[{"date_updated":"2026-08-07T09:35:25Z","oa_version":"Preprint","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"GradSch"},{"_id":"BiCh"}],"researchdata_availability":"no","publication_status":"published","external_id":{"pmid":["41368735 "],"arxiv":["2507.14302"]},"fulldoi":"https://doi.org/10.1021/acs.jctc.5c01400","issue":"24","abstract":[{"text":"Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which infers electrostatic interactions, polarization, and Born effective charges (BECs), just by learning from energy and force training data. Here, we present LES as a standalone library, compatible with any short-range MLIP, and demonstrate its integration with methods such as MACE, NequIP, Allegro, CACE, CHGNet, and UMA. We benchmark LES-enhanced models on distinct systems, including bulk water, polar dipeptides, and gold dimer adsorption on defective substrates, and show that LES not only captures correct electrostatics but also improves accuracy. Additionally, we scale LES to large and chemically diverse data by training MACELES-OFF on the SPICE set containing molecules and clusters, making a universal MLIP with electrostatics for organic systems, including biomolecules. MACELES-OFF is more accurate than its short-range counterpart (MACE-OFF) trained on the same data set, predicts dipoles and BECs reliably, and has better descriptions of bulk liquids. By enabling efficient long-range electrostatics without directly training on electrical properties, LES paves the way for electrostatic foundation MLIPs.","lang":"eng"}],"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"doi":"10.1021/acs.jctc.5c01400","acknowledgement":"Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number R35GM159986. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K. and B.C. acknowledge funding from Toyota Research Institute Synthesis Advanced Research Challenge. T.J.I., D.S.K. and P.Z. acknowledge funding from BIDMaP Postdoctoral Fellowship. T.J.I. used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ′GenAI@NERSC’. The authors thank Bowen Deng for valuable discussions on MatGL implementation, and thank Gabor Csanyi for stimulating discussions.","status":"public","year":"2025","citation":{"mla":"Kim, Dongjin, et al. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 24, American Chemical Society, 2025, pp. 12709–24, doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01400\">10.1021/acs.jctc.5c01400</a>.","chicago":"Kim, Dongjin, Xiaoyu Wang, Santiago Vargas, Peichen Zhong, Daniel S. King, Theo Jaffrelot Inizan, and Bingqing Cheng. “A Universal Augmentation Framework for Long-Range Electrostatics in Machine Learning Interatomic Potentials.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.jctc.5c01400\">https://doi.org/10.1021/acs.jctc.5c01400</a>.","short":"D. Kim, X. Wang, S. Vargas, P. Zhong, D.S. King, T.J. Inizan, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 12709–12724.","ama":"Kim D, Wang X, Vargas S, et al. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. <i>Journal of Chemical Theory and Computation</i>. 2025;21(24):12709-12724. doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01400\">10.1021/acs.jctc.5c01400</a>","ieee":"D. Kim <i>et al.</i>, “A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials,” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 24. American Chemical Society, pp. 12709–12724, 2025.","ista":"Kim D, Wang X, Vargas S, Zhong P, King DS, Inizan TJ, Cheng B. 2025. A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. Journal of Chemical Theory and Computation. 21(24), 12709–12724.","apa":"Kim, D., Wang, X., Vargas, S., Zhong, P., King, D. S., Inizan, T. J., &#38; Cheng, B. (2025). A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.5c01400\">https://doi.org/10.1021/acs.jctc.5c01400</a>"},"supplementarymaterial":"no","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2507.14302"}],"dataavailabilitystatement":"The training sets, training scripts, and trained potentials are available at https://github.com/ChengUCB/les_fit. The 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.","type":"journal_article","day":"10","language":[{"iso":"eng"}],"arxiv":1,"corr_author":"1","date_published":"2025-12-10T00:00:00Z","OA_place":"repository","pmid":1,"quality_controlled":"1","volume":21,"OA_type":"green","author":[{"first_name":"Dongjin","last_name":"Kim","full_name":"Kim, Dongjin"},{"first_name":"Xiaoyu","last_name":"Wang","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","full_name":"Wang, Xiaoyu"},{"full_name":"Vargas, Santiago","last_name":"Vargas","first_name":"Santiago"},{"full_name":"Zhong, Peichen","last_name":"Zhong","first_name":"Peichen"},{"full_name":"King, Daniel S.","first_name":"Daniel S.","last_name":"King"},{"first_name":"Theo Jaffrelot","last_name":"Inizan","full_name":"Inizan, Theo Jaffrelot"},{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"title":"A universal augmentation framework for long-range electrostatics in machine learning interatomic potentials","article_type":"original","date_created":"2026-01-04T23:01:33Z","oa":1,"publication":"Journal of Chemical Theory and Computation","scopus_import":"1","intvolume":"        21","page":"12709-12724","das_tickbox":"1","_id":"20926","publisher":"American Chemical Society"},{"year":"2025","acknowledgement":"The authors thank for valuable discussions with Pinchen Xie, David Limmer, Jeff Neaton, and Greg Voth. The authors thank Sebastien Hamel for providing the DFT MD trajectories for superionic water, and help clarifying questions related to the pseudopotentials. The authors thank Federico Grasselli and Stefano Baroni for providing data and notebooks for computing the conductivity of a molten salt. This research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California, Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). D.S.K. and P.Z. acknowledge funding from the BIDMaP Postdoctoral Fellowship.","status":"public","doi":"10.1038/s41524-025-01911-z","publication_identifier":{"eissn":["2057-3960"]},"abstract":[{"lang":"eng","text":"Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods, but do not by themselves incorporate electrical response. Here, we show that polarization and Born effective charge (BEC) tensors can be directly extracted from long-range MLIPs within the Latent Ewald Summation (LES) framework, solely by learning from energy and force data. Using this approach, we predict the infrared spectra of bulk water under zero or finite external electric fields, ionic conductivities of high-pressure superionic ice, and the phase transition and hysteresis in ferroelectric PbTiO3 perovskite. This work thus extends the capability of MLIPs to predict electrical response –without training on charges or polarization or BECs– and enables accurate modeling of electric-field-driven processes in diverse systems at scale."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2026-01-20T07:22:04Z","type":"journal_article","day":"29","license":"https://creativecommons.org/licenses/by/4.0/","dataavailabilitystatement":"The training sets, training scripts, BEC inference scripts, and trained CACE potentials are available at https://github.com/BingqingCheng/LES-BEC.","month":"12","supplementarymaterial":"no","citation":{"mla":"Zhong, Peichen, et al. “Machine Learning Interatomic Potential Can Infer Electrical Response.” <i>Npj Computational Materials</i>, vol. 11, 384, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41524-025-01911-z\">10.1038/s41524-025-01911-z</a>.","chicago":"Zhong, Peichen, Dongjin Kim, Daniel S. King, and Bingqing Cheng. “Machine Learning Interatomic Potential Can Infer Electrical Response.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41524-025-01911-z\">https://doi.org/10.1038/s41524-025-01911-z</a>.","short":"P. Zhong, D. Kim, D.S. King, B. Cheng, Npj Computational Materials 11 (2025).","ama":"Zhong P, Kim D, King DS, Cheng B. Machine learning interatomic potential can infer electrical response. <i>npj Computational Materials</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41524-025-01911-z\">10.1038/s41524-025-01911-z</a>","apa":"Zhong, P., Kim, D., King, D. S., &#38; Cheng, B. (2025). Machine learning interatomic potential can infer electrical response. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-025-01911-z\">https://doi.org/10.1038/s41524-025-01911-z</a>","ista":"Zhong P, Kim D, King DS, Cheng B. 2025. Machine learning interatomic potential can infer electrical response. npj Computational Materials. 11, 384.","ieee":"P. Zhong, D. Kim, D. S. King, and B. Cheng, “Machine learning interatomic potential can infer electrical response,” <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","article_processing_charge":"Yes","article_number":"384","date_updated":"2026-08-07T09:38:09Z","fulldoi":"https://doi.org/10.1038/s41524-025-01911-z","researchdata_availability":"yes","publication_status":"published","department":[{"_id":"BiCh"}],"_id":"20990","ddc":["540"],"das_tickbox":"1","scopus_import":"1","intvolume":"        11","publication":"npj Computational Materials","date_created":"2026-01-15T12:17:07Z","oa":1,"article_type":"original","has_accepted_license":"1","publisher":"Springer Nature","file":[{"checksum":"cc999804ba3bfed809ae46c73869e4e3","access_level":"open_access","file_id":"21005","relation":"main_file","success":1,"file_size":2686255,"date_created":"2026-01-20T07:22:04Z","date_updated":"2026-01-20T07:22:04Z","content_type":"application/pdf","creator":"dernst","file_name":"2025_npj_Zhong.pdf"}],"corr_author":"1","date_published":"2025-12-29T00:00:00Z","language":[{"iso":"eng"}],"title":"Machine learning interatomic potential can infer electrical response","author":[{"first_name":"Peichen","last_name":"Zhong","full_name":"Zhong, Peichen"},{"last_name":"Kim","first_name":"Dongjin","full_name":"Kim, Dongjin"},{"last_name":"King","first_name":"Daniel S.","full_name":"King, Daniel S."},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"OA_type":"gold","volume":11,"PlanS_conform":"1","quality_controlled":"1","OA_place":"publisher"},{"has_accepted_license":"1","article_type":"original","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"oa":1,"date_created":"2025-10-19T22:01:31Z","publication":"Proceedings of the National Academy of Sciences","scopus_import":"1","intvolume":"       122","page":"e2415664122","das_tickbox":"1","ddc":["540"],"_id":"20492","isi":1,"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"corr_author":"1","date_published":"2025-10-14T00:00:00Z","file":[{"creator":"dernst","file_name":"2025_PNAS_Zeng.pdf","content_type":"application/pdf","date_updated":"2025-10-21T10:02:15Z","date_created":"2025-10-21T10:02:15Z","success":1,"file_size":12244843,"file_id":"20513","relation":"main_file","access_level":"open_access","checksum":"3f9cd0d67ffe9110fb238407671584b7"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity"}]},"OA_place":"publisher","quality_controlled":"1","pmid":1,"volume":122,"PlanS_conform":"1","OA_type":"hybrid","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3","author":[{"full_name":"Zeng, Zezhu","orcid":"0000-0001-5126-4928","last_name":"Zeng","first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"last_name":"Fan","first_name":"Zheyong","full_name":"Fan, Zheyong"},{"full_name":"Simoncelli, Michele","last_name":"Simoncelli","first_name":"Michele"},{"first_name":"Chen","last_name":"Chen","full_name":"Chen, Chen"},{"full_name":"Liang, Ting","last_name":"Liang","first_name":"Ting"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"},{"full_name":"Thornton, Geoff","first_name":"Geoff","last_name":"Thornton"},{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"issue":"41","abstract":[{"lang":"eng","text":"The glassy thermal conductivities observed in crystalline inorganic perovskites such as Cs3Bi2I6Cl3 are perplexing and lacking theoretical explanations. Here, we first experimentally measure its thermal transport behavior from 20 to 300 K, after synthesizing Cs3Bi2I6Cl3 single crystals. Using path-integral molecular dynamics simulations driven by machine learning potentials, we reveal that Cs3Bi2I6Cl3 has large lattice distortions at low temperatures, which may be related to the large atomic size mismatch. Employing the Wigner formulation of thermal transport, we reproduce theexperimental thermal conductivities based on lattice-distorted structures. This studythus provides a framework for predicting and understanding glassy thermal transportin materials with strong lattice disorder."}],"doi":"10.1073/pnas.2415664122","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"Z.Z. acknowledges the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. We acknowledge the high-performance computing facilities offered by Institute of Science and Technology Austria and The University of Hong Kong.","status":"public","year":"2025","citation":{"chicago":"Zeng, Zezhu, Zheyong Fan, Michele Simoncelli, Chen Chen, Ting Liang, Yue Chen, Geoff Thornton, and Bingqing Cheng. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2415664122\">https://doi.org/10.1073/pnas.2415664122</a>.","mla":"Zeng, Zezhu, et al. “Lattice Distortion Leads to Glassy Thermal Transport in Crystalline Cs3Bi2I6Cl3.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 41, National Academy of Sciences, 2025, p. e2415664122, doi:<a href=\"https://doi.org/10.1073/pnas.2415664122\">10.1073/pnas.2415664122</a>.","short":"Z. Zeng, Z. Fan, M. Simoncelli, C. Chen, T. Liang, Y. Chen, G. Thornton, B. Cheng, Proceedings of the National Academy of Sciences 122 (2025) e2415664122.","apa":"Zeng, Z., Fan, Z., Simoncelli, M., Chen, C., Liang, T., Chen, Y., … Cheng, B. (2025). Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2415664122\">https://doi.org/10.1073/pnas.2415664122</a>","ieee":"Z. Zeng <i>et al.</i>, “Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 41. National Academy of Sciences, p. e2415664122, 2025.","ama":"Zeng Z, Fan Z, Simoncelli M, et al. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(41):e2415664122. doi:<a href=\"https://doi.org/10.1073/pnas.2415664122\">10.1073/pnas.2415664122</a>","ista":"Zeng Z, Fan Z, Simoncelli M, Chen C, Liang T, Chen Y, Thornton G, Cheng B. 2025. Lattice distortion leads to glassy thermal transport in crystalline Cs3Bi2I6Cl3. Proceedings of the National Academy of Sciences. 122(41), e2415664122."},"month":"10","supplementarymaterial":"no","ec_funded":1,"dataavailabilitystatement":"Primitive Data Types have been deposited in GitHub (Cs3Bi2I6Cl3_heat_conductivity) (https://github.com/ZengZezhu/Cs3Bi2I6Cl3_heat_conductivity) (74).","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"14","type":"journal_article","file_date_updated":"2025-10-21T10:02:15Z","date_updated":"2026-08-07T10:11:03Z","article_processing_charge":"No","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BiCh"}],"researchdata_availability":"no","publication_status":"published","external_id":{"pmid":["41052324"],"isi":["001600415200001"]},"fulldoi":"https://doi.org/10.1073/pnas.2415664122"},{"related_material":{"link":[{"relation":"software","url":"https://github.com/ZengZezhu/heat-conductivity-a-HfO2"}]},"file":[{"date_created":"2025-12-30T09:13:06Z","date_updated":"2025-12-30T09:13:06Z","creator":"dernst","file_name":"2025_ACSMaterialsLetters_Zeng.pdf","content_type":"application/pdf","checksum":"d61e63439ddeaef29e9a2ee0f65c4ec1","access_level":"open_access","success":1,"file_size":2402059,"relation":"main_file","file_id":"20903"}],"date_published":"2025-06-30T00:00:00Z","corr_author":"1","language":[{"iso":"eng"}],"title":"Thermal transport of amorphous hafnia across the glass transition","author":[{"orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng"},{"last_name":"Liang","first_name":"Xia","full_name":"Liang, Xia"},{"full_name":"Fan, Zheyong","first_name":"Zheyong","last_name":"Fan"},{"last_name":"Chen","first_name":"Yue","full_name":"Chen, Yue"},{"full_name":"Simoncelli, Michele","last_name":"Simoncelli","first_name":"Michele"},{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"OA_type":"hybrid","quality_controlled":"1","OA_place":"publisher","_id":"20011","das_tickbox":"1","page":"2695-2701","ddc":["530"],"scopus_import":"1","publication":"ACS Materials Letters","oa":1,"date_created":"2025-07-13T22:01:24Z","article_type":"original","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"has_accepted_license":"1","publisher":"American Chemical Society","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-08-07T10:06:48Z","fulldoi":"https://doi.org/10.1021/acsmaterialslett.5c00263","external_id":{"isi":["001520226300001"]},"researchdata_availability":"no","publication_status":"published","department":[{"_id":"BiCh"}],"year":"2025","acknowledgement":"We thank Ludovic Berthier for fruitful discussions and Ting Liang for providing the initial structures of a-SiO2. Z.Z. acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Programme, under Marie Skłodowska-Curie grant agreement No. 101034413. The authors also acknowledge the research computing facilities provided by HPC ISTA and ITS HKU.","status":"public","publication_identifier":{"eissn":["2639-4979"]},"doi":"10.1021/acsmaterialslett.5c00263","abstract":[{"lang":"eng","text":"Heat transport in glasses over a wide temperature range is critical for applications in gate dielectrics and thermal insulators but remains poorly understood due to the challenges in modeling vibrational anharmonicity and configurational dynamics across the glass transition. Recent predictions show an unusual decrease in thermal conductivity (κ) with temperature in amorphous hafnia (a-HfO2), contrasting with the typical trend in glasses. Using molecular dynamics with a machine-learning-based neuroevolution potential, we compute κ of a-HfO2 from 50 K to 2000 K. At low temperatures, the Wigner transport equation captures both anharmonicity and quantum statistics. Above 1200 K, atomic diffusion invalidates the quasiparticle picture, and we resort to the Green–Kubo method to capture convective transport. We further extend the Wigner transport equation to supercooled a-HfO2, revealing the crucial role of low-frequency modes in facilitating heat transport. The computed κ, based on both Green–Kubo and Wigner transport theories, increases continuously with temperature up to 2000 K."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2025-12-30T09:13:06Z","day":"30","type":"journal_article","dataavailabilitystatement":"All necessary source data files generated for this study are available in the GitHub repository https://github.com/ZengZezhu/heat-conductivity-a-HfO2.","ec_funded":1,"month":"06","supplementarymaterial":"no","citation":{"ama":"Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. Thermal transport of amorphous hafnia across the glass transition. <i>ACS Materials Letters</i>. 2025:2695-2701. doi:<a href=\"https://doi.org/10.1021/acsmaterialslett.5c00263\">10.1021/acsmaterialslett.5c00263</a>","ieee":"Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, and B. Cheng, “Thermal transport of amorphous hafnia across the glass transition,” <i>ACS Materials Letters</i>. American Chemical Society, pp. 2695–2701, 2025.","ista":"Zeng Z, Liang X, Fan Z, Chen Y, Simoncelli M, Cheng B. 2025. Thermal transport of amorphous hafnia across the glass transition. ACS Materials Letters., 2695–2701.","apa":"Zeng, Z., Liang, X., Fan, Z., Chen, Y., Simoncelli, M., &#38; Cheng, B. (2025). Thermal transport of amorphous hafnia across the glass transition. <i>ACS Materials Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsmaterialslett.5c00263\">https://doi.org/10.1021/acsmaterialslett.5c00263</a>","chicago":"Zeng, Zezhu, Xia Liang, Zheyong Fan, Yue Chen, Michele Simoncelli, and Bingqing Cheng. “Thermal Transport of Amorphous Hafnia across the Glass Transition.” <i>ACS Materials Letters</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acsmaterialslett.5c00263\">https://doi.org/10.1021/acsmaterialslett.5c00263</a>.","mla":"Zeng, Zezhu, et al. “Thermal Transport of Amorphous Hafnia across the Glass Transition.” <i>ACS Materials Letters</i>, American Chemical Society, 2025, pp. 2695–701, doi:<a href=\"https://doi.org/10.1021/acsmaterialslett.5c00263\">10.1021/acsmaterialslett.5c00263</a>.","short":"Z. Zeng, X. Liang, Z. Fan, Y. Chen, M. Simoncelli, B. Cheng, ACS Materials Letters (2025) 2695–2701."}},{"article_processing_charge":"Yes","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"80","date_updated":"2026-08-07T10:04:17Z","external_id":{"arxiv":["2408.15165"],"isi":["001453622900002"]},"fulldoi":"https://doi.org/10.1038/s41524-025-01577-7","department":[{"_id":"BiCh"}],"researchdata_availability":"unclear","publication_status":"published","publication_identifier":{"eissn":["2057-3960"]},"doi":"10.1038/s41524-025-01577-7","year":"2025","status":"public","acknowledgement":"B. C. thanks David Limmer for providing the water slab dataset, and Carolin Faller for the NaCl dataset.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Machine learning interatomic potentials (MLIPs) often neglect long-range interactions, such as electrostatic and dispersion forces. In this work, we introduce a straightforward and efficient method to account for long-range interactions by learning a hidden variable from local atomic descriptors and applying an Ewald summation to this variable. We demonstrate that in systems including charged and polar molecular dimers, bulk water, and water-vapor interface, standard short-ranged MLIPs can lead to unphysical predictions even when employing message passing. The long-range models effectively eliminate these artifacts, with only about twice the computational cost of short-range MLIPs.","lang":"eng"}],"dataavailabilitystatement":"The training scripts, trained CACE potentials, and MD input files are available at https://github.com/BingqingCheng/cace-lr-fit.","file_date_updated":"2025-04-08T09:34:58Z","type":"journal_article","day":"26","citation":{"chicago":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>.","mla":"Cheng, Bingqing. “Latent Ewald Summation for Machine Learning of Long-Range Interactions.” <i>Npj Computational Materials</i>, vol. 11, 80, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>.","short":"B. Cheng, Npj Computational Materials 11 (2025).","ieee":"B. Cheng, “Latent Ewald summation for machine learning of long-range interactions,” <i>npj Computational Materials</i>, vol. 11. Springer Nature, 2025.","ista":"Cheng B. 2025. Latent Ewald summation for machine learning of long-range interactions. npj Computational Materials. 11, 80.","ama":"Cheng B. Latent Ewald summation for machine learning of long-range interactions. <i>npj Computational Materials</i>. 2025;11. doi:<a href=\"https://doi.org/10.1038/s41524-025-01577-7\">10.1038/s41524-025-01577-7</a>","apa":"Cheng, B. (2025). Latent Ewald summation for machine learning of long-range interactions. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-025-01577-7\">https://doi.org/10.1038/s41524-025-01577-7</a>"},"supplementarymaterial":"no","month":"03","file":[{"date_updated":"2025-04-08T09:34:58Z","date_created":"2025-04-08T09:34:58Z","file_name":"2025_npjCompMaterials_Cheng.pdf","creator":"dernst","content_type":"application/pdf","access_level":"open_access","checksum":"cc99b7407a12139d9b2d8457961935ae","success":1,"file_size":1608315,"relation":"main_file","file_id":"19528"}],"date_published":"2025-03-26T00:00:00Z","corr_author":"1","arxiv":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"title":"Latent Ewald summation for machine learning of long-range interactions","OA_place":"publisher","volume":11,"OA_type":"gold","quality_controlled":"1","intvolume":"        11","scopus_import":"1","publication":"npj Computational Materials","_id":"19495","das_tickbox":"1","ddc":["000"],"article_type":"original","has_accepted_license":"1","oa":1,"date_created":"2025-04-06T22:01:32Z","isi":1,"publisher":"Springer Nature","DOAJ_listed":"1"},{"type":"journal_article","day":"02","file_date_updated":"2025-12-01T08:41:32Z","dataavailabilitystatement":"Code has been deposited to https://github.com/GagliardiGroup/CEONet (83). Data has been deposited to https://doi.org/10.5281/zenodo.16934624 (84).","supplementarymaterial":"no","month":"12","citation":{"ista":"King DS, Grzenda D, Zhu R, Hudson N, Foster I, Cheng B, Gagliardi L. 2025. Cartesian equivariant representations for learning and understanding molecular orbitals. Proceedings of the National Academy of Sciences. 122(48), e2510235122.","ieee":"D. S. King <i>et al.</i>, “Cartesian equivariant representations for learning and understanding molecular orbitals,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48. National Academy of Sciences, 2025.","apa":"King, D. S., Grzenda, D., Zhu, R., Hudson, N., Foster, I., Cheng, B., &#38; Gagliardi, L. (2025). Cartesian equivariant representations for learning and understanding molecular orbitals. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2510235122\">https://doi.org/10.1073/pnas.2510235122</a>","ama":"King DS, Grzenda D, Zhu R, et al. Cartesian equivariant representations for learning and understanding molecular orbitals. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(48). doi:<a href=\"https://doi.org/10.1073/pnas.2510235122\">10.1073/pnas.2510235122</a>","mla":"King, Daniel S., et al. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48, e2510235122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2510235122\">10.1073/pnas.2510235122</a>.","chicago":"King, Daniel S., Daniel Grzenda, Ray Zhu, Nathaniel Hudson, Ian Foster, Bingqing Cheng, and Laura Gagliardi. “Cartesian Equivariant Representations for Learning and Understanding Molecular Orbitals.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2510235122\">https://doi.org/10.1073/pnas.2510235122</a>.","short":"D.S. King, D. Grzenda, R. Zhu, N. Hudson, I. Foster, B. Cheng, L. Gagliardi, Proceedings of the National Academy of Sciences 122 (2025)."},"acknowledgement":"This work is supported as part of the Catalyst Design for Decarbonization Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under award no. DE-SC0023383. We thank the Research Computing Center at the University of Chicago and for access to computational resources. Additionally, this research used the Savio computational cluster resource provided by the Berkeley Research Computing program at the University of California (UC), Berkeley (supported by the UC Berkeley Chancellor, Vice Chancellor for Research, and Chief Information Officer). Furthermore, we thank Matthew Hennefarth and Matt Hermes for useful discussions.","status":"public","year":"2025","publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.2510235122","issue":"48","abstract":[{"lang":"eng","text":"Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"fulldoi":"https://doi.org/10.1073/pnas.2510235122","external_id":{"pmid":["41269783"]},"researchdata_availability":"no","publication_status":"published","department":[{"_id":"BiCh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-08-07T10:27:53Z","article_number":"e2510235122","publisher":"National Academy of Sciences","ddc":["540"],"das_tickbox":"1","_id":"20702","publication":"Proceedings of the National Academy of Sciences","scopus_import":"1","intvolume":"       122","date_created":"2025-11-30T23:02:06Z","oa":1,"has_accepted_license":"1","article_type":"original","author":[{"full_name":"King, Daniel S.","last_name":"King","first_name":"Daniel S."},{"full_name":"Grzenda, Daniel","last_name":"Grzenda","first_name":"Daniel"},{"last_name":"Zhu","first_name":"Ray","full_name":"Zhu, Ray"},{"first_name":"Nathaniel","last_name":"Hudson","full_name":"Hudson, Nathaniel"},{"full_name":"Foster, Ian","last_name":"Foster","first_name":"Ian"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Gagliardi","first_name":"Laura","full_name":"Gagliardi, Laura"}],"title":"Cartesian equivariant representations for learning and understanding molecular orbitals","pmid":1,"quality_controlled":"1","volume":122,"OA_type":"hybrid","OA_place":"publisher","related_material":{"link":[{"url":"https://github.com/GagliardiGroup/CEONet ","relation":"software"}]},"date_published":"2025-12-02T00:00:00Z","corr_author":"1","file":[{"file_size":27607870,"success":1,"file_id":"20719","relation":"main_file","access_level":"open_access","checksum":"58051539a884c7a97306fd3afdb539ac","creator":"dernst","file_name":"2025_PNAS_King.pdf","content_type":"application/pdf","date_created":"2025-12-01T08:41:32Z","date_updated":"2025-12-01T08:41:32Z"}],"language":[{"iso":"eng"}]},{"supplementarymaterial":"no","month":"10","citation":{"ista":"Tuo P, Zeng Z, Chen J, Cheng B. 2025. Scalable multitemperature free energy sampling of classical Ising spin states. Journal of Chemical Theory and Computation. 21(22), 11427–11435.","apa":"Tuo, P., Zeng, Z., Chen, J., &#38; Cheng, B. (2025). Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>","ama":"Tuo P, Zeng Z, Chen J, Cheng B. Scalable multitemperature free energy sampling of classical Ising spin states. <i>Journal of Chemical Theory and Computation</i>. 2025;21(22):11427-11435. doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>","ieee":"P. Tuo, Z. Zeng, J. Chen, and B. Cheng, “Scalable multitemperature free energy sampling of classical Ising spin states,” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22. American Chemical Society, pp. 11427–11435, 2025.","short":"P. Tuo, Z. Zeng, J. Chen, B. Cheng, Journal of Chemical Theory and Computation 21 (2025) 11427–11435.","chicago":"Tuo, Ping, Zezhu Zeng, Jiale Chen, and Bingqing Cheng. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2025. <a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">https://doi.org/10.1021/acs.jctc.5c01248</a>.","mla":"Tuo, Ping, et al. “Scalable Multitemperature Free Energy Sampling of Classical Ising Spin States.” <i>Journal of Chemical Theory and Computation</i>, vol. 21, no. 22, American Chemical Society, 2025, pp. 11427–35, doi:<a href=\"https://doi.org/10.1021/acs.jctc.5c01248\">10.1021/acs.jctc.5c01248</a>."},"type":"journal_article","day":"31","ec_funded":1,"issue":"22","abstract":[{"lang":"eng","text":"Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a discrete flow matching model, tailored for systems with discrete phase-space coordinates (e.g., the Ising model or a multicomponent system on a lattice). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead, and the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate our approach on the 2D Ising model, showing efficient and reliable free energy sampling. These results highlight the potential of flow matching for low-cost, scalable free energy sampling in discrete systems and suggest promising extensions to alchemical degrees of freedom in crystalline materials. The codebase developed for this work is openly available at https://github.com/tuoping/alchemicalFES."}],"status":"public","acknowledgement":"P.T. acknowledges funding from FFG MAGNIFICO and the BIDMaP Postdoctoral Fellowship. Z.Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 101034413. The authors acknowledge the research computing facilities provided by the Institute of Science and Technology Austria (ISTA), and resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy Office of Science User Facility using NERSC award DOEERCAP0031751 ’GenAI@NERSC’. P.T. acknowledges valued discussions with Dr. Daniel King, Dr. Lei Wang, and Dr. Fuzhi Dai.","year":"2025","doi":"10.1021/acs.jctc.5c01248","publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"researchdata_availability":"no","publication_status":"published","department":[{"_id":"BiCh"},{"_id":"DaAl"}],"fulldoi":"https://doi.org/10.1021/acs.jctc.5c01248","external_id":{"isi":["001605927900001"],"pmid":["41172130"]},"date_updated":"2026-08-07T10:29:06Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","article_processing_charge":"No","publisher":"American Chemical Society","isi":1,"date_created":"2025-11-30T23:02:06Z","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"article_type":"original","page":"11427-11435","das_tickbox":"0","_id":"20704","publication":"Journal of Chemical Theory and Computation","intvolume":"        21","scopus_import":"1","quality_controlled":"1","pmid":1,"volume":21,"OA_type":"closed access","title":"Scalable multitemperature free energy sampling of classical Ising spin states","author":[{"full_name":"Tuo, Ping","first_name":"Ping","last_name":"Tuo","id":"6e5644c0-c180-11ed-a2da-facc4c9f4f09"},{"orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","last_name":"Zeng","first_name":"Zezhu"},{"full_name":"Chen, Jiale","orcid":"0000-0001-5337-5875","last_name":"Chen","first_name":"Jiale","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/tuoping/alchemicalFES","relation":"software"}]},"corr_author":"1","date_published":"2025-10-31T00:00:00Z"},{"file_date_updated":"2025-04-22T09:46:27Z","day":"03","type":"journal_article","citation":{"mla":"Schmied, Verena, et al. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” <i>Journal of Neuroinflammation</i>, vol. 22, no. 1, 98, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1186/s12974-025-03366-x\">10.1186/s12974-025-03366-x</a>.","chicago":"Schmied, Verena, Medina Korkut, Alessandro Venturino, Juan Pablo Maya-Arteaga, and Sandra Siegert. “Microglia Determine an Immune-Challenged Environment and Facilitate Ibuprofen Action in Human Retinal Organoids.” <i>Journal of Neuroinflammation</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1186/s12974-025-03366-x\">https://doi.org/10.1186/s12974-025-03366-x</a>.","short":"V. Schmied, M. Korkut, A. Venturino, J.P. Maya-Arteaga, S. Siegert, Journal of Neuroinflammation 22 (2025).","ista":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. 2025. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. Journal of Neuroinflammation. 22(1), 98.","ama":"Schmied V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. <i>Journal of Neuroinflammation</i>. 2025;22(1). doi:<a href=\"https://doi.org/10.1186/s12974-025-03366-x\">10.1186/s12974-025-03366-x</a>","ieee":"V. Schmied, M. Korkut, A. Venturino, J. P. Maya-Arteaga, and S. Siegert, “Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids,” <i>Journal of Neuroinflammation</i>, vol. 22, no. 1. Springer Nature, 2025.","apa":"Schmied, V., Korkut, M., Venturino, A., Maya-Arteaga, J. P., &#38; Siegert, S. (2025). Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. <i>Journal of Neuroinflammation</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12974-025-03366-x\">https://doi.org/10.1186/s12974-025-03366-x</a>"},"month":"04","doi":"10.1186/s12974-025-03366-x","APC_amount":"3948 EUR","publication_identifier":{"eissn":["1742-2094"]},"year":"2025","status":"public","acknowledgement":"We thank the scientific service units at ISTA, specifically the Lab Support Facility (LSF), the Molecular Biology Services/Virus Services Team, specifically Flavia Gama Gomes Leite and Mark Andrew Smyth, for the virus production, and the Imaging and Optics Facility (IOF). We thank all members of the Siegert group and Marco Benevento for their constant feedback on the project and comments on the manuscript. A special thanks to Rouven Schulz for input on statistical analysis and sharing R-scripts, Gloria Colombo for the introduction to cell sorting, Negar Vehdani and Florianne Schoot Uiterkamp for their support in cell culture. This research was supported by the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development."}],"issue":"1","external_id":{"isi":["001459311800002"],"pmid":["40181459"]},"fulldoi":"https://doi.org/10.1186/s12974-025-03366-x","department":[{"_id":"SaSi"}],"publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"98","date_updated":"2026-08-12T08:45:16Z","publisher":"Springer Nature","isi":1,"DOAJ_listed":"1","scopus_import":"1","intvolume":"        22","publication":"Journal of Neuroinflammation","_id":"19593","ddc":["570"],"article_type":"original","project":[{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"},{"name":"IST Austria Open Access 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Pablo"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"OA_place":"publisher","volume":22,"PlanS_conform":"1","OA_type":"gold","pmid":1,"quality_controlled":"1","file":[{"date_created":"2025-04-22T09:46:27Z","date_updated":"2025-04-22T09:46:27Z","file_name":"2025_JourNeuroinflammation_Schmied.pdf","creator":"dernst","content_type":"application/pdf","checksum":"dcc355c21ab713e45fda5c61b5fa5299","access_level":"open_access","success":1,"file_size":4482167,"file_id":"19607","relation":"main_file"}],"corr_author":"1","date_published":"2025-04-03T00:00:00Z","related_material":{"link":[{"relation":"press_release","description":"News on ISTA 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Verena"}],"title":"Human microglia impact neuronal development in retinal organoids","supervisor":[{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert"}],"OA_place":"publisher","page":"151","ddc":["570"],"_id":"20074","oa":1,"date_created":"2025-07-24T12:37:22Z","has_accepted_license":"1","project":[{"name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-017"}],"degree_awarded":"PhD","doi_confirm":"1","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"No","date_updated":"2026-08-12T08:45:16Z","fulldoi":"https://doi.org/10.15479/AT-ISTA-20074","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"status":"public","year":"2025","doi":"10.15479/AT-ISTA-20074","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-060-2"]},"abstract":[{"text":"Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. \r\nIn chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. \r\nIn chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. \r\nIn summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"type":"dissertation","day":"24","file_date_updated":"2025-07-30T09:29:09Z","month":"07","citation":{"chicago":"Schmied, Verena. “Human Microglia Impact Neuronal Development in Retinal Organoids.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>.","mla":"Schmied, Verena. <i>Human Microglia Impact Neuronal Development in Retinal Organoids</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>.","short":"V. Schmied, Human Microglia Impact Neuronal Development in Retinal Organoids, Institute of Science and Technology Austria, 2025.","ieee":"V. Schmied, “Human microglia impact neuronal development in retinal organoids,” Institute of Science and Technology Austria, 2025.","ista":"Schmied V. 2025. Human microglia impact neuronal development in retinal organoids. Institute of Science and Technology Austria.","apa":"Schmied, V. (2025). <i>Human microglia impact neuronal development in retinal organoids</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20074\">https://doi.org/10.15479/AT-ISTA-20074</a>","ama":"Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20074\">10.15479/AT-ISTA-20074</a>"}},{"type":"journal_article","day":"23","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.16373"}],"month":"02","citation":{"ama":"Brooks M, Mitrouskas DJ. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. 2025;6(1):281-325. doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>","ieee":"M. Brooks and D. J. Mitrouskas, “Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling,” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1. Mathematical Sciences Publishers, pp. 281–325, 2025.","ista":"Brooks M, Mitrouskas DJ. 2025. Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. Probability and Mathematical Physics. 6(1), 281–325.","apa":"Brooks, M., &#38; Mitrouskas, D. J. (2025). Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling. <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>","short":"M. Brooks, D.J. Mitrouskas, Probability and Mathematical Physics 6 (2025) 281–325.","chicago":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>. Mathematical Sciences Publishers, 2025. <a href=\"https://doi.org/10.2140/pmp.2025.6.281\">https://doi.org/10.2140/pmp.2025.6.281</a>.","mla":"Brooks, Morris, and David Johannes Mitrouskas. “Asymptotic Series for Low-Energy Excitations of the Fröhlich Polaron at Strong Coupling.” <i>Probability and Mathematical Physics</i>, vol. 6, no. 1, Mathematical Sciences Publishers, 2025, pp. 281–325, doi:<a href=\"https://doi.org/10.2140/pmp.2025.6.281\">10.2140/pmp.2025.6.281</a>."},"status":"public","acknowledgement":"M.B. gratefully acknowledges funding from the ERC Advanced Grant ERC-AdG CLaQS, grant agreement n. 83478.","year":"2025","doi":"10.2140/pmp.2025.6.281","publication_identifier":{"eissn":["2690-1005"],"issn":["2690-0998"]},"issue":"1","abstract":[{"lang":"eng","text":"We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field."}],"fulldoi":"https://doi.org/10.2140/pmp.2025.6.281","external_id":{"arxiv":["2306.16373"]},"publication_status":"published","department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","oa_version":"Preprint","date_updated":"2026-08-12T08:44:53Z","publisher":"Mathematical Sciences Publishers","page":"281-325","_id":"19372","publication":"Probability and Mathematical Physics","intvolume":"         6","scopus_import":"1","oa":1,"date_created":"2025-03-09T23:01:28Z","article_type":"original","title":"Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling","author":[{"orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","last_name":"Brooks"},{"full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas","first_name":"David Johannes"}],"quality_controlled":"1","volume":6,"OA_type":"green","OA_place":"repository","corr_author":"1","date_published":"2025-02-23T00:00:00Z","language":[{"iso":"eng"}],"arxiv":1},{"language":[{"iso":"eng"}],"arxiv":1,"related_material":{"record":[{"id":"13221","relation":"earlier_version","status":"public"},{"relation":"dissertation_contains","status":"public","id":"20147"}]},"date_published":"2025-04-08T00:00:00Z","corr_author":"1","file":[{"content_type":"application/pdf","creator":"esarac","file_name":"2307.06016.pdf","date_updated":"2025-09-11T12:17:12Z","date_created":"2025-09-11T12:17:12Z","file_id":"20343","relation":"main_file","success":1,"file_size":709584,"access_level":"open_access","checksum":"0b4d477bd981379724c35a4de2c176e5"}],"quality_controlled":"1","volume":21,"OA_type":"gold","PlanS_conform":"1","OA_place":"publisher","title":"Safety and liveness of quantitative properties and automata","author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"oa":1,"date_created":"2025-09-11T12:17:52Z","has_accepted_license":"1","article_type":"original","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"ddc":["000"],"_id":"20342","publication":"Logical Methods in Computer Science","scopus_import":"1","intvolume":"        21","DOAJ_listed":"1","publisher":"EPI Sciences","isi":1,"date_updated":"2026-08-12T08:46:05Z","article_number":"13149","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"fulldoi":"https://doi.org/10.46298/lmcs-21(2:2)2025","external_id":{"isi":["001468887900001"],"arxiv":["2307.06016"]},"issue":"2","abstract":[{"lang":"eng","text":"Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 and the Israel Science Foundation grant 2410/22. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication.","year":"2025","doi":"10.46298/lmcs-21(2:2)2025","publication_identifier":{"eissn":["1860-5974"]},"month":"04","citation":{"ista":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. 2025. Safety and liveness of quantitative properties and automata. Logical Methods in Computer Science. 21(2), 13149.","ama":"Boker U, Henzinger TA, Mazzocchi NA, Sarac NE. Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. 2025;21(2). doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>","apa":"Boker, U., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2025). Safety and liveness of quantitative properties and automata. <i>Logical Methods in Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>","ieee":"U. Boker, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Safety and liveness of quantitative properties and automata,” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2. EPI Sciences, 2025.","mla":"Boker, Udi, et al. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>, vol. 21, no. 2, 13149, EPI Sciences, 2025, doi:<a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">10.46298/lmcs-21(2:2)2025</a>.","chicago":"Boker, Udi, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Safety and Liveness of Quantitative Properties and Automata.” <i>Logical Methods in Computer Science</i>. EPI Sciences, 2025. <a href=\"https://doi.org/10.46298/lmcs-21(2:2)2025\">https://doi.org/10.46298/lmcs-21(2:2)2025</a>.","short":"U. Boker, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, Logical Methods in Computer Science 21 (2025)."},"type":"journal_article","day":"08","file_date_updated":"2025-09-11T12:17:12Z","ec_funded":1},{"oa":1,"date_created":"2025-05-18T22:02:50Z","has_accepted_license":"1","project":[{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"article_type":"original","ddc":["570"],"page":"249-274","_id":"19701","publication":"Annual Review of Biophysics","intvolume":"        54","scopus_import":"1","publisher":"Annual Reviews","isi":1,"language":[{"iso":"eng"}],"corr_author":"1","date_published":"2025-05-01T00:00:00Z","file":[{"file_name":"2025_AnnualReviewBiophysics_Tkacik.pdf","creator":"dernst","content_type":"application/pdf","date_created":"2025-05-19T07:55:51Z","date_updated":"2025-05-19T07:55:51Z","success":1,"file_size":317925,"file_id":"19710","relation":"main_file","access_level":"open_access","checksum":"9ab623b2bc45dcd5fdd2c9577ea8ae9f"}],"quality_controlled":"1","pmid":1,"OA_type":"hybrid","volume":54,"OA_place":"publisher","title":"Information processing in biochemical networks","author":[{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pieter Rein Ten","last_name":"Wolde","full_name":"Wolde, Pieter Rein Ten"}],"abstract":[{"text":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","acknowledgement":"G.T. acknowledges the support of the Human Frontiers Science Program (HFSP), the Austrian Science Fund (FWF 10.55776/P34015, 10.55776/P28844), and the European Research Council Synergy DYNATRANS (ERC-2023-SyG 101118866) grant. P.R.t.W. performed his work at the research institute AMOLF and acknowledges support from the Dutch Research Council (NWO) and funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 885065).","year":"2025","doi":"10.1146/annurev-biophys-060524-102720","publication_identifier":{"eissn":["1936-1238"]},"month":"05","citation":{"chicago":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>.","mla":"Tkačik, Gašper, and Pieter Rein Ten Wolde. “Information Processing in Biochemical Networks.” <i>Annual Review of Biophysics</i>, vol. 54, Annual Reviews, 2025, pp. 249–74, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>.","short":"G. Tkačik, P.R.T. Wolde, Annual Review of Biophysics 54 (2025) 249–274.","ama":"Tkačik G, Wolde PRT. Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. 2025;54:249-274. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">10.1146/annurev-biophys-060524-102720</a>","ista":"Tkačik G, Wolde PRT. 2025. Information processing in biochemical networks. Annual Review of Biophysics. 54, 249–274.","ieee":"G. Tkačik and P. R. T. Wolde, “Information processing in biochemical networks,” <i>Annual Review of Biophysics</i>, vol. 54. Annual Reviews, pp. 249–274, 2025.","apa":"Tkačik, G., &#38; Wolde, P. R. T. (2025). Information processing in biochemical networks. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-060524-102720\">https://doi.org/10.1146/annurev-biophys-060524-102720</a>"},"type":"journal_article","day":"01","file_date_updated":"2025-05-19T07:55:51Z","date_updated":"2026-08-12T09:25:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","department":[{"_id":"GaTk"}],"fulldoi":"https://doi.org/10.1146/annurev-biophys-060524-102720","external_id":{"isi":["001488641500013"],"pmid":["39929539"]}},{"title":"Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation","author":[{"full_name":"Moriyama, Yuuta","orcid":"0000-0002-2853-8051","first_name":"Yuuta","last_name":"Moriyama","id":"addc9b8c-67a0-11f0-b374-a2e094825470"},{"last_name":"Mitsui","first_name":"Toshiyuki","full_name":"Mitsui, Toshiyuki"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"OA_place":"publisher","pmid":1,"quality_controlled":"1","OA_type":"hybrid","volume":152,"PlanS_conform":"1","date_published":"2025-06-27T00:00:00Z","corr_author":"1","file":[{"access_level":"open_access","checksum":"808d8aa28df79d23fb661838d1fdc1be","relation":"main_file","file_id":"20070","success":1,"file_size":25935563,"date_updated":"2025-07-23T08:43:01Z","date_created":"2025-07-23T08:43:01Z","content_type":"application/pdf","creator":"dernst","file_name":"2025_Development_Moriyama.pdf"}],"language":[{"iso":"eng"}],"isi":1,"publisher":"Company of Biologists","publication":"Development","intvolume":"       152","scopus_import":"1","ddc":["570"],"_id":"20048","has_accepted_license":"1","article_type":"original","oa":1,"date_created":"2025-07-21T08:10:32Z","external_id":{"pmid":["40576478"],"isi":["001525252300001"]},"fulldoi":"https://doi.org/10.1242/dev.204261","department":[{"_id":"CaHe"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-08-12T10:01:31Z","article_number":"dev204261","day":"27","type":"journal_article","file_date_updated":"2025-07-23T08:43:01Z","citation":{"ieee":"Y. Moriyama, T. Mitsui, and C.-P. J. Heisenberg, “Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation,” <i>Development</i>, vol. 152, no. 12. Company of Biologists, 2025.","ista":"Moriyama Y, Mitsui T, Heisenberg C-PJ. 2025. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. Development. 152(12), dev204261.","ama":"Moriyama Y, Mitsui T, Heisenberg C-PJ. Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. 2025;152(12). doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>","apa":"Moriyama, Y., Mitsui, T., &#38; Heisenberg, C.-P. J. (2025). Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>","short":"Y. Moriyama, T. Mitsui, C.-P.J. Heisenberg, Development 152 (2025).","mla":"Moriyama, Yuuta, et al. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>, vol. 152, no. 12, dev204261, Company of Biologists, 2025, doi:<a href=\"https://doi.org/10.1242/dev.204261\">10.1242/dev.204261</a>.","chicago":"Moriyama, Yuuta, Toshiyuki Mitsui, and Carl-Philipp J Heisenberg. “Hoxb Genes Determine the Timing of Cell Ingression by Regulating Cell Surface Fluctuations during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2025. <a href=\"https://doi.org/10.1242/dev.204261\">https://doi.org/10.1242/dev.204261</a>."},"month":"06","doi":"10.1242/dev.204261","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"acknowledgement":"We thank all the Heisenberg lab members for discussions and comments on the manuscript, and the Bioimaging and Life Science facilities of ISTA for support with microscopy and fish maintenance, respectively. This study was funded by a Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship and a Japan Science and Technology Agency PRESTO grant (JPMJPR214B) to Y.M. Open Access funding provided by the Japan Science and Technology Agency. Deposited in PMC for immediate release.","status":"public","year":"2025","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"12","abstract":[{"text":"During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.","lang":"eng"}]},{"month":"10","supplementarymaterial":"no","citation":{"short":"T.D. Browning, S. Chan, Journal de l’Ecole Polytechnique - Mathematiques 12 (2025) 1677–1691.","mla":"Browning, Timothy D., and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12, Ecole Polytechnique, 2025, pp. 1677–91, doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>.","chicago":"Browning, Timothy D, and Stephanie Chan. “Solubility of a Resultant Equation and Applications.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2025. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>.","ieee":"T. D. Browning and S. Chan, “Solubility of a resultant equation and applications,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 12. Ecole Polytechnique, pp. 1677–1691, 2025.","ama":"Browning TD, Chan S. Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2025;12:1677-1691. doi:<a href=\"https://doi.org/10.5802/jep.320\">10.5802/jep.320</a>","ista":"Browning TD, Chan S. 2025. Solubility of a resultant equation and applications. Journal de l’Ecole Polytechnique - Mathematiques. 12, 1677–1691.","apa":"Browning, T. D., &#38; Chan, S. (2025). Solubility of a resultant equation and applications. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.320\">https://doi.org/10.5802/jep.320</a>"},"day":"21","type":"journal_article","file_date_updated":"2026-02-24T07:56:34Z","abstract":[{"lang":"eng","text":"The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x],\r\nsuch that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q.\r\nGiven a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all\r\nquadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common\r\nroot in Fp. Using recent work of Landesman, an application to the average size of the odd part\r\nof the class group of quadratic number fields is also given"},{"lang":"fre","text":" Le grand crible est utilisé pour estimer la densité des polynômes quadratiques Q ∈ Z[x] tels qu’il existe un polynôme de degré impair défini sur Z dont le résultant avec Q est égal à ±1. Étant donné un polynôme unitaire R ∈ Z[x] de degré impair, on s’en sert pour montrer que, pour presque tous les polynômes quadratiques Q ∈ Z[x], il existe un nombre premier p tel que Q et R aient une racine commune dans Fp. En utilisant des travaux récents de Landesman, on obtient également une application concernant la taille moyenne de la partie impaire du groupe de classe des corps quadratiques."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","acknowledgement":"While working on this paper, the first author was supported by a FWF grant (DOI 10.55776/P36278).","year":"2025","publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"doi":"10.5802/jep.320","researchdata_availability":"no","publication_status":"published","department":[{"_id":"TiBr"}],"fulldoi":"https://doi.org/10.5802/jep.320","external_id":{"arxiv":["2411.09264"]},"date_updated":"2026-08-12T11:17:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"Yes","DOAJ_listed":"1","publisher":"Ecole Polytechnique","oa":1,"date_created":"2026-02-22T23:01:36Z","has_accepted_license":"1","project":[{"grant_number":"P36278","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","name":"Rational curves via function field analytic number theory"}],"article_type":"original","ddc":["510"],"das_tickbox":"0","page":"1677-1691","_id":"21343","publication":"Journal de l'Ecole Polytechnique - Mathematiques","intvolume":"        12","scopus_import":"1","quality_controlled":"1","volume":12,"PlanS_conform":"1","OA_type":"gold","OA_place":"publisher","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","last_name":"Browning"},{"id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1","last_name":"Chan","first_name":"Yik Tung","orcid":"0000-0001-8467-4106","full_name":"Chan, Yik Tung"}],"title":"Solubility of a resultant equation and applications","language":[{"iso":"eng"}],"arxiv":1,"date_published":"2025-10-21T00:00:00Z","corr_author":"1","file":[{"access_level":"open_access","checksum":"828577ea48ac6109d3e9dd1aeddd45c4","file_size":1003689,"success":1,"relation":"main_file","file_id":"21356","date_created":"2026-02-24T07:56:34Z","date_updated":"2026-02-24T07:56:34Z","creator":"dernst","file_name":"2025_JEP_Browning.pdf","content_type":"application/pdf"}]},{"dataavailabilitystatement":"The data used in Sections 6 and 9 is hosted on the Göttingen Research Online Data repository [https://doi.org/10.25625/4FLFH8]. The code used to determine the data in Sections 6.2, 9.1 and 9.2 is found on the second author’s github page.","file_date_updated":"2025-09-03T06:44:44Z","day":"01","type":"journal_article","citation":{"chicago":"Browning, Timothy D, and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>.","mla":"Browning, Timothy D., and Florian Alexander Wilsch. “Integral Points on Cubic Surfaces: Heuristics and Numerics.” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4, 81, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>.","short":"T.D. Browning, F.A. Wilsch, Selecta Mathematica New Series 31 (2025).","ista":"Browning TD, Wilsch FA. 2025. Integral points on cubic surfaces: heuristics and numerics. Selecta Mathematica New Series. 31(4), 81.","ama":"Browning TD, Wilsch FA. Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. 2025;31(4). doi:<a href=\"https://doi.org/10.1007/s00029-025-01074-1\">10.1007/s00029-025-01074-1</a>","ieee":"T. D. Browning and F. A. Wilsch, “Integral points on cubic surfaces: heuristics and numerics,” <i>Selecta Mathematica New Series</i>, vol. 31, no. 4. Springer Nature, 2025.","apa":"Browning, T. D., &#38; Wilsch, F. A. (2025). Integral points on cubic surfaces: heuristics and numerics. <i>Selecta Mathematica New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-025-01074-1\">https://doi.org/10.1007/s00029-025-01074-1</a>"},"month":"09","supplementarymaterial":"yes","doi":"10.1007/s00029-025-01074-1","publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"year":"2025","acknowledgement":"The authors owe a debt of thanks to Yonatan Harpaz for asking about circle method heuristics for log K3 surfaces. His contribution to the resulting discussion is gratefully acknowledged. Thanks are also due to Andrew Sutherland for help with numerical data for the equation x^3 + y^3 + z^3 = 1, together with Alex Gamburd, Amit Ghosh, Peter Sarnak and Matteo Verzobio for their interest in this paper. Special thanks are due to Victor Wang for helpful conversations about the circle method heuristics and to the anonymous referee for several useful comments. While working on this paper, the authors were supported by a FWF grant (DOI 10.55776/P32428), and the first author was supported by a further FWF grant (DOI 10.55776/P36278) and a grant from the School of Mathematics at the Institute for Advanced Study in Princeton.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.","lang":"eng"}],"issue":"4","external_id":{"arxiv":["2407.16315"],"isi":["001552779800001"]},"fulldoi":"https://doi.org/10.1007/s00029-025-01074-1","department":[{"_id":"TiBr"}],"publication_status":"published","researchdata_availability":"yes","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"81","date_updated":"2026-08-12T12:15:32Z","isi":1,"publisher":"Springer Nature","scopus_import":"1","intvolume":"        31","publication":"Selecta Mathematica New Series","_id":"20249","das_tickbox":"1","ddc":["500"],"article_type":"original","project":[{"_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","grant_number":"P32428","call_identifier":"FWF","name":"New frontiers of the Manin conjecture"},{"name":"Rational curves via function field analytic number theory","_id":"bd8a4fdc-d553-11ed-ba76-80a0167441a3","grant_number":"P36278"}],"has_accepted_license":"1","date_created":"2025-08-31T22:01:31Z","oa":1,"author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","first_name":"Florian Alexander","last_name":"Wilsch","orcid":"0000-0001-7302-8256","full_name":"Wilsch, Florian Alexander"}],"title":"Integral points on cubic surfaces: heuristics and numerics","OA_place":"publisher","OA_type":"hybrid","PlanS_conform":"1","volume":31,"quality_controlled":"1","file":[{"date_updated":"2025-09-03T06:44:44Z","date_created":"2025-09-03T06:44:44Z","content_type":"application/pdf","file_name":"2025_SelectaMathematica_Browning.pdf","creator":"dernst","checksum":"89352f1f7e8d2b367ae5f4e9bf9eb1f5","access_level":"open_access","relation":"main_file","file_id":"20281","file_size":2484757,"success":1}],"corr_author":"1","date_published":"2025-09-01T00:00:00Z","related_material":{"link":[{"url":"https://github.com/fwilsch/cubicpts","relation":"software"}],"record":[{"status":"public","relation":"research_data","id":"22234"}]},"arxiv":1,"language":[{"iso":"eng"}]},{"department":[{"_id":"JePa"}],"publication_status":"published","external_id":{"arxiv":["2407.10623"],"isi":["001550090200001"]},"fulldoi":"https://doi.org/10.1088/1361-648X/adebd3","date_updated":"2026-08-12T14:00:12Z","article_number":"333501","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Volpe, Giorgio, Nuno A.M. Araújo, Maria Guix, Mark Miodownik, Nicolas Martin, Laura Alvarez, Juliane Simmchen, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>.","mla":"Volpe, Giorgio, et al. “Roadmap for Animate Matter.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33, 333501, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>.","short":"G. Volpe, N.A.M. Araújo, M. Guix, M. Miodownik, N. Martin, L. Alvarez, J. Simmchen, R.D. Leonardo, N. Pellicciotta, Q. Martinet, J.A. Palacci, W.K. Ng, D. Saxena, R. Sapienza, S. Nadine, J.F. Mano, R. Mahdavi, C. Beck Adiels, J. Forth, C. Santangelo, S. Palagi, J.M. Seok, V.A. Webster-Wood, S. Wang, L. Yao, A. Aghakhani, T. Barois, H. Kellay, C. Coulais, M. Van Hecke, C.J. Pierce, T. Wang, B. Chong, D.I. Goldman, A. Reina, V. Trianni, G. Volpe, R. Beckett, S.P. Nair, R. Armstrong, Journal of Physics: Condensed Matter 37 (2025).","apa":"Volpe, G., Araújo, N. A. M., Guix, M., Miodownik, M., Martin, N., Alvarez, L., … Armstrong, R. (2025). Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/adebd3\">https://doi.org/10.1088/1361-648X/adebd3</a>","ama":"Volpe G, Araújo NAM, Guix M, et al. Roadmap for animate matter. <i>Journal of Physics: Condensed Matter</i>. 2025;37(33). doi:<a href=\"https://doi.org/10.1088/1361-648X/adebd3\">10.1088/1361-648X/adebd3</a>","ieee":"G. Volpe <i>et al.</i>, “Roadmap for animate matter,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 33. IOP Publishing, 2025.","ista":"Volpe G, Araújo NAM, Guix M, Miodownik M, Martin N, Alvarez L, Simmchen J, Leonardo RD, Pellicciotta N, Martinet Q, Palacci JA, Ng WK, Saxena D, Sapienza R, Nadine S, Mano JF, Mahdavi R, Beck Adiels C, Forth J, Santangelo C, Palagi S, Seok JM, Webster-Wood VA, Wang S, Yao L, Aghakhani A, Barois T, Kellay H, Coulais C, Van Hecke M, Pierce CJ, Wang T, Chong B, Goldman DI, Reina A, Trianni V, Volpe G, Beckett R, Nair SP, Armstrong R. 2025. Roadmap for animate matter. Journal of Physics: Condensed Matter. 37(33), 333501."},"month":"08","day":"18","type":"journal_article","file_date_updated":"2025-09-02T07:22:48Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"33","abstract":[{"text":"Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner.","lang":"eng"}],"doi":"10.1088/1361-648X/adebd3","publication_identifier":{"issn":["0953-8984"],"eissn":["1361-648X"]},"acknowledgement":"Living Architecture is Funded by the EU Horizon 2020 Future Emerging Technologies Open programme (2016–2019) Grant Agreement 686585 a consortium of 6 collaborating institutions—Newcastle University, University of Trento, University of the West of England, Spanish National Research Council, Explora Biotech and Liquifer Systems Group.\r\n\r\nThe Active Living Infrastructure: Controlled Environment (ALICE) project is funded by an EU Innovation Award for the development of a bio-digital ‘brick’ prototype, a collaboration between Newcastle University, Translating Nature, and the University of the West of England (2019–2021) under EU Grant Agreement No. 851246.\r\n\r\nMicrobial Hydroponics: Circular Sustainable Electrobiosynthesis (Mi-Hy) is Funded by the European Union under Grant Agreement Number 101114746, which is a collaboration between Beneficiaries, KU Leuven (Belgium), the University of Southampton (UK), SONY Computer Science Laboratory (France), BioFaction KG (Austria), Spanish National Research Council (Spain), and Associated Partners, the University of the West of England (UK) and University of Southampton (UK). Mi-Hy is also supported through the interdisciplinary KU Leuven Institute for Cultural Heritage (HERKUL).","status":"public","year":"2025","OA_place":"publisher","quality_controlled":"1","volume":37,"PlanS_conform":"1","OA_type":"hybrid","author":[{"last_name":"Volpe","first_name":"Giorgio","full_name":"Volpe, Giorgio"},{"full_name":"Araújo, Nuno A.M.","first_name":"Nuno A.M.","last_name":"Araújo"},{"full_name":"Guix, Maria","last_name":"Guix","first_name":"Maria"},{"first_name":"Mark","last_name":"Miodownik","full_name":"Miodownik, Mark"},{"last_name":"Martin","first_name":"Nicolas","full_name":"Martin, Nicolas"},{"last_name":"Alvarez","first_name":"Laura","full_name":"Alvarez, Laura"},{"full_name":"Simmchen, Juliane","last_name":"Simmchen","first_name":"Juliane"},{"last_name":"Leonardo","first_name":"Roberto Di","full_name":"Leonardo, Roberto Di"},{"full_name":"Pellicciotta, Nicola","first_name":"Nicola","last_name":"Pellicciotta"},{"full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","first_name":"Quentin","last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"first_name":"Wai Kit","last_name":"Ng","full_name":"Ng, Wai Kit"},{"last_name":"Saxena","first_name":"Dhruv","full_name":"Saxena, Dhruv"},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"},{"last_name":"Nadine","first_name":"Sara","full_name":"Nadine, Sara"},{"first_name":"João F.","last_name":"Mano","full_name":"Mano, João F."},{"full_name":"Mahdavi, Reza","first_name":"Reza","last_name":"Mahdavi"},{"first_name":"Caroline","last_name":"Beck Adiels","full_name":"Beck Adiels, Caroline"},{"first_name":"Joe","last_name":"Forth","full_name":"Forth, Joe"},{"full_name":"Santangelo, Christian","first_name":"Christian","last_name":"Santangelo"},{"full_name":"Palagi, Stefano","first_name":"Stefano","last_name":"Palagi"},{"first_name":"Ji Min","last_name":"Seok","full_name":"Seok, Ji Min"},{"full_name":"Webster-Wood, Victoria A.","first_name":"Victoria A.","last_name":"Webster-Wood"},{"full_name":"Wang, Shuhong","last_name":"Wang","first_name":"Shuhong"},{"last_name":"Yao","first_name":"Lining","full_name":"Yao, Lining"},{"full_name":"Aghakhani, Amirreza","first_name":"Amirreza","last_name":"Aghakhani"},{"last_name":"Barois","first_name":"Thomas","full_name":"Barois, Thomas"},{"full_name":"Kellay, Hamid","first_name":"Hamid","last_name":"Kellay"},{"last_name":"Coulais","first_name":"Corentin","full_name":"Coulais, Corentin"},{"first_name":"Martin","last_name":"Van Hecke","full_name":"Van Hecke, Martin"},{"last_name":"Pierce","first_name":"Christopher J.","full_name":"Pierce, Christopher J."},{"first_name":"Tianyu","last_name":"Wang","full_name":"Wang, Tianyu"},{"full_name":"Chong, Baxi","first_name":"Baxi","last_name":"Chong"},{"full_name":"Goldman, Daniel I.","first_name":"Daniel I.","last_name":"Goldman"},{"full_name":"Reina, Andreagiovanni","last_name":"Reina","first_name":"Andreagiovanni"},{"full_name":"Trianni, Vito","last_name":"Trianni","first_name":"Vito"},{"last_name":"Volpe","first_name":"Giovanni","full_name":"Volpe, Giovanni"},{"full_name":"Beckett, Richard","last_name":"Beckett","first_name":"Richard"},{"full_name":"Nair, Sean P.","last_name":"Nair","first_name":"Sean P."},{"full_name":"Armstrong, Rachel","last_name":"Armstrong","first_name":"Rachel"}],"title":"Roadmap for animate matter","language":[{"iso":"eng"}],"arxiv":1,"date_published":"2025-08-18T00:00:00Z","file":[{"creator":"dernst","file_name":"2025_CondensedMatter_Volpe.pdf","content_type":"application/pdf","date_created":"2025-09-02T07:22:48Z","date_updated":"2025-09-02T07:22:48Z","file_size":8997829,"success":1,"file_id":"20271","relation":"main_file","access_level":"open_access","checksum":"7309274f78bed785b158bd290337f456"}],"publisher":"IOP Publishing","isi":1,"has_accepted_license":"1","article_type":"original","oa":1,"date_created":"2025-08-24T22:01:30Z","publication":"Journal of Physics: Condensed Matter","scopus_import":"1","intvolume":"        37","ddc":["530"],"_id":"20218"},{"month":"10","citation":{"short":"H. Farooq, M. Nauman, Journal of Physics: Condensed Matter 37 (2025).","mla":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40, 405801, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>.","chicago":"Farooq, Hamza, and Muhammad Nauman. “Non-Linear Magnetotropic Susceptibility in FePS3.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>.","ieee":"H. Farooq and M. Nauman, “Non-linear magnetotropic susceptibility in FePS3,” <i>Journal of Physics: Condensed Matter</i>, vol. 37, no. 40. IOP Publishing, 2025.","ista":"Farooq H, Nauman M. 2025. Non-linear magnetotropic susceptibility in FePS3. Journal of Physics: Condensed Matter. 37(40), 405801.","ama":"Farooq H, Nauman M. Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. 2025;37(40). doi:<a href=\"https://doi.org/10.1088/1361-648X/ae0913\">10.1088/1361-648X/ae0913</a>","apa":"Farooq, H., &#38; Nauman, M. (2025). Non-linear magnetotropic susceptibility in FePS3. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ae0913\">https://doi.org/10.1088/1361-648X/ae0913</a>"},"day":"06","type":"journal_article","file_date_updated":"2025-10-13T06:34:15Z","issue":"40","abstract":[{"lang":"eng","text":"Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"acknowledgement":"We thank Kimberly A. Modic for her support and discussions regarding the technique in the context of a project indirectly related to, but distinct from, the present work. We also thank Brad J. Ramshaw and Arkady Shekhter for scientific discussions not directly related to this study, but whose insights proved helpful. We are grateful to Valeska Zambra, Amit Nathwani, Hamza Nasir, and Tayyaba Hussain for informal discussions on various aspects of the technique, and to Naoya Iwahara for his thoughtful and constructive feedback. The experimental curve shown in figures 3(b) and 6, from the Thermodynamics of Quantum Materials (TQM) group at ISTA, was measured by Muhammad Nauman for an unrelated project. We thank Kimberly Modic for granting access to the laboratory facilities. Je Geun Park provided the crystal used for that measurement via Younjung Jo, whose contribution we gratefully acknowledge. Institutional support from the Institute of Science and Technology Austria (ISTA) is also gratefully acknowledged.","status":"public","year":"2025","doi":"10.1088/1361-648X/ae0913","publication_identifier":{"eissn":["1361-648X"],"issn":["0953-8984"]},"publication_status":"published","department":[{"_id":"KiMo"}],"fulldoi":"https://doi.org/10.1088/1361-648X/ae0913","external_id":{"isi":["001585824100001"],"pmid":["40967257"]},"date_updated":"2026-08-12T14:00:34Z","article_number":"405801","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","isi":1,"publisher":"IOP Publishing","date_created":"2025-10-12T22:01:26Z","oa":1,"has_accepted_license":"1","article_type":"original","ddc":["530"],"_id":"20453","publication":"Journal of Physics: Condensed Matter","scopus_import":"1","intvolume":"        37","pmid":1,"quality_controlled":"1","OA_type":"hybrid","PlanS_conform":"1","volume":37,"OA_place":"publisher","author":[{"first_name":"Hamza","last_name":"Farooq","full_name":"Farooq, Hamza"},{"full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","first_name":"Muhammad","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"}],"title":"Non-linear magnetotropic susceptibility in FePS3","language":[{"iso":"eng"}],"date_published":"2025-10-06T00:00:00Z","corr_author":"1","file":[{"access_level":"open_access","checksum":"b182856a5a655496e149afa49ec464f3","success":1,"file_size":1709516,"file_id":"20458","relation":"main_file","date_created":"2025-10-13T06:34:15Z","date_updated":"2025-10-13T06:34:15Z","file_name":"2025_JourPhysicsCondMatter_Farooq.pdf","creator":"dernst","content_type":"application/pdf"}]},{"publication_status":"published","department":[{"_id":"SyCr"}],"fulldoi":"https://doi.org/10.1098/rsif.2025.0202","external_id":{"isi":["001548084900001"],"pmid":["40799050"]},"date_updated":"2026-08-12T14:09:20Z","article_number":"20250202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","article_processing_charge":"No","month":"08","citation":{"short":"O. Ayalon, H. Rajendran, Journal of the Royal Society Interface 22 (2025).","chicago":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>. Royal Society, 2025. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>.","mla":"Ayalon, Oran, and Harikrishnan Rajendran. “Interplay of Asexual and Sexual Reproduction in Bifunctional Insects.” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229, 20250202, Royal Society, 2025, doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>.","ama":"Ayalon O, Rajendran H. Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. 2025;22(229). doi:<a href=\"https://doi.org/10.1098/rsif.2025.0202\">10.1098/rsif.2025.0202</a>","apa":"Ayalon, O., &#38; Rajendran, H. (2025). Interplay of asexual and sexual reproduction in bifunctional insects. <i>Journal of the Royal Society Interface</i>. Royal Society. <a href=\"https://doi.org/10.1098/rsif.2025.0202\">https://doi.org/10.1098/rsif.2025.0202</a>","ieee":"O. Ayalon and H. Rajendran, “Interplay of asexual and sexual reproduction in bifunctional insects,” <i>Journal of the Royal Society Interface</i>, vol. 22, no. 229. Royal Society, 2025.","ista":"Ayalon O, Rajendran H. 2025. Interplay of asexual and sexual reproduction in bifunctional insects. Journal of the Royal Society Interface. 22(229), 20250202."},"type":"journal_article","day":"13","issue":"229","abstract":[{"text":"Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.","lang":"eng"}],"status":"public","acknowledgement":"We acknowledge Prof. Uri Alon for introducing us to the topic of systems biology during the graduate course at the Weizmann Institute of Science, whose insights and teachings have greatly inspired this work.","year":"2025","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"doi":"10.1098/rsif.2025.0202","pmid":1,"quality_controlled":"1","OA_type":"closed access","volume":22,"title":"Interplay of asexual and sexual reproduction in bifunctional insects","author":[{"full_name":"Ayalon, Oran","last_name":"Ayalon","first_name":"Oran"},{"id":"876b6b34-8ff4-11ec-97c9-8d95a7aae416","first_name":"Harikrishnan","last_name":"Rajendran","full_name":"Rajendran, Harikrishnan"}],"language":[{"iso":"eng"}],"date_published":"2025-08-13T00:00:00Z","corr_author":"1","publisher":"Royal Society","isi":1,"date_created":"2025-08-24T22:01:30Z","article_type":"original","_id":"20219","publication":"Journal of the Royal Society Interface","scopus_import":"1","intvolume":"        22"},{"date_published":"2025-05-23T00:00:00Z","language":[{"iso":"eng"}],"title":"Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development","author":[{"first_name":"Adrián","last_name":"Cárdenas","full_name":"Cárdenas, Adrián"},{"full_name":"Çelik, Irem","last_name":"Çelik","first_name":"Irem"},{"first_name":"Alexandre","last_name":"Espinós","full_name":"Espinós, Alexandre"},{"full_name":"Streicher, Carmen","first_name":"Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"López-González","first_name":"Lara","full_name":"López-González, Lara"},{"last_name":"del-Valle-Anton","first_name":"Lucia","full_name":"del-Valle-Anton, Lucia"},{"first_name":"Virginia","last_name":"Fernández","full_name":"Fernández, Virginia"},{"full_name":"Amin, Salma","first_name":"Salma","last_name":"Amin"},{"full_name":"Negri, Enrico","last_name":"Negri","first_name":"Enrico"},{"full_name":"Ortuño, Eduardo Fernández","last_name":"Ortuño","first_name":"Eduardo Fernández"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Borrell","first_name":"Víctor","full_name":"Borrell, Víctor"}],"OA_type":"green","OA_place":"repository","_id":"19762","publication":"bioRxiv","oa":1,"date_created":"2025-05-29T10:45:55Z","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","date_updated":"2026-08-13T07:18:38Z","fulldoi":"https://doi.org/10.1101/2025.05.22.655488","external_id":{"biorxivid":["10.1101/2025.05.22.655488"]},"publication_status":"submitted","department":[{"_id":"SiHi"}],"status":"public","acknowledgement":"We thank A. Iñigo for assistance with imaging, and members of the Borrell and Herrera labs for\r\ninsightful discussions and critical reading of the manuscript. Funding to our lab members was\r\nprovided by the Spanish Research Agency (AEI): FPI contract (BES-2016-077737) to L.dV.A., FPI SO contract (SEV-2017-0723-18-1) to A.E., JdC-Incorporación contract (IJC2020-044653-I) to V.F., and JAE-Intro fellowship (JAEICU23EX_0071) to I.C., as well as by La Caixa Foundation: La Caixa-Severo Ochoa fellowship (E-03-2016-0557140) to S.A., INPhINIT-Retaining fellowship (LCF/BQ/DR21/11880012) to E.F.O., INPhINIT-Incoming fellowship (LCF/BQ/DI22/11940006) to E.N., and Junior Leader-Retaining grant to A.C. (LCF/BQ/PR23/11980051). Work was supported by grants from FWF (SFB F78) to S.H.; AEI (PID2021-125618NB-I00) and European Research Council (101118729) to V.B., who also acknowledges financial support from AEI through the “Severo Ochoa” Programme for Centers of Excellence in R&D (CEX2021-001165-S).","year":"2025","doi":"10.1101/2025.05.22.655488","abstract":[{"text":"The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process.","lang":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"type":"preprint","day":"23","main_file_link":[{"url":"https://doi.org/10.1101/2025.05.22.655488","open_access":"1"}],"biorxivid":1,"month":"05","citation":{"chicago":"Cárdenas, Adrián, Irem Çelik, Alexandre Espinós, Carmen Streicher, Lara López-González, Lucia del-Valle-Anton, Virginia Fernández, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>.","mla":"Cárdenas, Adrián, et al. “Early Indirect Neurogenesis Transitions to Late Direct Neurogenesis in Mouse Cerebral Cortex Development.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","short":"A. Cárdenas, I. Çelik, A. Espinós, C. Streicher, L. López-González, L. del-Valle-Anton, V. Fernández, S. Amin, E. Negri, E.F. Ortuño, S. Hippenmeyer, V. Borrell, BioRxiv (n.d.).","ieee":"A. Cárdenas <i>et al.</i>, “Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development,” <i>bioRxiv</i>. .","ama":"Cárdenas A, Çelik I, Espinós A, et al. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>","ista":"Cárdenas A, Çelik I, Espinós A, Streicher C, López-González L, del-Valle-Anton L, Fernández V, Amin S, Negri E, Ortuño EF, Hippenmeyer S, Borrell V. Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.22.655488\">10.1101/2025.05.22.655488</a>.","apa":"Cárdenas, A., Çelik, I., Espinós, A., Streicher, C., López-González, L., del-Valle-Anton, L., … Borrell, V. (n.d.). Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.22.655488\">https://doi.org/10.1101/2025.05.22.655488</a>"}},{"fulldoi":"https://doi.org/10.1101/2025.05.07.652665","title":"Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis","author":[{"first_name":"I","last_name":"Varela-Martínez","full_name":"Varela-Martínez, I"},{"id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","first_name":"Ana","last_name":"Villalba Requena","orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana"},{"first_name":"J.","last_name":"Garcia-Marqués","full_name":"Garcia-Marqués, J."},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Nieto, M.","first_name":"M.","last_name":"Nieto"}],"publication_status":"submitted","OA_type":"green","OA_place":"repository","department":[{"_id":"SiHi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","date_published":"2025-05-07T00:00:00Z","date_updated":"2026-08-13T07:16:48Z","language":[{"iso":"eng"}],"day":"07","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.07.652665"}],"month":"05","citation":{"chicago":"Varela-Martínez, I, Ana Villalba Requena, J. Garcia-Marqués, Simon Hippenmeyer, and M. Nieto. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>.","mla":"Varela-Martínez, I., et al. “Early Emergence of Projection-Subtype Fate-Restricted Radial Glial Progenitors Orchestrates Neocortical Neurogenesis.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","short":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, M. Nieto, BioRxiv (n.d.).","ista":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>.","ama":"Varela-Martínez I, Villalba Requena A, Garcia-Marqués J, Hippenmeyer S, Nieto M. Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.07.652665\">10.1101/2025.05.07.652665</a>","apa":"Varela-Martínez, I., Villalba Requena, A., Garcia-Marqués, J., Hippenmeyer, S., &#38; Nieto, M. (n.d.). Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.07.652665\">https://doi.org/10.1101/2025.05.07.652665</a>","ieee":"I. Varela-Martínez, A. Villalba Requena, J. Garcia-Marqués, S. Hippenmeyer, and M. Nieto, “Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis,” <i>bioRxiv</i>. ."},"year":"2025","_id":"19717","status":"public","acknowledgement":"We thank M. Caouyette for the plasmid construction for Pou3f1 overexpression; C. Varela747 Martínez for help with the code for graphical analysis; all members from the Nieto’s lab for\r\ncomment on the manuscript, specially to F. Martín for the insightful discussions;J.C. Oliveros\r\nand J.A. García from the computational service of the CNB for help with the analysis of\r\nRNAseq dataset, C.O. Sorzano for the help with statistical analysis, and the service of\r\nAdvance Optical Microscopy of the CNB for their technical advice.\r\nI.V.M holds a fellowship funded by MCICIU (PRE-2018-083376), the work was funded by\r\nPID2020-112831GB-I00 funded by MCIN/AEI /10.13039/501100011033.\r\n","publication":"bioRxiv","doi":"10.1101/2025.05.07.652665","abstract":[{"text":"Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.","lang":"eng"}],"oa":1,"date_created":"2025-05-20T10:19:29Z"}]