--- OA_place: repository OA_type: free access _id: '21439' abstract: - lang: eng text: These files contain supplementary movies accompanying the PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” by Zuzana Dunajova (2026). The videos provide additional visual material supporting the experiments and results described in the thesis. acknowledged_ssus: - _id: Bio - _id: ScienComp article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova citation: ama: Dunajova Z. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” 2026. doi:10.15479/AT-ISTA-21439 apa: Dunajova, Z. (2026). Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21439 chicago: Dunajova, Zuzana. “Supplementary Movies to PhD Thesis ‘Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.’” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21439. ieee: Z. Dunajova, “Supplementary movies to PhD thesis ‘Geometry-driven self-organization of migrating cells and chiral filaments.’” Institute of Science and Technology Austria, 2026. ista: Dunajova Z. 2026. Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments”, Institute of Science and Technology Austria, 10.15479/AT-ISTA-21439. mla: Dunajova, Zuzana. Supplementary Movies to PhD Thesis “Geometry-Driven Self-Organization of Migrating Cells and Chiral Filaments.” Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21439. short: Z. Dunajova, (2026). contributor: - contributor_type: researcher first_name: Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - contributor_type: researcher first_name: Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' corr_author: '1' date_created: 2026-03-11T21:05:20Z date_published: 2026-03-12T00:00:00Z date_updated: 2026-03-18T14:11:36Z day: '12' ddc: - '570' department: - _id: GradSch - _id: EdHa doi: 10.15479/AT-ISTA-21439 file: - access_level: open_access checksum: 47809a9a31b748b16e21e92d11ddc87f content_type: application/zip creator: zdunajov date_created: 2026-03-11T20:41:28Z date_updated: 2026-03-11T20:41:28Z file_id: '21440' file_name: Supplementary_movies_Thesis_Dunajova.zip file_size: 154465214 relation: main_file success: 1 - access_level: open_access checksum: a64a174bc6abf0a5e77631e4fd121f1f content_type: text/plain creator: zdunajov date_created: 2026-03-11T20:52:39Z date_updated: 2026-03-11T20:52:39Z file_id: '21441' file_name: readme.txt file_size: 2289 relation: main_file success: 1 file_date_updated: 2026-03-11T20:52:39Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '03' oa: 1 oa_version: None project: - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public - id: '21427' relation: used_in_publication status: public - id: '21423' relation: used_in_publication status: public status: public title: Supplementary movies to PhD thesis “Geometry-driven self-organization of migrating cells and chiral filaments” 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21370' abstract: - lang: eng text: Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of ML for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences. article_number: '012501' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Giovanni full_name: Volpe, Giovanni last_name: Volpe - first_name: Carolina full_name: Wählby, Carolina last_name: Wählby - first_name: Lei full_name: Tian, Lei last_name: Tian - first_name: Michael full_name: Hecht, Michael last_name: Hecht - first_name: Artur full_name: Yakimovich, Artur last_name: Yakimovich - first_name: Kristina full_name: Monakhova, Kristina last_name: Monakhova - first_name: Laura full_name: Waller, Laura last_name: Waller - first_name: Ivo F. full_name: Sbalzarini, Ivo F. last_name: Sbalzarini - first_name: Christopher A. full_name: Metzler, Christopher A. last_name: Metzler - first_name: Mingyang full_name: Xie, Mingyang last_name: Xie - first_name: Kevin full_name: Zhang, Kevin last_name: Zhang - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Halina full_name: Rubinsztein-Dunlop, Halina last_name: Rubinsztein-Dunlop - first_name: Daniel full_name: Brunner, Daniel last_name: Brunner - first_name: Bijie full_name: Bai, Bijie last_name: Bai - first_name: Aydogan full_name: Ozcan, Aydogan last_name: Ozcan - first_name: Daniel full_name: Midtvedt, Daniel last_name: Midtvedt - first_name: Hao full_name: Wang, Hao last_name: Wang - first_name: Tongyu full_name: Li, Tongyu last_name: Li - first_name: Nataša full_name: Sladoje, Nataša last_name: Sladoje - first_name: Joakim full_name: Lindblad, Joakim last_name: Lindblad - first_name: Jason T. full_name: Smith, Jason T. last_name: Smith - first_name: Marien full_name: Ochoa, Marien last_name: Ochoa - first_name: Margarida full_name: Barroso, Margarida last_name: Barroso - first_name: Xavier full_name: Intes, Xavier last_name: Intes - first_name: Tong full_name: Qiu, Tong last_name: Qiu - first_name: Li Yu full_name: Yu, Li Yu last_name: Yu - first_name: Sixian full_name: You, Sixian last_name: You - first_name: Yongtao full_name: Liu, Yongtao last_name: Liu - first_name: Maxim A. full_name: Ziatdinov, Maxim A. last_name: Ziatdinov - first_name: Sergei V. full_name: Kalinin, Sergei V. last_name: Kalinin - first_name: Arlo full_name: Sheridan, Arlo last_name: Sheridan - first_name: Uri full_name: Manor, Uri last_name: Manor - first_name: Elias full_name: Nehme, Elias last_name: Nehme - first_name: Ofri full_name: Goldenberg, Ofri last_name: Goldenberg - first_name: Yoav full_name: Shechtman, Yoav last_name: Shechtman - first_name: Henrik K. full_name: Moberg, Henrik K. last_name: Moberg - first_name: Christoph full_name: Langhammer, Christoph last_name: Langhammer - first_name: Barbora full_name: Špačková, Barbora last_name: Špačková - first_name: Saga full_name: Helgadottir, Saga last_name: Helgadottir - first_name: Benjamin full_name: Midtvedt, Benjamin last_name: Midtvedt - first_name: Aykut full_name: Argun, Aykut last_name: Argun - first_name: Tobias full_name: Thalheim, Tobias last_name: Thalheim - first_name: Frank full_name: Cichos, Frank last_name: Cichos - first_name: Stefano full_name: Bo, Stefano last_name: Bo - first_name: Lars full_name: Hubatsch, Lars last_name: Hubatsch - first_name: Jesus full_name: Pineda, Jesus last_name: Pineda - first_name: Carlo full_name: Manzo, Carlo last_name: Manzo - first_name: Harshith full_name: Bachimanchi, Harshith last_name: Bachimanchi - first_name: Erik full_name: Selander, Erik last_name: Selander - first_name: Antoni full_name: Homs-Corbera, Antoni last_name: Homs-Corbera - first_name: Martin full_name: Fränzl, Martin last_name: Fränzl - first_name: Kevin full_name: De Haan, Kevin last_name: De Haan - first_name: Yair full_name: Rivenson, Yair last_name: Rivenson - first_name: Zofia full_name: Korczak, Zofia last_name: Korczak - first_name: Caroline Beck full_name: Adiels, Caroline Beck last_name: Adiels - first_name: Mite full_name: Mijalkov, Mite last_name: Mijalkov - first_name: Dániel full_name: Veréb, Dániel last_name: Veréb - first_name: Yu Wei full_name: Chang, Yu Wei last_name: Chang - first_name: Joana B. full_name: Pereira, Joana B. last_name: Pereira - first_name: Damian full_name: Matuszewski, Damian last_name: Matuszewski - first_name: Gustaf full_name: Kylberg, Gustaf last_name: Kylberg - first_name: Ida Maria full_name: Sintorn, Ida Maria last_name: Sintorn - first_name: Juan C. full_name: Caicedo, Juan C. last_name: Caicedo - first_name: Beth A. full_name: Cimini, Beth A. last_name: Cimini - first_name: Muyinatu A. full_name: Lediju Bell, Muyinatu A. last_name: Lediju Bell - first_name: Bruno M. full_name: Saraiva, Bruno M. last_name: Saraiva - first_name: Guillaume full_name: Jacquemet, Guillaume last_name: Jacquemet - first_name: Ricardo full_name: Henriques, Ricardo last_name: Henriques - first_name: Wei full_name: Ouyang, Wei last_name: Ouyang - first_name: Trang full_name: Le, Trang last_name: Le - first_name: Estibaliz full_name: Gómez-De-Mariscal, Estibaliz last_name: Gómez-De-Mariscal - first_name: Daniel full_name: Sage, Daniel last_name: Sage - first_name: Arrate full_name: Muñoz-Barrutia, Arrate last_name: Muñoz-Barrutia - first_name: Ebba Josefson full_name: Lindqvist, Ebba Josefson last_name: Lindqvist - first_name: Johanna full_name: Bergman, Johanna last_name: Bergman citation: ama: 'Volpe G, Wählby C, Tian L, et al. Roadmap on deep learning for microscopy. Journal of Physics: Photonics. 2026;8(1). doi:10.1088/2515-7647/ae0fd1' apa: 'Volpe, G., Wählby, C., Tian, L., Hecht, M., Yakimovich, A., Monakhova, K., … Bergman, J. (2026). Roadmap on deep learning for microscopy. Journal of Physics: Photonics. IOP Publishing. https://doi.org/10.1088/2515-7647/ae0fd1' chicago: 'Volpe, Giovanni, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, et al. “Roadmap on Deep Learning for Microscopy.” Journal of Physics: Photonics. IOP Publishing, 2026. https://doi.org/10.1088/2515-7647/ae0fd1.' ieee: 'G. Volpe et al., “Roadmap on deep learning for microscopy,” Journal of Physics: Photonics, vol. 8, no. 1. IOP Publishing, 2026.' ista: 'Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton IC, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Li T, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, De Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Lediju Bell MA, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-De-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. 2026. Roadmap on deep learning for microscopy. Journal of Physics: Photonics. 8(1), 012501.' mla: 'Volpe, Giovanni, et al. “Roadmap on Deep Learning for Microscopy.” Journal of Physics: Photonics, vol. 8, no. 1, 012501, IOP Publishing, 2026, doi:10.1088/2515-7647/ae0fd1.' short: 'G. Volpe, C. Wählby, L. Tian, M. Hecht, A. Yakimovich, K. Monakhova, L. Waller, I.F. Sbalzarini, C.A. Metzler, M. Xie, K. Zhang, I.C. Lenton, H. Rubinsztein-Dunlop, D. Brunner, B. Bai, A. Ozcan, D. Midtvedt, H. Wang, T. Li, N. Sladoje, J. Lindblad, J.T. Smith, M. Ochoa, M. Barroso, X. Intes, T. Qiu, L.Y. Yu, S. You, Y. Liu, M.A. Ziatdinov, S.V. Kalinin, A. Sheridan, U. Manor, E. Nehme, O. Goldenberg, Y. Shechtman, H.K. Moberg, C. Langhammer, B. Špačková, S. Helgadottir, B. Midtvedt, A. Argun, T. Thalheim, F. Cichos, S. Bo, L. Hubatsch, J. Pineda, C. Manzo, H. Bachimanchi, E. Selander, A. Homs-Corbera, M. Fränzl, K. De Haan, Y. Rivenson, Z. Korczak, C.B. Adiels, M. Mijalkov, D. Veréb, Y.W. Chang, J.B. Pereira, D. Matuszewski, G. Kylberg, I.M. Sintorn, J.C. Caicedo, B.A. Cimini, M.A. Lediju Bell, B.M. Saraiva, G. Jacquemet, R. Henriques, W. Ouyang, T. Le, E. Gómez-De-Mariscal, D. Sage, A. Muñoz-Barrutia, E.J. Lindqvist, J. Bergman, Journal of Physics: Photonics 8 (2026).' date_created: 2026-03-01T23:01:39Z date_published: 2026-03-01T00:00:00Z date_updated: 2026-03-23T13:18:11Z day: '01' ddc: - '530' department: - _id: ScWa doi: 10.1088/2515-7647/ae0fd1 external_id: arxiv: - '2303.03793' file: - access_level: open_access checksum: 172720f1f0c5c9d06a282e52023a0030 content_type: application/pdf creator: dernst date_created: 2026-03-02T09:05:53Z date_updated: 2026-03-02T09:05:53Z file_id: '21375' file_name: 2026_JPhysPhotonics_Volpe.pdf file_size: 16789781 relation: main_file success: 1 file_date_updated: 2026-03-02T09:05:53Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version publication: 'Journal of Physics: Photonics' publication_identifier: eissn: - 2515-7647 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Roadmap on deep learning for microscopy 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: 8 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21470' abstract: - lang: eng text: Despite its pivotal role in optical manipulation, high capacity communications, and quantum information, a general measure of orbital angular momentum (OAM) in structured light remains elusive. In optical fields, where multiple vortices coexist, the local nature of vortex OAM and the absence of a common rotation axis make the total OAM of the field difficult to quantify. Here, we introduce the R index—a metric that captures the intrinsic OAM content of any structured optical field, from pure Laguerre–Gaussian modes to arbitrary multi vortex superpositions. Not only does this metric quantify the total OAM, it also assesses field purity, providing insight into the fidelity and robustness of the OAM generation. By unifying OAM characterization into a single figure of merit, the R index enables direct comparison across diverse beam profiles and facilitates the identification of optimal configurations for both foundational studies and applied technologies. acknowledgement: This research was funded in whole or in part by the Austrian Science Fund (FWF) [10.55776/F1004]. For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. article_number: '015071' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Monika full_name: Bahl, Monika last_name: Bahl - first_name: Georgios full_name: Koutentakis, Georgios id: d7b23d3a-9e21-11ec-b482-f76739596b95 last_name: Koutentakis - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 - first_name: Tom full_name: Jungnickel, Tom last_name: Jungnickel - first_name: Timo full_name: Gaßen, Timo last_name: Gaßen - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Oliver H. full_name: Heckl, Oliver H. last_name: Heckl citation: ama: 'Bahl M, Koutentakis G, Maslov M, et al. The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. Journal of Physics: Photonics. 2026;8(1). doi:10.1088/2515-7647/ae3506' apa: 'Bahl, M., Koutentakis, G., Maslov, M., Jungnickel, T., Gaßen, T., Lemeshko, M., & Heckl, O. H. (2026). The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. Journal of Physics: Photonics. IOP Publishing. https://doi.org/10.1088/2515-7647/ae3506' chicago: 'Bahl, Monika, Georgios Koutentakis, Mikhail Maslov, Tom Jungnickel, Timo Gaßen, Mikhail Lemeshko, and Oliver H. Heckl. “The R-Index: A Universal Metric for Evaluating OAM Content and Mode Purity in Optical Fields.” Journal of Physics: Photonics. IOP Publishing, 2026. https://doi.org/10.1088/2515-7647/ae3506.' ieee: 'M. Bahl et al., “The R-index: A universal metric for evaluating OAM content and mode purity in optical fields,” Journal of Physics: Photonics, vol. 8, no. 1. IOP Publishing, 2026.' ista: 'Bahl M, Koutentakis G, Maslov M, Jungnickel T, Gaßen T, Lemeshko M, Heckl OH. 2026. The R-index: A universal metric for evaluating OAM content and mode purity in optical fields. Journal of Physics: Photonics. 8(1), 015071.' mla: 'Bahl, Monika, et al. “The R-Index: A Universal Metric for Evaluating OAM Content and Mode Purity in Optical Fields.” Journal of Physics: Photonics, vol. 8, no. 1, 015071, IOP Publishing, 2026, doi:10.1088/2515-7647/ae3506.' short: 'M. Bahl, G. Koutentakis, M. Maslov, T. Jungnickel, T. Gaßen, M. Lemeshko, O.H. Heckl, Journal of Physics: Photonics 8 (2026).' corr_author: '1' date_created: 2026-03-22T23:04:32Z date_published: 2026-03-10T00:00:00Z date_updated: 2026-03-23T13:26:26Z day: '10' ddc: - '530' department: - _id: MiLe doi: 10.1088/2515-7647/ae3506 external_id: arxiv: - '2508.12973' file: - access_level: open_access checksum: 0ec8a2d3f9efa704203a41f068344974 content_type: application/pdf creator: dernst date_created: 2026-03-23T13:24:01Z date_updated: 2026-03-23T13:24:01Z file_id: '21476' file_name: 2026_JPhysPhotonics_Bahl.pdf file_size: 1150404 relation: main_file success: 1 file_date_updated: 2026-03-23T13:24:01Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3 grant_number: F100403 name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions publication: 'Journal of Physics: Photonics' publication_identifier: eissn: - 2515-7647 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'The R-index: A universal metric for evaluating OAM content and mode purity in optical fields' 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: 8 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21469' abstract: - lang: eng text: "Terahertz (THz) spectroscopy is a powerful probe of low-energy excitations in complex materials. Extending it into the nonlinear regime broadens its scope and can provide valuable insight into interactions among these modes. However, interpreting nonlinear spectra is challenging because resonant features in this case do not always reflect intrinsic material dynamics. Here, we study nonlinear THz-induced Kerr effect in a generic material LaAlO3. After detailed analysis of temporal oscillations of the Kerr signal, we identify an \U0001D438\U0001D454 Raman mode at 1.1 THz excited through a two-photon process, while two additional peaks (0.86 and 0.36 THz) arise from phase matching of the near-infrared probe beam with co- and counterpropagating THz pump fields, mediated by off-resonant electronic hyperpolarizability. These results demonstrate the crucial role of kinematic effects in shaping THz-induced Kerr response and establish a framework for interpreting nonlinear spectroscopies in complex materials." acknowledgement: Z. A. acknowledges support from the collaborative research project SFB Q-M&S funded by the Austrian Science Fund (FWF, Grant No. PR1050F8602). S. F. M. acknowledges support and funding from the Deutsche Forschungsgemeinschaft (DFG, Grant No. 469405347). article_number: '106901' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Chao full_name: Shen, Chao id: f84c083e-dc8d-11ea-abe3-aaf3d822a8bb last_name: Shen - first_name: Maximilian full_name: Frenzel, Maximilian last_name: Frenzel - first_name: Sebastian F. full_name: Maehrlein, Sebastian F. last_name: Maehrlein - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: Shen C, Frenzel M, Maehrlein SF, Alpichshev Z. Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. Physical Review Letters. 2026;136(10). doi:10.1103/1c5k-9z82 apa: Shen, C., Frenzel, M., Maehrlein, S. F., & Alpichshev, Z. (2026). Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. Physical Review Letters. American Physical Society. https://doi.org/10.1103/1c5k-9z82 chicago: Shen, Chao, Maximilian Frenzel, Sebastian F. Maehrlein, and Zhanybek Alpichshev. “Disentangling Electronic and Ionic Nonlinear Polarization Effects in Bulk THz Kerr Response.” Physical Review Letters. American Physical Society, 2026. https://doi.org/10.1103/1c5k-9z82. ieee: C. Shen, M. Frenzel, S. F. Maehrlein, and Z. Alpichshev, “Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response,” Physical Review Letters, vol. 136, no. 10. American Physical Society, 2026. ista: Shen C, Frenzel M, Maehrlein SF, Alpichshev Z. 2026. Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response. Physical Review Letters. 136(10), 106901. mla: Shen, Chao, et al. “Disentangling Electronic and Ionic Nonlinear Polarization Effects in Bulk THz Kerr Response.” Physical Review Letters, vol. 136, no. 10, 106901, American Physical Society, 2026, doi:10.1103/1c5k-9z82. short: C. Shen, M. Frenzel, S.F. Maehrlein, Z. Alpichshev, Physical Review Letters 136 (2026). corr_author: '1' date_created: 2026-03-22T23:04:31Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-03-23T13:11:09Z day: '13' ddc: - '530' department: - _id: ZhAl - _id: GradSch doi: 10.1103/1c5k-9z82 file: - access_level: open_access checksum: 712b05b4b0e0fbe9fd426a8c9d41ce20 content_type: application/pdf creator: dernst date_created: 2026-03-23T13:08:06Z date_updated: 2026-03-23T13:08:06Z file_id: '21475' file_name: 2026_PhysicalReviewLetters_Shen.pdf file_size: 1375532 relation: main_file success: 1 file_date_updated: 2026-03-23T13:08:06Z has_accepted_license: '1' intvolume: ' 136' issue: '10' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 34a97cc6-11ca-11ed-8bc3-9acbba792f33 grant_number: F8602 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Nonlinear THz spectroscopy of quantum critical materials' publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response 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: 136 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21472' abstract: - lang: eng text: We study the ground state energy of a gas of spin 1/2 fermions with repulsive short-range interactions. We derive an upper bound that agrees, at low density e, with the Huang–Yang conjecture. The latter captures the first three terms in an asymptotic low-density expansion, and in particular the Huang–Yang correction term of order e^7/3. Our trial state is constructed using an adaptation of the bosonic Bogoliubov theory to the Fermi system, where the correlation structure of fermionic particles is incorporated by quasi-bosonic Bogoliubov transformations. In the latter, it is important to consider a modified zero-energy scattering equation that takes into account the presence of the Fermi sea, in the spirit of the Bethe–Goldstone equation. acknowledgement: "We thank the referees for valuable remarks. This work was partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the TRR 352 – Project-ID 470903074. PTN was partially supported by the European Research Council via the ERC Consolidator Grant RAMBAS – Project-Nr. 10104424.\r\nOpen access publishing facilitated by Università degli Studi di Milano, as part of the Wiley - CRUI-CARE agreement." article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Emanuela L. full_name: Giacomelli, Emanuela L. last_name: Giacomelli - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Phan Thành full_name: Nam, Phan Thành last_name: Nam - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Giacomelli EL, Hainzl C, Nam PT, Seiringer R. The Huang–Yang formula for the low-density Fermi gas: Upper bound. Communications on Pure and Applied Mathematics. 2026. doi:10.1002/cpa.70040' apa: 'Giacomelli, E. L., Hainzl, C., Nam, P. T., & Seiringer, R. (2026). The Huang–Yang formula for the low-density Fermi gas: Upper bound. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.70040' chicago: 'Giacomelli, Emanuela L., Christian Hainzl, Phan Thành Nam, and Robert Seiringer. “The Huang–Yang Formula for the Low-Density Fermi Gas: Upper Bound.” Communications on Pure and Applied Mathematics. Wiley, 2026. https://doi.org/10.1002/cpa.70040.' ieee: 'E. L. Giacomelli, C. Hainzl, P. T. Nam, and R. Seiringer, “The Huang–Yang formula for the low-density Fermi gas: Upper bound,” Communications on Pure and Applied Mathematics. Wiley, 2026.' ista: 'Giacomelli EL, Hainzl C, Nam PT, Seiringer R. 2026. The Huang–Yang formula for the low-density Fermi gas: Upper bound. Communications on Pure and Applied Mathematics.' mla: 'Giacomelli, Emanuela L., et al. “The Huang–Yang Formula for the Low-Density Fermi Gas: Upper Bound.” Communications on Pure and Applied Mathematics, Wiley, 2026, doi:10.1002/cpa.70040.' short: E.L. Giacomelli, C. Hainzl, P.T. Nam, R. Seiringer, Communications on Pure and Applied Mathematics (2026). date_created: 2026-03-22T23:04:33Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-03-23T13:32:14Z day: '13' department: - _id: RoSe doi: 10.1002/cpa.70040 external_id: arxiv: - '2409.17914' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/cpa.70040 month: '03' oa: 1 oa_version: Published Version publication: Communications on Pure and Applied Mathematics publication_identifier: eissn: - 1097-0312 issn: - 0010-3640 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'The Huang–Yang formula for the low-density Fermi gas: Upper bound' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21473' abstract: - lang: eng text: Physical exercise acutely improves hippocampus-dependent memory. Whereas animal studies have offered cellular- and synaptic-level accounts of these effects, human neuroimaging studies show that exercise improves hippocampal-cortical connectivity at the macroscale level. However, the neurophysiological basis of exercise-induced effects on hippocampal-cortical circuits remains unknown. Experimental evidence supports the idea that hippocampal sharp wave-ripples (SWR) play a critical role in learning and memory. Coupling between SWRs in the hippocampus and neocortex may reflect modulations in inter-regional connectivity required by mnemonic processes. Here, we examine the hypothesis that exercise modulates hippocampal-cortical ripple dynamics in the human brain. We performed intracranial recordings in epilepsy patients undergoing pre-surgical evaluation, during awake resting state, before and after an exercise session. Exercise increased ripple rate in the hippocampus. Exercise also enhanced the coupling and phase-synchrony between cortical ripples in the limbic and the default mode (DM) cortical networks and hippocampal SWRs. Further, a higher heart rate during exercise, reflecting exercise intensity, was related to a subsequent increase in resting state ripples across specific cortical networks, including the DM network. These results offer the first direct evidence that a single exercise session elicits changes in ripple events, a well-established neurophysiological marker of mnemonic processing. The characterisation and anatomical distribution of the described modulation points to hippocampal ripples as a potential mechanism by which exercise elicits its reported short-term effects in cognition. acknowledgement: We acknowledge the generosity of the patients, who contributed time and effort to take part in this study. article_number: fcag041 article_processing_charge: Yes article_type: original author: - first_name: Araceli R. full_name: Cardenas, Araceli R. last_name: Cardenas - first_name: Juan F full_name: Ramirez Villegas, Juan F id: 44B06F76-F248-11E8-B48F-1D18A9856A87 last_name: Ramirez Villegas - first_name: Christopher K. full_name: Kovach, Christopher K. last_name: Kovach - first_name: Phillip E. full_name: Gander, Phillip E. last_name: Gander - first_name: Rachel C. full_name: Cole, Rachel C. last_name: Cole - first_name: Andrew J. full_name: Grossbach, Andrew J. last_name: Grossbach - first_name: Hiroto full_name: Kawasaki, Hiroto last_name: Kawasaki - first_name: Jeremy D.W. full_name: Greenlee, Jeremy D.W. last_name: Greenlee - first_name: Matthew A. full_name: Howard, Matthew A. last_name: Howard - first_name: Kirill V. full_name: Nourski, Kirill V. last_name: Nourski - first_name: Matthew I. full_name: Banks, Matthew I. last_name: Banks - first_name: Michelle W. full_name: Voss, Michelle W. last_name: Voss citation: ama: Cardenas AR, Ramirez Villegas JF, Kovach CK, et al. Exercise enhances hippocampal-cortical ripple interactions in the human brain. Brain Communications. 2026;8(2). doi:10.1093/braincomms/fcag041 apa: Cardenas, A. R., Ramirez Villegas, J. F., Kovach, C. K., Gander, P. E., Cole, R. C., Grossbach, A. J., … Voss, M. W. (2026). Exercise enhances hippocampal-cortical ripple interactions in the human brain. Brain Communications. Oxford University Press. https://doi.org/10.1093/braincomms/fcag041 chicago: Cardenas, Araceli R., Juan F Ramirez Villegas, Christopher K. Kovach, Phillip E. Gander, Rachel C. Cole, Andrew J. Grossbach, Hiroto Kawasaki, et al. “Exercise Enhances Hippocampal-Cortical Ripple Interactions in the Human Brain.” Brain Communications. Oxford University Press, 2026. https://doi.org/10.1093/braincomms/fcag041. ieee: A. R. Cardenas et al., “Exercise enhances hippocampal-cortical ripple interactions in the human brain,” Brain Communications, vol. 8, no. 2. Oxford University Press, 2026. ista: Cardenas AR, Ramirez Villegas JF, Kovach CK, Gander PE, Cole RC, Grossbach AJ, Kawasaki H, Greenlee JDW, Howard MA, Nourski KV, Banks MI, Voss MW. 2026. Exercise enhances hippocampal-cortical ripple interactions in the human brain. Brain Communications. 8(2), fcag041. mla: Cardenas, Araceli R., et al. “Exercise Enhances Hippocampal-Cortical Ripple Interactions in the Human Brain.” Brain Communications, vol. 8, no. 2, fcag041, Oxford University Press, 2026, doi:10.1093/braincomms/fcag041. short: A.R. Cardenas, J.F. Ramirez Villegas, C.K. Kovach, P.E. Gander, R.C. Cole, A.J. Grossbach, H. Kawasaki, J.D.W. Greenlee, M.A. Howard, K.V. Nourski, M.I. Banks, M.W. Voss, Brain Communications 8 (2026). corr_author: '1' date_created: 2026-03-22T23:04:34Z date_published: 2026-03-09T00:00:00Z date_updated: 2026-03-23T14:30:47Z day: '09' ddc: - '570' department: - _id: JoCs doi: 10.1093/braincomms/fcag041 file: - access_level: open_access checksum: b5b45c16defeaf88056fc3b939bd0350 content_type: application/pdf creator: dernst date_created: 2026-03-23T14:27:39Z date_updated: 2026-03-23T14:27:39Z file_id: '21478' file_name: 2026_BrainCommunications_Cardenas.pdf file_size: 33974419 relation: main_file success: 1 file_date_updated: 2026-03-23T14:27:39Z has_accepted_license: '1' intvolume: ' 8' issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Brain Communications publication_identifier: eissn: - 2632-1297 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Exercise enhances hippocampal-cortical ripple interactions in the human brain 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: 8 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21471' acknowledgement: We thank the Barton group at the Institute of Scienceand Technology Austria for many fruitful conversationsthat triggered the germination of the ideas and questions discussed here. N. H. Barton, P. Surendranadh, A. Pal,Z. Mérai, and two anonymous reviewers provided useful comments on the manuscript. article_number: e70175 article_processing_charge: No article_type: letter_note author: - first_name: Sofia Maria full_name: Backlund, Sofia Maria id: a19ed178-1337-11ed-9389-c30ab879a82a last_name: Backlund - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Rosina Matilde full_name: Soler Schaller, Rosina Matilde id: 9e668447-8c32-11ed-b0c7-8dc2d7b80803 last_name: Soler Schaller citation: ama: 'Backlund SM, Stankowski S, Soler Schaller RM. Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? American Journal of Botany. 2026;113(3). doi:10.1002/ajb2.70175' apa: 'Backlund, S. M., Stankowski, S., & Soler Schaller, R. M. (2026). Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? American Journal of Botany. Wiley. https://doi.org/10.1002/ajb2.70175' chicago: 'Backlund, Sofia Maria, Sean Stankowski, and Rosina Matilde Soler Schaller. “Seeds as Space-Time Travelers: How Does Evolution Balance the Joint Benefits and Trade-Offs of Dormancy and Dispersal?” American Journal of Botany. Wiley, 2026. https://doi.org/10.1002/ajb2.70175.' ieee: 'S. M. Backlund, S. Stankowski, and R. M. Soler Schaller, “Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal?,” American Journal of Botany, vol. 113, no. 3. Wiley, 2026.' ista: 'Backlund SM, Stankowski S, Soler Schaller RM. 2026. Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal? American Journal of Botany. 113(3), e70175.' mla: 'Backlund, Sofia Maria, et al. “Seeds as Space-Time Travelers: How Does Evolution Balance the Joint Benefits and Trade-Offs of Dormancy and Dispersal?” American Journal of Botany, vol. 113, no. 3, e70175, Wiley, 2026, doi:10.1002/ajb2.70175.' short: S.M. Backlund, S. Stankowski, R.M. Soler Schaller, American Journal of Botany 113 (2026). corr_author: '1' date_created: 2026-03-22T23:04:33Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-03-23T14:47:52Z day: '11' ddc: - '580' - '570' department: - _id: NiBa - _id: GradSch doi: 10.1002/ajb2.70175 external_id: pmid: - '41814642' file: - access_level: open_access checksum: 6116108a12c4a5cc91fc653d67885309 content_type: application/pdf creator: dernst date_created: 2026-03-23T14:01:44Z date_updated: 2026-03-23T14:01:44Z file_id: '21477' file_name: 2026_AmericanJourBotany_Backlund.pdf file_size: 495080 relation: main_file success: 1 file_date_updated: 2026-03-23T14:01:44Z has_accepted_license: '1' intvolume: ' 113' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: American Journal of Botany publication_identifier: eissn: - 1537-2197 issn: - 0002-9122 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal?' 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: 113 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: diamond PlanS_conform: '1' _id: '21481' abstract: - lang: eng text: 'The Hα emission line in galaxies is a powerful tracer of their recent star formation activity. With the advent of JWST, we are now able to routinely observe Hα in galaxies at high redshift (z ≳ 3) and thus measure their star formation rates (SFRs). However, using classical SFR(Hα) calibrations to derive the SFRs leads to biased results because high-redshift galaxies are commonly characterized by low metallicities and bursty star formation histories, affecting the conversion factor between the Hα luminosity (LHα) and the SFR. We developed a set of new SFR(Hα) calibrations that allowed us to predict the SFRs of Hα-emitters at z ≳ 3 with very little error. We used the SPHINX cosmological simulations to select a sample of star-forming galaxies representative of the Hα-emitter population observed with JWST. We then derived linear corrections to the classical SFR(Hα) calibrations that took variations in the physical properties (e.g., stellar metallicities) among individual galaxies into account. We obtained two new SFR(Hα) calibrations that compared to the classical calibrations reduce the root mean squared error (RMSE) in the predicted SFRs by ΔRMSE ≈ 0.04 dex and ΔRMSE ≈ 0.06 dex, respectively. Using the recent JWST NIRCam/grism observations of Hα-emitters at z ∼ 6, we show that the new calibrations affect the high-redshift galaxy population statistics: (i) the estimated cosmic SFR density decreases by ΔρSFR ≈ 12%, and (ii) the observed slope of the star formation main sequence increases by Δ∂logSFR/∂logM★ = 0.08 ± 0.02.' acknowledgement: "We thank the anonymous referee for the insightful comments that helped improve the manuscript. We also thank Thibault Garel, Pascal Oesch, Irene Shivaei, Charlotte Simmonds, Andrew Hopkins, Daniel Schaerer, and Rashmi Gottumukkala for useful comments and productive discussions. We gratefully acknowledge support from the CBPsmn (PSMN, Pôle Scientifique de Modélisation Numérique) of the ENS de Lyon for the computing resources.\r\nFunded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. This work made extensive use of several open-source software packages, and we gratefully acknowledge the efforts of their authors: numpy (Harris et al. 2020), astropy (Astropy Collaboration 2022), matplotlib (Hunter 2007), ipython (Perez & Granger 2007), and scikit-learn (Pedregosa et al. 2011)." article_number: A184 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Ivan full_name: Kramarenko, Ivan id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4 last_name: Kramarenko orcid: 0000-0001-5346-6048 - first_name: J. full_name: Rosdahl, J. last_name: Rosdahl - first_name: J. full_name: Blaizot, J. last_name: Blaizot - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: H. full_name: Katz, H. last_name: Katz - first_name: Claudia full_name: Di Cesare, Claudia id: 2d002343-372f-11ef-98ec-a164d20427cb last_name: Di Cesare citation: ama: Kramarenko I, Rosdahl J, Blaizot J, Matthee JJ, Katz H, Di Cesare C. H α as a tracer of star formation in the SPHINX cosmological simulations. Astronomy & Astrophysics. 2026;707. doi:10.1051/0004-6361/202557114 apa: Kramarenko, I., Rosdahl, J., Blaizot, J., Matthee, J. J., Katz, H., & Di Cesare, C. (2026). H α as a tracer of star formation in the SPHINX cosmological simulations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202557114 chicago: Kramarenko, Ivan, J. Rosdahl, J. Blaizot, Jorryt J Matthee, H. Katz, and Claudia Di Cesare. “H α as a Tracer of Star Formation in the SPHINX Cosmological Simulations.” Astronomy & Astrophysics. EDP Sciences, 2026. https://doi.org/10.1051/0004-6361/202557114. ieee: I. Kramarenko, J. Rosdahl, J. Blaizot, J. J. Matthee, H. Katz, and C. Di Cesare, “H α as a tracer of star formation in the SPHINX cosmological simulations,” Astronomy & Astrophysics, vol. 707. EDP Sciences, 2026. ista: Kramarenko I, Rosdahl J, Blaizot J, Matthee JJ, Katz H, Di Cesare C. 2026. H α as a tracer of star formation in the SPHINX cosmological simulations. Astronomy & Astrophysics. 707, A184. mla: Kramarenko, Ivan, et al. “H α as a Tracer of Star Formation in the SPHINX Cosmological Simulations.” Astronomy & Astrophysics, vol. 707, A184, EDP Sciences, 2026, doi:10.1051/0004-6361/202557114. short: I. Kramarenko, J. Rosdahl, J. Blaizot, J.J. Matthee, H. Katz, C. Di Cesare, Astronomy & Astrophysics 707 (2026). corr_author: '1' date_created: 2026-03-23T14:58:03Z date_published: 2026-03-05T00:00:00Z date_updated: 2026-03-23T15:46:31Z day: '05' ddc: - '520' department: - _id: JoMa doi: 10.1051/0004-6361/202557114 external_id: arxiv: - '2509.05403' file: - access_level: open_access checksum: 7429076b381dd498084f40ffd199e714 content_type: application/pdf creator: dernst date_created: 2026-03-23T15:44:09Z date_updated: 2026-03-23T15:44:09Z file_id: '21492' file_name: 2026_AstronomyAstrophysics_Kramarenko.pdf file_size: 904565 relation: main_file success: 1 file_date_updated: 2026-03-23T15:44:09Z has_accepted_license: '1' intvolume: ' 707' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: bd9b2118-d553-11ed-ba76-db24564edfea grant_number: '101076224' name: Young galaxies as tracers and agents of cosmic reionization publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' status: public title: H α as a tracer of star formation in the SPHINX cosmological simulations 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: 707 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21480' abstract: - lang: eng text: We present and test a protocol to learn the matrix-product operator (MPO) representation of an experimentally prepared quantum state. The protocol takes as input classical shadows corresponding to local randomized measurements, and outputs the tensors of an MPO maximizing a suitably defined fidelity with the experimental state. The tensor optimization is carried out sequentially, similarly to the well-known density matrix renormalization group algorithm. Our approach is provably efficient under certain technical conditions expected to be met in short-range correlated states and in typical noisy experimental settings. Under the same conditions, we also provide an efficient scheme to estimate fidelities between the learned and the experimental states. We experimentally demonstrate our protocol by learning entangled quantum states of up to N = 96 qubits in a superconducting quantum processor. Our method upgrades classical shadows to large-scale quantum computation and simulation experiments. acknowledgement: "We acknowledge insightful discussions with Antoine Browaeys, Mari Carmen Bañuls, Soonwon Choi, Thierry Lahaye, Daniel Stilck-França, Georgios Styliaris, and Xavier Waintal. The experimental data have been collected using the Qiskit library [103], and have been postprocessed using the RandomMeas [104] and ITensor [105] libraries. The work of M. V. and B. V. was funded by the French National Research Agency via the JCJC project QRand (No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (No. ANR-22-\r\nPETQ-0007), QUBITAF (No. ANR-22-PETQ-0004), and HQI (No. ANR-22-PNCQ-0002). We acknowledge the use of IBM Quantum Credits for this work. M. L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868. The work of C. L. was funded by the French National Research Agency via the PRC project ESQuisses (No. ANR-20-CE47-0014-01). J. I. C.\r\nacknowledges funding from the Federal Ministry of Education and Research Germany (BMBF) via the project FermiQP (No. 13N15889). Work at MPQ is part of the Munich Quantum Valley, which is supported by the Bavarian state government with funds from the Hightech Agenda\r\nBayern Plus. P. Z. acknowledges support by the European Union’s Horizon Europe research and innovation program under Grant Agreement No. 101113690 (PASQANS2). The work of L. P. was funded by the European Union (ERC, QUANTHEM, No. 101114881). We acknowledge support\r\nby the Erwin Schrödinger International Institute for Mathematics and Physics (ESI)." article_number: '090801' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Matteo full_name: Votto, Matteo last_name: Votto - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Cécilia full_name: Lancien, Cécilia last_name: Lancien - first_name: J. Ignacio full_name: Cirac, J. Ignacio last_name: Cirac - first_name: Peter full_name: Zoller, Peter last_name: Zoller - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Lorenzo full_name: Piroli, Lorenzo last_name: Piroli - first_name: Benoît full_name: Vermersch, Benoît last_name: Vermersch citation: ama: Votto M, Ljubotina M, Lancien C, et al. Learning mixed quantum states in large-scale experiments. Physical Review Letters. 2026;136(9). doi:10.1103/rbg2-f61m apa: Votto, M., Ljubotina, M., Lancien, C., Cirac, J. I., Zoller, P., Serbyn, M., … Vermersch, B. (2026). Learning mixed quantum states in large-scale experiments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/rbg2-f61m chicago: Votto, Matteo, Marko Ljubotina, Cécilia Lancien, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, Lorenzo Piroli, and Benoît Vermersch. “Learning Mixed Quantum States in Large-Scale Experiments.” Physical Review Letters. American Physical Society, 2026. https://doi.org/10.1103/rbg2-f61m. ieee: M. Votto et al., “Learning mixed quantum states in large-scale experiments,” Physical Review Letters, vol. 136, no. 9. American Physical Society, 2026. ista: Votto M, Ljubotina M, Lancien C, Cirac JI, Zoller P, Serbyn M, Piroli L, Vermersch B. 2026. Learning mixed quantum states in large-scale experiments. Physical Review Letters. 136(9), 090801. mla: Votto, Matteo, et al. “Learning Mixed Quantum States in Large-Scale Experiments.” Physical Review Letters, vol. 136, no. 9, 090801, American Physical Society, 2026, doi:10.1103/rbg2-f61m. short: M. Votto, M. Ljubotina, C. Lancien, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, B. Vermersch, Physical Review Letters 136 (2026). date_created: 2026-03-23T14:56:32Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-03-23T15:39:34Z day: '04' ddc: - '530' department: - _id: MaSe doi: 10.1103/rbg2-f61m external_id: arxiv: - '2507.12550' file: - access_level: open_access checksum: 12b16ce2d49c62b2909da95121bfaadb content_type: application/pdf creator: dernst date_created: 2026-03-23T15:35:27Z date_updated: 2026-03-23T15:35:27Z file_id: '21491' file_name: 2026_PhysicalReviewLetters_Votto.pdf file_size: 500041 relation: main_file success: 1 file_date_updated: 2026-03-23T15:35:27Z has_accepted_license: '1' intvolume: ' 136' issue: '9' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Learning mixed quantum states in large-scale experiments 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: 136 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21482' abstract: - lang: eng text: Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly and is highly relevant in material design and biology. Here, we show that specific but promiscuous short-range binding interactions make it possible to economically assemble linear filaments of user-defined length. Our approach leads to independent control over the mean and width of the filament size distribution and allows us to smoothly explore design trade-offs between assembly quality (spread in size) and cost (number of particle species). We employ a simple hierarchical assembly protocol to minimize assembly times and show that multiple stages of hierarchy make it possible to extend our approach to the assembly of higher-dimensional structures. Our work provides a conceptually simple solution to size control that is applicable to a broad range of systems, from DNA nanoparticles to supramolecular polymers and beyond. acknowledgement: We thank Maitane Muñoz-Basagoiti for helpful discussions. The research was supported by the Gesellschaft für Forschungsförderung Niederösterreich under Project No. FTI23-G-011. article_number: L012054 article_processing_charge: Yes article_type: original author: - first_name: Maximilian full_name: Hübl, Maximilian id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32 last_name: Hübl - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 citation: ama: Hübl M, Goodrich CP. Entropic size control of self-assembled filaments. Physical Review Research. 2026;8. doi:10.1103/68rs-3qgn apa: Hübl, M., & Goodrich, C. P. (2026). Entropic size control of self-assembled filaments. Physical Review Research. American Physical Society. https://doi.org/10.1103/68rs-3qgn chicago: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” Physical Review Research. American Physical Society, 2026. https://doi.org/10.1103/68rs-3qgn. ieee: M. Hübl and C. P. Goodrich, “Entropic size control of self-assembled filaments,” Physical Review Research, vol. 8. American Physical Society, 2026. ista: Hübl M, Goodrich CP. 2026. Entropic size control of self-assembled filaments. Physical Review Research. 8, L012054. mla: Hübl, Maximilian, and Carl Peter Goodrich. “Entropic Size Control of Self-Assembled Filaments.” Physical Review Research, vol. 8, L012054, American Physical Society, 2026, doi:10.1103/68rs-3qgn. short: M. Hübl, C.P. Goodrich, Physical Review Research 8 (2026). corr_author: '1' date_created: 2026-03-23T14:58:31Z date_published: 2026-03-05T00:00:00Z date_updated: 2026-03-23T15:59:11Z day: '05' ddc: - '530' department: - _id: CaGo - _id: GradSch doi: 10.1103/68rs-3qgn file: - access_level: open_access checksum: 6d8a68e4a19f8dad5abdf75f72316f3d content_type: application/pdf creator: dernst date_created: 2026-03-23T15:53:29Z date_updated: 2026-03-23T15:53:29Z file_id: '21493' file_name: 2026_PhysicalReviewResearch_Huebl.pdf file_size: 2680924 relation: main_file success: 1 file_date_updated: 2026-03-23T15:53:29Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5 grant_number: FTI23-G-011 name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Entropic size control of self-assembled filaments 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: 8 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21490' abstract: - lang: eng text: Auxin canalization is a self-organizing process that governs the flexible formation of vasculature by reinforcing the formation of auxin transport channels. A key prerequisite is the feedback between auxin signaling and directional auxin transport, mediated by PIN transporters. Despite the developmental importance of canalization, the molecular components linking auxin perception to the regulation of PIN auxin transporters remain poorly understood. Here, we identify TOW, a novel and essential component of auxin canalization that links intracellular auxin signaling with cell surface auxin perception. TOW is regulated downstream of TIR1/AFB-Aux/IAA-WRKY23 transcriptional auxin signaling. tow mutants exhibit defects in regeneration and de novo vasculature formation, along with impaired formation of polarized, PIN-expressing auxin channels. At the subcellular level, these mutants display disrupted auxin-induced PIN polarization and altered PIN endocytic trafficking dynamics. TOW localizes predominantly to the plasma membrane, where it interacts with receptor-like kinases involved in auxin canalization, including the TMK1 auxin co-receptor and the CAMEL-CANAR complex. TOW promotes PIN interaction with these kinases and stabilizes PINs at the cell surface. Together, our findings identify TOW as a molecular link between intracellular and cell surface auxin signaling mechanisms that converge on PIN trafficking and polarity, providing new insights into how auxin signaling regulates directional auxin transport for the self-organizing formation of vasculature during flexible plant development. acknowledged_ssus: - _id: MassSpec - _id: Bio - _id: LifeSc acknowledgement: We thank Dr. Z. Ge (ISTA) for providing vectors for the CRISPR-Cas9 system, Dr. Armel Nicolas and Dr. Bella Bruszel for phosphoproteomic analysis, Prof. Michael Wrzaczek (Czech Academy of Sciences, Czechia) for valuable suggestions, and Prof. Maciek Adamowski (University of Gdańsk) for technical assistance. We also acknowledge the support of the Mass Spectrometry and Proteomics Facility, the Imaging & Optics Facility, and the Lab Support Facility at the Institute of Science and Technology Austria. This research was supported by the Scientific Service Units (SSU) of ISTA, utilizing resources provided by the Imaging & Optics Facility (IOF) and the Lab Support Facility (LSF). The work conducted by the Friml group was funded by the European Research Council (ERC) under grant agreement no. 101142681 (CYNIPS) and by the Austrian Science Fund (FWF) under project ESP271. We acknowledge the core facility CELLIM supported by MEYS CR (LM2023050 Czech-BioImaging) and the Plant Sciences Core Facility of CEITEC Masaryk University. E.M. received support from the National Science Centre (NCN), Poland, through the OPUS call within the Weave programme (grant no. 2021/43/I/NZ1/01835). T.N. received support from TowArds Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of the ERDF Programme Johannes Amos Comenius. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mingyue full_name: Li, Mingyue id: 01f96916-0235-11eb-9379-a323192643b7 last_name: Li - first_name: Nikola full_name: Rydza, Nikola last_name: Rydza - first_name: Ewa full_name: Mazur, Ewa last_name: Mazur - first_name: Gergely full_name: Molnar, Gergely id: 34F1AF46-F248-11E8-B48F-1D18A9856A87 last_name: Molnar - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. Current Biology. 2026;36(6):1468-1480.e6. doi:10.1016/j.cub.2026.02.023 apa: Li, M., Rydza, N., Mazur, E., Molnar, G., Nodzyński, T., & Friml, J. (2026). Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2026.02.023 chicago: Li, Mingyue, Nikola Rydza, Ewa Mazur, Gergely Molnar, Tomasz Nodzyński, and Jiří Friml. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” Current Biology. Elsevier, 2026. https://doi.org/10.1016/j.cub.2026.02.023. ieee: M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, and J. Friml, “Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization,” Current Biology, vol. 36, no. 6. Elsevier, p. 1468–1480.e6, 2026. ista: Li M, Rydza N, Mazur E, Molnar G, Nodzyński T, Friml J. 2026. Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization. Current Biology. 36(6), 1468–1480.e6. mla: Li, Mingyue, et al. “Receptor-like-Kinase-Interacting Protein TOW Stabilizes PIN Transporters for Auxin Canalization.” Current Biology, vol. 36, no. 6, Elsevier, 2026, p. 1468–1480.e6, doi:10.1016/j.cub.2026.02.023. short: M. Li, N. Rydza, E. Mazur, G. Molnar, T. Nodzyński, J. Friml, Current Biology 36 (2026) 1468–1480.e6. corr_author: '1' date_created: 2026-03-23T15:11:16Z date_published: 2026-03-23T00:00:00Z date_updated: 2026-03-24T08:36:40Z day: '23' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.cub.2026.02.023 external_id: pmid: - '41831441' file: - access_level: open_access checksum: fe6c41fdab58a55df5f2a5860c02acdc content_type: application/pdf creator: dernst date_created: 2026-03-24T08:34:37Z date_updated: 2026-03-24T08:34:37Z file_id: '21496' file_name: 2026_CurrentBiology_Li.pdf file_size: 12986894 relation: main_file success: 1 file_date_updated: 2026-03-24T08:34:37Z has_accepted_license: '1' intvolume: ' 36' issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1468-1480.e6 pmid: 1 project: - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants - _id: bd906599-d553-11ed-ba76-abf8547645d7 grant_number: E271 name: Identification of a novel regulator in auxin canalization publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization 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: 36 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21484' abstract: - lang: eng text: An individual's phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents' DNA. Here, we derive how the genetic variance within a population is changed under the influence of indirect maternal, paternal and parent-of-origin effects under random mating. We also consider indirect effects of a sibling, in particular how the genetic variance is altered when looking at the phenotypic difference between two siblings. The calculations are then extended to include assortative mating (AM), which alters the variance by inducing increased homozygosity and correlations within and across loci. AM likely leads to covariance of parental genetic effects, a measure of the similarity of parents in the indirect effects they have on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait AM. Our theory shows how the resemblance among relatives increases under both AM, indirect and parent-of-origin effects. When our model is used to predict correlations among relatives in human height, we find that explaining the patterns observed in real data requires both indirect genetic effects and assortative mating. The degree to which direct, indirect and epigenetic effects shape the phenotypic variance of complex traits remains an open question that requires large-scale family data to be resolved. acknowledgement: We thank members of the Medical Genomics group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. article_number: iyag042 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Krätschmer I, Robinson MR. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. Genetics. 2026. doi:10.1093/genetics/iyag042 apa: Krätschmer, I., & Robinson, M. R. (2026). A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyag042 chicago: Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” Genetics. Oxford University Press, 2026. https://doi.org/10.1093/genetics/iyag042. ieee: I. Krätschmer and M. R. Robinson, “A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating,” Genetics. Oxford University Press, 2026. ista: Krätschmer I, Robinson MR. 2026. A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating. Genetics., iyag042. mla: Krätschmer, Ilse, and Matthew Richard Robinson. “A Quantitative Genetic Model for Indirect Genetic Effects and Genomic Imprinting under Random and Assortative Mating.” Genetics, iyag042, Oxford University Press, 2026, doi:10.1093/genetics/iyag042. short: I. Krätschmer, M.R. Robinson, Genetics (2026). corr_author: '1' date_created: 2026-03-23T15:02:54Z date_published: 2026-02-12T00:00:00Z date_updated: 2026-03-24T06:48:10Z day: '12' department: - _id: MaRo doi: 10.1093/genetics/iyag042 external_id: pmid: - '41677404' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/genetics/iyag042 month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Genetics publication_identifier: issn: - 1943-2631 publication_status: epub_ahead publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/medical-genomics-group/familyMC status: public title: A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating 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 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21486' abstract: - lang: eng text: Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes. acknowledgement: This work was supported by a grant from the Austrian Science Fund (FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback on an early version of the manuscript. We are grateful to Kamil Jaron and Julia Gries for helpful discussions and for sharing their unpublished work. Computational resources and support were provided by the Scientific Computing Unit at ISTA. article_number: qrag003 article_processing_charge: Yes article_type: original author: - first_name: Lorena Alexandra full_name: Layana Franco, Lorena Alexandra id: 02814589-eb8f-11eb-b029-a70074f3f18f last_name: Layana Franco orcid: 0000-0002-1253-6297 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters. 2026. doi:10.1093/evlett/qrag003 apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrag003 chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Evolution Letters. Oxford University Press, 2026. https://doi.org/10.1093/evlett/qrag003. ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera,” Evolution Letters. Oxford University Press, 2026. ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters., qrag003. mla: Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Evolution Letters, qrag003, Oxford University Press, 2026, doi:10.1093/evlett/qrag003. short: L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026). corr_author: '1' date_created: 2026-03-23T15:05:42Z date_published: 2026-03-12T00:00:00Z date_updated: 2026-03-24T07:14:08Z day: '12' ddc: - '570' department: - _id: BeVi - _id: GradSch doi: 10.1093/evlett/qrag003 has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/evlett/qrag003 month: '03' oa: 1 oa_version: Published Version project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development publication: Evolution Letters publication_identifier: eissn: - 2056-3744 publication_status: epub_ahead publisher: Oxford University Press quality_controlled: '1' status: public title: Causes and consequences of sex-chromosome turnovers in Diptera 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 year: '2026' ... --- OA_place: repository OA_type: free access _id: '21137' acknowledged_ssus: - _id: Bio - _id: EM-Fac - _id: ScienComp - _id: LifeSc acknowledgement: We thank all members of the Heisenberg, Henkes, and Hannezo groups for their support. We are also grateful to the Imaging and Optics, Scientific Computing, Life Science Support, and Cryo-Electron Microscopy facilities at ISTA for their technical assistance and support. Numerical simulations were performed using the computational resources from Lorentz Institute and the Academic Leiden Interdisciplinary Cluster Environment (ALICE) provided by Leiden University, and from PMMH provided by Sorbonne Université. S.N has received funding from European Union’s Horizon 2020 research and innovation programme (grant agreement No. 665385). This work was supported by the Austrian Science Fund (FWF) under projects PAT5044023 and W1250 awarded to C.-P.H. article_processing_charge: No author: - first_name: Suyash full_name: Naik, Suyash id: 2C0B105C-F248-11E8-B48F-1D18A9856A87 last_name: Naik orcid: 0000-0001-8421-5508 citation: ama: Naik S. Data associated with Keratins coordinate tissue spreading . 2026. doi:10.15479/AT-ISTA-21137 apa: Naik, S. (2026). Data associated with Keratins coordinate tissue spreading . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21137 chicago: Naik, Suyash. “Data Associated with Keratins Coordinate Tissue Spreading .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21137. ieee: S. Naik, “Data associated with Keratins coordinate tissue spreading .” Institute of Science and Technology Austria, 2026. ista: Naik S. 2026. Data associated with Keratins coordinate tissue spreading , Institute of Science and Technology Austria, 10.15479/AT-ISTA-21137. mla: Naik, Suyash. Data Associated with Keratins Coordinate Tissue Spreading . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21137. short: S. Naik, (2026). contributor: - contributor_type: researcher first_name: Yann-Edwin last_name: Keta - contributor_type: supervisor first_name: 'Silke ' last_name: Henkes - contributor_type: supervisor first_name: Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - contributor_type: supervisor first_name: Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 corr_author: '1' date_created: 2026-02-04T16:38:02Z date_published: 2026-03-24T00:00:00Z date_updated: 2026-03-24T08:32:00Z day: '24' department: - _id: GradSch - _id: CaHe - _id: EdHa doi: 10.15479/AT-ISTA-21137 ec_funded: 1 file: - access_level: open_access checksum: 5d1fda7e410f24c311fcf6bcf725698f content_type: application/zip creator: snaik date_created: 2026-03-16T11:51:10Z date_updated: 2026-03-16T11:51:10Z description: 'Python3 library written in C++20 to integrate vertex models. Please read the readme at https://github.com/yketa/cells/blob/main/README.md for detailed instructions for installation and usage of the code in this repository. ' file_id: '21461' file_name: cells-main.zip file_size: 725916 relation: main_file title: Cell git repository - access_level: open_access checksum: ee350c8eaed99f3ca348c47c8b190d3c content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-18T14:52:02Z date_updated: 2026-03-18T14:52:02Z file_id: '21464' file_name: DevBranchDataRepo.zip file_size: 282168895 relation: main_file success: 1 - access_level: open_access checksum: 1ecaf2c1a2ce8ff9c75a128cc02d0b8f content_type: text/markdown creator: snaik date_created: 2026-03-18T15:01:32Z date_updated: 2026-03-18T15:01:32Z file_id: '21466' file_name: ReadMe.md file_size: 2231 relation: main_file success: 1 - access_level: open_access checksum: da9a4687e5144b61a64ca341f922046a content_type: image/svg+xml creator: snaik date_created: 2026-03-18T15:12:57Z date_updated: 2026-03-18T15:12:57Z file_id: '21467' file_name: PaperSchematics.svg file_size: 1951210 relation: main_file success: 1 - access_level: open_access checksum: 9ac1054b16c212c6f34d402dce2c80e0 content_type: application/octet-stream creator: snaik date_created: 2026-03-21T03:37:43Z date_updated: 2026-03-21T03:37:43Z file_id: '21468' file_name: maxwell_sketch.tex file_size: 1897 relation: main_file success: 1 - access_level: open_access checksum: 7c9ecf78e2593b3830d96fa94baa08df content_type: application/x-zip-compressed creator: snaik date_created: 2026-03-24T07:21:43Z date_updated: 2026-03-24T07:21:43Z file_id: '21495' file_name: DataRepo.zip file_size: 749368723 relation: main_file success: 1 file_date_updated: 2026-03-24T07:21:43Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '3' oa: 1 oa_version: None project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 8f060199-16d5-11f0-9cad-f3253b266c46 grant_number: PAT 5044023 name: Keratins in epithelial tissue spreading - _id: 252C3B08-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1250-B20 name: Nano-Analytics of Cellular Systems publisher: Institute of Science and Technology Austria status: public title: 'Data associated with Keratins coordinate tissue spreading ' 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: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2026' ... --- _id: '21489' abstract: - lang: eng text: We study Kirillov algebras attached to minuscule highest weight representations of semisimple Lie algebras. They can be viewed as equivariant cohomology algebras of partial flag varieties. Real structures on the varieties then induce involutions of these algebras. We describe how these involutions act on the spectra of minuscule Kirillov algebras, and model the fixed points via the equivariant cohomology of real partial flag varieties. We then use this model to characterise freeness of the fixed point coordinate ring over the appropriate base. As an application, we recover a q = -1 phenomenon of Stembridge in the minuscule case by geometric means. acknowledgement: 'I would like to thank Tamás Hausel for introducing me to this area of mathematics and for his constant guidance. I would also like to thank Jakub Löwit and Miguel González for fruitful discussions and many helpful comments on this paper. This work was done during the author’s PhD studies at the Institute of Science and Technology Austria (ISTA). It was funded by the Austrian Science Fund (FWF) 10.55776/P35847. Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) arxiv: 1 author: - first_name: Mischa M full_name: Elkner, Mischa M id: 477faa59-080d-11ed-979a-c693ab7638ab last_name: Elkner citation: ama: Elkner MM. On involutions of minuscule Kirillov algebras induced by real structures. Transformation Groups. 2026. doi:10.1007/s00031-026-09958-y apa: Elkner, M. M. (2026). On involutions of minuscule Kirillov algebras induced by real structures. Transformation Groups. Springer Nature. https://doi.org/10.1007/s00031-026-09958-y chicago: Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” Transformation Groups. Springer Nature, 2026. https://doi.org/10.1007/s00031-026-09958-y. ieee: M. M. Elkner, “On involutions of minuscule Kirillov algebras induced by real structures,” Transformation Groups. Springer Nature, 2026. ista: Elkner MM. 2026. On involutions of minuscule Kirillov algebras induced by real structures. Transformation Groups. mla: Elkner, Mischa M. “On Involutions of Minuscule Kirillov Algebras Induced by Real Structures.” Transformation Groups, Springer Nature, 2026, doi:10.1007/s00031-026-09958-y. short: M.M. Elkner, Transformation Groups (2026). corr_author: '1' date_created: 2026-03-23T15:10:43Z date_published: 2026-03-14T00:00:00Z date_updated: 2026-03-24T08:26:10Z day: '14' ddc: - '510' department: - _id: TaHa doi: 10.1007/s00031-026-09958-y external_id: arxiv: - '2411.16270' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00031-026-09958-y month: '03' oa: 1 oa_version: None project: - _id: 34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3 grant_number: P35847 name: Geometry of the tip of the global nilpotent cone publication: Transformation Groups publication_identifier: eissn: - 1531-586X issn: - 1083-4362 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' status: public title: On involutions of minuscule Kirillov algebras induced by real structures 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 year: '2026' ... --- OA_place: repository _id: '21393' abstract: - lang: eng text: "This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS.\r\n\r\nWe formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star.\r\n\r\nOur second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight.\r\n\r\nOur third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved.\r\n\r\nIn the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X citation: ama: 'Dvorak M. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. 2026. doi:10.15479/AT-ISTA-21393' apa: 'Dvorak, M. (2026). Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21393' chicago: 'Dvorak, Martin. “Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21393.' ieee: 'M. Dvorak, “Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids,” Institute of Science and Technology Austria, 2026.' ista: 'Dvorak M. 2026. Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids. Institute of Science and Technology Austria.' mla: 'Dvorak, Martin. Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21393.' short: 'M. Dvorak, Pursuit of Truth and Beauty in Lean 4 : Formally Verified Theory of Grammars, Optimization, Matroids, Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-03-04T09:26:46Z date_published: 2026-03-04T00:00:00Z date_updated: 2026-03-27T12:37:00Z day: '04' ddc: - '511' - '000' degree_awarded: PhD department: - _id: GradSch - _id: VlKo doi: 10.15479/AT-ISTA-21393 file: - access_level: open_access checksum: cface6dc18152680962b5361575f6e4f content_type: application/pdf creator: mdvorak date_created: 2026-03-04T08:56:15Z date_updated: 2026-03-04T08:56:15Z file_id: '21394' file_name: 2026_Dvorak_Martin_Thesis.pdf file_size: 1771231 relation: main_file success: 1 - access_level: closed checksum: 290ddfacfb7e07fb07e6f0b334e67c90 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mdvorak date_created: 2026-03-04T09:03:37Z date_updated: 2026-03-04T09:03:37Z file_id: '21395' file_name: 2026_Dvorak_Martin_Thesis.docx file_size: 864585 relation: source_file file_date_updated: 2026-03-04T09:03:37Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '160' publication_identifier: isbn: - 978-3-99078-074-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - description: Full version of all definitions, statements, and proofs for Chapter 3.1 (Linear duality) relation: software url: https://github.com/madvorak/duality/tree/v3.5.0 - description: Full version of all definitions, statements, and proofs for Chapter 3.2 (Valued Constraint Satisfaction Problems) relation: software url: https://github.com/madvorak/vcsp/tree/v8.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 4 (Seymour project) relation: software url: https://github.com/Ivan-Sergeyev/seymour/tree/v1.2.0 - description: Full version of all definitions, statements, and proofs for Chapter 5 (Theory of grammars) relation: software url: https://github.com/madvorak/chomsky/tree/v1.2.0 - description: Old version (Lean 3) of the project about grammars relation: software url: https://github.com/madvorak/grammars - description: Demonstration of (minimal) requirements for selected algebraic classes used in my Ph.D. thesis relation: software url: https://github.com/madvorak/preliminaries/blob/main/Preliminaries.lean record: - id: '13120' relation: part_of_dissertation status: public - id: '21398' relation: part_of_dissertation status: public - id: '20071' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Jasmin full_name: Blanchette, Jasmin last_name: Blanchette title: 'Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids' 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: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold PlanS_conform: '1' _id: '21501' abstract: - lang: eng text: "Kinetically constrained models were originally introduced to capture slow relaxation in glassy systems, where dynamics are hindered by local constraints instead of energy barriers. Their quantum counterparts have recently drawn attention for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming from chiral symmetry. Yet, the structure and implications of these zero modes remain poorly understood. In this work, we focus on the properties of the zero mode subspace in quantum kinetically constrained models with a U(1) particle-conservation symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric U(1) East-West models to illustrate our two main results. First, we observe that the simultaneous presence of constraints and chiral symmetry generally leads to a parametric increase in the number of zero modes due to the fragmentation of the many-body\r\nHilbert space into disconnected sectors. Second, we generalize the concept of compact localized states from single-particle physics and introduce the notion of collective bound states, a special kind of nonergodic eigenstates that are robust to enlarging the system size. We formulate sufficient criteria for their existence, arguing that the degenerate zero mode subspace plays a central role, and demonstrate bound states in both example models and in a two-dimensional model, the U(1) North-East, and in the pairflip model, a system without particle conservation. Our results motivate a systematic study of bound states and their relation to ergodicity breaking, transport, and other properties of quantum kinetically constrained\r\nmodels. " acknowledgement: The authors acknowledge useful discussions with Berislav Buca. This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M.L. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111—390814868. This research was supported in part by grant NSF PHY-2309135 to the Kavli Institute for Theoretical Physics (KITP). article_number: '010352' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Eulalia full_name: Nicolau Jimenez, Eulalia id: 04b4791c-8fd7-11ee-a7df-be2fdc569c48 last_name: Nicolau Jimenez - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Nicolau Jimenez E, Ljubotina M, Serbyn M. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 2026;7. doi:10.1103/sl79-1xgb apa: Nicolau Jimenez, E., Ljubotina, M., & Serbyn, M. (2026). Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. American Physical Society. https://doi.org/10.1103/sl79-1xgb chicago: Nicolau Jimenez, Eulalia, Marko Ljubotina, and Maksym Serbyn. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” PRX Quantum. American Physical Society, 2026. https://doi.org/10.1103/sl79-1xgb. ieee: E. Nicolau Jimenez, M. Ljubotina, and M. Serbyn, “Fragmentation, zero modes, and collective bound states in constrained models,” PRX Quantum, vol. 7. American Physical Society, 2026. ista: Nicolau Jimenez E, Ljubotina M, Serbyn M. 2026. Fragmentation, zero modes, and collective bound states in constrained models. PRX Quantum. 7, 010352. mla: Nicolau Jimenez, Eulalia, et al. “Fragmentation, Zero Modes, and Collective Bound States in Constrained Models.” PRX Quantum, vol. 7, 010352, American Physical Society, 2026, doi:10.1103/sl79-1xgb. short: E. Nicolau Jimenez, M. Ljubotina, M. Serbyn, PRX Quantum 7 (2026). corr_author: '1' date_created: 2026-03-28T14:57:56Z date_published: 2026-03-13T00:00:00Z date_updated: 2026-03-30T06:09:28Z day: '13' ddc: - '530' department: - _id: MaSe doi: 10.1103/sl79-1xgb ec_funded: 1 external_id: arxiv: - '2504.17627' file: - access_level: open_access checksum: d155ffa9e1a8275702149165f4bf963c content_type: application/pdf creator: dernst date_created: 2026-03-30T06:08:07Z date_updated: 2026-03-30T06:08:07Z file_id: '21505' file_name: 2026_PRXQuantum_Nicolau.pdf file_size: 1848724 relation: main_file success: 1 file_date_updated: 2026-03-30T06:08:07Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication: PRX Quantum publication_identifier: eissn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Fragmentation, zero modes, and collective bound states in constrained models 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: 7 year: '2026' ... --- OA_place: publisher OA_type: hybrid _id: '21503' abstract: - lang: eng text: Currently, pharmacogenetics relies on partially annotated star alleles, leaving novel variants and complex haplotypes uninterpretable. Computational scoring frameworks could overcome these limitations. Here, we comprehensively evaluated the ability of existing (CADD, FATHMM-XF, PROVEAN, MutationAssessor, SIFT, PhyloP100, APF, APF2) and novel (PharmGScore and PharmMLScore) variant effect predictors to assess pharmacogenetic alleles in multiple scenarios. Altogether we analyzed 541 PharmVar alleles, high‑throughput CYP2C9 and CYP2C19 mutational maps, and 200 642 UK Biobank exomes linked with health records containing antidepressant treatment outcomes. Many evaluated tools, especially ensemble frameworks, matched or exceeded star allele classifications (ROC‑AUC up to 0.85 for allele definitions, 0.95 in vitro; TPR up to 0.99 for exomes) and accurately predicted severe antidepressant adverse events for carriers of deleterious variants in CYP2C19 (OR 1.20–1.35). Our findings show that computational predictors deliver star allele accuracy while overcoming their limitations. With additional validation, computational tools could enhance clinical decision frameworks by enabling continuous scoring, incorporating previously unknown variants, and providing genome-wide applicability. acknowledgement: "This research has been conducted using the UK Biobank Resource under Application Number 62979. We are grateful to the UK Biobank and all its voluntary participants. This work used data provided by patients and collected by the NHS as part of their care and support.\r\n\r\nThis study was funded by the National Science Center, Poland: PRELUDIUM BIS-3 grant no. 2021/43/O/NZ7/01187 (development and benchmarking of variant scores) and SONATINA 5 grant 2021/40/C/NZ2/00218 (UKB analyses). Additional support came from the statutory funds of the Maj Institute of Pharmacology PAS. We gratefully acknowledge Poland’s high-performance Infrastructure PLGrid ACK Cyfronet AGH, for providing computer facilities and support within computational grant no PLG/2022/015861. DMF and GEB were funded by NIH grants NIH R35GM152106 and UM1HG011969." article_number: '8' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jacek full_name: Hajto, Jacek last_name: Hajto - first_name: Marcin full_name: Piechota, Marcin last_name: Piechota - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Paula full_name: Konowalska, Paula last_name: Konowalska - first_name: Gabriel E. full_name: Boyle, Gabriel E. last_name: Boyle - first_name: Douglas M. full_name: Fowler, Douglas M. last_name: Fowler - first_name: Malgorzata full_name: Borczyk, Malgorzata last_name: Borczyk - first_name: Michal full_name: Korostynski, Michal last_name: Korostynski citation: ama: 'Hajto J, Piechota M, Krätschmer I, et al. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. Pharmacogenomics Journal. 2026;26(2). doi:10.1038/s41397-026-00399-0' apa: 'Hajto, J., Piechota, M., Krätschmer, I., Konowalska, P., Boyle, G. E., Fowler, D. M., … Korostynski, M. (2026). Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. Pharmacogenomics Journal. Springer Nature. https://doi.org/10.1038/s41397-026-00399-0' chicago: 'Hajto, Jacek, Marcin Piechota, Ilse Krätschmer, Paula Konowalska, Gabriel E. Boyle, Douglas M. Fowler, Malgorzata Borczyk, and Michal Korostynski. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” Pharmacogenomics Journal. Springer Nature, 2026. https://doi.org/10.1038/s41397-026-00399-0.' ieee: 'J. Hajto et al., “Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants,” Pharmacogenomics Journal, vol. 26, no. 2. Springer Nature, 2026.' ista: 'Hajto J, Piechota M, Krätschmer I, Konowalska P, Boyle GE, Fowler DM, Borczyk M, Korostynski M. 2026. Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants. Pharmacogenomics Journal. 26(2), 8.' mla: 'Hajto, Jacek, et al. “Computational Variant Predictors for Pharmacogenomics: From Evaluation of Single Alleles to Assessment of Adverse Drug Reactions to Antidepressants.” Pharmacogenomics Journal, vol. 26, no. 2, 8, Springer Nature, 2026, doi:10.1038/s41397-026-00399-0.' short: J. Hajto, M. Piechota, I. Krätschmer, P. Konowalska, G.E. Boyle, D.M. Fowler, M. Borczyk, M. Korostynski, Pharmacogenomics Journal 26 (2026). date_created: 2026-03-29T22:07:08Z date_published: 2026-03-09T00:00:00Z date_updated: 2026-03-30T07:10:50Z day: '09' ddc: - '570' department: - _id: MaRo doi: 10.1038/s41397-026-00399-0 external_id: pmid: - '41803106' file: - access_level: open_access checksum: 2fd3d7e48b779ac24245f6c35449b89a content_type: application/pdf creator: dernst date_created: 2026-03-30T07:04:08Z date_updated: 2026-03-30T07:04:08Z file_id: '21506' file_name: 2026_PharmacogenomicsJour_Hajto.pdf file_size: 2618963 relation: main_file success: 1 file_date_updated: 2026-03-30T07:04:08Z has_accepted_license: '1' intvolume: ' 26' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Pharmacogenomics Journal publication_identifier: eissn: - 1473-1150 issn: - ' 1470-269X' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants' 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: 26 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21509' abstract: - lang: eng text: Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes. acknowledgement: We thank D. Hess, V. Iesmantavicius, and J. Seebacher (FMI Proteomics and Protein Analysis Facility) for mass spectrometry support; S. Smallwood, K. Shimada, D. Klein, and M. Schütz-Stoffregen for technical assistance; J. Côté and C. Lachance for critical discussions; and members of the Thomä lab for helpful feedback. Support for this work was provided to N.H.T. by the European Research Council under the European Union’s Horizon 2020 research program (NucEM, no. 884331), the Novartis Research Foundation, the Swiss National Science Foundation (SNF 31003A_179541, 310030_214852, and Sinergia CRSII5_186230), and the Swiss Cancer Research (KFS-4980-02-2020 and KFS-5933-08-2023). S.D. was supported by the European Research Council (DONUTS, no. 101092623), the Knut and Alice Wallenberg Foundation (2024.0012), the Cancerfonden (25 4453 Pj), and the Swedish Research Council (VR 03255). A.K.M. was supported by a Human Frontier Science Program Long-Term Fellowship, and L.V. was supported by an EMBO fellowship (ALTF 549-2021). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Joscha full_name: Weiss, Joscha last_name: Weiss - first_name: Luca full_name: Vecchia, Luca last_name: Vecchia - first_name: David full_name: Domjan, David last_name: Domjan - first_name: Simone full_name: Cavadini, Simone last_name: Cavadini - first_name: Anton full_name: Sabantsev, Anton last_name: Sabantsev - first_name: Georg full_name: Kempf, Georg last_name: Kempf - first_name: Ganesh R. full_name: Pathare, Ganesh R. last_name: Pathare - first_name: Klaus full_name: Brackmann, Klaus last_name: Brackmann - first_name: Alicia full_name: Michael, Alicia id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael orcid: 0000-0002-6080-839X - first_name: Lukas full_name: Kater, Lukas last_name: Kater - first_name: Eric full_name: Hietter-Pfeiffer, Eric last_name: Hietter-Pfeiffer - first_name: Mina full_name: Haddawi, Mina last_name: Haddawi - first_name: Urja P. full_name: Kuber, Urja P. last_name: Kuber - first_name: Sandra full_name: Mühlhäusser, Sandra last_name: Mühlhäusser - first_name: Ralph S. full_name: Grand, Ralph S. last_name: Grand - first_name: Michael B. full_name: Stadler, Michael B. last_name: Stadler - first_name: Sebastian full_name: Deindl, Sebastian last_name: Deindl - first_name: Nicolas H. full_name: Thomä, Nicolas H. last_name: Thomä citation: ama: Weiss J, Vecchia L, Domjan D, et al. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 2026;86(4):625-639.e8. doi:10.1016/j.molcel.2026.01.021 apa: Weiss, J., Vecchia, L., Domjan, D., Cavadini, S., Sabantsev, A., Kempf, G., … Thomä, N. H. (2026). The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2026.01.021 chicago: Weiss, Joscha, Luca Vecchia, David Domjan, Simone Cavadini, Anton Sabantsev, Georg Kempf, Ganesh R. Pathare, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell. Elsevier, 2026. https://doi.org/10.1016/j.molcel.2026.01.021. ieee: J. Weiss et al., “The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2,” Molecular Cell, vol. 86, no. 4. Elsevier, p. 625–639.e8, 2026. ista: Weiss J, Vecchia L, Domjan D, Cavadini S, Sabantsev A, Kempf G, Pathare GR, Brackmann K, Michael AK, Kater L, Hietter-Pfeiffer E, Haddawi M, Kuber UP, Mühlhäusser S, Grand RS, Stadler MB, Deindl S, Thomä NH. 2026. The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2. Molecular Cell. 86(4), 625–639.e8. mla: Weiss, Joscha, et al. “The Human BAF Chromatin Remodeler Processes Nucleosomes Bound by Pioneer Transcription Factors OCT4–SOX2.” Molecular Cell, vol. 86, no. 4, Elsevier, 2026, p. 625–639.e8, doi:10.1016/j.molcel.2026.01.021. short: J. Weiss, L. Vecchia, D. Domjan, S. Cavadini, A. Sabantsev, G. Kempf, G.R. Pathare, K. Brackmann, A.K. Michael, L. Kater, E. Hietter-Pfeiffer, M. Haddawi, U.P. Kuber, S. Mühlhäusser, R.S. Grand, M.B. Stadler, S. Deindl, N.H. Thomä, Molecular Cell 86 (2026) 625–639.e8. date_created: 2026-03-30T11:58:48Z date_published: 2026-02-19T00:00:00Z date_updated: 2026-03-30T12:09:08Z day: '19' ddc: - '570' department: - _id: AlMi doi: 10.1016/j.molcel.2026.01.021 external_id: pmid: - '41679301' file: - access_level: open_access checksum: e16a7315b64a706184b177ea1621523c content_type: application/pdf creator: dernst date_created: 2026-03-30T12:04:38Z date_updated: 2026-03-30T12:04:38Z file_id: '21510' file_name: 2026_MolecularCell_Weiss.pdf file_size: 9786677 relation: main_file success: 1 file_date_updated: 2026-03-30T12:04:38Z has_accepted_license: '1' intvolume: ' 86' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 625-639.e8 pmid: 1 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2 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: 86 year: '2026' ... --- OA_place: publisher OA_type: hybrid PlanS_conform: '1' _id: '21483' abstract: - lang: eng text: 'Embryogenesis in the model plant Arabidopsis thaliana provides a framework for understanding how cell polarity and patterning coordinate with hormonal signalling to establish the plant body plan. Following fertilisation, the zygote divides asymmetrically to generate apical and basal lineages, establishing the apical–basal axis that defines future shoot and root poles. Genetic and molecular analyses of classical mutants including gnom, monopteros (mp), bodenlos (bdl) and topless revealed that localised auxin biosynthesis, directional transport and downstream transcriptional responses are central to apical–basal axis establishment and organ initiation. The main components of this regulation are polarly localised PIN auxin transporters and downstream modules involving MONOPTEROS and WUSCHEL-RELATED HOMEOBOX transcription factors. Advances in microscopy have transformed the study of Arabidopsis embryogenesis: fluorescence-compatible clearing reagents and three-dimensional reconstructions now permit quantitative analyses of cell geometry, division orientation, and cytoskeletal dynamics. Live ovule imaging setups with confocal laser scanning and multiphoton microscopes enable real-time observation of embryo development, while laser-assisted cell ablation can be used to probe cell-to-cell communication and fate plasticity. Together, these methodological breakthroughs position Arabidopsis embryos as a prime model for dissecting the chemical and biophysical cues that shape plant development.' acknowledgement: The authors would like to acknowledge the many colleagues whose valuable contributions to the field could not be included in this review due to space limitations and reference constraints. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ. article_number: nph.71072 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: David full_name: Babic, David id: db566d23-f6e0-11ea-865d-e6f270e968e7 last_name: Babic - first_name: Milan full_name: Zupunski, Milan id: f6a21fce-573e-11f0-a150-a8d96aee2539 last_name: Zupunski - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Babic D, Zupunski M, Friml J. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist. 2026. doi:10.1111/nph.71072 apa: Babic, D., Zupunski, M., & Friml, J. (2026). Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist. Wiley. https://doi.org/10.1111/nph.71072 chicago: Babic, David, Milan Zupunski, and Jiří Friml. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” New Phytologist. Wiley, 2026. https://doi.org/10.1111/nph.71072. ieee: D. Babic, M. Zupunski, and J. Friml, “Imaging and genetic toolbox to study Arabidopsis embryogenesis,” New Phytologist. Wiley, 2026. ista: Babic D, Zupunski M, Friml J. 2026. Imaging and genetic toolbox to study Arabidopsis embryogenesis. New Phytologist., nph. 71072. mla: Babic, David, et al. “Imaging and Genetic Toolbox to Study Arabidopsis Embryogenesis.” New Phytologist, nph. 71072, Wiley, 2026, doi:10.1111/nph.71072. short: D. Babic, M. Zupunski, J. Friml, New Phytologist (2026). corr_author: '1' date_created: 2026-03-23T14:59:06Z date_published: 2026-03-11T00:00:00Z date_updated: 2026-03-30T05:58:35Z day: '11' department: - _id: JiFr - _id: GradSch doi: 10.1111/nph.71072 external_id: pmid: - '41808651' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.71072 month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: epub_ahead publisher: Wiley quality_controlled: '1' status: public title: Imaging and genetic toolbox to study Arabidopsis embryogenesis 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 year: '2026' ...