--- OA_place: publisher OA_type: hybrid _id: '17219' abstract: - lang: eng text: 'We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.' acknowledgement: Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_number: '54' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Peter full_name: Synak, Peter id: 331776E2-F248-11E8-B48F-1D18A9856A87 last_name: Synak - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Irina-Malina full_name: Strugaru, Irina-Malina id: 2afc607f-f128-11eb-9611-8f2a0dfcf074 last_name: Strugaru - first_name: Arian full_name: Etemadihaghighi, Arian id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f last_name: Etemadihaghighi - first_name: Huidong full_name: Yang, Huidong last_name: Yang - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658223 apa: Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223 chicago: Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658223. ieee: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024. ista: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54. mla: Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223. short: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024). corr_author: '1' date_created: 2024-07-10T12:24:00Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-07T13:02:36Z day: '01' ddc: - '004' department: - _id: GradSch - _id: ChWo doi: 10.1145/3658223 external_id: isi: - '001289270900021' file: - access_level: open_access checksum: 1917067d4b52d7729019b03560004e43 content_type: application/pdf creator: dernst date_created: 2024-07-23T06:35:15Z date_updated: 2024-07-23T06:35:15Z file_id: '17317' file_name: 2024_ACMToG_HeissSynak.pdf file_size: 48763368 relation: main_file success: 1 - access_level: open_access checksum: a4f0e293184bfa034c0c585848806b17 content_type: video/mp4 creator: akalinov date_created: 2024-07-10T12:23:44Z date_updated: 2024-07-10T12:23:44Z file_id: '17221' file_name: sdtopofixer_final.mp4 file_size: 48021463 relation: main_file success: 1 - access_level: open_access checksum: 18fc310a78ec91651148c45a8b89fa44 content_type: application/pdf creator: akalinov date_created: 2025-11-11T09:50:52Z date_updated: 2025-11-11T09:50:52Z file_id: '20633' file_name: SuperDuperTopoFixer.pdf file_size: 48639581 relation: preprint title: Authors' version of the text file_date_updated: 2025-11-11T09:50:52Z has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '4' keyword: - surface tracking - topology change - non- manifold meshes - multi-material flows - solid modeling language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '19630' relation: dissertation_contains status: public - id: '18301' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multi-material mesh-based surface tracking with implicit topology changes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2024' ... --- _id: '17154' abstract: - lang: eng text: We compute the deterministic approximation for mixed fluctuation moments of products of deterministic matrices and general Sobolev functions of Wigner matrices. Restricting to polynomials, our formulas reproduce recent results of Male et al. (Random Matrices Theory Appl. 11(2):2250015, 2022), showing that the underlying combinatorics of non-crossing partitions and annular non-crossing permutations continue to stay valid beyond the setting of second-order free probability theory. The formulas obtained further characterize the variance in the functional central limit theorem given in the recent companion paper (Reker in Preprint, arXiv:2204.03419, 2023). and thus allow identifying the fluctuation around the thermal value in certain thermalization problems. article_number: '10' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker citation: ama: Reker J. Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. 2024;27(3). doi:10.1007/s11040-024-09483-y apa: Reker, J. (2024). Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. Springer Nature. https://doi.org/10.1007/s11040-024-09483-y chicago: Reker, Jana. “Fluctuation Moments for Regular Functions of Wigner Matrices.” Mathematical Physics, Analysis and Geometry. Springer Nature, 2024. https://doi.org/10.1007/s11040-024-09483-y. ieee: J. Reker, “Fluctuation moments for regular functions of Wigner Matrices,” Mathematical Physics, Analysis and Geometry, vol. 27, no. 3. Springer Nature, 2024. ista: Reker J. 2024. Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. 27(3), 10. mla: Reker, Jana. “Fluctuation Moments for Regular Functions of Wigner Matrices.” Mathematical Physics, Analysis and Geometry, vol. 27, no. 3, 10, Springer Nature, 2024, doi:10.1007/s11040-024-09483-y. short: J. Reker, Mathematical Physics, Analysis and Geometry 27 (2024). date_created: 2024-06-21T09:31:17Z date_published: 2024-06-20T00:00:00Z date_updated: 2026-04-07T13:02:12Z day: '20' ddc: - '519' department: - _id: LaEr doi: 10.1007/s11040-024-09483-y ec_funded: 1 external_id: arxiv: - '2307.11029' isi: - '001251464300001' file: - access_level: open_access checksum: 7d04318d66f765621bdcb648378d458e content_type: application/pdf creator: cchlebak date_created: 2024-06-26T11:26:42Z date_updated: 2024-06-26T11:26:42Z file_id: '17175' file_name: 2024_MathPhysAnaGeo_Reker.pdf file_size: 1327596 relation: main_file success: 1 file_date_updated: 2024-06-26T11:26:42Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Mathematical Physics, Analysis and Geometry publication_identifier: eissn: - 1572-9656 issn: - 1385-0172 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '17164' relation: dissertation_contains status: public scopus_import: '1' status: public title: Fluctuation moments for regular functions of Wigner Matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 27 year: '2024' ... --- OA_place: publisher _id: '18301' abstract: - lang: eng text: Physics simulation in computer graphics can bring triangle meshes into topologically invalid states. The method in this thesis contributed to Heiss-Synak* and Kalinov* et al. [2024] who devised a non-manifold hybrid surface tracker—a surface tracker that repairs explicit non-manifold triangle meshes with the help of the implicit domain. Specifically, this thesis provides an algorithm for filling the holes that are left after removing problematic parts of the mesh. alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Arian full_name: Etemadihaghighi, Arian id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f last_name: Etemadihaghighi citation: ama: Etemadi A. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. 2024. doi:10.15479/at:ista:18301 apa: Etemadi, A. (2024). Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18301 chicago: Etemadi, Arian. “Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18301. ieee: A. Etemadi, “Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking,” Institute of Science and Technology Austria, 2024. ista: Etemadi A. 2024. Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking. Institute of Science and Technology Austria. mla: Etemadi, Arian. Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18301. short: A. Etemadi, Filling the Holes of Non-Manifold Self-Intersecting Meshes for Implicit Topology Changes in Surface Tracking, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-11T19:52:20Z date_published: 2024-10-15T00:00:00Z date_updated: 2026-04-07T13:02:36Z day: '15' ddc: - '000' degree_awarded: MS department: - _id: GradSch - _id: ChWo doi: 10.15479/at:ista:18301 file: - access_level: open_access checksum: 80fb7923e229ad9d39253d7c8a8083d0 content_type: application/pdf creator: aetemadi date_created: 2024-10-24T14:34:42Z date_updated: 2024-10-24T14:34:42Z file_id: '18469' file_name: thesis-arian-etemadi.pdf file_size: 8914218 relation: main_file success: 1 - access_level: closed checksum: 1c02586ed7d441d5ec441867650568d1 content_type: application/x-zip-compressed creator: aetemadi date_created: 2024-10-24T14:34:54Z date_updated: 2024-10-24T14:34:54Z file_id: '18470' file_name: thesis-arian-etemadi-latex-source.zip file_size: 9802650 relation: source_file file_date_updated: 2024-10-24T14:34:54Z has_accepted_license: '1' keyword: - surface tracking - non-manifold - hole-filling - topology change - multi-material - solid-modeling language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa: 1 oa_version: Published Version page: '39' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17219' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 title: Filling the holes of non-manifold self-intersecting meshes for implicit topology changes in surface tracking tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository OA_type: green _id: '17047' abstract: - lang: eng text: We provide a dynamical study of a model of multiplicative perturbation of a unitary matrix introduced by Fyodorov. In particular, we identify a flow of deterministic domains that bound the spectrum with high probability, separating the outlier from the typical eigenvalues at all sub-critical timescales. These results are obtained under generic assumptions on U that hold for a variety of unitary random matrix models. article_number: '2450007' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Guillaume full_name: Dubach, Guillaume id: D5C6A458-10C4-11EA-ABF4-A4B43DDC885E last_name: Dubach orcid: 0000-0001-6892-8137 - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker citation: ama: 'Dubach G, Reker J. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. 2024;13(2). doi:10.1142/s2010326324500072' apa: 'Dubach, G., & Reker, J. (2024). Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. World Scientific Publishing. https://doi.org/10.1142/s2010326324500072' chicago: 'Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” Random Matrices: Theory and Applications. World Scientific Publishing, 2024. https://doi.org/10.1142/s2010326324500072.' ieee: 'G. Dubach and J. Reker, “Dynamics of a rank-one multiplicative perturbation of a unitary matrix,” Random Matrices: Theory and Applications, vol. 13, no. 2. World Scientific Publishing, 2024.' ista: 'Dubach G, Reker J. 2024. Dynamics of a rank-one multiplicative perturbation of a unitary matrix. Random Matrices: Theory and Applications. 13(2), 2450007.' mla: 'Dubach, Guillaume, and Jana Reker. “Dynamics of a Rank-One Multiplicative Perturbation of a Unitary Matrix.” Random Matrices: Theory and Applications, vol. 13, no. 2, 2450007, World Scientific Publishing, 2024, doi:10.1142/s2010326324500072.' short: 'G. Dubach, J. Reker, Random Matrices: Theory and Applications 13 (2024).' corr_author: '1' date_created: 2024-05-23T08:31:57Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-04-07T13:02:12Z day: '01' department: - _id: GradSch - _id: LaEr doi: 10.1142/s2010326324500072 ec_funded: 1 external_id: arxiv: - '2212.14638' isi: - '001229295200002' intvolume: ' 13' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2212.14638' month: '04' oa: 1 oa_version: Preprint project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: 'Random Matrices: Theory and Applications' publication_identifier: eissn: - 2010-3271 issn: - 2010-3263 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' related_material: record: - id: '17164' relation: dissertation_contains status: public scopus_import: '1' status: public title: Dynamics of a rank-one multiplicative perturbation of a unitary matrix type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 13 year: '2024' ... --- OA_place: publisher _id: '17850' abstract: - lang: eng text: "Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 citation: ama: Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:10.15479/at:ista:17850 apa: Gonzalez Somermeyer, L. (2024). Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17850 chicago: Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17850. ieee: L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024. ista: Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. mla: Gonzalez Somermeyer, Louisa. Fitness Landscapes of Orthologous Green Fluorescent Proteins. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17850. short: L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-06T12:57:44Z date_published: 2024-09-06T00:00:00Z date_updated: 2026-04-07T13:25:01Z day: '06' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FyKo doi: 10.15479/at:ista:17850 ec_funded: 1 file: - access_level: open_access checksum: d3303724e8d3c91321d71bbad4062048 content_type: application/pdf creator: lgonzale date_created: 2024-09-27T10:32:33Z date_updated: 2024-09-27T10:32:33Z file_id: '18151' file_name: louisa_thesis_draft__240904b.pdf file_size: 11219837 relation: main_file - access_level: closed checksum: 22e63f7f9014dffde2af7a47e7d1d014 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lgonzale date_created: 2024-09-27T10:34:34Z date_updated: 2024-09-27T10:34:34Z file_id: '18152' file_name: louisa_thesis_draft__240904b.docx file_size: 43338677 relation: source_file file_date_updated: 2024-09-27T10:34:34Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - relation: software url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks record: - id: '11448' relation: part_of_dissertation status: public status: public supervisor: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 title: Fitness landscapes of orthologous green fluorescent proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository OA_type: green _id: '21692' abstract: - lang: eng text: Scintillation, the process of converting high-energy radiation to detectable visible light, is pivotal in advanced technologies spanning from medical diagnostics to fundamental scientific research. Despite significant advancements toward faster and more efficient scintillators, there remains a fundamental limit arising from the intrinsic properties of scintillating materials. The scintillation process culminates in spontaneous emission of visible light, which is restricted in rate by the oscillator strength of individual emission centers. Here, we observe a novel collective emission phenomenon under X-ray excitation, breaking this limit and accelerating the emission. Our observation reveals that strong interactions between simultaneously excited coupled perovskite quantum dots can create collective radioluminescence. This effect is characterized by a spectral shift and an enhanced rate of emission, with an average lifetime of 230 ps, 14 times faster than their room temperature spontaneous emission. It has been established that such quantum dots exhibit superfluorescence under UV excitation. However, X-ray superfluorescence is inherently different, as each high-energy photon creates multiple synchronized excitation events, triggered by a photoelectron and resulting in even faster emission rates, a larger spectral shift, and a broader spectrum. This observation is consistent with a quantum-optical analysis explaining both the UV-driven and X-ray-driven effects. We use a Hanbury-Brown-Twiss g^(2) (τ) setup to analyze the temperature-dependent temporal response of these scintillators. Collective radioluminescence breaks the limit of scintillation lifetime based on spontaneous emission and could dramatically improve time-of-flight detector performance, introducing quantum enhancements to scintillation science. article_number: '2412.21101' article_processing_charge: No arxiv: 1 author: - first_name: Shaul full_name: Katznelson, Shaul last_name: Katznelson - first_name: Shai full_name: Levy, Shai last_name: Levy - first_name: Alexey full_name: Gorlach, Alexey last_name: Gorlach - first_name: Nathan full_name: Regev, Nathan last_name: Regev - first_name: Michael full_name: Birk, Michael last_name: Birk - first_name: Chen full_name: Mechel, Chen last_name: Mechel - first_name: Offek full_name: Tziperman, Offek last_name: Tziperman - first_name: Roman full_name: Schuetz, Roman last_name: Schuetz - first_name: Rotem full_name: Strassberg, Rotem last_name: Strassberg - first_name: Georgy full_name: Dosovitsky, Georgy last_name: Dosovitsky - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yehonadav full_name: Bekenstein, Yehonadav last_name: Bekenstein - first_name: Ido full_name: Kaminer, Ido last_name: Kaminer citation: ama: Katznelson S, Levy S, Gorlach A, et al. Superfluorescent scintillation from coupled perovskite quantum dots. arXiv. doi:10.48550/arXiv.2412.21101 apa: Katznelson, S., Levy, S., Gorlach, A., Regev, N., Birk, M., Mechel, C., … Kaminer, I. (n.d.). Superfluorescent scintillation from coupled perovskite quantum dots. arXiv. https://doi.org/10.48550/arXiv.2412.21101 chicago: Katznelson, Shaul, Shai Levy, Alexey Gorlach, Nathan Regev, Michael Birk, Chen Mechel, Offek Tziperman, et al. “Superfluorescent Scintillation from Coupled Perovskite Quantum Dots.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.21101. ieee: S. Katznelson et al., “Superfluorescent scintillation from coupled perovskite quantum dots,” arXiv. . ista: Katznelson S, Levy S, Gorlach A, Regev N, Birk M, Mechel C, Tziperman O, Schuetz R, Strassberg R, Dosovitsky G, Roques-Carmes C, Bekenstein Y, Kaminer I. Superfluorescent scintillation from coupled perovskite quantum dots. arXiv, 2412.21101. mla: Katznelson, Shaul, et al. “Superfluorescent Scintillation from Coupled Perovskite Quantum Dots.” ArXiv, 2412.21101, doi:10.48550/arXiv.2412.21101. short: S. Katznelson, S. Levy, A. Gorlach, N. Regev, M. Birk, C. Mechel, O. Tziperman, R. Schuetz, R. Strassberg, G. Dosovitsky, C. Roques-Carmes, Y. Bekenstein, I. Kaminer, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-30T00:00:00Z date_updated: 2026-04-13T09:48:01Z day: '30' doi: 10.48550/arXiv.2412.21101 extern: '1' external_id: arxiv: - '2412.21101' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2412.21101' month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Superfluorescent scintillation from coupled perovskite quantum dots type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21686' abstract: - lang: eng text: Scintillation describes the conversion of high-energy particles into light in transparent media and finds diverse applications such as high-energy particle detection and industrial and medical imaging. This process operates on multiple timescales, with the final radiative step consisting of spontaneous emission, which can be modeled within the framework of quasi-equilibrium fluctuational electrodynamics. Scintillation can therefore be controlled and enhanced via nanophotonic effects, which has been proposed and experimentally demonstrated. Such designs have thus far obeyed Lorentz reciprocity, meaning there is a direct equivalence between scintillation emission and absorption by the scintillator. However, scintillators that do not obey Lorentz reciprocity have not been explored, even though they represent a novel platform for probing emission which is both nonequilibrium and nonreciprocal in nature. In this work, we propose to harness nonreciprocity to achieve directional control of scintillation emission, granting an additional degree of control over scintillation. Such directionality of light output is important in improving collection efficiencies along the directions where detectors are located. We present the design of a nonreciprocal scintillator using a one-dimensional magnetophotonic crystal in the Voigt configuration. Our work demonstrates the potential of controlling nonequilibrium emission such as scintillation by breaking reciprocity and expands the space of nanophotonic design for achieving such control. article_number: '2409.17002' article_processing_charge: No arxiv: 1 author: - first_name: Olivia Y. full_name: Long, Olivia Y. last_name: Long - first_name: Simo full_name: Pajovic, Simo last_name: Pajovic - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yoichiro full_name: Tsurimaki, Yoichiro last_name: Tsurimaki - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić - first_name: Svetlana V. full_name: Boriskina, Svetlana V. last_name: Boriskina - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Long OY, Pajovic S, Roques-Carmes C, et al. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv. doi:10.48550/arXiv.2409.17002 apa: Long, O. Y., Pajovic, S., Roques-Carmes, C., Tsurimaki, Y., Rivera, N., Soljačić, M., … Fan, S. (n.d.). Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv. https://doi.org/10.48550/arXiv.2409.17002 chicago: Long, Olivia Y., Simo Pajovic, Charles Roques-Carmes, Yoichiro Tsurimaki, Nicholas Rivera, Marin Soljačić, Svetlana V. Boriskina, and Shanhui Fan. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.17002. ieee: O. Y. Long et al., “Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals,” arXiv. . ista: Long OY, Pajovic S, Roques-Carmes C, Tsurimaki Y, Rivera N, Soljačić M, Boriskina SV, Fan S. Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals. arXiv, 2409.17002. mla: Long, Olivia Y., et al. “Nonreciprocal Scintillation Using One-Dimensional Magneto-Optical Photonic Crystals.” ArXiv, 2409.17002, doi:10.48550/arXiv.2409.17002. short: O.Y. Long, S. Pajovic, C. Roques-Carmes, Y. Tsurimaki, N. Rivera, M. Soljačić, S.V. Boriskina, S. Fan, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-09-25T00:00:00Z date_updated: 2026-04-13T10:48:09Z day: '25' doi: 10.48550/arXiv.2409.17002 extern: '1' external_id: arxiv: - '2409.17002' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.17002 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Nonreciprocal scintillation using one-dimensional magneto-optical photonic crystals type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21685' abstract: - lang: eng text: Nonlinear optics has become the workhorse for countless applications in classical and quantum optics, from optical bistability to single photon pair generation. However, the intrinsic weakness of optical nonlinearity has meant that large input powers and weak output powers are often a necessity in nonlinear frequency conversion. Here, motivated by recent advances in using non-Hermitian photonics and gain/loss engineering to enable non-reciprocal light transport, we explore how the interplay between non-Hermiticity and optical nonlinearity leads to a fundamentally new regime of nonlinear frequency conversion. We show how non-Hermitian coupling between discrete frequency modes can result in non-reciprocal flow of energy in the frequency dimension, closely resembling the non-Hermitian skin effect (NHSE). Applying our theory to a multimode nonlinear cavity supporting cascaded nonlinear processes, we create an asymmetric infrared (IR) comb that features a ``skin'' frequency mode populated with efficiency exceeding 85\%. Furthermore, we demonstrate how three-wave mixing processes in the non-reciprocal infrared comb we generate enables terahertz (THz) generation exceeding the Manley-Rowe limit. We then show how the non-reciprocal frequency conversion is robust against cavity defects and disorder that cause random fluctuations in the dissipation rate for different modes. Moreover, in certain regimes, the nonlinear, non-Hermitian system supports stable limit cycles that can enable multimode pulsing with picosecond pulse widths and GHz repetition rates. Finally, we explore how the system can be applied to generate simultaneous IR and THz frequency combs, potentially unlocking novel applications in spectroscopy and metrology. article_number: '2409.14299' article_processing_charge: No arxiv: 1 author: - first_name: Sahil full_name: Pontula, Sahil last_name: Pontula - first_name: Sachin full_name: Vaidya, Sachin last_name: Vaidya - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Shiekh Zia full_name: Uddin, Shiekh Zia last_name: Uddin - first_name: Marin full_name: Soljacic, Marin last_name: Soljacic - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin citation: ama: Pontula S, Vaidya S, Roques-Carmes C, Uddin SZ, Soljacic M, Salamin Y. Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv. doi:10.48550/arXiv.2409.14299 apa: Pontula, S., Vaidya, S., Roques-Carmes, C., Uddin, S. Z., Soljacic, M., & Salamin, Y. (n.d.). Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv. https://doi.org/10.48550/arXiv.2409.14299 chicago: Pontula, Sahil, Sachin Vaidya, Charles Roques-Carmes, Shiekh Zia Uddin, Marin Soljacic, and Yannick Salamin. “Non-Reciprocal Frequency Conversion in a Multimode Nonlinear System.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.14299. ieee: S. Pontula, S. Vaidya, C. Roques-Carmes, S. Z. Uddin, M. Soljacic, and Y. Salamin, “Non-reciprocal frequency conversion in a multimode nonlinear system,” arXiv. . ista: Pontula S, Vaidya S, Roques-Carmes C, Uddin SZ, Soljacic M, Salamin Y. Non-reciprocal frequency conversion in a multimode nonlinear system. arXiv, 2409.14299. mla: Pontula, Sahil, et al. “Non-Reciprocal Frequency Conversion in a Multimode Nonlinear System.” ArXiv, 2409.14299, doi:10.48550/arXiv.2409.14299. short: S. Pontula, S. Vaidya, C. Roques-Carmes, S.Z. Uddin, M. Soljacic, Y. Salamin, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-09-22T00:00:00Z date_updated: 2026-04-13T10:49:12Z day: '22' doi: 10.48550/arXiv.2409.14299 extern: '1' external_id: arxiv: - '2409.14299' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.14299 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Non-reciprocal frequency conversion in a multimode nonlinear system type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21689' abstract: - lang: eng text: Metasurfaces -- ultrathin structures composed of subwavelength optical elements -- have revolutionized light manipulation by enabling precise control over electromagnetic waves' amplitude, phase, polarization, and spectral properties. Concurrently, computational imaging leverages algorithms to reconstruct images from optically processed signals, overcoming limitations of traditional imaging systems. This review explores the synergistic integration of metaoptics and computational imaging, "computational metaoptics," which combines the physical wavefront shaping ability of metasurfaces with advanced computational algorithms to enhance imaging performance beyond conventional limits. We discuss how computational metaoptics addresses the inherent limitations of single-layer metasurfaces in achieving multifunctionality without compromising efficiency. By treating metasurfaces as physical preconditioners and co-designing them with reconstruction algorithms through end-to-end (inverse) design, it is possible to jointly optimize the optical hardware and computational software. This holistic approach allows for the automatic discovery of optimal metasurface designs and reconstruction methods that significantly improve imaging capabilities. Advanced applications enabled by computational metaoptics are highlighted, including phase imaging and quantum state measurement, which benefit from the metasurfaces' ability to manipulate complex light fields and the computational algorithms' capacity to reconstruct high-dimensional information. We also examine performance evaluation challenges, emphasizing the need for new metrics that account for the combined optical and computational nature of these systems. Finally, we identify new frontiers in computational metaoptics which point toward a future where computational metaoptics may play a central role in advancing imaging science and technology. article_number: '2411.09133' article_processing_charge: No arxiv: 1 author: - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Kai full_name: Wang, Kai last_name: Wang - first_name: Yuanmu full_name: Yang, Yuanmu last_name: Yang - first_name: Arka full_name: Majumdar, Arka last_name: Majumdar - first_name: Zin full_name: Lin, Zin last_name: Lin citation: ama: Roques-Carmes C, Wang K, Yang Y, Majumdar A, Lin Z. Computational metaoptics for imaging. arXiv. doi:10.48550/arXiv.2411.09133 apa: Roques-Carmes, C., Wang, K., Yang, Y., Majumdar, A., & Lin, Z. (n.d.). Computational metaoptics for imaging. arXiv. https://doi.org/10.48550/arXiv.2411.09133 chicago: Roques-Carmes, Charles, Kai Wang, Yuanmu Yang, Arka Majumdar, and Zin Lin. “Computational Metaoptics for Imaging.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2411.09133. ieee: C. Roques-Carmes, K. Wang, Y. Yang, A. Majumdar, and Z. Lin, “Computational metaoptics for imaging,” arXiv. . ista: Roques-Carmes C, Wang K, Yang Y, Majumdar A, Lin Z. Computational metaoptics for imaging. arXiv, 2411.09133. mla: Roques-Carmes, Charles, et al. “Computational Metaoptics for Imaging.” ArXiv, 2411.09133, doi:10.48550/arXiv.2411.09133. short: C. Roques-Carmes, K. Wang, Y. Yang, A. Majumdar, Z. Lin, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-11-14T00:00:00Z date_updated: 2026-04-13T09:53:49Z day: '14' doi: 10.48550/arXiv.2411.09133 extern: '1' external_id: arxiv: - '2411.09133' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2411.09133 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Computational metaoptics for imaging type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21690' abstract: - lang: eng text: Many quantum systems exhibit high sensitivity to their initial conditions, where microscopic quantum fluctuations can significantly influence macroscopic observables. Understanding how quantum states may influence the behavior of nonlinear dynamic systems may open new avenues in controlling light-matter interactions. To explore this issue, we analyze the sensitivity of a fundamental quantum optical process - parametric oscillation - to quantum initializations. Focusing on optical parametric oscillators (OPOs), we demonstrate that the quantum statistics of arbitrary initial states are imprinted in the early-stage dynamics and can persist in the steady-state probabilities. We derive the "quantum sensitivity" of parametric oscillators, linking the initial quantum state to the system's steady-state outcomes, highlighting how losses and parametric gain govern the system's quantum sensitivity. Moreover, we show that these findings extend beyond OPOs to a broader class of nonlinear systems, including Josephson junction based superconducting circuits. Our work opens the way to a new class of experiments that can test the sensitivity of macroscopic systems to quantum initial conditions and offers a pathway for controlling systems with quantum degrees of freedom. article_number: :2412.02887 article_processing_charge: No arxiv: 1 author: - first_name: Alex full_name: Gu, Alex last_name: Gu - first_name: Jamison full_name: Sloan, Jamison last_name: Sloan - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Seou full_name: Choi, Seou last_name: Choi - first_name: Eric I. full_name: Rosenthal, Eric I. last_name: Rosenthal - first_name: Michael full_name: Horodynski, Michael last_name: Horodynski - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Jelena full_name: Vučković, Jelena last_name: Vučković - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić citation: ama: Gu A, Sloan J, Roques-Carmes C, et al. Quantum sensitivity of parametric oscillators. arXiv. doi:10.48550/arXiv.2412.02887 apa: Gu, A., Sloan, J., Roques-Carmes, C., Choi, S., Rosenthal, E. I., Horodynski, M., … Soljačić, M. (n.d.). Quantum sensitivity of parametric oscillators. arXiv. https://doi.org/10.48550/arXiv.2412.02887 chicago: Gu, Alex, Jamison Sloan, Charles Roques-Carmes, Seou Choi, Eric I. Rosenthal, Michael Horodynski, Yannick Salamin, Jelena Vučković, and Marin Soljačić. “Quantum Sensitivity of Parametric Oscillators.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.02887. ieee: A. Gu et al., “Quantum sensitivity of parametric oscillators,” arXiv. . ista: Gu A, Sloan J, Roques-Carmes C, Choi S, Rosenthal EI, Horodynski M, Salamin Y, Vučković J, Soljačić M. Quantum sensitivity of parametric oscillators. arXiv, :2412.02887. mla: Gu, Alex, et al. “Quantum Sensitivity of Parametric Oscillators.” ArXiv, :2412.02887, doi:10.48550/arXiv.2412.02887. short: A. Gu, J. Sloan, C. Roques-Carmes, S. Choi, E.I. Rosenthal, M. Horodynski, Y. Salamin, J. Vučković, M. Soljačić, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-03T00:00:00Z date_updated: 2026-04-13T09:52:34Z day: '03' doi: 10.48550/arXiv.2412.02887 extern: '1' external_id: arxiv: - '2412.02887' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.02887 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Quantum sensitivity of parametric oscillators type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21691' 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. article_number: '2412.15068' article_processing_charge: No arxiv: 1 author: - first_name: Trung Kiên full_name: Lê, Trung Kiên last_name: Lê - first_name: Daniil M. full_name: Lukin, Daniil M. last_name: Lukin - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Eran full_name: Lustig, Eran last_name: Lustig - first_name: Melissa A. full_name: Guidry, Melissa A. last_name: Guidry - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan - first_name: Jelena full_name: Vučković, Jelena last_name: Vučković citation: ama: Lê TK, Lukin DM, Roques-Carmes C, et al. Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir. arXiv. doi:10.48550/arXiv.2412.15068 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. arXiv. https://doi.org/10.48550/arXiv.2412.15068 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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.15068. ieee: T. K. Lê et al., “Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir,” arXiv. . 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. mla: Lê, Trung Kiên, et al. “Cavity Quantum Electrodynamics in Finite-Bandwidth Squeezed Reservoir.” ArXiv, 2412.15068, doi:10.48550/arXiv.2412.15068. short: T.K. Lê, D.M. Lukin, C. Roques-Carmes, A. Karnieli, E. Lustig, M.A. Guidry, S. Fan, J. Vučković, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-12-19T00:00:00Z date_updated: 2026-04-13T09:50:09Z day: '19' doi: 10.48550/arXiv.2412.15068 extern: '1' external_id: arxiv: - '2412.15068' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.15068 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Cavity quantum electrodynamics in finite-bandwidth squeezed reservoir type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21684' 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. article_number: '2406.15058' article_processing_charge: No arxiv: 1 author: - first_name: Avner full_name: Shultzman, Avner last_name: Shultzman - first_name: Roman full_name: Schütz, Roman last_name: Schütz - first_name: Yaniv full_name: Kurman, Yaniv last_name: Kurman - first_name: Neta full_name: Lahav, Neta last_name: Lahav - first_name: George full_name: Dosovitskiy, George last_name: Dosovitskiy - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yehonadav full_name: Bekenstein, Yehonadav last_name: Bekenstein - first_name: Georgios full_name: Konstantinou, Georgios last_name: Konstantinou - first_name: Riccardo full_name: Latella, Riccardo last_name: Latella - first_name: Lei full_name: Zhang, Lei last_name: Zhang - first_name: Francis Loignon-Houle full_name: Francis Loignon-Houle, Francis Loignon-Houle last_name: Francis Loignon-Houle - first_name: Antonio J. full_name: Gonzalez, Antonio J. last_name: Gonzalez - first_name: José María full_name: Benlloch, José María last_name: Benlloch - first_name: Ido full_name: Kaminer, Ido last_name: Kaminer - first_name: Paul full_name: Lecoq, Paul last_name: Lecoq citation: ama: Shultzman A, Schütz R, Kurman Y, et al. Towards a second generation of metascintillators using the Purcell effect. arXiv. doi:10.48550/arXiv.2406.15058 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. arXiv. https://doi.org/10.48550/arXiv.2406.15058 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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.15058. ieee: A. Shultzman et al., “Towards a second generation of metascintillators using the Purcell effect,” arXiv. . 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. mla: Shultzman, Avner, et al. “Towards a Second Generation of Metascintillators Using the Purcell Effect.” ArXiv, 2406.15058, doi:10.48550/arXiv.2406.15058. 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.). date_created: 2026-04-09T09:10:41Z date_published: 2024-06-21T00:00:00Z date_updated: 2026-04-13T10:50:23Z day: '21' doi: 10.48550/arXiv.2406.15058 extern: '1' external_id: arxiv: - '2406.15058' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2406.15058 month: '06' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Towards a second generation of metascintillators using the Purcell effect type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21680' 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. article_number: '2405.05201' article_processing_charge: No arxiv: 1 author: - first_name: Sahil full_name: Pontula, Sahil last_name: Pontula - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Marin full_name: Soljacic, Marin last_name: Soljacic citation: ama: Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing through cascaded nonlinear optical processes. arXiv. doi:10.48550/arXiv.2405.05201 apa: Pontula, S., Salamin, Y., Roques-Carmes, C., & Soljacic, M. (n.d.). Multimode amplitude squeezing through cascaded nonlinear optical processes. arXiv. https://doi.org/10.48550/arXiv.2405.05201 chicago: Pontula, Sahil, Yannick Salamin, Charles Roques-Carmes, and Marin Soljacic. “Multimode Amplitude Squeezing through Cascaded Nonlinear Optical Processes.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.05201. ieee: S. Pontula, Y. Salamin, C. Roques-Carmes, and M. Soljacic, “Multimode amplitude squeezing through cascaded nonlinear optical processes,” arXiv. . ista: Pontula S, Salamin Y, Roques-Carmes C, Soljacic M. Multimode amplitude squeezing through cascaded nonlinear optical processes. arXiv, 2405.05201. mla: Pontula, Sahil, et al. “Multimode Amplitude Squeezing through Cascaded Nonlinear Optical Processes.” ArXiv, 2405.05201, doi:10.48550/arXiv.2405.05201. short: S. Pontula, Y. Salamin, C. Roques-Carmes, M. Soljacic, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-05-08T00:00:00Z date_updated: 2026-04-13T10:51:17Z day: '08' doi: 10.48550/arXiv.2405.05201 extern: '1' external_id: arxiv: - '2405.05201' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.05201 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Multimode amplitude squeezing through cascaded nonlinear optical processes type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21679' abstract: - lang: eng 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.' article_number: '2403.13071' article_processing_charge: No arxiv: 1 author: - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Nicholas full_name: Rivera, Nicholas last_name: Rivera - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. arXiv. doi:10.48550/arXiv.2403.13071 apa: Karnieli, A., Roques-Carmes, C., Rivera, N., & Fan, S. (n.d.). Strong coupling and single-photon nonlinearity in free-electron quantum optics. arXiv. https://doi.org/10.48550/arXiv.2403.13071 chicago: Karnieli, Aviv, Charles Roques-Carmes, Nicholas Rivera, and Shanhui Fan. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.13071. ieee: A. Karnieli, C. Roques-Carmes, N. Rivera, and S. Fan, “Strong coupling and single-photon nonlinearity in free-electron quantum optics,” arXiv. . ista: Karnieli A, Roques-Carmes C, Rivera N, Fan S. Strong coupling and single-photon nonlinearity in free-electron quantum optics. arXiv, 2403.13071. mla: Karnieli, Aviv, et al. “Strong Coupling and Single-Photon Nonlinearity in Free-Electron Quantum Optics.” ArXiv, 2403.13071, doi:10.48550/arXiv.2403.13071. short: A. Karnieli, C. Roques-Carmes, N. Rivera, S. Fan, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-03-19T00:00:00Z date_updated: 2026-04-13T10:57:33Z day: '19' doi: 10.48550/arXiv.2403.13071 extern: '1' external_id: arxiv: - '2403.13071' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2403.13071 month: '03' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Strong coupling and single-photon nonlinearity in free-electron quantum optics type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21681' abstract: - lang: eng 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. article_number: '2405.20241' article_processing_charge: No arxiv: 1 author: - first_name: Aviv full_name: Karnieli, Aviv last_name: Karnieli - first_name: Offek full_name: Tziperman, Offek last_name: Tziperman - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Shanhui full_name: Fan, Shanhui last_name: Fan citation: ama: Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv. doi:10.48550/arXiv.2405.20241 apa: Karnieli, A., Tziperman, O., Roques-Carmes, C., & Fan, S. (n.d.). Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv. https://doi.org/10.48550/arXiv.2405.20241 chicago: Karnieli, Aviv, Offek Tziperman, Charles Roques-Carmes, and Shanhui Fan. “Decoherence-Free Many-Body Hamiltonians in Nonlinear Waveguide Quantum Electrodynamics.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.20241. ieee: A. Karnieli, O. Tziperman, C. Roques-Carmes, and S. Fan, “Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics,” arXiv. . ista: Karnieli A, Tziperman O, Roques-Carmes C, Fan S. Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics. arXiv, 2405.20241. mla: Karnieli, Aviv, et al. “Decoherence-Free Many-Body Hamiltonians in Nonlinear Waveguide Quantum Electrodynamics.” ArXiv, 2405.20241, doi:10.48550/arXiv.2405.20241. short: A. Karnieli, O. Tziperman, C. Roques-Carmes, S. Fan, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-05-30T00:00:00Z date_updated: 2026-04-13T10:53:32Z day: '30' doi: 10.48550/arXiv.2405.20241 extern: '1' external_id: arxiv: - '2405.20241' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.20241 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Decoherence-free many-body Hamiltonians in nonlinear waveguide quantum electrodynamics type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '21683' 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. article_number: '2406.04000' article_processing_charge: No arxiv: 1 author: - first_name: Michael full_name: Horodynski, Michael last_name: Horodynski - first_name: Charles full_name: Roques-Carmes, Charles id: e2e68fc9-6505-11ef-a541-eb4e72cc3e82 last_name: Roques-Carmes - first_name: Yannick full_name: Salamin, Yannick last_name: Salamin - first_name: Seou full_name: Choi, Seou last_name: Choi - first_name: Jamison full_name: Sloan, Jamison last_name: Sloan - first_name: Di full_name: Luo, Di last_name: Luo - first_name: Marin full_name: Soljačić, Marin last_name: Soljačić citation: ama: Horodynski M, Roques-Carmes C, Salamin Y, et al. Stochastic logic in biased coupled photonic probabilistic bits. arXiv. doi:10.48550/arXiv.2406.04000 apa: Horodynski, M., Roques-Carmes, C., Salamin, Y., Choi, S., Sloan, J., Luo, D., & Soljačić, M. (n.d.). Stochastic logic in biased coupled photonic probabilistic bits. arXiv. https://doi.org/10.48550/arXiv.2406.04000 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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.04000. ieee: M. Horodynski et al., “Stochastic logic in biased coupled photonic probabilistic bits,” arXiv. . 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. mla: Horodynski, Michael, et al. “Stochastic Logic in Biased Coupled Photonic Probabilistic Bits.” ArXiv, 2406.04000, doi:10.48550/arXiv.2406.04000. short: M. Horodynski, C. Roques-Carmes, Y. Salamin, S. Choi, J. Sloan, D. Luo, M. Soljačić, ArXiv (n.d.). date_created: 2026-04-09T09:10:41Z date_published: 2024-06-06T00:00:00Z date_updated: 2026-04-13T10:52:25Z day: '06' doi: 10.48550/arXiv.2406.04000 extern: '1' external_id: arxiv: - '2406.04000' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2406.04000 month: '06' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted scopus_import: '1' status: public title: Stochastic logic in biased coupled photonic probabilistic bits type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '12875' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: LifeSc - _id: PreCl 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. " article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Thomas full_name: Krausgruber, Thomas last_name: Krausgruber - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Martin full_name: Schrammel, Martin id: f13e7cae-e8bd-11ed-841a-96dedf69f46d last_name: Schrammel - first_name: Natalie Y full_name: Özgen, 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 full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009 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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009 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.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009. ieee: G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024. 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. mla: Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009. 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. corr_author: '1' date_created: 2023-04-27T09:41:48Z date_published: 2024-01-17T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '17' ddc: - '570' department: - _id: SiHi - _id: RySh doi: 10.1016/j.neuron.2023.11.009 external_id: isi: - '001163937900001' pmid: - '38096816' file: - access_level: open_access checksum: 32b3788f7085cf44a84108d8faaff3ce content_type: application/pdf creator: dernst date_created: 2024-02-06T13:56:15Z date_updated: 2024-02-06T13:56:15Z file_id: '14944' file_name: 2024_Neuron_Cheung.pdf file_size: 5942467 relation: main_file success: 1 file_date_updated: 2024-02-06T13:56:15Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 230-246.e11 pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-pedigree-of-brain-cells/ scopus_import: '1' status: public title: Multipotent progenitors instruct ontogeny of the superior colliculus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2024' ... --- _id: '14683' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio - _id: PreCl 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. article_number: '102771' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2024;5(1). doi:10.1016/j.xpro.2023.102771 apa: Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2024). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771 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.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2023.102771. 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,” STAR Protocols, vol. 5, no. 1. Elsevier, 2024. 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.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2024, doi:10.1016/j.xpro.2023.102771. short: N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2023-12-13T11:48:05Z date_published: 2024-03-15T00:00:00Z date_updated: 2025-04-15T08:23:06Z day: '15' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2023.102771 ec_funded: 1 external_id: pmid: - '38070137' file: - access_level: open_access checksum: 3f0ee62e04bf5a44b45b035662826e95 content_type: application/pdf creator: dernst date_created: 2024-07-16T11:50:03Z date_updated: 2024-07-16T11:50:03Z file_id: '17260' file_name: 2024_STARProtoc_Amberg.pdf file_size: 8871807 relation: main_file success: 1 file_date_updated: 2024-07-16T11:50:03Z has_accepted_license: '1' intvolume: ' 5' issue: '1' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Neuroscience language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T01031 name: Role of Eed in neural stem cell lineage progression - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17187' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio - _id: PreCl 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' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103157 apa: Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157 chicago: Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157. ieee: G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. 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. mla: Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols, vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157. short: G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-06-30T22:01:04Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:11Z day: '20' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2024.103157 ec_funded: 1 external_id: pmid: - '38935508' file: - access_level: open_access checksum: d8a8cdba82a394e731aa699ace1ae433 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:12:40Z date_updated: 2025-01-09T12:12:40Z file_id: '18809' file_name: 2024_STARProtoc_Cheung.pdf file_size: 5186071 relation: main_file success: 1 file_date_updated: 2025-01-09T12:12:40Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17232' 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" acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: PreCl 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). article_number: '103168' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168 apa: Cheung, G. T., 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. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168 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.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168. 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,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. 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. mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168. short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-07-14T22:01:10Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '20' ddc: - '570' department: - _id: SiHi - _id: PreCl doi: 10.1016/j.xpro.2024.103168 external_id: pmid: - '38968076' file: - access_level: open_access checksum: 464f52ecc6ec92f509552823bb82bf79 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:16:53Z date_updated: 2025-01-09T12:16:53Z file_id: '18810' file_name: 2024_STARProtoc_Cheung2.pdf file_size: 6445556 relation: main_file success: 1 file_date_updated: 2025-01-09T12:16:53Z has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ...