[{"day":"17","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-08-03T13:21:14Z","OA_place":"publisher","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","OA_type":"hybrid","publication":"Letters in Mathematical Physics","title":"Dyson expansion for form-bounded perturbations and applications to the polaron problem","intvolume":"       116","file":[{"file_id":"22641","creator":"dernst","relation":"main_file","date_created":"2026-08-04T05:55:58Z","checksum":"1b90ff7da16b9604d6fe2c6281493456","access_level":"open_access","success":1,"file_name":"2026_LettersMathPhysics_Desio.pdf","file_size":371840,"date_updated":"2026-08-04T05:55:58Z","content_type":"application/pdf"}],"volume":116,"month":"07","article_processing_charge":"Yes (via OA deal)","type":"journal_article","status":"public","year":"2026","publication_status":"published","file_date_updated":"2026-08-04T05:55:58Z","supplementarymaterial":"no","quality_controlled":"1","das_tickbox":"0","article_number":"87","doi":"10.1007/s11005-026-02107-2","publication_identifier":{"issn":["1573-0530"]},"_id":"22639","oa":1,"article_type":"original","has_accepted_license":"1","researchdata_availability":"no","corr_author":"1","author":[{"id":"ea10a57b-23f6-11ef-9085-80d8596d52ef","last_name":"Desio","first_name":"Davide","orcid":"0000-0001-9840-3809","full_name":"Desio, Davide"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"D. Desio and R. Seiringer, “Dyson expansion for form-bounded perturbations and applications to the polaron problem,” <i>Letters in Mathematical Physics</i>, vol. 116, no. 4. Springer Nature, 2026.","chicago":"Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1007/s11005-026-02107-2\">https://doi.org/10.1007/s11005-026-02107-2</a>.","mla":"Desio, Davide, and Robert Seiringer. “Dyson Expansion for Form-Bounded Perturbations and Applications to the Polaron Problem.” <i>Letters in Mathematical Physics</i>, vol. 116, no. 4, 87, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1007/s11005-026-02107-2\">10.1007/s11005-026-02107-2</a>.","ista":"Desio D, Seiringer R. 2026. Dyson expansion for form-bounded perturbations and applications to the polaron problem. Letters in Mathematical Physics. 116(4), 87.","ama":"Desio D, Seiringer R. Dyson expansion for form-bounded perturbations and applications to the polaron problem. <i>Letters in Mathematical Physics</i>. 2026;116(4). doi:<a href=\"https://doi.org/10.1007/s11005-026-02107-2\">10.1007/s11005-026-02107-2</a>","short":"D. Desio, R. Seiringer, Letters in Mathematical Physics 116 (2026).","apa":"Desio, D., &#38; Seiringer, R. (2026). Dyson expansion for form-bounded perturbations and applications to the polaron problem. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-026-02107-2\">https://doi.org/10.1007/s11005-026-02107-2</a>"},"PlanS_conform":"1","arxiv":1,"date_published":"2026-07-17T00:00:00Z","publisher":"Springer Nature","license":"https://creativecommons.org/licenses/by/4.0/","issue":"4","external_id":{"arxiv":["2512.13443"]},"ddc":["510"],"abstract":[{"text":"We present an abstract Dyson expansion for perturbations that are merely relatively form-bounded, and apply it to the polaron problem. For a large class of polaron-type models, including the Fröhlich and Nelson models, we prove that the vacuum expectation value of the heat semi-group is a completely monotone function of the square of the total momentum. Consequently, the ground-state energy is a concave function of the square of the momentum, a result recently proved for the Fröhlich model in [14] using a probabilistic approach via Wiener integrals.","lang":"eng"}],"department":[{"_id":"RoSe"},{"_id":"GradSch"}],"date_updated":"2026-08-04T05:57:21Z"},{"issue":"27","publisher":"American Chemical Society","date_published":"2026-06-15T00:00:00Z","date_updated":"2026-08-04T05:52:13Z","department":[{"_id":"PaSc"}],"abstract":[{"text":"The one-bond proton-carbon coupling constant (1JCH) is an insightful probe of carbohydrate configuration. Equatorial and axial protons at the C1 position typically exhibit distinct 1JCH values, enabling NMR measurements to distinguish α- and β-configurations in carbohydrates. In principle, such measurements could provide insights into carbohydrates in the cell walls of intact microbes. However, traditionally, these measurements are performed by solution NMR with carbohydrates that were extracted, solubilized and fractionated, leaving the biological relevance of the measurements uncertain. Here, we demonstrate that 1H-detected solid-state NMR with fast magic-angle spinning allows quantitative measurements of 1JCH couplings for mobile capsular polysaccharides, directly on submilligram amounts of pathogenic cells. Our approach is demonstrated on intact cells of the pathogenic yeast Cryptococcus neoformans. High-resolution proton-detected spectra enabled the determination of coupling constants for five mobile polysaccharide units of the cryptococcal capsule, revealing their native configurations and confirming previous solution NMR-based anomeric configuration assignments.","lang":"eng"}],"external_id":{"pmid":["42377973"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Lends, Alons","last_name":"Lends","first_name":"Alons"},{"first_name":"Gaelle","last_name":"Lamon","full_name":"Lamon, Gaelle"},{"last_name":"Vallet","first_name":"Alicia","full_name":"Vallet, Alicia"},{"last_name":"Grélard","first_name":"Axelle","full_name":"Grélard, Axelle"},{"first_name":"Estelle","last_name":"Morvan","full_name":"Morvan, Estelle"},{"full_name":"Aimanianda, Vishukumar","last_name":"Aimanianda","first_name":"Vishukumar"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Loquet, Antoine","last_name":"Loquet","first_name":"Antoine"}],"researchdata_availability":"no","citation":{"apa":"Lends, A., Lamon, G., Vallet, A., Grélard, A., Morvan, E., Aimanianda, V., … Loquet, A. (2026). On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.6c06064\">https://doi.org/10.1021/jacs.6c06064</a>","short":"A. Lends, G. Lamon, A. Vallet, A. Grélard, E. Morvan, V. Aimanianda, P. Schanda, A. Loquet, Journal of the American Chemical Society 148 (2026) 28037–28042.","ama":"Lends A, Lamon G, Vallet A, et al. On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. <i>Journal of the American Chemical Society</i>. 2026;148(27):28037-28042. doi:<a href=\"https://doi.org/10.1021/jacs.6c06064\">10.1021/jacs.6c06064</a>","chicago":"Lends, Alons, Gaelle Lamon, Alicia Vallet, Axelle Grélard, Estelle Morvan, Vishukumar Aimanianda, Paul Schanda, and Antoine Loquet. “On-Cell Detection of Polysaccharide One-Bond1Jch Couplings by Proton-Detected Solid-State NMR.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2026. <a href=\"https://doi.org/10.1021/jacs.6c06064\">https://doi.org/10.1021/jacs.6c06064</a>.","ieee":"A. Lends <i>et al.</i>, “On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR,” <i>Journal of the American Chemical Society</i>, vol. 148, no. 27. American Chemical Society, pp. 28037–28042, 2026.","mla":"Lends, Alons, et al. “On-Cell Detection of Polysaccharide One-Bond1Jch Couplings by Proton-Detected Solid-State NMR.” <i>Journal of the American Chemical Society</i>, vol. 148, no. 27, American Chemical Society, 2026, pp. 28037–42, doi:<a href=\"https://doi.org/10.1021/jacs.6c06064\">10.1021/jacs.6c06064</a>.","ista":"Lends A, Lamon G, Vallet A, Grélard A, Morvan E, Aimanianda V, Schanda P, Loquet A. 2026. On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR. Journal of the American Chemical Society. 148(27), 28037–28042."},"language":[{"iso":"eng"}],"oa_version":"None","das_tickbox":"0","quality_controlled":"1","supplementarymaterial":"yes","year":"2026","publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"22638","doi":"10.1021/jacs.6c06064","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"publication":"Journal of the American Chemical Society","OA_type":"closed access","scopus_import":"1","acknowledgement":"We thank the ANR (ANR-16-CE11-0020-02 to A. Loquet and V.A. and ANR-21-CE17-0032 to V.A.) as well as the Swiss National Science Foundation for early postdoc mobility project P2EZP2_184258 to A. Lends. This work has benefited from the Biophysical and Structural Chemistry Platform at Institut Européen de Chimie et Biologie IECB, Centre National de la Recherche Scientifique CNRS Unité d’Appui et de Recherche UAR 3033, INSERM US001, and the CNRS (IR-RMN FR3050 and Infranalytics FR2054).","date_created":"2026-08-03T13:20:41Z","pmid":1,"day":"15","article_processing_charge":"No","month":"06","volume":148,"intvolume":"       148","page":"28037-28042","title":"On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR"},{"das_tickbox":"0","quality_controlled":"1","supplementarymaterial":"no","publication_status":"epub_ahead","year":"2026","type":"journal_article","status":"public","has_accepted_license":"1","article_type":"original","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/S0017089526101074"}],"_id":"22644","doi":"10.1017/s0017089526101074","publication_identifier":{"issn":["0017-0895"],"eissn":["1469-509X"]},"publication":"Glasgow Mathematical Journal","OA_type":"hybrid","scopus_import":"1","OA_place":"publisher","acknowledgement":"I am deeply grateful to my advisor Tim Browning for suggesting this problem and for the many valuable discussions that shaped this work. I would also like to thank Efthymios Sofos, Matteo Verzobio, and Shuntaro Yamagishi for discussions and insights that contributed to this paper. I am also very grateful to the anonymous referee for their careful reading and for the considerable effort they put into improving the manuscript.","date_created":"2026-08-04T06:15:04Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"21","article_processing_charge":"Yes (via OA deal)","month":"07","title":"Liouville function, von Mangoldt function, and norm forms at random binary forms","page":"1-34","publisher":"Cambridge University Press","date_published":"2026-07-21T00:00:00Z","PlanS_conform":"1","arxiv":1,"date_updated":"2026-08-04T06:28:01Z","department":[{"_id":"TiBr"},{"_id":"GradSch"}],"abstract":[{"text":"We analyze the average behavior of various arithmetic functions at the values of degree 𝑑 binary forms ordered by height, with probability 1. This approach yields averaged versions of the Chowla conjecture and the Bateman–Horn conjecture for random binary forms. Furthermore, we show that the rational Hasse principle holds for almost all Châtelet varieties defined by a fixed norm form of degree 𝑒 and by varying binary forms of fixed degree 𝑑, provided 𝑒 divides 𝑑. This proves an average version of a conjecture of Colliot-Thélène.","lang":"eng"}],"mathsc":["11N32","11N37","11D57","11G35"],"ddc":["500"],"external_id":{"arxiv":["2506.18065"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yijie","last_name":"Diao","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","full_name":"Diao, Yijie","orcid":"0000-0002-4989-5330"}],"corr_author":"1","researchdata_availability":"no","citation":{"apa":"Diao, Y. (2026). Liouville function, von Mangoldt function, and norm forms at random binary forms. <i>Glasgow Mathematical Journal</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/s0017089526101074\">https://doi.org/10.1017/s0017089526101074</a>","short":"Y. Diao, Glasgow Mathematical Journal (2026) 1–34.","ama":"Diao Y. Liouville function, von Mangoldt function, and norm forms at random binary forms. <i>Glasgow Mathematical Journal</i>. 2026:1-34. doi:<a href=\"https://doi.org/10.1017/s0017089526101074\">10.1017/s0017089526101074</a>","chicago":"Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” <i>Glasgow Mathematical Journal</i>. Cambridge University Press, 2026. <a href=\"https://doi.org/10.1017/s0017089526101074\">https://doi.org/10.1017/s0017089526101074</a>.","ieee":"Y. Diao, “Liouville function, von Mangoldt function, and norm forms at random binary forms,” <i>Glasgow Mathematical Journal</i>. Cambridge University Press, pp. 1–34, 2026.","ista":"Diao Y. 2026. Liouville function, von Mangoldt function, and norm forms at random binary forms. Glasgow Mathematical Journal., 1–34.","mla":"Diao, Yijie. “Liouville Function, von Mangoldt Function, and Norm Forms at Random Binary Forms.” <i>Glasgow Mathematical Journal</i>, Cambridge University Press, 2026, pp. 1–34, doi:<a href=\"https://doi.org/10.1017/s0017089526101074\">10.1017/s0017089526101074</a>."},"language":[{"iso":"eng"}],"oa_version":"Published Version"},{"citation":{"ieee":"A. Kalinov, M. Ly, C. Hafner, and C. Wojtan, “Physics-inspired procedural texturing of extremely deformable surfaces,” <i>ACM Transactions on Graphics</i>, vol. 45, no. 4. Association for Computing Machinery, 2026.","chicago":"Kalinov, Aleksei, Mickaël Ly, Christian Hafner, and Chris Wojtan. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2026. <a href=\"https://doi.org/10.1145/3811353\">https://doi.org/10.1145/3811353</a>.","mla":"Kalinov, Aleksei, et al. “Physics-Inspired Procedural Texturing of Extremely Deformable Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 45, no. 4, 154, Association for Computing Machinery, 2026, doi:<a href=\"https://doi.org/10.1145/3811353\">10.1145/3811353</a>.","ista":"Kalinov A, Ly M, Hafner C, Wojtan C. 2026. Physics-inspired procedural texturing of extremely deformable surfaces. ACM Transactions on Graphics. 45(4), 154.","short":"A. Kalinov, M. Ly, C. Hafner, C. Wojtan, ACM Transactions on Graphics 45 (2026).","ama":"Kalinov A, Ly M, Hafner C, Wojtan C. Physics-inspired procedural texturing of extremely deformable surfaces. <i>ACM Transactions on Graphics</i>. 2026;45(4). doi:<a href=\"https://doi.org/10.1145/3811353\">10.1145/3811353</a>","apa":"Kalinov, A., Ly, M., Hafner, C., &#38; Wojtan, C. (2026). Physics-inspired procedural texturing of extremely deformable surfaces. <i>ACM Transactions on Graphics</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3811353\">https://doi.org/10.1145/3811353</a>"},"language":[{"iso":"eng"}],"oa_version":"Published Version","author":[{"id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","first_name":"Aleksei","full_name":"Kalinov, Aleksei","orcid":"0000-0003-2189-3904"},{"full_name":"Ly, Mickaël","last_name":"Ly","first_name":"Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"full_name":"Hafner, Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","researchdata_availability":"no","abstract":[{"lang":"eng","text":"The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation.\r\nWe present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge."}],"date_updated":"2026-08-04T09:07:44Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"ddc":["006"],"publisher":"Association for Computing Machinery","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/infinite-deformation-and-shape-computation/","relation":"press_release"}]},"conference":{"start_date":"2026-07-19","location":"Los Angeles, CA, United States","end_date":"2026-07-23","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"issue":"4","date_published":"2026-07-01T00:00:00Z","volume":45,"file":[{"content_type":"video/mp4","date_updated":"2026-05-29T13:19:33Z","file_size":77337231,"file_name":"tog454-article154-supplemental.mp4","success":1,"access_level":"open_access","date_created":"2026-05-29T13:19:33Z","checksum":"ea165bf731ddd3045f83878dcb833672","relation":"main_file","file_id":"21924","creator":"akalinov"},{"date_updated":"2026-05-29T13:19:37Z","content_type":"video/mp4","file_size":226633977,"file_name":"tog454-article154-video.mp4","success":1,"access_level":"open_access","checksum":"6274cfb15ea5ba7324b74afc7b0d9629","date_created":"2026-05-29T13:19:37Z","file_id":"21925","creator":"akalinov","relation":"main_file"},{"checksum":"9d41b322a7876be9a3311017b9973183","date_created":"2026-05-29T13:19:33Z","relation":"main_file","file_id":"21926","creator":"akalinov","success":1,"access_level":"open_access","file_name":"tog454-article154-supplemental.pdf","date_updated":"2026-05-29T13:19:33Z","content_type":"application/pdf","file_size":6793867},{"access_level":"open_access","success":1,"file_id":"21927","creator":"akalinov","relation":"main_file","date_created":"2026-05-29T13:19:36Z","checksum":"51bc60d2de867fbfa570652dec7993b4","file_size":84173392,"content_type":"application/pdf","date_updated":"2026-05-29T13:19:36Z","file_name":"tog454-article154-main-1.pdf"}],"article_processing_charge":"Yes","month":"07","title":"Physics-inspired procedural texturing of extremely deformable surfaces","intvolume":"        45","keyword":["Procedural animation"],"project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"publication":"ACM Transactions on Graphics","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","scopus_import":"1","OA_type":"gold","OA_place":"publisher","acknowledgement":"We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback. We also thank Jonathan Gagnon for their help with running the Lapped Textures codes and SideFX for the Houdini Education software licenses.\r\nImages in Fig. 2 by Kisoulou and Vultured on Unsplash, Michal Jarmoluk and Public Domain Pictures from Pixabay and Hawai‘i Volcanoes NPS on flickr. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing and was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","date_created":"2026-05-29T13:25:16Z","article_type":"original","oa":1,"has_accepted_license":"1","article_number":"154","_id":"21923","publication_identifier":{"issn":["0730-0301"]},"doi":"10.1145/3811353","das_tickbox":"0","publication_status":"published","file_date_updated":"2026-05-29T13:19:37Z","year":"2026","type":"journal_article","status":"public","quality_controlled":"1","supplementarymaterial":"yes"},{"citation":{"ista":"Zoller B, Benichou A, Gregor T, Tkačik G. 2026. Invariant nonequilibrium dynamics in gene regulation optimize information flow. Proceedings of the National Academy of Sciences of the United States of America. 123(28), e2524855123.","mla":"Zoller, Benjamin, et al. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 123, no. 28, e2524855123, National Academy of Sciences, 2026, doi:<a href=\"https://doi.org/10.1073/pnas.2524855123\">10.1073/pnas.2524855123</a>.","chicago":"Zoller, Benjamin, Alexis Benichou, Thomas Gregor, and Gašper Tkačik. “Invariant Nonequilibrium Dynamics in Gene Regulation Optimize Information Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2026. <a href=\"https://doi.org/10.1073/pnas.2524855123\">https://doi.org/10.1073/pnas.2524855123</a>.","ieee":"B. Zoller, A. Benichou, T. Gregor, and G. Tkačik, “Invariant nonequilibrium dynamics in gene regulation optimize information flow,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 123, no. 28. National Academy of Sciences, 2026.","apa":"Zoller, B., Benichou, A., Gregor, T., &#38; Tkačik, G. (2026). Invariant nonequilibrium dynamics in gene regulation optimize information flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2524855123\">https://doi.org/10.1073/pnas.2524855123</a>","ama":"Zoller B, Benichou A, Gregor T, Tkačik G. Invariant nonequilibrium dynamics in gene regulation optimize information flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2026;123(28). doi:<a href=\"https://doi.org/10.1073/pnas.2524855123\">10.1073/pnas.2524855123</a>","short":"B. Zoller, A. Benichou, T. Gregor, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 123 (2026)."},"oa_version":"Published Version","language":[{"iso":"eng"}],"dataavailabilitystatement":"Software code data have been deposited in Institute Pasteur GitHub (https://gitlab.pasteur.fr/tglab/invariantpromoterdynamicspaper) (51).","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Benjamin","last_name":"Zoller","full_name":"Zoller, Benjamin"},{"full_name":"Benichou, Alexis","last_name":"Benichou","first_name":"Alexis","id":"3a67230c-5fc0-11ef-a673-de9a2ffadafe"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"researchdata_availability":"yes","corr_author":"1","department":[{"_id":"GaTk"}],"date_updated":"2026-08-04T09:21:10Z","abstract":[{"text":"Eukaryotic gene regulation relies on stochastic yet controlled promoter switching, in which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies have revealed a surprising invariance of the “switching correlation time” (TC)—the characteristic decay time of the autocorrelation function of promoter activity fluctuations—across gene expression levels in multiple genes and organisms. A biophysically plausible explanation for this invariance has so far been lacking. Here, we show that this empirical constraint imposes stringent requirements on minimal yet realistic models of transcriptional regulation. Specifically, reproducing TC–invariance requires regulatory architectures with at least four internal states and nonequilibrium dynamics that break detailed balance. Using Bayesian inference on Drosophila gap gene expression data, we demonstrate that such models i) quantitatively reproduce the observed TC–invariance, ii) remain robust to parameter perturbations, and iii) maximize information transmission from transcription factor concentration to gene expression. Remarkably, the TC-invariant modulation strategy we identify as optimal closely parallels contemporary control-theoretic results on the modulation of stochastic switching systems. Taken together, our results suggest that eukaryotic transcriptional regulation operates in a nonequilibrium regime to balance precision, reaction-rate limitations, and energy dissipation, thereby achieving near-optimal information transmission under fundamental physical constraints.","lang":"eng"}],"external_id":{"pmid":["42406962"]},"ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"28","publisher":"National Academy of Sciences","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/the-art-of-proper-flickering/","description":"News on ISTA website"}]},"date_published":"2026-07-14T00:00:00Z","month":"07","article_processing_charge":"Yes","file":[{"file_size":24580098,"date_updated":"2026-07-20T13:12:47Z","content_type":"application/pdf","file_name":"2026_PNAS_Zoller.pdf","access_level":"open_access","success":1,"creator":"dernst","file_id":"22376","relation":"main_file","date_created":"2026-07-20T13:12:47Z","checksum":"f4d82dd706ff1629db68d71190288350"}],"volume":123,"project":[{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"intvolume":"       123","title":"Invariant nonequilibrium dynamics in gene regulation optimize information flow","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2026-07-19T22:01:46Z","OA_place":"publisher","acknowledgement":"This work was supported by the French NationalResearch Agency (ANR-20-CE12-0028 “ChroDynE” and ANR-23-CE13-0021“GastruCyp” and ANR-10 LABX-73 “Revive;” all T.G.), and by funding from theEuropean Research Council (ERC-2023-SyG, “Dynatrans,” 101118866, T.G. andG.T.). This work was also supported in part by the U.S. NSF, through the Centerfor the Physics of Biological Function (PHY-1734030, T.G.), and by NIH GrantsR01GM097275, U01DA047730, and U01DK127429 (T.G.)","scopus_import":"1","OA_type":"hybrid","day":"14","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"pmid":1,"has_accepted_license":"1","oa":1,"article_type":"original","doi":"10.1073/pnas.2524855123","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"22363","article_number":"e2524855123","das_tickbox":"1","supplementarymaterial":"yes","quality_controlled":"1","status":"public","type":"journal_article","file_date_updated":"2026-07-20T13:12:47Z","publication_status":"published","year":"2026"},{"title":"Distributing stationary qubit entanglement through a nonlocal squeezed reservoir","project":[{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105"},{"grant_number":"101089099","name":"Cavity Quantum Electro Optics: Microwave photonics with nonclassical states","_id":"bdadfa0d-d553-11ed-ba76-fb85edbd456a"}],"intvolume":"        16","file":[{"file_name":"2026_PhysicalReviewX_AndresJuanes.pdf","content_type":"application/pdf","date_updated":"2026-08-04T05:40:41Z","file_size":5301241,"checksum":"2bab109f975545d096c21dd72c738b6e","date_created":"2026-08-04T05:40:41Z","relation":"main_file","creator":"dernst","file_id":"22640","success":1,"access_level":"open_access"}],"volume":16,"month":"07","article_processing_charge":"Yes","day":"13","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"acknowledgement":"We thank A. Trioni and C. N. Borja for assistance in device fabrication, C. Siegele for fruitful discussions, IBM for donating the JPC used in this work, and the MIBA machine shop and the ISTA nanofabrication facility for technical support. This work was funded in part by the Austrian Science Fund (FWF) through the excellence cluster quantA 10.55776/COE1 and the SFB BeyondC 10.55776/F71, as well as the European Union—NextGenerationEU, and ISTA. J. F. and L. K. acknowledge support from the Horizon Europe Program HORIZON-CL4-2022-QUANTUM-01-SGA via Project No. 101113946 OpenSuperQPlus100, and J. F. from the European Research Council No. 101089099 (ERC CoG cQEO). J. A. acknowledges support from the QUANTERA project MOLAR with reference No. PCI2024-153449, funded by MICIU/AEI/10.13039/501100011033 and the European Union. This research is part of the Munich Quantum Valley, which is supported by the Bavarian state government with funds from the Hightech Agenda Bayern Plus.","date_created":"2026-08-03T13:19:31Z","OA_place":"publisher","DOAJ_listed":"1","scopus_import":"1","OA_type":"gold","publication":"Physical Review X","article_number":"031005","publication_identifier":{"eissn":["2160-3308"]},"doi":"10.1103/r4jt-j39w","_id":"22637","oa":1,"article_type":"original","has_accepted_license":"1","status":"public","type":"journal_article","publication_status":"published","year":"2026","file_date_updated":"2026-08-04T05:40:41Z","supplementarymaterial":"yes","quality_controlled":"1","das_tickbox":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"apa":"Andres Juanes, A., Agustí, J., Sett, R., Redchenko, E., Kapoor, L., Hawaldar, S., … Fink, J. M. (2026). Distributing stationary qubit entanglement through a nonlocal squeezed reservoir. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/r4jt-j39w\">https://doi.org/10.1103/r4jt-j39w</a>","short":"A. Andres Juanes, J. Agustí, R. Sett, E. Redchenko, L. Kapoor, S. Hawaldar, P. Rabl, J.M. Fink, Physical Review X 16 (2026).","ama":"Andres Juanes A, Agustí J, Sett R, et al. Distributing stationary qubit entanglement through a nonlocal squeezed reservoir. <i>Physical Review X</i>. 2026;16(3). doi:<a href=\"https://doi.org/10.1103/r4jt-j39w\">10.1103/r4jt-j39w</a>","chicago":"Andres Juanes, Alejandro, J. Agustí, Riya Sett, Elena Redchenko, Lucky Kapoor, Samarth Hawaldar, P. Rabl, and Johannes M Fink. “Distributing Stationary Qubit Entanglement through a Nonlocal Squeezed Reservoir.” <i>Physical Review X</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/r4jt-j39w\">https://doi.org/10.1103/r4jt-j39w</a>.","ieee":"A. Andres Juanes <i>et al.</i>, “Distributing stationary qubit entanglement through a nonlocal squeezed reservoir,” <i>Physical Review X</i>, vol. 16, no. 3. American Physical Society, 2026.","ista":"Andres Juanes A, Agustí J, Sett R, Redchenko E, Kapoor L, Hawaldar S, Rabl P, Fink JM. 2026. Distributing stationary qubit entanglement through a nonlocal squeezed reservoir. Physical Review X. 16(3), 031005.","mla":"Andres Juanes, Alejandro, et al. “Distributing Stationary Qubit Entanglement through a Nonlocal Squeezed Reservoir.” <i>Physical Review X</i>, vol. 16, no. 3, 031005, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/r4jt-j39w\">10.1103/r4jt-j39w</a>."},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"researchdata_availability":"yes","corr_author":"1","author":[{"full_name":"Andres Juanes, Alejandro","last_name":"Andres Juanes","first_name":"Alejandro","id":"7601fd3a-5355-11ee-ae5a-a20ca6f3cfb9"},{"last_name":"Agustí","first_name":"J.","full_name":"Agustí, J."},{"last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7641-8348","full_name":"Sett, Riya"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"},{"last_name":"Kapoor","first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky"},{"orcid":"0000-0002-1965-4309","full_name":"Hawaldar, Samarth","first_name":"Samarth","last_name":"Hawaldar","id":"221708e1-1ff6-11ee-9fa6-85146607433e"},{"first_name":"P.","last_name":"Rabl","full_name":"Rabl, P."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"dataavailabilitystatement":"The data that support the findings of this article are openly available  https://zenodo.org/records/19099731.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["530"],"abstract":[{"lang":"eng","text":"The distribution of entanglement across distant qubits is a central challenge for the operation of scalable quantum computers and large-scale quantum networks. Existing approaches rely on deterministic state transfer, or probabilistic protocols that require active control or measurements and postselection. Here, we demonstrate a fundamentally different, fully autonomous process, where two remote qubits are entangled through their coupling to a quantum-correlated photonic reservoir. In our experiment, a Josephson parametric converter produces a Gaussian, continuous-variable entangled state of propagating microwave fields that drives two spatially separated superconducting transmon qubits into a stationary, discrete-variable entangled state. We also show how qubit tomography unlocks a direct and sensitive verification of two-mode squeezing in the microwave domain. These results establish networks of qubits interfaced with distributed continuous-variable entangled states as a powerful platform for foundational studies and quantum-technology applications."}],"department":[{"_id":"JoFi"},{"_id":"GradSch"}],"date_updated":"2026-08-04T09:18:57Z","PlanS_conform":"1","date_published":"2026-07-13T00:00:00Z","publisher":"American Physical Society","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/quantum-bath-syncs-distant-qubits/","description":"News on ISTA website"}]},"issue":"3"},{"article_type":"original","_id":"22315","doi":"10.1126/science.adw6568","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"article_number":"eadw6568","das_tickbox":"1","quality_controlled":"1","supplementarymaterial":"yes","publication_status":"published","year":"2026","status":"public","type":"journal_article","month":"07","article_processing_charge":"No","volume":393,"intvolume":"       393","project":[{"name":"Cyclic nucleotides as second messengers in plants","grant_number":"101142681","_id":"8f347782-16d5-11f0-9cad-8c19706ee739"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"title":"Roots navigate around decay regions by sensing local pH gradients","publication":"Science","OA_type":"closed access","scopus_import":"1","date_created":"2026-07-13T14:57:10Z","acknowledgement":"We are grateful to H. Guo and L. Liu (Department of Biology, Southern University of Science and Technology) for providing the rgf1/2/3, rgi1/2/3/4, tpst-1, and pepr1/2 lines. We thank K.-h. Liu (College of Life Science, Northwest A&F University) for generously providing the ABA biosensor nlsABACUS2-400n. We also thank J. Li and J. Chang (School of Life Sciences, Lanzhou University) for providing the ahk2-5/cre1-2, ahp1/2/3, arr16/arr17, and pTCSn::GFP lines. Our thanks further extend to D. Qian, also from the School of Life Sciences at Lanzhou University, for sharing Arabidopsis line pTUB6::mCherry-TUB6. We are grateful to Y. Zhao (CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) for providing nced3/5, snrk2.2/2.3/2.6, and pyl duodecuple mutants. We also acknowledge the Teaching and Research Core Facility at the College of Life Sciences, Northwest A&F University, particularly N. Fan, for their invaluable technical assistance. We also thank Life Science Research Core Services (LSRCS), Northwest A&F University, for helping with characterization, including CLSM (X. Liu). Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China JYB2025XDXM706 (Y.Z.); Qin Chuangyuan High-level Innovation and Entrepreneurship Talent Program QCYRCXM-2022-237 (Y.Z.); Fundamental Research Funds for the Central Universities K20200168 (Y.Z.); National Natural Science Foundation of China 32570375 (Y.Z.); National Natural Science Foundation of China 32400699 (A.Z.); European Research Council (ERC, CYNIPS) 101142681 (J.F.); Austrian Science Fund (FWF): P 37051-B (J.F.).","pmid":1,"day":"09","date_updated":"2026-08-04T09:22:49Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Plant tropisms enable roots to navigate complex soils by responding to directional environmental cues. Biological decay, although central to nutrient cycling, also creates microbially active and potentially hostile niches. In this work, we identified “saprotropism,” a previously unrecognized growth response that enables roots to actively bend away from decaying plant-derived matter. Fungal-driven microbial decomposition released organic acids and formed stable pH gradients in surrounding soil, allowing roots to pinpoint decay without direct contact. Root epidermal cells sensed this acidic gradient through the root meristem growth factor peptide-receptor module, converting external pH asymmetry into asymmetric abscisic acid (ABA) distribution. ABA asymmetry drove microtubule reorganization, which was decoded into decay-avoidant root bending. Together, these findings establish microbial decay–derived chemical gradients as an instructive signal for root navigation and expand the framework of microbe-soil-plant communication.","lang":"eng"}],"external_id":{"pmid":["42424472"]},"issue":"6807","related_material":{"link":[{"url":"https://ista.ac.at/en/news/roots-steer-clear-of-plant-rot/","description":"News on ISTA website","relation":"press_release"}]},"publisher":"American Association for the Advancement of Science","date_published":"2026-07-09T00:00:00Z","citation":{"apa":"Bao, Z., Wang, H., Zhang, A., Gao, R., Gu, W., Fan, N., … Zhang, Y. (2026). Roots navigate around decay regions by sensing local pH gradients. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adw6568\">https://doi.org/10.1126/science.adw6568</a>","ama":"Bao Z, Wang H, Zhang A, et al. Roots navigate around decay regions by sensing local pH gradients. <i>Science</i>. 2026;393(6807). doi:<a href=\"https://doi.org/10.1126/science.adw6568\">10.1126/science.adw6568</a>","short":"Z. Bao, H. Wang, A. Zhang, R. Gao, W. Gu, N. Fan, J. Friml, Y. Zhang, Science 393 (2026).","ista":"Bao Z, Wang H, Zhang A, Gao R, Gu W, Fan N, Friml J, Zhang Y. 2026. Roots navigate around decay regions by sensing local pH gradients. Science. 393(6807), eadw6568.","mla":"Bao, Zhulatai, et al. “Roots Navigate around Decay Regions by Sensing Local PH Gradients.” <i>Science</i>, vol. 393, no. 6807, eadw6568, American Association for the Advancement of Science, 2026, doi:<a href=\"https://doi.org/10.1126/science.adw6568\">10.1126/science.adw6568</a>.","chicago":"Bao, Zhulatai, Huihui Wang, Ai Zhang, Ruxi Gao, Wen Gu, Ni Fan, Jiří Friml, and Yuzhou Zhang. “Roots Navigate around Decay Regions by Sensing Local PH Gradients.” <i>Science</i>. American Association for the Advancement of Science, 2026. <a href=\"https://doi.org/10.1126/science.adw6568\">https://doi.org/10.1126/science.adw6568</a>.","ieee":"Z. Bao <i>et al.</i>, “Roots navigate around decay regions by sensing local pH gradients,” <i>Science</i>, vol. 393, no. 6807. American Association for the Advancement of Science, 2026."},"language":[{"iso":"eng"}],"oa_version":"None","dataavailabilitystatement":"All data are available in the manuscript or the supplementary materials. The raw RNA-seq data have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE315473. Microbiome sequencing data have been deposited in the Sequence Read Archive (SRA) under BioProject number PRJNA1397137. Materials are available upon request from the corresponding author.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Zhulatai","last_name":"Bao","full_name":"Bao, Zhulatai"},{"last_name":"Wang","first_name":"Huihui","full_name":"Wang, Huihui"},{"full_name":"Zhang, Ai","last_name":"Zhang","first_name":"Ai"},{"full_name":"Gao, Ruxi","first_name":"Ruxi","last_name":"Gao"},{"last_name":"Gu","first_name":"Wen","full_name":"Gu, Wen"},{"first_name":"Ni","last_name":"Fan","full_name":"Fan, Ni"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang"}],"researchdata_availability":"yes"},{"pmid":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"17","scopus_import":"1","OA_type":"hybrid","acknowledgement":"We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical assistance; A. Stichelberger and S. Liegenfeld for the management of our animal colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance; C. Jansen and the Scientific Computing Facility for bioinformatics support and technical assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted in Fig. 1; and all members of the laboratory of G.N. for their support and discussions. This study was supported by the Scientific Service Units of ISTA through resources provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities, member of the Vienna BioCenter. This work was supported by a European Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding provided by Institute of Science and Technology (IST Austria).","OA_place":"publisher","date_created":"2026-07-13T09:47:21Z","publication":"Nature","title":"Cortical development dynamics across autism spectrum disorder mouse models","project":[{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","grant_number":"101044865"},{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232","call_identifier":"FWF"},{"_id":"ebb38b5d-77a9-11ec-83b8-a42e08120a88","name":"Neurobiology of anxiety in autism spectrum disorders","grant_number":"FG1803 49015"}],"article_processing_charge":"Yes (via OA deal)","month":"06","publication_status":"epub_ahead","year":"2026","type":"journal_article","status":"public","quality_controlled":"1","supplementarymaterial":"yes","_id":"22295","main_file_link":[{"url":"https://doi.org/10.1038/s41586-026-10679-1","open_access":"1"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"doi":"10.1038/s41586-026-10679-1","article_type":"original","oa":1,"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"corr_author":"1","researchdata_availability":"yes","author":[{"full_name":"Schwarz, Lena A","first_name":"Lena A","last_name":"Schwarz","id":"29A8453C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","first_name":"Christoph"},{"first_name":"Sergey","last_name":"Isaev","full_name":"Isaev, Sergey"},{"full_name":"Lisi, Michela","id":"39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c","first_name":"Michela","last_name":"Lisi"},{"last_name":"Malzl","first_name":"Daniel","full_name":"Malzl, Daniel"},{"full_name":"Büschl, Christoph","first_name":"Christoph","last_name":"Büschl","id":"2a8c054c-0913-11ee-9159-f8ef515809ed"},{"full_name":"Ladstätter, Sabrina","last_name":"Ladstätter","first_name":"Sabrina"},{"first_name":"Bárbara","last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara"},{"last_name":"Barel","first_name":"Matteo","id":"8959927b-2236-11ed-bd6e-ea83d94ade0e","full_name":"Barel, Matteo"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173"},{"first_name":"Chaitanya","last_name":"Chintaluri","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya"},{"full_name":"Gorkiewicz, Sarah","first_name":"Sarah","last_name":"Gorkiewicz","id":"f141a35d-15a9-11ec-9fb2-fef6becc7b6f"},{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad"},{"full_name":"Belinova, Tereza","last_name":"Belinova","first_name":"Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368"},{"full_name":"Reichl, Stephan","first_name":"Stephan","last_name":"Reichl"},{"id":"dd6d52f2-c50d-11eb-9548-bcf0ff82b344","last_name":"Sendžikaitė","first_name":"Gintarė","full_name":"Sendžikaitė, Gintarė"},{"full_name":"Arcot Jayaram, Satish","orcid":"0000-0002-2479-2669","last_name":"Arcot Jayaram","first_name":"Satish","id":"b0bbee33-09f7-11eb-909c-8b358058d28a"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"last_name":"Adameyko","first_name":"Igor","full_name":"Adameyko, Igor"},{"full_name":"Kharchenko, Peter Vasili","id":"0095641e-7eb7-11f1-8665-aec51a2ab5e0","first_name":"Peter Vasili","last_name":"Kharchenko"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"dataavailabilitystatement":"Single-nucleus multiomics data are available from the Gene Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz). Source data are provided with this paper. Scripts and analyses that support the main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter, B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi, T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M. Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino, Nature (2026).","ama":"Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across autism spectrum disorder mouse models. <i>Nature</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41586-026-10679-1\">10.1038/s41586-026-10679-1</a>","apa":"Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino, G. (2026). Cortical development dynamics across autism spectrum disorder mouse models. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-026-10679-1\">https://doi.org/10.1038/s41586-026-10679-1</a>","ieee":"L. A. Schwarz <i>et al.</i>, “Cortical development dynamics across autism spectrum disorder mouse models,” <i>Nature</i>. Springer Nature, 2026.","chicago":"Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl, Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” <i>Nature</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41586-026-10679-1\">https://doi.org/10.1038/s41586-026-10679-1</a>.","mla":"Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum Disorder Mouse Models.” <i>Nature</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41586-026-10679-1\">10.1038/s41586-026-10679-1</a>.","ista":"Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics across autism spectrum disorder mouse models. Nature."},"PlanS_conform":"1","date_published":"2026-06-17T00:00:00Z","publisher":"Springer Nature","related_material":{"link":[{"url":"https://ista.ac.at/en/news/patterns-in-genetic-chaos/","description":"News on ISTA website","relation":"press_release"}]},"ddc":["570"],"external_id":{"pmid":["42310454"]},"abstract":[{"lang":"eng","text":"Despite the functional diversity of over 100 causal genes1,2,3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD."}],"date_updated":"2026-08-04T09:29:55Z","department":[{"_id":"AnKi"},{"_id":"GaNo"},{"_id":"TiVo"},{"_id":"ScienComp"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"PreCl"}]},{"has_accepted_license":"1","article_type":"original","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-026-03166-5"}],"_id":"22268","doi":"10.1038/s41587-026-03166-5","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"das_tickbox":"1","quality_controlled":"1","supplementarymaterial":"yes","year":"2026","publication_status":"epub_ahead","status":"public","type":"journal_article","article_processing_charge":"Yes (via OA deal)","month":"06","title":"Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles","publication":"Nature Biotechnology","OA_type":"hybrid","scopus_import":"1","acknowledgement":"A. Marx acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. A.M.B. and P.S. are supported by the Institute of Science and Technology Austria Internal Project Call grant Generative Protein NMR. S.V. was supported in part by funding from the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard. Open access funding provided by Institute of Science and Technology (IST Austria).","OA_place":"publisher","date_created":"2026-07-12T22:02:19Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"day":"29","date_updated":"2026-08-04T09:25:18Z","department":[{"_id":"PaSc"},{"_id":"AlBr"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"AlphaFold3 predicts highly accurate protein structures from sequence but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work, we show that AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM) experiments and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology generates compact structural ensembles whose ensemble-averaged observables agree with experiment, with fewer distance restraint violations than traditionally resolved NMR structures and with unmodeled alternate conformations uncovered in electron density. This methodology paves the way for experimentally aware predictive models that generate structural ensembles consistent with the measurements, potentially over multiple modalities, and that can be further refined toward thermodynamically grounded ensembles by incorporating energetics."}],"ddc":["570"],"external_id":{"pmid":["42374114"]},"publisher":"Springer Nature","related_material":{"link":[{"url":"https://ista.ac.at/en/news/toward-experiment-guided-alphafold/","description":"News on ISTA website","relation":"press_release"}]},"date_published":"2026-06-29T00:00:00Z","PlanS_conform":"1","citation":{"apa":"Maddipatla, S. A., Sellam, N. E., Bojan, M. I., Masalitin, V., Vedula, S., Schanda, P., … Bronstein, A. M. (2026). Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-026-03166-5\">https://doi.org/10.1038/s41587-026-03166-5</a>","ama":"Maddipatla SA, Sellam NE, Bojan MI, et al. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. <i>Nature Biotechnology</i>. 2026. doi:<a href=\"https://doi.org/10.1038/s41587-026-03166-5\">10.1038/s41587-026-03166-5</a>","short":"S.A. Maddipatla, N.E. Sellam, M.I. Bojan, V. Masalitin, S. Vedula, P. Schanda, A. Marx, A.M. Bronstein, Nature Biotechnology (2026).","ista":"Maddipatla SA, Sellam NE, Bojan MI, Masalitin V, Vedula S, Schanda P, Marx A, Bronstein AM. 2026. Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles. Nature Biotechnology.","mla":"Maddipatla, Sai A., et al. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” <i>Nature Biotechnology</i>, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41587-026-03166-5\">10.1038/s41587-026-03166-5</a>.","chicago":"Maddipatla, Sai A, Nadav E Sellam, Meital I Bojan, Vova Masalitin, Sanketh Vedula, Paul Schanda, Ailie Marx, and Alex M. Bronstein. “Experiment-Guided AlphaFold3 Resolves Measurement-Consistent Protein Ensembles.” <i>Nature Biotechnology</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41587-026-03166-5\">https://doi.org/10.1038/s41587-026-03166-5</a>.","ieee":"S. A. Maddipatla <i>et al.</i>, “Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles,” <i>Nature Biotechnology</i>. Springer Nature, 2026."},"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","dataavailabilitystatement":"All structures and metrics reported in this paper are openly available on Harvard Dataverse - https://doi.org/10.7910/DVN/PLYUHN. All code is openly available on GitHub (https://github.com/sai-advaith/guided_alphafold); the version used for this paper (version 0.9.1) is permanently archived on Zenodo https://doi.org/10.5281/zenodo.17307005","author":[{"id":"e957f5e5-91c9-11f0-a95f-e090f66ecb4d","last_name":"Maddipatla","first_name":"Sai A","full_name":"Maddipatla, Sai A"},{"first_name":"Nadav E","last_name":"Sellam","id":"ef280fe0-91c9-11f0-a95f-8dea3f5bc513","full_name":"Sellam, Nadav E"},{"last_name":"Bojan","first_name":"Meital I","id":"11d88cf5-91ca-11f0-a95f-edf9f08f47b7","full_name":"Bojan, Meital I"},{"id":"ff7958eb-91c9-11f0-a95f-f3bf65828cf6","first_name":"Vova","last_name":"Masalitin","full_name":"Masalitin, Vova"},{"full_name":"Vedula, Sanketh","first_name":"Sanketh","last_name":"Vedula"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"},{"first_name":"Alexander","last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730"}],"corr_author":"1","researchdata_availability":"yes"},{"keyword":["direct genetic effects","DGE","indirect genetic effects","IGE","parent-of-origin effects","phenotypic variation","assortative mating","within-family GWAS","MoBa","EstBB"],"project":[{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk"}],"intvolume":"         6","title":"Separating direct, indirect, and parent-of-origin genetic effects in the human population","month":"07","article_processing_charge":"Yes","file":[{"file_name":"2026_CellGenomics_Kraetschmer.pdf","file_size":3679297,"date_updated":"2026-07-28T07:24:50Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"22597","date_created":"2026-07-28T07:24:50Z","checksum":"f896b510480d2d4e4a7fd46c2e2761f4","access_level":"open_access","success":1}],"volume":6,"date_created":"2026-06-10T07:39:08Z","acknowledgement":"We thank Zoltan Kutalik, Peter Visscher, and members of the Robinson group at ISTA for their comments, which improved this manuscript. This work was funded by an SNSF Eccellenza Grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria.\r\nThe Norwegian Mother, Father, and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. We thank the Norwegian Institute of Public Health (NIPH) for generating high-quality genomic data. The research is part of the HARVEST collaboration, supported by the Research Council of Norway (#229624). We also thank the NORMENT Center for providing genotype data, funded by the Research Council of Norway (#223273), South East Norway Health Authorities, and Stiftelsen Kristian Gerhard Jebsen, and in collaboration with deCODE Genetics. We further thank the Center for Diabetes Research, the University of Bergen for providing genotype data funded by the ERC AdG project SELECTionPREDISPOSED, Stiftelsen Kristian Gerhard Jebsen, Trond Mohn Foundation, the Research Council of Norway, the Novo Nordisk Foundation, the University of Bergen, and the Western Norway Health Authorities. The MoBa work was performed on the TSD (Tjeneste for Sensitive Data) facilities, owned by the University of Oslo, operated and developed by the TSD service group at the University of Oslo, IT Department (USIT, tsd-drift@usit.uio.no). E.Y. is supported by the European Union (grant numbers 101045526 and 101073237) and the Research Council of Norway (grant numbers 336078, 288083, and 331640).\r\nWe would like to acknowledge the participants and investigators of the Generation Scotland Cohort study. Generation Scotland received core support from the Chief Scientist Office of the Scottish Government Health Directorates (CZD/16/6) and the Scottish Funding Council (HR03006). Genotyping and methylation typing of the GS:SFHS samples was carried out by the Genetics Core Laboratory at the Wellcome Trust Clinical Research Facility, Edinburgh, Scotland and was funded by the Medical Research Council UK and the Wellcome Trust (Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally” [STRADL] ref. 104036/Z/14/Z).\r\nWe would like to thank and acknowledge the participants and investigators of the Estonian Biobank (EstBB) study. The research was conducted using the Estonian Center of Genomics/Roadmap II funded by the Estonian Research Council (project number TT17).\r\nNorwegian analyses were performed on resources provided by Sigma2 - the National Infrastructure for High-Performance Computing and Data Storage in Norway. Estonian Data analysis was carried out in the High-Performance Computing Center cloud provided by University of Tartu. Analysis of the Generation Scotland data and the summary statistics obtained from the other analyses was conducted at IST Austria and is supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","OA_place":"publisher","DOAJ_listed":"1","OA_type":"gold","scopus_import":"1","day":"08","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"pmid":1,"publication":"Cell Genomics","doi":"10.1016/j.xgen.2026.101277","publication_identifier":{"eissn":["2666-979X"]},"_id":"21987","article_number":"101277","has_accepted_license":"1","oa":1,"article_type":"original","supplementarymaterial":"yes","quality_controlled":"1","type":"journal_article","status":"public","year":"2026","publication_status":"published","file_date_updated":"2026-07-28T07:24:50Z","das_tickbox":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"short":"I. Krätschmer, L. Hegemann, R.J. Hofmeister, E.C. Corfield, M. Mahmoudi, O. Delaneau, O.A. Andreassen, A. Campbell, C. Hayward, R.E. Marioni, E. Ystrom, A. Havdahl, M.R. Robinson, Cell Genomics 6 (2026).","ama":"Krätschmer I, Hegemann L, Hofmeister RJ, et al. Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. 2026;6(7). doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>","apa":"Krätschmer, I., Hegemann, L., Hofmeister, R. J., Corfield, E. C., Mahmoudi, M., Delaneau, O., … Robinson, M. R. (2026). Separating direct, indirect, and parent-of-origin genetic effects in the human population. <i>Cell Genomics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>","ieee":"I. Krätschmer <i>et al.</i>, “Separating direct, indirect, and parent-of-origin genetic effects in the human population,” <i>Cell Genomics</i>, vol. 6, no. 7. Elsevier, 2026.","chicago":"Krätschmer, Ilse, Laura Hegemann, Robin J. Hofmeister, Elizabeth C. Corfield, Mahdi Mahmoudi, Olivier Delaneau, Ole A. Andreassen, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">https://doi.org/10.1016/j.xgen.2026.101277</a>.","mla":"Krätschmer, Ilse, et al. “Separating Direct, Indirect, and Parent-of-Origin Genetic Effects in the Human Population.” <i>Cell Genomics</i>, vol. 6, no. 7, 101277, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.xgen.2026.101277\">10.1016/j.xgen.2026.101277</a>.","ista":"Krätschmer I, Hegemann L, Hofmeister RJ, Corfield EC, Mahmoudi M, Delaneau O, Andreassen OA, Campbell A, Hayward C, Marioni RE, Ystrom E, Havdahl A, Robinson MR. 2026. Separating direct, indirect, and parent-of-origin genetic effects in the human population. Cell Genomics. 6(7), 101277."},"researchdata_availability":"yes","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","dataavailabilitystatement":"Information on how to access the MoBaPsychGen post-imputation QC data are available here: https://www.fhi.no/en/me/the-psychgen-centre-for-genetic-epidemiology-and-mental-health/access-to-genetic-data-after-quality-control-by-the-mobapsychgen-pipeline-v/.\r\nEstonian Biobank data (https://genomics.ut.ee/en/content/estonian-biobank) were used in this project. For access to be granted to the Estonian Biobank genotypic and corresponding phenotypic data, a preliminary application must be presented to the oversight committee, who must first approve the project. Ethics permission must then be obtained from the Estonian Committee on Bioethics and Human Research. Finally, a full project must be submitted and approved by the Estonian Biobank.\r\nAccess to the Generation Scotland data is available with appropriate permission from the Generation Scotland Access Committee. Applications should be made to access@generationscotland.org (https://genscot.ed.ac.uk/).\r\nThe code for JODIE developed in this work is open source and is publicly available on zenodo (https://doi.org/10.5281/zenodo.19593928) and GitHub (https://github.com/medical-genomics-group/JODIE).\r\nHaplotype Reference Consortium Release 1.1 data (https://ega-archive.org/datasets/EGAD00001002729) are available by application to a Data Access Committee (DAC) of the Wellcome Trust Sanger Institute.\r\nThe Common Metabolic Diseases Atlas can be accessed here: https://cmdga.org.","author":[{"full_name":"Krätschmer, Ilse","orcid":"0000-0002-5636-9259","id":"30d4014e-7753-11eb-b44b-db6d61112e73","last_name":"Krätschmer","first_name":"Ilse"},{"full_name":"Hegemann, Laura","last_name":"Hegemann","first_name":"Laura"},{"full_name":"Hofmeister, Robin J.","last_name":"Hofmeister","first_name":"Robin J."},{"full_name":"Corfield, Elizabeth C.","last_name":"Corfield","first_name":"Elizabeth C."},{"full_name":"Mahmoudi, Mahdi","first_name":"Mahdi","last_name":"Mahmoudi"},{"full_name":"Delaneau, Olivier","first_name":"Olivier","last_name":"Delaneau"},{"last_name":"Andreassen","first_name":"Ole A.","full_name":"Andreassen, Ole A."},{"first_name":"Archie","last_name":"Campbell","full_name":"Campbell, Archie"},{"full_name":"Hayward, Caroline","first_name":"Caroline","last_name":"Hayward"},{"first_name":"Riccardo E.","last_name":"Marioni","full_name":"Marioni, Riccardo E."},{"last_name":"Ystrom","first_name":"Eivind","full_name":"Ystrom, Eivind"},{"full_name":"Havdahl, Alexandra","last_name":"Havdahl","first_name":"Alexandra"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"external_id":{"pmid":["40909755"]},"ddc":["570"],"department":[{"_id":"MaRo"}],"date_updated":"2026-08-04T09:34:08Z","abstract":[{"lang":"eng","text":"We introduce JODIE, a genetic joint modeling approach that estimates how DNA loci influence human traits by partitioning genetic effects into four components: direct effects (from a child’s alleles), indirect maternal and paternal effects (from parents’ alleles), and parent-of-origin (PofO) effects (dependent on parental transmission of alleles), while uniquely accounting for assortative mating. We analyze 30,000 child-mother-father trios from the Estonian Biobank and the Norwegian Mother, Father, and Child Cohort, focusing on height, body mass index, and childhood educational test scores. We find direct effects to be the largest contributor to trait variation, but combined, indirect parental and PofO effects are similarly substantial. We support our results by within-family genome-wide association testing and identify 276 independently associated DNA regions with a complex interplay between direct, indirect, and PofO effects. By joint modeling, we show that direct, indirect, and PofO effects collectively shape human phenotypic variation across loci genome-wide."}],"date_published":"2026-07-08T00:00:00Z","issue":"7","publisher":"Elsevier","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/human-traits-beyond-inherited-genes/","description":"News on ISTA website"}]}},{"corr_author":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"NMR"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"ieee":"L. M. Becker, “Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR,” Institute of Science and Technology Austria, 2026.","chicago":"Becker, Lea Marie. “Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-22334\">https://doi.org/10.15479/AT-ISTA-22334</a>.","mla":"Becker, Lea Marie. <i>Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22334\">10.15479/AT-ISTA-22334</a>.","ista":"Becker LM. 2026. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. Institute of Science and Technology Austria.","short":"L.M. Becker, Exploring Protein Dynamics Using Specific Labeling Approaches for Solid-State MAS NMR, Institute of Science and Technology Austria, 2026.","ama":"Becker LM. Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-22334\">10.15479/AT-ISTA-22334</a>","apa":"Becker, L. M. (2026). <i>Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-22334\">https://doi.org/10.15479/AT-ISTA-22334</a>"},"date_published":"2026-07-13T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"12675","relation":"part_of_dissertation","status":"public"},{"id":"21777","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12114"},{"status":"public","relation":"part_of_dissertation","id":"22105"}]},"ddc":["572"],"doi_confirm":"1","date_updated":"2026-08-04T09:32:45Z","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"supervisor":[{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"abstract":[{"text":"Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters.\r\nFunctionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies.\r\nTaken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function.\r\n","lang":"eng"}],"date_created":"2026-07-14T08:08:51Z","acknowledgement":"During the work on this thesis, I was the recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01).","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"day":"13","project":[{"name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0"}],"title":"Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR","page":"205","month":"07","article_processing_charge":"No","file":[{"file_name":"2026_Becker_Lea_source_files.zip","date_updated":"2026-07-16T09:17:08Z","content_type":"application/zip","file_size":99472908,"date_created":"2026-07-16T09:17:08Z","checksum":"8b85114eff543916c0e1445cd2189555","relation":"source_file","file_id":"22346","creator":"lbecker","access_level":"closed"},{"file_id":"22347","creator":"lbecker","relation":"main_file","date_created":"2026-07-16T09:17:05Z","checksum":"6c526862bc6dbd1e4c80ecb34580bc58","access_level":"open_access","success":1,"file_name":"2026_Becker_Lea_Thesis.pdf","file_size":74647289,"content_type":"application/pdf","date_updated":"2026-07-16T09:17:05Z"}],"year":"2026","publication_status":"published","file_date_updated":"2026-07-16T09:17:08Z","status":"public","type":"dissertation","das_tickbox":"1","alternative_title":["ISTA Thesis"],"_id":"22334","doi":"10.15479/AT-ISTA-22334","publication_identifier":{"isbn":["978-3-99078-084-8"],"issn":["2663-337X"]},"has_accepted_license":"1","oa":1},{"has_accepted_license":"1","article_type":"original","oa":1,"_id":"22105","doi":"10.1038/s41557-026-02155-0","publication_identifier":{"eissn":["17554349"],"issn":["17554330"]},"das_tickbox":"1","quality_controlled":"1","supplementarymaterial":"yes","file_date_updated":"2026-07-28T06:58:35Z","publication_status":"published","year":"2026","type":"journal_article","status":"public","month":"07","article_processing_charge":"Yes (via OA deal)","volume":18,"file":[{"access_level":"open_access","success":1,"relation":"main_file","file_id":"22595","creator":"dernst","checksum":"1069fb27949fd2cb641b043b3a96a580","date_created":"2026-07-28T06:58:35Z","file_size":2618184,"content_type":"application/pdf","date_updated":"2026-07-28T06:58:35Z","file_name":"2026_NatureChemistry_Becker.pdf"}],"intvolume":"        18","project":[{"_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","grant_number":"26777","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"page":"1221-1230","title":"Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes","publication":"Nature Chemistry","scopus_import":"1","OA_type":"hybrid","date_created":"2026-06-21T22:03:01Z","acknowledgement":"We thank N. R. Skrynnikov and O. O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to T. Schubeis (Lyon) for advice on GB1 crystallization and R. Schmid for initial crystallization trials. We thank C. Mueller-Dieckmann for assistance with room-temperature X-ray crystallography data collection on beamline ID30B at the ESRF, which is acknowledged for providing beamtime through its In-House Research programme. We thank S. Falkner for assistance with constructing the structural model of the IgG:GB1 complex. We thank J. Lewandowski for providing feedback on the paper and granting access to backbone relaxation data of IgG:GB1T2Q and GB1T2Q microcrystals. This research was supported by the Scientific Service Units (SSU) of the Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank P. Rovó and M. V. Falcón for excellent support of the NMR facility. L.M.B. is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant number PR10660EAW01). C.C. acknowledges the European Research Council (grant project 101097272 ‘MilliInMicro’) and the Métropole du Grand Nancy (grant project ‘ARC’). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.Open access funding provided by Institute of Science and Technology (IST Austria).","OA_place":"publisher","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"day":"01","date_updated":"2026-08-04T09:32:45Z","department":[{"_id":"PaSc"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein–protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions."}],"ddc":["540"],"external_id":{"pmid":["42271006"]},"related_material":{"record":[{"id":"20641","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"21145"},{"relation":"dissertation_contains","status":"public","id":"22334"}],"link":[{"url":"https://ista.ac.at/en/news/how-proteins-breathe/","description":"News on ISTA website","relation":"research_data"}]},"publisher":"Springer Nature","date_published":"2026-07-01T00:00:00Z","PlanS_conform":"1","citation":{"ista":"Becker LM, Fu H, Tatman B, Dreydoppel M, Kapitonova A, Balazs D, Weininger U, Engilberge S, Chipot C, Schanda P. 2026. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. Nature Chemistry. 18, 1221–1230.","mla":"Becker, Lea Marie, et al. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>, vol. 18, Springer Nature, 2026, pp. 1221–30, doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>.","ieee":"L. M. Becker <i>et al.</i>, “Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes,” <i>Nature Chemistry</i>, vol. 18. Springer Nature, pp. 1221–1230, 2026.","chicago":"Becker, Lea Marie, Haohao Fu, Benjamin Tatman, Matthias Dreydoppel, Anna Kapitonova, Daniel Balazs, Ulrich Weininger, Sylvain Engilberge, Christophe Chipot, and Paul Schanda. “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” <i>Nature Chemistry</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>.","ama":"Becker LM, Fu H, Tatman B, et al. Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. 2026;18:1221-1230. doi:<a href=\"https://doi.org/10.1038/s41557-026-02155-0\">10.1038/s41557-026-02155-0</a>","short":"L.M. Becker, H. Fu, B. Tatman, M. Dreydoppel, A. Kapitonova, D. Balazs, U. Weininger, S. Engilberge, C. Chipot, P. Schanda, Nature Chemistry 18 (2026) 1221–1230.","apa":"Becker, L. M., Fu, H., Tatman, B., Dreydoppel, M., Kapitonova, A., Balazs, D., … Schanda, P. (2026). Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-026-02155-0\">https://doi.org/10.1038/s41557-026-02155-0</a>"},"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","dataavailabilitystatement":"The cryo and room-temperature crystal structures of GB1QDD are deposited at the PDB under the access codes 9I2I and 9T8Z, respectively. The solid-state NMR backbone assignment of GB1QDD is deposited at the BMRB under the access code 53330. NMR spectra, analysis scripts and raw data are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-20641)120. Files to reproduce the enhanced-sampling MD simulations are publicly available at the ISTA research explorer (https://doi.org/10.15479/AT-ISTA-21145)121.","author":[{"orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie"},{"last_name":"Fu","first_name":"Haohao","full_name":"Fu, Haohao"},{"full_name":"Tatman, Benjamin","last_name":"Tatman","first_name":"Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"},{"last_name":"Dreydoppel","first_name":"Matthias","full_name":"Dreydoppel, Matthias"},{"id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","first_name":"Anna","full_name":"Kapitonova, Anna"},{"orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"last_name":"Weininger","first_name":"Ulrich","full_name":"Weininger, Ulrich"},{"first_name":"Sylvain","last_name":"Engilberge","full_name":"Engilberge, Sylvain"},{"full_name":"Chipot, Christophe","last_name":"Chipot","first_name":"Christophe"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"}],"corr_author":"1","researchdata_availability":"yes","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}]},{"oa_version":"Published Version","citation":{"apa":"Becker, L. M., Schanda, P., &#38; Chipot, C. (2026). Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>","short":"L.M. Becker, P. Schanda, C. Chipot, (2026).","ama":"Becker LM, Schanda P, Chipot C. Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>","chicago":"Becker, Lea Marie, Paul Schanda, and Christophe Chipot. “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">https://doi.org/10.15479/AT-ISTA-21145</a>.","ieee":"L. M. Becker, P. Schanda, and C. Chipot, “Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.’” Institute of Science and Technology Austria, 2026.","ista":"Becker LM, Schanda P, Chipot C. 2026. Additional Data for ‘Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>.","mla":"Becker, Lea Marie, et al. <i>Additional Data for “Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21145\">10.15479/AT-ISTA-21145</a>."},"contributor":[{"last_name":"Fu","first_name":"Haohao","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Benjamin","last_name":"Tatman","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"},{"contributor_type":"researcher","first_name":"Matthias","last_name":"Dreydoppel"},{"contributor_type":"researcher","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","last_name":"Kapitonova","first_name":"Anna"},{"first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Ulrich","last_name":"Weininger"},{"contributor_type":"researcher","first_name":"Sylvain","last_name":"Engilberge"}],"corr_author":"1","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"}],"ddc":["572"],"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"date_updated":"2026-08-04T09:32:45Z","abstract":[{"text":"Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. ","lang":"eng"}],"date_published":"2026-02-09T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","related_material":{"record":[{"id":"20641","relation":"earlier_version","status":"public"},{"id":"22105","status":"public","relation":"used_in_publication"}]},"publisher":"Institute of Science and Technology Austria","project":[{"_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches","grant_number":"26777"}],"title":"Additional Data for \"Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes\"","month":"02","article_processing_charge":"No","file":[{"checksum":"02a419cce8cea450bc952f35488d2df5","date_created":"2026-02-05T13:52:37Z","relation":"table_of_contents","file_id":"21146","creator":"lbecker","access_level":"open_access","file_name":"README.txt","date_updated":"2026-02-05T13:52:37Z","content_type":"text/plain","file_size":4263},{"success":1,"access_level":"open_access","date_created":"2026-02-05T13:52:41Z","checksum":"b0b82b1aa73985b0b308a3fa52d21aea","relation":"main_file","file_id":"21147","creator":"lbecker","date_updated":"2026-02-05T13:52:41Z","content_type":"application/zip","file_size":50647107,"file_name":"Research_Data.zip"}],"date_created":"2026-02-05T13:54:39Z","acknowledgement":"We thank Nikolai R. Skrynnikov and Olga O. Lebedenko (St. Petersburg) for insightful discussions and for performing exploratory MD simulations. We are grateful to Tobias Schubeis (Lyon) for advice with GB1 crystallization, and Rebecca Schmid for initial crystallization trials.\r\nWe thank Sebastian Falkner for assistance with constructing the structural model of the IgG:GB1 complex.\r\nThis research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance and the Lab Support Facilities. We thank Petra Rovó and Margarita Valhondo Falcón for excellent support of the NMR facility.\r\nLea M. Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (grant no. PR10660EAW01). Christophe Chipot acknowledges the European Research Council (grant project 101097272 ``MilliInMicro'') and the Métropole du Grand Nancy (grant project ``ARC''). BM07-FIP2 is supported by the French ANR PIA3 (France 2030) EquipEx+ project MAGNIFIX under grant agreement ANR-21-ESRE-0011.","day":"09","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"doi":"10.15479/AT-ISTA-21145","_id":"21145","has_accepted_license":"1","oa":1,"type":"research_data","status":"public","file_date_updated":"2026-02-05T13:52:41Z","year":"2026"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"P.N. Petrov, J.T. Zhang, J.J. Axelrod, P.K. Olshin, H. Müller, Nature Communications 17 (2026).","ama":"Petrov PN, Zhang JT, Axelrod JJ, Olshin PK, Müller H. Crossed laser phase plates for transmission electron microscopy. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-74060-6\">10.1038/s41467-026-74060-6</a>","apa":"Petrov, P. N., Zhang, J. T., Axelrod, J. J., Olshin, P. K., &#38; Müller, H. (2026). Crossed laser phase plates for transmission electron microscopy. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-74060-6\">https://doi.org/10.1038/s41467-026-74060-6</a>","ieee":"P. N. Petrov, J. T. Zhang, J. J. Axelrod, P. K. Olshin, and H. Müller, “Crossed laser phase plates for transmission electron microscopy,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","chicago":"Petrov, Petar N, Jessie T. Zhang, Jeremy J. Axelrod, Pavel K. Olshin, and Holger Müller. “Crossed Laser Phase Plates for Transmission Electron Microscopy.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-74060-6\">https://doi.org/10.1038/s41467-026-74060-6</a>.","ista":"Petrov PN, Zhang JT, Axelrod JJ, Olshin PK, Müller H. 2026. Crossed laser phase plates for transmission electron microscopy. Nature Communications. 17, 7199.","mla":"Petrov, Petar N., et al. “Crossed Laser Phase Plates for Transmission Electron Microscopy.” <i>Nature Communications</i>, vol. 17, 7199, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-74060-6\">10.1038/s41467-026-74060-6</a>."},"researchdata_availability":"no","author":[{"id":"b1d6732d-8cb6-11f0-baab-bd460ee3a287","last_name":"Petrov","first_name":"Petar N","full_name":"Petrov, Petar N"},{"last_name":"Zhang","first_name":"Jessie T.","full_name":"Zhang, Jessie T."},{"full_name":"Axelrod, Jeremy J.","first_name":"Jeremy J.","last_name":"Axelrod"},{"first_name":"Pavel K.","last_name":"Olshin","full_name":"Olshin, Pavel K."},{"first_name":"Holger","last_name":"Müller","full_name":"Müller, Holger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"The simulated apoferritin exit wave and associated image simulation and analysis code used for generating the figures are available on Code Ocean (https://www.codeocean.com/).","ddc":["530"],"abstract":[{"text":"A phase plate has long been sought in transmission electron microscopy (TEM) to maximize the image contrast of weakly-scattering objects like biomolecules. The laser phase plate (LPP) has recently demonstrated that an amplified, focused laser standing wave reliably phase shifts the electron beam, achieving phase-contrast TEM. Building on the single-beam LPP, here we introduce the crossed laser phase plate (XLPP): two laser standing waves which intersect in the diffraction plane. We present a theoretical model for the XLPP inside the microscope and show that, relative to the original LPP, it increases information transfer at low spatial frequencies while suppressing ghost images formed by Kapitza-Dirac diffraction. We also present a simple acquisition scheme, enabled by the XLPP, which further suppresses ghosts. Finally, we discuss practical considerations of XLPP design and show experimental results from a prototype. The results of this study chart the course for future developments of LPP hardware.","lang":"eng"}],"date_updated":"2026-08-05T09:27:39Z","department":[{"_id":"MiLe"}],"PlanS_conform":"1","date_published":"2026-06-05T00:00:00Z","publisher":"Springer Nature","title":"Crossed laser phase plates for transmission electron microscopy","intvolume":"        17","volume":17,"file":[{"date_updated":"2026-08-03T06:48:08Z","content_type":"application/pdf","file_size":2052058,"file_name":"2026_NatureComm_Petrov.pdf","success":1,"access_level":"open_access","checksum":"9bbcbaed3fd78e99cd728877332953c1","date_created":"2026-08-03T06:48:08Z","creator":"dernst","file_id":"22624","relation":"main_file"}],"month":"06","article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"05","DOAJ_listed":"1","OA_type":"gold","scopus_import":"1","OA_place":"publisher","date_created":"2026-08-02T22:01:51Z","publication":"Nature Communications","article_number":"7199","_id":"22613","doi":"10.1038/s41467-026-74060-6","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","oa":1,"has_accepted_license":"1","file_date_updated":"2026-08-03T06:48:08Z","publication_status":"published","year":"2026","status":"public","type":"journal_article","quality_controlled":"1","supplementarymaterial":"yes","das_tickbox":"1"},{"researchdata_availability":"yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","dataavailabilitystatement":"The datasets are publicly available in the Electron Microscopy Public Image Archive [A1: EMPIAR-13528 (on), EMPIAR-13527 (off); A2: EMPIAR-13529 (on), EMPIAR-13526 (off); A3: EMPIAR-13530 (on), EMPIAR-13525 (off); H1: EMPIAR-13535 (on), EMPIAR-13533 (off); H2: EMPIAR-13534 (on), EMPIAR-13532 (off); H3: EMPIAR-13537 (on), EMPIAR-13531 (off)]. The final reconstructed maps are deposited in the Electron Microscopy Data Bank [A1: EMD-76790 (on), EMD-76791 (off); A2: EMD-76792 (on), EMD-76793 (off); A3: EMD-76794 (on), EMD-76797 (off); H1: EMD-76802 (on), EMD-76804 (off); H2: EMD-76805 (on), EMD-76806 (off); H3: EMD-76807 (on), EMD-76809 (off)]. The initial structures in Fig. 3 are deposited at EMD-76810 (on) and EMD-76811 (off). Code for converting EER movies to binned TIF format with proper accounting for electron dose is deposited in Zenodo (47) and available on GitHub at https://github.com/matterwaves/eer2tiff/releases/tag/v0.1.0. All specimen preparation materials are commercially available.","author":[{"full_name":"Petrov, Petar N","first_name":"Petar N","last_name":"Petrov","id":"b1d6732d-8cb6-11f0-baab-bd460ee3a287"},{"last_name":"Zhang","first_name":"Jessie T.","full_name":"Zhang, Jessie T."},{"full_name":"Remis, Jonathan","last_name":"Remis","first_name":"Jonathan"},{"full_name":"Axelrod, Jeremy J.","last_name":"Axelrod","first_name":"Jeremy J."},{"last_name":"Cheng","first_name":"Hang","full_name":"Cheng, Hang"},{"last_name":"Cooper","first_name":"Eric S.","full_name":"Cooper, Eric S."},{"full_name":"Hicklin, Ian K.","last_name":"Hicklin","first_name":"Ian K."},{"last_name":"Sandhaus","first_name":"Shahar","full_name":"Sandhaus, Shahar"},{"first_name":"Cooper","last_name":"Schnurr","full_name":"Schnurr, Cooper"},{"last_name":"Glaeser","first_name":"Robert M.","full_name":"Glaeser, Robert M."},{"last_name":"Müller","first_name":"Holger","full_name":"Müller, Holger"}],"oa_version":"None","language":[{"iso":"eng"}],"citation":{"apa":"Petrov, P. N., Zhang, J. T., Remis, J., Axelrod, J. J., Cheng, H., Cooper, E. S., … Müller, H. (2026). Laser phase plate improves structure determination of small proteins by cryo-EM. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aeh0665\">https://doi.org/10.1126/science.aeh0665</a>","ama":"Petrov PN, Zhang JT, Remis J, et al. Laser phase plate improves structure determination of small proteins by cryo-EM. <i>Science</i>. 2026;393(6807):195-196. doi:<a href=\"https://doi.org/10.1126/science.aeh0665\">10.1126/science.aeh0665</a>","short":"P.N. Petrov, J.T. Zhang, J. Remis, J.J. Axelrod, H. Cheng, E.S. Cooper, I.K. Hicklin, S. Sandhaus, C. Schnurr, R.M. Glaeser, H. Müller, Science 393 (2026) 195–196.","mla":"Petrov, Petar N., et al. “Laser Phase Plate Improves Structure Determination of Small Proteins by Cryo-EM.” <i>Science</i>, vol. 393, no. 6807, AAAS, 2026, pp. 195–96, doi:<a href=\"https://doi.org/10.1126/science.aeh0665\">10.1126/science.aeh0665</a>.","ista":"Petrov PN, Zhang JT, Remis J, Axelrod JJ, Cheng H, Cooper ES, Hicklin IK, Sandhaus S, Schnurr C, Glaeser RM, Müller H. 2026. Laser phase plate improves structure determination of small proteins by cryo-EM. Science. 393(6807), 195–196.","chicago":"Petrov, Petar N, Jessie T. Zhang, Jonathan Remis, Jeremy J. Axelrod, Hang Cheng, Eric S. Cooper, Ian K. Hicklin, et al. “Laser Phase Plate Improves Structure Determination of Small Proteins by Cryo-EM.” <i>Science</i>. AAAS, 2026. <a href=\"https://doi.org/10.1126/science.aeh0665\">https://doi.org/10.1126/science.aeh0665</a>.","ieee":"P. N. Petrov <i>et al.</i>, “Laser phase plate improves structure determination of small proteins by cryo-EM,” <i>Science</i>, vol. 393, no. 6807. AAAS, pp. 195–196, 2026."},"date_published":"2026-07-09T00:00:00Z","issue":"6807","publisher":"AAAS","external_id":{"pmid":["42275466"]},"ddc":["570"],"department":[{"_id":"MiLe"}],"date_updated":"2026-08-05T09:27:38Z","abstract":[{"lang":"eng","text":"Phase plates can, in principle, overcome the poor image contrast in cryo–electron microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. However, previous designs have been unstable and compromised the high-resolution signal and have thus been unable to surpass results achieved by standard cryo-EM. Here, we show that the laser phase plate (LPP), installed in a modern, custom Titan Krios microscope, enhances the resolution in single-particle reconstruction of small proteins by improving specimen-motion correction and recovery of information from the early frames, as well as particle visualization, three-dimensional classification, and alignment. These advances use standard defocus ranges and reconstruction procedures but open the door to LPP-tailored protocols, offering further improvements by leveraging the LPP demonstrated here."}],"date_created":"2026-07-19T22:01:46Z","acknowledgement":"The authors thank O. Schwartz and S. Scheres for helpful remarks and discussions; D. Agard, B. Carragher, C. Potter, and P. Olshin for close collaboration; A. Singh, L. Maisenbacher, S. Strasser, and I. Pope for help with mirror inspection; J. Fang, E. Nogales, and J. Hurley for sharing their lab space and assisting with sample preparation; B. Buijsse, W. Hagen, B. Jiang, and T. Coyle at Thermo Fisher Scientific for the design of the custom transfer optics and technical support; G. Long and T. Gutierrez at the UC Berkeley Physics R&D Machine Shop for machining cavity components and tooling. This work was supported by the following: Chan Zuckerberg Initiative award numbers 2021-234606 and 2025-367757, National Institutes of Health grant R01GM126011, Gordon and Betty Moore Foundation grant 9366, Lawrence Berkeley National Laboratory Directed Research and Development Program grant 25-111, and Cooperative Research and Development Agreement award AWD00004352 (to H.M.); National Institutes of Health fellowship F32GM149186 (to P.N.P.).","scopus_import":"1","OA_type":"closed access","day":"09","pmid":1,"publication":"Science","intvolume":"       393","title":"Laser phase plate improves structure determination of small proteins by cryo-EM","page":"195-196","article_processing_charge":"No","month":"07","volume":393,"supplementarymaterial":"yes","quality_controlled":"1","status":"public","type":"journal_article","year":"2026","publication_status":"published","das_tickbox":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"doi":"10.1126/science.aeh0665","_id":"22365","has_accepted_license":"1","article_type":"original"},{"quality_controlled":"1","status":"public","type":"journal_article","year":"2026","publication_status":"published","das_tickbox":"1","publication_identifier":{"eissn":["2328-4277"]},"doi":"10.1029/2026ef008857","_id":"22443","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2026EF008857"}],"article_number":"e2026EF008857","oa":1,"article_type":"original","date_created":"2026-07-27T12:30:23Z","OA_place":"publisher","scopus_import":"1","DOAJ_listed":"1","OA_type":"gold","day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Earth's Future","intvolume":"        14","title":"Reimagining how flood warnings can inform decision‐making and community actions","month":"06","article_processing_charge":"No","volume":14,"date_published":"2026-06-01T00:00:00Z","issue":"6","publisher":"American Geophysical Union","date_updated":"2026-08-06T09:02:33Z","abstract":[{"lang":"eng","text":"Society faces increasingly severe flood hazards, intensifying demand for flood early warning systems (FEWS) that deliver accurate and actionable information. However, most existing FEWS remain prediction‐centric, treating decision‐making as a downstream consumer of hazard forecasts while offering limited support for uncertainty interpretation, risk communication, and real‐world response. This Perspective presents a vision and blueprint for a novel inland FEWS‐decision‐making (FEWS‐DM) framework that repositions decision‐making as an equal partner in the forecasting process—not a passive recipient of its outputs. The framework is built on three tightly coupled, co‐evolving thrusts: Physical Science (T1), which advances flood prediction with quantified uncertainty informed by decision relevance; Human Science (T2), which incorporates psychology, behavior, and cultural and institutional context; and Decision Science (T3), which unifies physical predictions and human factors through principled, utility‐based decision support with end‐to‐end uncertainty management. Rather than treating T1 as a solved problem, FEWS‐DM recognizes that forecast development itself must be shaped by decision needs through continuous bidirectional feedback. We identify key scientific, behavioral, and operational challenges limiting such integration and discuss the enabling role of AI, while emphasizing human‐centered design and community feedback as essential for building trust and improving flood risk management.</jats:p>"}],"extern":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Vinh Ngoc","last_name":"Tran","full_name":"Tran, Vinh Ngoc"},{"full_name":"Huan, Xun","last_name":"Huan","first_name":"Xun"},{"full_name":"Antar, Anindya Das","first_name":"Anindya Das","last_name":"Antar"},{"first_name":"Nikola","last_name":"Banovic","full_name":"Banovic, Nikola"},{"full_name":"Bednar, Jeff H.","first_name":"Jeff H.","last_name":"Bednar"},{"first_name":"Shannon Marie","last_name":"Bergt","full_name":"Bergt, Shannon Marie"},{"last_name":"Cheng","first_name":"Chen","full_name":"Cheng, Chen"},{"full_name":"Dominguez, Francina","last_name":"Dominguez","first_name":"Francina"},{"first_name":"Simone","last_name":"Fatichi","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","full_name":"Fatichi, Simone"},{"full_name":"Gonzalez, Richard","last_name":"Gonzalez","first_name":"Richard"},{"full_name":"Gray, Kevin","last_name":"Gray","first_name":"Kevin"},{"first_name":"Brian","last_name":"Jewett","full_name":"Jewett, Brian"},{"full_name":"Kim, Jongho","last_name":"Kim","first_name":"Jongho"},{"full_name":"Le, Phong V.V.","first_name":"Phong V.V.","last_name":"Le"},{"full_name":"Lu, Dan","first_name":"Dan","last_name":"Lu"},{"first_name":"Snehal","last_name":"Prabhudesai","full_name":"Prabhudesai, Snehal"},{"full_name":"Putri, Deffi","last_name":"Putri","first_name":"Deffi"},{"full_name":"Rath, Sudhansu","first_name":"Sudhansu","last_name":"Rath"},{"first_name":"Khachik","last_name":"Sargsyan","full_name":"Sargsyan, Khachik"},{"full_name":"Whitaker, Sarah H.","first_name":"Sarah H.","last_name":"Whitaker"},{"first_name":"Daniel B.","last_name":"Wright","full_name":"Wright, Daniel B."},{"first_name":"Donghui","last_name":"Xu","full_name":"Xu, Donghui"},{"last_name":"Ziker","first_name":"John P.","full_name":"Ziker, John P."},{"first_name":"Valeriy Y.","last_name":"Ivanov","full_name":"Ivanov, Valeriy Y."}],"oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ama":"Tran VN, Huan X, Antar AD, et al. Reimagining how flood warnings can inform decision‐making and community actions. <i>Earth’s Future</i>. 2026;14(6). doi:<a href=\"https://doi.org/10.1029/2026ef008857\">10.1029/2026ef008857</a>","short":"V.N. Tran, X. Huan, A.D. Antar, N. Banovic, J.H. Bednar, S.M. Bergt, C. Cheng, F. Dominguez, S. Fatichi, R. Gonzalez, K. Gray, B. Jewett, J. Kim, P.V.V. Le, D. Lu, S. Prabhudesai, D. Putri, S. Rath, K. Sargsyan, S.H. Whitaker, D.B. Wright, D. Xu, J.P. Ziker, V.Y. Ivanov, Earth’s Future 14 (2026).","apa":"Tran, V. N., Huan, X., Antar, A. D., Banovic, N., Bednar, J. H., Bergt, S. M., … Ivanov, V. Y. (2026). Reimagining how flood warnings can inform decision‐making and community actions. <i>Earth’s Future</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2026ef008857\">https://doi.org/10.1029/2026ef008857</a>","ista":"Tran VN, Huan X, Antar AD, Banovic N, Bednar JH, Bergt SM, Cheng C, Dominguez F, Fatichi S, Gonzalez R, Gray K, Jewett B, Kim J, Le PVV, Lu D, Prabhudesai S, Putri D, Rath S, Sargsyan K, Whitaker SH, Wright DB, Xu D, Ziker JP, Ivanov VY. 2026. Reimagining how flood warnings can inform decision‐making and community actions. Earth’s Future. 14(6), e2026EF008857.","mla":"Tran, Vinh Ngoc, et al. “Reimagining How Flood Warnings Can Inform Decision‐making and Community Actions.” <i>Earth’s Future</i>, vol. 14, no. 6, e2026EF008857, American Geophysical Union, 2026, doi:<a href=\"https://doi.org/10.1029/2026ef008857\">10.1029/2026ef008857</a>.","ieee":"V. N. Tran <i>et al.</i>, “Reimagining how flood warnings can inform decision‐making and community actions,” <i>Earth’s Future</i>, vol. 14, no. 6. American Geophysical Union, 2026.","chicago":"Tran, Vinh Ngoc, Xun Huan, Anindya Das Antar, Nikola Banovic, Jeff H. Bednar, Shannon Marie Bergt, Chen Cheng, et al. “Reimagining How Flood Warnings Can Inform Decision‐making and Community Actions.” <i>Earth’s Future</i>. American Geophysical Union, 2026. <a href=\"https://doi.org/10.1029/2026ef008857\">https://doi.org/10.1029/2026ef008857</a>."}},{"oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"short":"D. Kim, B. Cheng, The Journal of Chemical Physics 164 (2026).","ama":"Kim D, Cheng B. Long-range electrostatics for machine learning interatomic potentials is easier than we thought. <i>The Journal of Chemical Physics</i>. 2026;164(6). doi:<a href=\"https://doi.org/10.1063/5.0316886\">10.1063/5.0316886</a>","apa":"Kim, D., &#38; Cheng, B. (2026). Long-range electrostatics for machine learning interatomic potentials is easier than we thought. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0316886\">https://doi.org/10.1063/5.0316886</a>","mla":"Kim, Dongjin, and Bingqing Cheng. “Long-Range Electrostatics for Machine Learning Interatomic Potentials Is Easier than We Thought.” <i>The Journal of Chemical Physics</i>, vol. 164, no. 6, 060901, AIP Publishing, 2026, doi:<a href=\"https://doi.org/10.1063/5.0316886\">10.1063/5.0316886</a>.","ista":"Kim D, Cheng B. 2026. Long-range electrostatics for machine learning interatomic potentials is easier than we thought. The Journal of Chemical Physics. 164(6), 060901.","ieee":"D. Kim and B. Cheng, “Long-range electrostatics for machine learning interatomic potentials is easier than we thought,” <i>The Journal of Chemical Physics</i>, vol. 164, no. 6. AIP Publishing, 2026.","chicago":"Kim, Dongjin, and Bingqing Cheng. “Long-Range Electrostatics for Machine Learning Interatomic Potentials Is Easier than We Thought.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2026. <a href=\"https://doi.org/10.1063/5.0316886\">https://doi.org/10.1063/5.0316886</a>."},"researchdata_availability":"yes","corr_author":"1","author":[{"last_name":"Kim","first_name":"Dongjin","full_name":"Kim, Dongjin"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"dataavailabilitystatement":"The RPBE-D3 bulk water dataset, training scripts, evaluation scripts, the trained CACE E + F + Qeq model, and CACE LES and MACE LES models used to produce results shown in Figs. 2(c)–2(e) are available at https://github.com/ChengUCB/les_fit.\r\n\r\nThe LES library is publicly available at https://github.com/ChengUCB/les. The CACE package with the LES implementation is available at https://github.com/BingqingCheng/cace. The MACE package with the LES implementation is available at https://github.com/ACEsuit/mace. The NequIP and Allegro LES extension package is available at https://github.com/ChengUCB/NequIP-LES. The MatGL package with the LES implementation is available at https://github.com/ChengUCB/matgl. The UMA package with the LES implementation is available at https://github.com/santi921/fairchem/tree/les_branch.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2512.18029"]},"abstract":[{"lang":"eng","text":"The lack of long-range electrostatics is a key limitation of modern machine learning interatomic potentials (MLIPs), hindering reliable applications to interfaces, charge-transfer reactions, polar and ionic materials, and biomolecules. In this Perspective, we distill two design principles behind the Latent Ewald Summation framework, which can capture long-range interactions, charges, and electrical response just by learning from standard energy and force training data: (i) use a Coulomb functional form with environment-dependent charges to capture electrostatic interactions, and (ii) avoid explicit training on ambiguous density functional theory partial charges. When both principles are satisfied, substantial flexibility remains: essentially any short-range MLIP can be augmented; charge equilibration schemes can be added when desired; dipoles and Born effective charges can be inferred or fine-tuned; and charge/spin-state embeddings or tensorial targets can be further incorporated. We also discuss current limitations and open challenges. Together, these minimal, physics-guided design rules suggest that incorporating long-range electrostatics into MLIPs is simpler and perhaps more broadly applicable than is commonly assumed."}],"department":[{"_id":"BiCh"}],"date_updated":"2026-08-07T09:33:14Z","arxiv":1,"date_published":"2026-02-14T00:00:00Z","publisher":"AIP Publishing","issue":"6","title":"Long-range electrostatics for machine learning interatomic potentials is easier than we thought","intvolume":"       164","volume":164,"month":"02","article_processing_charge":"No","day":"14","date_created":"2026-03-02T10:06:46Z","OA_place":"repository","acknowledgement":"B.C. thanks Christoph Dellago for his mentorship and influence. In addition to his seminal contributions to statistical mechanics, Christoph Dellago is an early developer and adopter of machine learning interatomic potentials. B.C. did two exchanges in the groups of Christoph Dellago and Jörg Behler in 2018, with transformative impact on her research directions.\r\n\r\nWe thank Peichen Zhong and Daniel S. King for useful feedback on the manuscript and for the collaborations on the LES method.\r\n\r\nFunding acknowledgment: Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award No. R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.","scopus_import":"1","OA_type":"free access","publication":"The Journal of Chemical Physics","article_number":"060901","doi":"10.1063/5.0316886","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2512.18029","open_access":"1"}],"_id":"21381","oa":1,"article_type":"original","status":"public","type":"journal_article","publication_status":"published","year":"2026","supplementarymaterial":"no","quality_controlled":"1","das_tickbox":"1"},{"citation":{"chicago":"Luo, Zhaoyang, Jianning Ren, and Simone Fatichi. “Air and Soil Warming Have Different Effects on Soil Organic Carbon Storage.” <i>Communications Earth &#38; Environment</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s43247-026-03367-5\">https://doi.org/10.1038/s43247-026-03367-5</a>.","ieee":"Z. Luo, J. Ren, and S. Fatichi, “Air and soil warming have different effects on soil organic carbon storage,” <i>Communications Earth &#38; Environment</i>, vol. 7. Springer Nature, 2026.","ista":"Luo Z, Ren J, Fatichi S. 2026. Air and soil warming have different effects on soil organic carbon storage. Communications Earth &#38; Environment. 7, 394.","mla":"Luo, Zhaoyang, et al. “Air and Soil Warming Have Different Effects on Soil Organic Carbon Storage.” <i>Communications Earth &#38; Environment</i>, vol. 7, 394, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s43247-026-03367-5\">10.1038/s43247-026-03367-5</a>.","apa":"Luo, Z., Ren, J., &#38; Fatichi, S. (2026). Air and soil warming have different effects on soil organic carbon storage. <i>Communications Earth &#38; Environment</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43247-026-03367-5\">https://doi.org/10.1038/s43247-026-03367-5</a>","short":"Z. Luo, J. Ren, S. Fatichi, Communications Earth &#38; Environment 7 (2026).","ama":"Luo Z, Ren J, Fatichi S. Air and soil warming have different effects on soil organic carbon storage. <i>Communications Earth &#38; Environment</i>. 2026;7. doi:<a href=\"https://doi.org/10.1038/s43247-026-03367-5\">10.1038/s43247-026-03367-5</a>"},"oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"full_name":"Luo, Zhaoyang","last_name":"Luo","first_name":"Zhaoyang"},{"last_name":"Ren","first_name":"Jianning","full_name":"Ren, Jianning"},{"id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","last_name":"Fatichi","first_name":"Simone","full_name":"Fatichi, Simone"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","extern":"1","abstract":[{"lang":"eng","text":"Warming impacts both net primary production (NPP) and soil organic carbon (SOC) decomposition, and consequently, SOC storage. However, the role of warming in regulating SOC storage remains debated. Here, we leverage literature data of warming experiments and a mechanistic model to explore SOC responses to warming by partitioning the effects of air and soil warming. Both the literature data and numerical model show that air and soil warming play distinct roles in regulating SOC storage, with insignificant SOC responses under air warming and negative responses to soil warming. Soil warming decreases SOC storage because of temperature-driven increases in decomposition rate. Air warming effects on SOC are more complex. In some cases, air warming can lead to a lower NPP and higher decomposition rate. In others, air warming can stimulate NPP and enhance soil moisture depletion that inhibits SOC decomposition. Once the latter mechanisms dominate, SOC storage increases with air warming."}],"date_updated":"2026-08-07T09:28:26Z","publisher":"Springer Nature","date_published":"2026-05-05T00:00:00Z","volume":7,"article_processing_charge":"No","month":"05","title":"Air and soil warming have different effects on soil organic carbon storage","intvolume":"         7","publication":"Communications Earth & Environment","day":"05","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2026-07-27T12:30:23Z","OA_place":"publisher","OA_type":"gold","DOAJ_listed":"1","scopus_import":"1","oa":1,"article_type":"original","article_number":"394","publication_identifier":{"eissn":["2662-4435"]},"doi":"10.1038/s43247-026-03367-5","main_file_link":[{"url":"https://doi.org/10.1038/s43247-026-03367-5","open_access":"1"}],"_id":"22441","das_tickbox":"1","status":"public","type":"journal_article","publication_status":"published","year":"2026","quality_controlled":"1"},{"das_tickbox":"1","status":"public","type":"journal_article","year":"2026","publication_status":"published","quality_controlled":"1","oa":1,"article_type":"original","article_number":"9","publication_identifier":{"eissn":["2662-4435"]},"doi":"10.1038/s43247-025-03035-0","_id":"22528","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s43247-025-03035-0"}],"publication":"Communications Earth & Environment","day":"05","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"OA_place":"publisher","date_created":"2026-07-27T12:30:24Z","scopus_import":"1","OA_type":"gold","DOAJ_listed":"1","volume":7,"article_processing_charge":"No","month":"01","title":"Limited capability of current satellite solar-induced chlorophyll fluorescence reconstructions to capture stomatal responses to environmental stresses","intvolume":"         7","publisher":"Springer Nature","date_published":"2026-01-05T00:00:00Z","abstract":[{"lang":"eng","text":"Quantification of the impact of environmental stress on terrestrial vegetation photosynthesis is crucial for our understanding of the global carbon cycle, particularly under a changing climate. Vegetation responses to environmental stress manifest first as plant physiological changes, and at later stages through changes in canopy structure. Here we leverage CO2 and water flux data from 103 eddy covariance towers and satellite thermal images to assess whether current satellite reconstructions of solar-induced chlorophyll fluorescence capture these plant mechanisms. After removing seasonality using standardized anomalies (z-scores), we found that the relationship between tower-observed gross primary productivity and fluorescence reconstructions considerably weakened across a wide range of biomes. This loss of correlation results from a decoupling between stomatal responses and the physiological emission yield (ΦF) of fluorescence reconstructions during soil and atmospheric dry periods. The consequence is that productivity derived from fluorescence reconstructions will be progressively overestimated as dry conditions persist."}],"date_updated":"2026-08-07T10:34:55Z","author":[{"full_name":"Zhao, Jiacheng","last_name":"Zhao","first_name":"Jiacheng"},{"first_name":"Athanasios","last_name":"Paschalis","full_name":"Paschalis, Athanasios"},{"full_name":"Gentine, Pierre","last_name":"Gentine","first_name":"Pierre"},{"full_name":"Feng, Zhaozhong","last_name":"Feng","first_name":"Zhaozhong"},{"full_name":"Fatichi, Simone","id":"cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6","first_name":"Simone","last_name":"Fatichi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","extern":"1","citation":{"chicago":"Zhao, Jiacheng, Athanasios Paschalis, Pierre Gentine, Zhaozhong Feng, and Simone Fatichi. “Limited Capability of Current Satellite Solar-Induced Chlorophyll Fluorescence Reconstructions to Capture Stomatal Responses to Environmental Stresses.” <i>Communications Earth &#38; Environment</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s43247-025-03035-0\">https://doi.org/10.1038/s43247-025-03035-0</a>.","ieee":"J. Zhao, A. Paschalis, P. Gentine, Z. Feng, and S. Fatichi, “Limited capability of current satellite solar-induced chlorophyll fluorescence reconstructions to capture stomatal responses to environmental stresses,” <i>Communications Earth &#38; Environment</i>, vol. 7. Springer Nature, 2026.","mla":"Zhao, Jiacheng, et al. “Limited Capability of Current Satellite Solar-Induced Chlorophyll Fluorescence Reconstructions to Capture Stomatal Responses to Environmental Stresses.” <i>Communications Earth &#38; Environment</i>, vol. 7, 9, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s43247-025-03035-0\">10.1038/s43247-025-03035-0</a>.","ista":"Zhao J, Paschalis A, Gentine P, Feng Z, Fatichi S. 2026. Limited capability of current satellite solar-induced chlorophyll fluorescence reconstructions to capture stomatal responses to environmental stresses. Communications Earth &#38; Environment. 7, 9.","apa":"Zhao, J., Paschalis, A., Gentine, P., Feng, Z., &#38; Fatichi, S. (2026). Limited capability of current satellite solar-induced chlorophyll fluorescence reconstructions to capture stomatal responses to environmental stresses. <i>Communications Earth &#38; Environment</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43247-025-03035-0\">https://doi.org/10.1038/s43247-025-03035-0</a>","short":"J. Zhao, A. Paschalis, P. Gentine, Z. Feng, S. Fatichi, Communications Earth &#38; Environment 7 (2026).","ama":"Zhao J, Paschalis A, Gentine P, Feng Z, Fatichi S. Limited capability of current satellite solar-induced chlorophyll fluorescence reconstructions to capture stomatal responses to environmental stresses. <i>Communications Earth &#38; Environment</i>. 2026;7. doi:<a href=\"https://doi.org/10.1038/s43247-025-03035-0\">10.1038/s43247-025-03035-0</a>"},"oa_version":"Published Version","language":[{"iso":"eng"}]},{"scopus_import":"1","DOAJ_listed":"1","OA_type":"diamond","OA_place":"publisher","date_created":"2026-08-10T07:53:32Z","acknowledgement":"The authors thank the referee for their helpful and constructive report, which has significantly enhanced the quality of the manuscript.\r\nThe authors thank I. Caiazzo, L. Ferrario, and L. Buchele for very useful discussions. L. Barrault, L. Bugnet, and L. Einramhof gratefully acknowledge support from the European Research Council (ERC) under the Horizon Europe\r\nprogramme (Calcifer; Starting Grant agreement N◦101165631). L. Barrault\r\nacknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 27648.\r\nWhile partially funded by the European Union, views and opinions expressed\r\nare, however, those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union\r\nnor the granting authority can be held responsible for them.","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","publication":"Astronomy & Astrophysics","intvolume":"       708","project":[{"name":"Unveiling the mysteries of stellar dynamics: a pioneering journey in magnetoasteroseismology","grant_number":"101165631","_id":"914d8549-16d5-11f0-9cad-bbe6324c93a9"},{"_id":"5b62812b-ab3d-11f0-914f-8f3a9cdb4af7","grant_number":"27648","name":"Unveiling the structure and dynamics of the deep convective core - radiative zone boundary throughout stellar evolution"}],"title":"Magneto-archeology of white dwarfs","month":"04","article_processing_charge":"No","volume":708,"file":[{"success":1,"access_level":"open_access","checksum":"61edee776603d7b879b06b3ea8d2bc89","date_created":"2026-08-11T05:46:02Z","relation":"main_file","creator":"dernst","file_id":"22671","date_updated":"2026-08-11T05:46:02Z","content_type":"application/pdf","file_size":3739424,"file_name":"2026_AstronomyAstrophysics_Einramhof.pdf"}],"quality_controlled":"1","supplementarymaterial":"yes","file_date_updated":"2026-08-11T05:46:02Z","year":"2026","publication_status":"published","status":"public","type":"journal_article","das_tickbox":"1","_id":"22663","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"doi":"10.1051/0004-6361/202659069","article_number":"L14","has_accepted_license":"1","article_type":"original","oa":1,"corr_author":"1","researchdata_availability":"yes","dataavailabilitystatement":"We used MESA version 24.08.1. All inlists and relevant files are available on Zenodo at https://doi.org/10.5281/zenodo.19232789","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"f1497a1a-72ef-11ef-b75a-fd877bbf6e8c","first_name":"Lukas","last_name":"Einramhof","full_name":"Einramhof, Lukas"},{"last_name":"Bugnet","first_name":"Lisa Annabelle","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000"},{"first_name":"L. M.","last_name":"Calcaferro","full_name":"Calcaferro, L. M."},{"id":"4471a8fd-32c1-11ee-a9a4-fb670d398f64","first_name":"Lucas","last_name":"Barrault","full_name":"Barrault, Lucas"},{"full_name":"Das, S. B.","first_name":"S. B.","last_name":"Das"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"ieee":"L. Einramhof, L. A. Bugnet, L. M. Calcaferro, L. Barrault, and S. B. Das, “Magneto-archeology of white dwarfs,” <i>Astronomy &#38; Astrophysics</i>, vol. 708. EDP Sciences, 2026.","chicago":"Einramhof, Lukas, Lisa Annabelle Bugnet, L. M. Calcaferro, Lucas Barrault, and S. B. Das. “Magneto-Archeology of White Dwarfs.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2026. <a href=\"https://doi.org/10.1051/0004-6361/202659069\">https://doi.org/10.1051/0004-6361/202659069</a>.","ista":"Einramhof L, Bugnet LA, Calcaferro LM, Barrault L, Das SB. 2026. Magneto-archeology of white dwarfs. Astronomy &#38; Astrophysics. 708, L14.","mla":"Einramhof, Lukas, et al. “Magneto-Archeology of White Dwarfs.” <i>Astronomy &#38; Astrophysics</i>, vol. 708, L14, EDP Sciences, 2026, doi:<a href=\"https://doi.org/10.1051/0004-6361/202659069\">10.1051/0004-6361/202659069</a>.","ama":"Einramhof L, Bugnet LA, Calcaferro LM, Barrault L, Das SB. Magneto-archeology of white dwarfs. <i>Astronomy &#38; Astrophysics</i>. 2026;708. doi:<a href=\"https://doi.org/10.1051/0004-6361/202659069\">10.1051/0004-6361/202659069</a>","short":"L. Einramhof, L.A. Bugnet, L.M. Calcaferro, L. Barrault, S.B. Das, Astronomy &#38; Astrophysics 708 (2026).","apa":"Einramhof, L., Bugnet, L. A., Calcaferro, L. M., Barrault, L., &#38; Das, S. B. (2026). Magneto-archeology of white dwarfs. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202659069\">https://doi.org/10.1051/0004-6361/202659069</a>"},"date_published":"2026-04-01T00:00:00Z","PlanS_conform":"1","arxiv":1,"publisher":"EDP Sciences","ddc":["520"],"external_id":{"arxiv":["2601.15203"]},"date_updated":"2026-08-11T05:49:20Z","department":[{"_id":"LiBu"},{"_id":"GradSch"}],"abstract":[{"lang":"eng","text":"The detection of strong, large-scale magnetic fields at the surfaces of the oldest white dwarfs might point toward a hidden internal magnetic field slowly rising to the surface. In addition, strong magnetic fields have recently been measured through asteroseismology in the radiative interiors of red giant stars, the progenitors of white dwarfs. To investigate the potential connection between these observations, we revisited the fossil field framework using asteroseismic detections to constrain the strength of such magnetic fields as red giants evolve into the white dwarf stage. We assumed that the magnetic field was either created during the core convection on the main sequence or that it fills the radiative interior as the star evolves on the red giant branch. From these initial conditions, we evolved the magnetic flux, allowing for magnetic diffusion along the evolution of a modeled 1.5 M⊙ star. We find that measured field strengths in red giants attributed to the hydrogen-burning shell are compatible with the field amplitudes and emergence timescales of magnetized white dwarfs. On the contrary, magnetic fields generated solely from a convective-core dynamo on the main sequence and detectable on the red giant branch would be buried too deep in the star and would not match the breakout timescales or the field strengths of magnetic white dwarfs. Therefore, for us to connect magnetic fields observed along the late evolution of stars via a fossil field we would need to find a broadly magnetized internal radiative zone on the red giant branch."}]}]