universalities in BCS theory","file":[{"file_size":3648831,"checksum":"c7bc3b31e430d57c65393051ca439575","success":1,"date_created":"2024-09-26T13:11:24Z","date_updated":"2024-09-26T13:11:24Z","file_id":"18147","creator":"alaurits","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"Lauritsen-thesis-final.pdf"},{"file_size":1625888,"checksum":"39f6b1b7f83e25a3bf9f933f1ea0bc06","date_created":"2024-09-26T13:12:55Z","date_updated":"2024-09-26T13:12:55Z","creator":"alaurits","file_id":"18148","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","file_name":"Lauritsen-thesis-source.zip"}],"status":"public","language":[{"iso":"eng"}],"_id":"18135"},{"_id":"14931","publication":"Journal of Functional Analysis","language":[{"iso":"eng"}],"article_type":"original","status":"public","scopus_import":"1","file":[{"file_id":"17305","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2024_JourFunctAnalysis_Lauritsen.pdf","checksum":"ee203cf2dc4420ad90d3c9970d246a78","file_size":1381063,"date_created":"2024-07-22T11:11:56Z","success":1,"date_updated":"2024-07-22T11:11:56Z"}],"title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","ddc":["510"],"publication_status":"published","date_updated":"2026-04-16T08:17:56Z","author":[{"last_name":"Lauritsen","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"month":"04","ec_funded":1,"abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"year":"2024","isi":1,"volume":286,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"external_id":{"isi":["001170294000001"],"arxiv":["2301.04894"]},"related_material":{"record":[{"id":"18135","relation":"dissertation_contains","status":"public"}]},"date_created":"2024-02-04T23:00:53Z","oa_version":"Published Version","issue":"7","publisher":"Elsevier","department":[{"_id":"RoSe"}],"citation":{"mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>, vol. 286, no. 7, 110320, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>.","apa":"Lauritsen, A. B., &#38; Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” <i>Journal of Functional Analysis</i>, vol. 286, no. 7. Elsevier, 2024.","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” <i>Journal of Functional Analysis</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">https://doi.org/10.1016/j.jfa.2024.110320</a>.","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. <i>Journal of Functional Analysis</i>. 2024;286(7). doi:<a href=\"https://doi.org/10.1016/j.jfa.2024.110320\">10.1016/j.jfa.2024.110320</a>","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024)."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"article_processing_charge":"Yes (via OA deal)","arxiv":1,"day":"01","quality_controlled":"1","date_published":"2024-04-01T00:00:00Z","intvolume":"       286","type":"journal_article","file_date_updated":"2024-07-22T11:11:56Z","oa":1,"doi":"10.1016/j.jfa.2024.110320","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"110320","corr_author":"1"}]