[{"status":"public","OA_type":"hybrid","type":"journal_article","ddc":["540"],"title":"Response matching for generating materials and molecules","file":[{"access_level":"open_access","file_name":"2024_JCTC_Cheng.pdf","date_created":"2025-01-13T09:11:09Z","content_type":"application/pdf","date_updated":"2025-01-13T09:11:09Z","success":1,"relation":"main_file","checksum":"aca0011bba4846140809b5af583daa9a","creator":"dernst","file_id":"18832","file_size":4758251}],"publication_status":"published","fulldoi":"https://doi.org/10.1021/acs.jctc.4c00998","arxiv":1,"isi":1,"has_accepted_license":"1","file_date_updated":"2025-01-13T09:11:09Z","article_processing_charge":"Yes (in subscription journal)","oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/cace"}]},"dataavailabilitystatement":"The training scripts, trained models, and training data are available at https://github.com/BingqingCheng/cace-rm.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"9259-9266","language":[{"iso":"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)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","supplementarymaterial":"no","OA_place":"publisher","corr_author":"1","date_updated":"2026-09-24T11:30:58Z","author":[{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"publication":"Journal of Chemical Theory and Computation","date_created":"2024-10-20T22:02:07Z","year":"2024","citation":{"chicago":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">https://doi.org/10.1021/acs.jctc.4c00998</a>.","short":"B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.","ieee":"B. Cheng, “Response matching for generating materials and molecules,” <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20. American Chemical Society, pp. 9259–9266, 2024.","mla":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20, American Chemical Society, 2024, pp. 9259–66, doi:<a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">10.1021/acs.jctc.4c00998</a>.","ista":"Cheng B. 2024. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 20(20), 9259–9266.","ama":"Cheng B. Response matching for generating materials and molecules. <i>Journal of Chemical Theory and Computation</i>. 2024;20(20):9259-9266. doi:<a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">10.1021/acs.jctc.4c00998</a>","apa":"Cheng, B. (2024). Response matching for generating materials and molecules. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">https://doi.org/10.1021/acs.jctc.4c00998</a>"},"doi":"10.1021/acs.jctc.4c00998","date_published":"2024-10-22T00:00:00Z","day":"22","abstract":[{"lang":"eng","text":"Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration."}],"scopus_import":"1","das_tickbox":"1","external_id":{"arxiv":["2405.09057"],"isi":["001330001500001"],"pmid":["39365029"]},"month":"10","oa_version":"Published Version","publisher":"American Chemical Society","_id":"18452","department":[{"_id":"BiCh"}],"acknowledgement":"B.C. thanks Chris Pickard for enlightening discussions.","pmid":1,"issue":"20","quality_controlled":"1","researchdata_availability":"no","volume":20,"publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"article_type":"original","intvolume":"        20"},{"ddc":["000"],"type":"journal_article","OA_type":"gold","status":"public","isi":1,"arxiv":1,"fulldoi":"https://doi.org/10.1038/s41524-024-01332-4","publication_status":"published","title":"Cartesian atomic cluster expansion for machine learning interatomic potentials","file":[{"creator":"dernst","checksum":"e6b4d1a45a9ef1e9be35b313d96ebd6f","file_size":1659509,"file_id":"18813","date_created":"2025-01-09T12:36:48Z","content_type":"application/pdf","access_level":"open_access","file_name":"2024_npjComputationalMaterials_Cheng.pdf","date_updated":"2025-01-09T12:36:48Z","relation":"main_file","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"The water dataset is from https://github.com/BingqingCheng/ab-initio-thermodynamics-of-water. MD17-ethanol is from http://www.sgdml.org/#datasets. BPA is from ref. 43, downloaded from https://github.com/davkovacs/BOTNet-datasets. The HEA25 dataset is from ref. 45, downloaded from https://archive.materialscloud.org/record/2023.57. The training scripts, trained CACE potentials, and MD input files are available at https://github.com/BingqingCheng/cacefit.","oa":1,"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2025-01-09T12:36:48Z","corr_author":"1","OA_place":"publisher","supplementarymaterial":"no","citation":{"apa":"Cheng, B. (2024). Cartesian atomic cluster expansion for machine learning interatomic potentials. <i>Npj Computational Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41524-024-01332-4\">https://doi.org/10.1038/s41524-024-01332-4</a>","ista":"Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 10, 157.","ama":"Cheng B. Cartesian atomic cluster expansion for machine learning interatomic potentials. <i>npj Computational Materials</i>. 2024;10. doi:<a href=\"https://doi.org/10.1038/s41524-024-01332-4\">10.1038/s41524-024-01332-4</a>","short":"B. Cheng, Npj Computational Materials 10 (2024).","ieee":"B. Cheng, “Cartesian atomic cluster expansion for machine learning interatomic potentials,” <i>npj Computational Materials</i>, vol. 10. Springer Nature, 2024.","mla":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” <i>Npj Computational Materials</i>, vol. 10, 157, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41524-024-01332-4\">10.1038/s41524-024-01332-4</a>.","chicago":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” <i>Npj Computational Materials</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41524-024-01332-4\">https://doi.org/10.1038/s41524-024-01332-4</a>."},"year":"2024","date_created":"2024-07-28T22:01:08Z","publication":"npj Computational Materials","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng"}],"date_updated":"2026-09-24T11:30:25Z","das_tickbox":"1","abstract":[{"text":"Machine learning interatomic potentials are revolutionizing large-scale, accurate atomistic modeling in material science and chemistry. Many potentials use atomic cluster expansion or equivariant message-passing frameworks. Such frameworks typically use spherical harmonics as angular basis functions, followed by Clebsch-Gordan contraction to maintain rotational symmetry. We propose a mathematically equivalent and simple alternative that performs all operations in the Cartesian coordinates. This approach provides a complete set of polynormially independent features of atomic environments while maintaining interaction body orders. Additionally, we integrate low-dimensional embeddings of various chemical elements, trainable radial channel coupling, and inter-atomic message passing. The resulting potential, named Cartesian Atomic Cluster Expansion (CACE), exhibits good accuracy, stability, and generalizability. We validate its performance in diverse systems, including bulk water, small molecules, and 25-element high-entropy alloys.","lang":"eng"}],"scopus_import":"1","DOAJ_listed":"1","date_published":"2024-07-18T00:00:00Z","day":"18","doi":"10.1038/s41524-024-01332-4","acknowledgement":"B.C. thanks Ralf Drautz and Ngoc Cuong Nguyen for illuminating discussions.","department":[{"_id":"BiCh"}],"_id":"17322","publisher":"Springer Nature","month":"07","oa_version":"Published Version","external_id":{"isi":["001271730700001"],"arxiv":["2402.07472"]},"intvolume":"        10","article_type":"original","publication_identifier":{"eissn":["2057-3960"]},"volume":10,"researchdata_availability":"no","quality_controlled":"1","article_number":"157"},{"status":"public","ec_funded":1,"type":"journal_article","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1103/physrevb.109.054305","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"supplementarymaterial":"yes","author":[{"last_name":"Cheng","first_name":"Ruihuan","full_name":"Cheng, Ruihuan"},{"last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu"},{"first_name":"Chen","last_name":"Wang","full_name":"Wang, Chen"},{"first_name":"Niuchang","last_name":"Ouyang","full_name":"Ouyang, Niuchang"},{"last_name":"Chen","first_name":"Yue","full_name":"Chen, Yue"}],"date_updated":"2026-09-24T11:19:44Z","date_created":"2024-03-04T07:41:23Z","year":"2024","citation":{"ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. 2024;109(5). doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>","apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., &#38; Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>.","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>.","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” <i>Physical Review B</i>, vol. 109, no. 5. American Physical Society, 2024.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024)."},"publication":"Physical Review B","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}],"scopus_import":"1","doi":"10.1103/physrevb.109.054305","day":"14","date_published":"2024-02-14T00:00:00Z","das_tickbox":"0","oa_version":"None","month":"02","publisher":"American Physical Society","external_id":{"isi":["001198615900003"]},"acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","_id":"15052","department":[{"_id":"BiCh"}],"quality_controlled":"1","article_number":"054305","issue":"5","intvolume":"       109","volume":109,"researchdata_availability":"no","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_type":"original"},{"month":"12","oa_version":"Published Version","publisher":"Elsevier","external_id":{"pmid":["39547223"],"isi":["001395711300001"]},"acknowledgement":"We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF) and the Preclinical Facility (PCF). This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer Institute is supported by institutional grants of the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI (VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for Scientific Research.","_id":"18553","department":[{"_id":"CaBe"}],"quality_controlled":"1","issue":"24","pmid":1,"intvolume":"        84","researchdata_availability":"yes","volume":84,"publication_identifier":{"issn":["1097-2765"]},"article_type":"original","author":[{"full_name":"Ramadhin, Anisha R.","last_name":"Ramadhin","first_name":"Anisha R."},{"full_name":"Lee, Shun-Hsiao","first_name":"Shun-Hsiao","last_name":"Lee"},{"full_name":"Zhou, Di","last_name":"Zhou","first_name":"Di"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"full_name":"Gonzalo-Hansen, Camila","last_name":"Gonzalo-Hansen","first_name":"Camila"},{"first_name":"Marjolein","last_name":"van Sluis","full_name":"van Sluis, Marjolein"},{"last_name":"Blom","first_name":"Cindy M.A.","full_name":"Blom, Cindy M.A."},{"full_name":"Janssens, Roel C.","first_name":"Roel C.","last_name":"Janssens"},{"last_name":"Raams","first_name":"Anja","full_name":"Raams, Anja"},{"full_name":"Dekkers, Dick","first_name":"Dick","last_name":"Dekkers"},{"full_name":"Bezstarosti, Karel","last_name":"Bezstarosti","first_name":"Karel"},{"last_name":"Slade","first_name":"Dea","full_name":"Slade, Dea"},{"first_name":"Wim","last_name":"Vermeulen","full_name":"Vermeulen, Wim"},{"full_name":"Pines, Alex","first_name":"Alex","last_name":"Pines"},{"full_name":"Demmers, Jeroen A.A.","first_name":"Jeroen A.A.","last_name":"Demmers"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"},{"last_name":"Sixma","first_name":"Titia K.","full_name":"Sixma, Titia K."},{"first_name":"Jurgen A.","last_name":"Marteijn","full_name":"Marteijn, Jurgen A."}],"date_updated":"2026-10-01T08:20:39Z","year":"2024","date_created":"2024-11-15T12:12:54Z","citation":{"chicago":"Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>.","short":"A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen, M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti, D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A. Marteijn, Molecular Cell 84 (2024) 4740–4757.e12.","ieee":"A. R. Ramadhin <i>et al.</i>, “STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,” <i>Molecular Cell</i>, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.","mla":"Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” <i>Molecular Cell</i>, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>.","ista":"Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.","ama":"Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. 2024;84(24):4740-4757.e12. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">10.1016/j.molcel.2024.10.030</a>","apa":"Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen, C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2024.10.030\">https://doi.org/10.1016/j.molcel.2024.10.030</a>"},"publication":"Molecular Cell","scopus_import":"1","abstract":[{"lang":"eng","text":"Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol II stability and initiating DNA damage excision by TFIIH recruitment. However, the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a TC-NER factor, which is essential for correct DNA damage removal and subsequent transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA, UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as a core TC-NER component."}],"doi":"10.1016/j.molcel.2024.10.030","date_published":"2024-12-19T00:00:00Z","day":"19","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"das_tickbox":"1","oa":1,"related_material":{"record":[{"status":"public","id":"23013","relation":"research_data"}]},"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2025-01-13T11:17:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"4740-4757.e12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"dataavailabilitystatement":"Proteomics data is deposited at the ProteomeXchange Consortium through the PRIDE partner repository with dataset identifier PXD051720. Imaging data are deposited at Mendeley Data at https://doi.org/10.17632/wp9sf6sp4z.1. Cryo-EM reconstructions and structure coordinates are deposited to the Electron Microscopy Database (EMDB) and to the PDB under the following accession codes: for RNA Pol II-TC-NER-STK19 complex model (PDB: 9FD2), composite map (EMD-50325) and consensus map (EMD-50292). Focused maps of CSA-DDB1-DDA1-UVSSA-STK19 (EMD-50293), RNA Pol II-ELOF1 (EMD-50294), CRL4CSA (EMD-50295), and CSA-DDB1-DDA1-CSB (EMD-50306).\r\nThis paper does not report original code.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","supplementarymaterial":"yes","OA_place":"publisher","status":"public","ddc":["570"],"OA_type":"hybrid","type":"journal_article","title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","file":[{"file_size":25071994,"file_id":"18844","creator":"dernst","checksum":"e051e2766b2d424983778f742cb7c5ed","success":1,"date_updated":"2025-01-13T11:17:35Z","relation":"main_file","content_type":"application/pdf","date_created":"2025-01-13T11:17:35Z","file_name":"2024_MolecularCell_Ramadhin.pdf","access_level":"open_access"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.molcel.2024.10.030"},{"fulldoi":"https://doi.org/10.1021/acs.jmedchem.3c02250","title":"Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε","publication_status":"published","OA_type":"closed access","type":"journal_article","status":"public","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"8609-8629","language":[{"iso":"eng"}],"dataavailabilitystatement":"Atomic coordinates and experimental data have been deposited in the PDB with the following PDB ID codes: 6CNX (VRK1 bound to 2); 6CFM (VRK1 bound to 3); 6CQH (VRK1 bound to 4); 6CMM (VRK1 bound to 7); 6VXU (VRK1 bound to 8); 6VZH (VRK1 bound to 11); 6CSW (VRK1 bound to 13); 8V42 (VRK1 bound to 21); 6NPN (VRK1 bound to 24).","article_processing_charge":"No","das_tickbox":"1","scopus_import":"1","abstract":[{"text":"Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.","lang":"eng"}],"doi":"10.1021/acs.jmedchem.3c02250","day":"23","date_published":"2024-05-23T00:00:00Z","year":"2024","date_created":"2025-01-29T09:14:19Z","citation":{"ista":"de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B, Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR, Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG, Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629.","ama":"de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. <i>Journal of Medicinal Chemistry</i>. 2024;67(11):8609-8629. doi:<a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">10.1021/acs.jmedchem.3c02250</a>","apa":"de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim, R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε. <i>Journal of Medicinal Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">https://doi.org/10.1021/acs.jmedchem.3c02250</a>","chicago":"Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” <i>Journal of Medicinal Chemistry</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">https://doi.org/10.1021/acs.jmedchem.3c02250</a>.","mla":"de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” <i>Journal of Medicinal Chemistry</i>, vol. 67, no. 11, American Chemical Society, 2024, pp. 8609–29, doi:<a href=\"https://doi.org/10.1021/acs.jmedchem.3c02250\">10.1021/acs.jmedchem.3c02250</a>.","ieee":"F. H. de Souza Gama <i>et al.</i>, “Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε,” <i>Journal of Medicinal Chemistry</i>, vol. 67, no. 11. American Chemical Society, pp. 8609–8629, 2024.","short":"F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim, M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas, A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo, S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins, O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M. Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629."},"publication":"Journal of Medicinal Chemistry","author":[{"last_name":"de Souza Gama","first_name":"Fernando H.","full_name":"de Souza Gama, Fernando H."},{"full_name":"Dutra, Luiz A.","first_name":"Luiz A.","last_name":"Dutra"},{"first_name":"Michael","last_name":"Hawgood","full_name":"Hawgood, Michael"},{"first_name":"Caio Vinícius","last_name":"dos Reis","full_name":"dos Reis, Caio Vinícius"},{"last_name":"Serafim","first_name":"Ricardo A. M.","full_name":"Serafim, Ricardo A. M."},{"full_name":"Ferreira, Marcos A.","first_name":"Marcos A.","last_name":"Ferreira"},{"full_name":"Teodoro, Bruno V. M.","first_name":"Bruno V. M.","last_name":"Teodoro"},{"full_name":"Takarada, Jéssica Emi","last_name":"Takarada","first_name":"Jéssica Emi"},{"full_name":"Santiago, André S.","last_name":"Santiago","first_name":"André S."},{"full_name":"Balourdas, Dimitrios-Ilias","first_name":"Dimitrios-Ilias","last_name":"Balourdas"},{"full_name":"Nilsson, Ann-Sofie","last_name":"Nilsson","first_name":"Ann-Sofie"},{"full_name":"Urien, Bruno","last_name":"Urien","first_name":"Bruno"},{"last_name":"Almeida","first_name":"Vitor M.","full_name":"Almeida, Vitor M."},{"full_name":"Gileadi, Carina","last_name":"Gileadi","first_name":"Carina"},{"last_name":"Ramos","first_name":"Priscila Z.","full_name":"Ramos, Priscila Z."},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"last_name":"Vasconcelos","first_name":"Stanley N. S.","full_name":"Vasconcelos, Stanley N. S."},{"full_name":"Cunha, Micael R.","last_name":"Cunha","first_name":"Micael R."},{"last_name":"Mueller","first_name":"Susanne","full_name":"Mueller, Susanne"},{"full_name":"Knapp, Stefan","first_name":"Stefan","last_name":"Knapp"},{"first_name":"Katlin B.","last_name":"Massirer","full_name":"Massirer, Katlin B."},{"full_name":"Elkins, Jonathan M.","first_name":"Jonathan M.","last_name":"Elkins"},{"last_name":"Gileadi","first_name":"Opher","full_name":"Gileadi, Opher"},{"full_name":"Mascarello, Alessandra","last_name":"Mascarello","first_name":"Alessandra"},{"last_name":"Lemmens","first_name":"Bennie B. L. G.","full_name":"Lemmens, Bennie B. L. G."},{"last_name":"Guimarães","first_name":"Cristiano R. W.","full_name":"Guimarães, Cristiano R. W."},{"full_name":"Azevedo, Hatylas","first_name":"Hatylas","last_name":"Azevedo"},{"first_name":"Rafael M.","last_name":"Couñago","full_name":"Couñago, Rafael M."}],"date_updated":"2026-10-01T08:26:28Z","intvolume":"        67","researchdata_availability":"yes","volume":67,"article_type":"original","publication_identifier":{"eissn":["1520-4804"],"issn":["0022-2623"]},"quality_controlled":"1","issue":"11","pmid":1,"acknowledgement":"R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0), Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by the Structural Genomics Consortium, a registered charity (1097737) that receives funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck & Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7), A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C. (2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00) and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis. We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We thank the staff at the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24. The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang (KI) for valuable discussions and technical support.","_id":"18945","department":[{"_id":"CaBe"}],"month":"05","oa_version":"None","publisher":"American Chemical Society","external_id":{"pmid":["38780468"]}},{"oa":1,"article_processing_charge":"Yes","file_date_updated":"2024-08-12T07:56:38Z","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"dataavailabilitystatement":"The authors declare that the data supporting the findings of this study are available within the paper and its Supplementary Information files","supplementarymaterial":"yes","OA_place":"publisher","corr_author":"1","status":"public","ddc":["530"],"APC_amount":"3534 EUR","OA_type":"gold","type":"journal_article","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file":[{"date_updated":"2024-08-12T07:56:38Z","relation":"main_file","success":1,"file_name":"2024_CommMaterials_Zu.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-08-12T07:56:38Z","file_id":"17416","file_size":9824134,"checksum":"d6f74e242db5f46bb0e380ee23a268af","creator":"dernst"}],"title":"Designing athermal disordered solids with automatic differentiation","publication_status":"published","fulldoi":"https://doi.org/10.1038/s43246-024-00583-4","arxiv":1,"month":"08","oa_version":"Published Version","publisher":"Springer Nature","external_id":{"arxiv":["2404.15101"]},"acknowledgement":"We thank M. Lechner for helpful discussions.","_id":"17407","department":[{"_id":"CaGo"}],"quality_controlled":"1","article_number":"141","intvolume":"         5","volume":5,"researchdata_availability":"yes (supplementary data)","article_type":"original","publication_identifier":{"eissn":["2662-4443"]},"author":[{"full_name":"Zu, Mengjie","last_name":"Zu","first_name":"Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2"},{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"date_updated":"2026-10-01T08:28:59Z","date_created":"2024-08-11T22:01:11Z","year":"2024","citation":{"chicago":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” <i>Communications Materials</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s43246-024-00583-4\">https://doi.org/10.1038/s43246-024-00583-4</a>.","short":"M. Zu, C.P. Goodrich, Communications Materials 5 (2024).","ieee":"M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic differentiation,” <i>Communications Materials</i>, vol. 5. Springer Nature, 2024.","mla":"Zu, Mengjie, and Carl Peter Goodrich. “Designing Athermal Disordered Solids with Automatic Differentiation.” <i>Communications Materials</i>, vol. 5, 141, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s43246-024-00583-4\">10.1038/s43246-024-00583-4</a>.","ama":"Zu M, Goodrich CP. Designing athermal disordered solids with automatic differentiation. <i>Communications Materials</i>. 2024;5. doi:<a href=\"https://doi.org/10.1038/s43246-024-00583-4\">10.1038/s43246-024-00583-4</a>","ista":"Zu M, Goodrich CP. 2024. Designing athermal disordered solids with automatic differentiation. Communications Materials. 5, 141.","apa":"Zu, M., &#38; Goodrich, C. P. (2024). Designing athermal disordered solids with automatic differentiation. <i>Communications Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43246-024-00583-4\">https://doi.org/10.1038/s43246-024-00583-4</a>"},"publication":"Communications Materials","abstract":[{"lang":"eng","text":"The ability to control forces between sub-micron-scale building blocks offers significant potential for designing new materials through self-assembly. Traditionally, this involves identifying a crystal structure with a desired property and then designing building-block interactions so that it assembles spontaneously. However, this paradigm fails for structurally disordered solids, which lack a well-defined structure. Here, we show that disordered solids can still be treated from an inverse self-assembly perspective by bypassing structure and directly targeting material properties. Using the Poisson’s ratio as a primary example, we demonstrate how differentiable programming links interaction parameters with emergent behavior, enabling iterative training to achieve the desired Poisson’s ratio. We also tune other properties, including pressure and local 8-fold structural order, and can even control multiple properties simultaneously. This robust, transferable, and scalable approach can handle a wide variety of systems and properties, demonstrating the utility of disordered solids as a practical avenue for self-assembly platforms."}],"scopus_import":"1","doi":"10.1038/s43246-024-00583-4","day":"01","date_published":"2024-08-01T00:00:00Z","das_tickbox":"1"},{"supplementarymaterial":"unclear","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-07-29T10:56:01Z","has_accepted_license":"1","oa":1,"page":"487-510","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"grant_number":"ALTF 44-2021","_id":"eb872896-77a9-11ec-83b8-f59a38ec17f8","name":"Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy"}],"file":[{"checksum":"e0505553b3cee624fa865f0cc5a99ecc","creator":"dernst","file_id":"17339","file_size":1276645,"access_level":"open_access","file_name":"2024_AnnualReviewBiophys_Lo.pdf","content_type":"application/pdf","date_created":"2024-07-29T10:56:01Z","success":1,"date_updated":"2024-07-29T10:56:01Z","relation":"main_file"}],"title":"Bacterial Electrophysiology","publication_status":"published","fulldoi":"https://doi.org/10.1146/annurev-biophys-030822-032215","isi":1,"status":"public","type":"journal_article","ddc":["570"],"pmid":1,"quality_controlled":"1","researchdata_availability":"no","volume":53,"article_type":"original","publication_identifier":{"issn":["1936-122X"],"eissn":["1936-1238"]},"intvolume":"        53","external_id":{"pmid":["38382113"],"isi":["001278237500021"]},"oa_version":"Published Version","month":"07","publisher":"Annual Reviews","_id":"17325","department":[{"_id":"CaGu"}],"acknowledgement":"We would like to thank all members of the Pilizota lab, as well as Calin Guet, Orkun Soyer, Munehiro Asally, Peter Swain, and in particular Matt Scott and Ariel Amir, for their support, comments, and useful discussions. T.P. and W.-C.L. were supported by the Leverhulme Trust, grant RPG-2019-187, and T.P. is supported by EPSRC Fellowship EP/V03264X/1. E.K. was supported by a European Molecular Biology Organization Long-Term Postdoctoral Fellowship, ALTF 44-2021.","doi":"10.1146/annurev-biophys-030822-032215","day":"01","date_published":"2024-07-01T00:00:00Z","abstract":[{"text":"Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.","lang":"eng"}],"scopus_import":"1","das_tickbox":"0","date_updated":"2026-10-01T08:29:37Z","author":[{"full_name":"Lo, Wei Chang","last_name":"Lo","first_name":"Wei Chang"},{"first_name":"Ekaterina","id":"1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A","last_name":"Krasnopeeva","full_name":"Krasnopeeva, Ekaterina"},{"first_name":"Teuta","last_name":"Pilizota","full_name":"Pilizota, Teuta"}],"publication":"Annual Review of Biophysics","year":"2024","date_created":"2024-07-28T22:01:09Z","citation":{"apa":"Lo, W. C., Krasnopeeva, E., &#38; Pilizota, T. (2024). Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>","ista":"Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510.","ama":"Lo WC, Krasnopeeva E, Pilizota T. Bacterial Electrophysiology. <i>Annual Review of Biophysics</i>. 2024;53:487-510. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>","ieee":"W. C. Lo, E. Krasnopeeva, and T. Pilizota, “Bacterial Electrophysiology,” <i>Annual Review of Biophysics</i>, vol. 53. Annual Reviews, pp. 487–510, 2024.","short":"W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510.","mla":"Lo, Wei Chang, et al. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>, vol. 53, Annual Reviews, 2024, pp. 487–510, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">10.1146/annurev-biophys-030822-032215</a>.","chicago":"Lo, Wei Chang, Ekaterina Krasnopeeva, and Teuta Pilizota. “Bacterial Electrophysiology.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2024. <a href=\"https://doi.org/10.1146/annurev-biophys-030822-032215\">https://doi.org/10.1146/annurev-biophys-030822-032215</a>."}},{"quality_controlled":"1","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"article_type":"original","volume":20,"researchdata_availability":"yes","intvolume":"        20","external_id":{"isi":["001232300600001"]},"publisher":"Springer Nature","month":"08","oa_version":"None","department":[{"_id":"BjHo"}],"_id":"17128","acknowledgement":"We gratefully acknowledge the assistance of J. M. Lopez with DNSs at an early stage of this work. This work was partially supported by two grants from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST 111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing resources of CRIANN (Normandy, France).","date_published":"2024-08-01T00:00:00Z","day":"01","doi":"10.1038/s41567-024-02513-0","abstract":[{"text":"The onset of turbulence in pipe flow has defied detailed understanding ever since the first observations of the spatially heterogeneous nature of the transition. Recent theoretical studies and experiments in simpler, shear-driven flows suggest that the onset of turbulence is a directed-percolation non-equilibrium phase transition, but whether these findings are generic and also apply to open or pressure-driven flows is unknown. In pipe flow, the extremely long time scales near the transition make direct observations of critical behaviour virtually impossible. Here we find a technical solution to that limitation and show that the universality class of the transition is directed percolation, from which a jammed phase of puffs emerges above the critical point. Our method is to experimentally characterize all pairwise interactions between localized patches of turbulence puffs and use these interactions as input for renormalization group and computer simulations of minimal models that extrapolate to long length and time scales. The strong interactions in the jamming regime enable us to explicitly measure the turbulent fraction and confirm model predictions. Our work shows that directed-percolation scaling applies beyond simple closed shear flows and underscores how statistical mechanics can lead to profound, quantitative and predictive insights on turbulent flows and their phases.","lang":"eng"}],"scopus_import":"1","das_tickbox":"1","date_updated":"2026-10-01T07:50:32Z","author":[{"full_name":"Lemoult, Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M","last_name":"Lemoult"},{"full_name":"Vasudevan, Mukund","last_name":"Vasudevan","first_name":"Mukund","id":"3C5A959A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shih","first_name":"Hong Yan","full_name":"Shih, Hong Yan"},{"last_name":"Linga","first_name":"Gaute","full_name":"Linga, Gaute"},{"first_name":"Joachim","last_name":"Mathiesen","full_name":"Mathiesen, Joachim"},{"first_name":"Nigel","last_name":"Goldenfeld","full_name":"Goldenfeld, Nigel"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"publication":"Nature Physics","citation":{"apa":"Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld, N., &#38; Hof, B. (2024). Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>","ama":"Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming near the transition to pipe turbulence. <i>Nature Physics</i>. 2024;20:1339-1345. doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>","ista":"Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence. Nature Physics. 20, 1339–1345.","short":"G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld, B. Hof, Nature Physics 20 (2024) 1339–1345.","ieee":"G. M. Lemoult <i>et al.</i>, “Directed percolation and puff jamming near the transition to pipe turbulence,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1339–1345, 2024.","mla":"Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1339–45, doi:<a href=\"https://doi.org/10.1038/s41567-024-02513-0\">10.1038/s41567-024-02513-0</a>.","chicago":"Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming near the Transition to Pipe Turbulence.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02513-0\">https://doi.org/10.1038/s41567-024-02513-0</a>."},"year":"2024","date_created":"2024-06-09T22:01:03Z","supplementarymaterial":"yes","corr_author":"1","article_processing_charge":"No","related_material":{"record":[{"relation":"research_data","id":"23012","status":"public"}]},"dataavailabilitystatement":"All experimental data presented in this article are available online in the Zenodo repository at https://doi.org/10.5281/zenodo.10308791","language":[{"iso":"eng"}],"page":"1339-1345","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","title":"Directed percolation and puff jamming near the transition to pipe turbulence","project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960"}],"fulldoi":"https://doi.org/10.1038/s41567-024-02513-0","isi":1,"status":"public","type":"journal_article"},{"language":[{"iso":"eng"}],"page":"R1230-R1232","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","corr_author":"1","supplementarymaterial":"no","type":"journal_article","OA_type":"closed access","status":"public","isi":1,"fulldoi":"https://doi.org/10.1016/j.cub.2024.10.065","publication_status":"published","title":"Development: Turing mechanics","department":[{"_id":"CaHe"}],"_id":"18651","publisher":"Elsevier","oa_version":"None","month":"12","external_id":{"pmid":["39689690"],"isi":["001392077000001"]},"intvolume":"        34","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"article_type":"letter_note","volume":34,"researchdata_availability":"no","quality_controlled":"1","issue":"24","pmid":1,"citation":{"short":"N. Hino, C. Santos Fernandes Lasbarrères Camelo, C.-P.J. Heisenberg, Current Biology 34 (2024) R1230–R1232.","ieee":"N. Hino, C. Santos Fernandes Lasbarrères Camelo, and C.-P. J. Heisenberg, “Development: Turing mechanics,” <i>Current Biology</i>, vol. 34, no. 24. Elsevier, pp. R1230–R1232, 2024.","mla":"Hino, Naoya, et al. “Development: Turing Mechanics.” <i>Current Biology</i>, vol. 34, no. 24, Elsevier, 2024, pp. R1230–32, doi:<a href=\"https://doi.org/10.1016/j.cub.2024.10.065\">10.1016/j.cub.2024.10.065</a>.","chicago":"Hino, Naoya, Carolina Santos Fernandes Lasbarrères Camelo, and Carl-Philipp J Heisenberg. “Development: Turing Mechanics.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2024.10.065\">https://doi.org/10.1016/j.cub.2024.10.065</a>.","apa":"Hino, N., Santos Fernandes Lasbarrères Camelo, C., &#38; Heisenberg, C.-P. J. (2024). Development: Turing mechanics. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2024.10.065\">https://doi.org/10.1016/j.cub.2024.10.065</a>","ista":"Hino N, Santos Fernandes Lasbarrères Camelo C, Heisenberg C-PJ. 2024. Development: Turing mechanics. Current Biology. 34(24), R1230–R1232.","ama":"Hino N, Santos Fernandes Lasbarrères Camelo C, Heisenberg C-PJ. Development: Turing mechanics. <i>Current Biology</i>. 2024;34(24):R1230-R1232. doi:<a href=\"https://doi.org/10.1016/j.cub.2024.10.065\">10.1016/j.cub.2024.10.065</a>"},"year":"2024","date_created":"2024-12-15T23:01:49Z","publication":"Current Biology","author":[{"last_name":"Hino","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","first_name":"Naoya","full_name":"Hino, Naoya"},{"id":"6347dca5-074c-11ed-af92-a80f860d9d5b","first_name":"Carolina","last_name":"Santos Fernandes Lasbarrères Camelo","full_name":"Santos Fernandes Lasbarrères Camelo, Carolina"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_updated":"2026-10-01T08:30:45Z","das_tickbox":"0","scopus_import":"1","abstract":[{"text":"Embryo axis formation begins with the localized expression of biochemical signals, which organize cell movements and determine cell fate. A quail study finds that tissue contraction and resulting long-range changes in tissue tension restrict the area where these biochemical signals are expressed.","lang":"eng"}],"day":"16","date_published":"2024-12-16T00:00:00Z","doi":"10.1016/j.cub.2024.10.065"},{"type":"research_data_reference","main_file_link":[{"url":"https://doi.org/10.17632/wp9sf6sp4z.1","open_access":"1"}],"OA_type":"green","citation":{"ista":"Marteijn  Jurgen. 2024. Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al., Mendeley Data, <a href=\"https://doi.org/10.17632/wp9sf6sp4z.1\">10.17632/wp9sf6sp4z.1</a>.","ama":"Marteijn  Jurgen. Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al. 2024. doi:<a href=\"https://doi.org/10.17632/wp9sf6sp4z.1\">10.17632/wp9sf6sp4z.1</a>","apa":"Marteijn,  Jurgen. (2024). Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al. Mendeley Data. <a href=\"https://doi.org/10.17632/wp9sf6sp4z.1\">https://doi.org/10.17632/wp9sf6sp4z.1</a>","chicago":"Marteijn,  Jurgen. “Study of STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, Pol II Ubiquitylation and TFIIH Recruitment by Ramadhin et Al.” Mendeley Data, 2024. <a href=\"https://doi.org/10.17632/wp9sf6sp4z.1\">https://doi.org/10.17632/wp9sf6sp4z.1</a>.","mla":"Marteijn,  Jurgen. <i>Study of STK19 Drives Transcription-Coupled Repair by Stimulating Repair Complex Stability, Pol II Ubiquitylation and TFIIH Recruitment by Ramadhin et Al.</i> Mendeley Data, 2024, doi:<a href=\"https://doi.org/10.17632/wp9sf6sp4z.1\">10.17632/wp9sf6sp4z.1</a>.","ieee":"Jurgen Marteijn, “Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al.” Mendeley Data, 2024.","short":"Jurgen Marteijn, (2024)."},"ddc":["570"],"year":"2024","date_created":"2026-10-01T08:20:32Z","date_updated":"2026-10-01T08:20:39Z","author":[{"last_name":"Marteijn","first_name":" Jurgen","full_name":"Marteijn,  Jurgen"}],"status":"public","fulldoi":"https://doi.org/10.17632/wp9sf6sp4z.1","date_published":"2024-10-01T00:00:00Z","day":"01","doi":"10.17632/wp9sf6sp4z.1","abstract":[{"lang":"eng","text":"Raw data of figures in our manuscript 'Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment'  by Ramadhin et al. "}],"title":"Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al.","department":[{"_id":"CaBe"}],"_id":"23013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","related_material":{"record":[{"id":"18553","status":"public","relation":"used_in_publication"}]},"publisher":"Mendeley Data","oa":1,"month":"10","oa_version":"None","OA_place":"repository"},{"publication":"Nature Physics","year":"2024","date_created":"2024-01-21T23:00:57Z","citation":{"ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 20, 310–321.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. <i>Nature Physics</i>. 2024;20:310-321. doi:<a href=\"https://doi.org/10.1038/s41567-023-02302-1\">10.1038/s41567-023-02302-1</a>","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02302-1\">https://doi.org/10.1038/s41567-023-02302-1</a>","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-023-02302-1\">https://doi.org/10.1038/s41567-023-02302-1</a>.","mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 310–21, doi:<a href=\"https://doi.org/10.1038/s41567-023-02302-1\">10.1038/s41567-023-02302-1</a>.","ieee":"S. Caballero Mancebo <i>et al.</i>, “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 310–321, 2024.","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics 20 (2024) 310–321."},"date_updated":"2026-10-01T08:33:51Z","author":[{"orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"},{"full_name":"Shinde, Rushikesh","first_name":"Rushikesh","last_name":"Shinde"},{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison","last_name":"Bolger-Munro","full_name":"Bolger-Munro, Madison","orcid":"0000-0002-8176-4824"},{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"full_name":"Szep, Gregory","last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari","full_name":"Steccari, Irene"},{"id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David","last_name":"Labrousse Arias","full_name":"Labrousse Arias, David"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"last_name":"Callan-Jones","first_name":"Andrew","full_name":"Callan-Jones, Andrew"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"das_tickbox":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"doi":"10.1038/s41567-023-02302-1","day":"01","date_published":"2024-02-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces.","lang":"eng"}],"_id":"14846","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27).","external_id":{"pmid":["38370025"],"isi":["001138880800005"]},"month":"02","oa_version":"Published Version","publisher":"Springer Nature","volume":20,"researchdata_availability":"yes","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"article_type":"original","intvolume":"        20","pmid":1,"quality_controlled":"1","type":"journal_article","ddc":["530"],"status":"public","fulldoi":"https://doi.org/10.1038/s41567-023-02302-1","isi":1,"file":[{"file_name":"2024_NaturePhysics_CaballeroMancebo.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-07-16T12:12:43Z","relation":"main_file","date_updated":"2024-07-16T12:12:43Z","success":1,"checksum":"7891ebe7c900ae47469ab127031dd1ec","creator":"dernst","file_id":"17267","file_size":9897883}],"title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","project":[{"call_identifier":"FWF","grant_number":"I03601","_id":"2646861A-B435-11E9-9278-68D0E5697425","name":"Control of embryonic cleavage pattern"}],"publication_status":"published","dataavailabilitystatement":"Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on request","page":"310-321","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-07-16T12:12:43Z","has_accepted_license":"1","oa":1,"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"corr_author":"1","supplementarymaterial":"yes"},{"author":[{"last_name":"Arslan","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"date_updated":"2026-10-01T08:33:05Z","citation":{"ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. 2024;34(1):171-182.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., &#38; Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>","chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” <i>Current Biology</i>, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>."},"date_created":"2024-01-14T23:00:56Z","year":"2024","publication":"Current Biology","scopus_import":"1","abstract":[{"text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells.","lang":"eng"}],"date_published":"2024-01-08T00:00:00Z","day":"08","doi":"10.1016/j.cub.2023.11.067","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"das_tickbox":"1","publisher":"Elsevier","oa_version":"Published Version","month":"01","external_id":{"isi":["001154500400001"],"pmid":["38134934"]},"acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"_id":"14795","quality_controlled":"1","pmid":1,"issue":"1","intvolume":"        34","article_type":"original","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"researchdata_availability":"upon request","volume":34,"status":"public","ddc":["570"],"ec_funded":1,"type":"journal_article","publication_status":"published","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"access_level":"open_access","file_name":"2024_CurrentBiology_Arslan.pdf","date_created":"2024-01-16T10:53:31Z","content_type":"application/pdf","date_updated":"2024-01-16T10:53:31Z","success":1,"relation":"main_file","checksum":"51220b76d72a614208f84bdbfbaf9b72","creator":"dernst","file_size":5183861,"file_id":"14813"}],"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","isi":1,"fulldoi":"https://doi.org/10.1016/j.cub.2023.11.067","oa":1,"has_accepted_license":"1","file_date_updated":"2024-01-16T10:53:31Z","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"page":"171-182.e8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"All original microscopy data any additional information reported in this paper is available from the lead contact upon request. All original code is available from the lead contact upon request","supplementarymaterial":"yes","corr_author":"1"},{"article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-03-04T07:24:43Z","has_accepted_license":"1","oa":1,"related_material":{"record":[{"relation":"research_data","id":"14926","status":"public"}]},"dataavailabilitystatement":"A custom MATLAB script for analyzing cell dispersal has been deposited in the ISTA library (doi:10.15479/AT:ISTA:14926)","page":"1-18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"supplementarymaterial":"yes","corr_author":"1","status":"public","type":"journal_article","ec_funded":1,"ddc":["570"],"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"file":[{"success":1,"relation":"main_file","date_updated":"2024-03-04T07:24:43Z","file_name":"2024_Development_Schauer.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-03-04T07:24:43Z","file_size":14839986,"file_id":"15050","checksum":"6961ea10012bf0d266681f9628bb8f13","creator":"dernst"}],"publication_status":"published","fulldoi":"https://doi.org/10.1242/dev.202316","isi":1,"external_id":{"isi":["001170580200001"],"pmid":["38372390"]},"month":"02","oa_version":"Published Version","publisher":"Company of Biologists","_id":"15048","department":[{"_id":"CaHe"},{"_id":"Bio"}],"acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","issue":"4","pmid":1,"quality_controlled":"1","researchdata_availability":"yes","volume":151,"article_type":"original","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"intvolume":"       151","date_updated":"2026-10-01T08:32:34Z","author":[{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"publication":"Development","date_created":"2024-03-03T23:00:50Z","year":"2024","citation":{"apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18. doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, Company of Biologists, 2024, pp. 1–18, doi:<a href=\"https://doi.org/10.1242/dev.202316\">10.1242/dev.202316</a>.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>, vol. 151, no. 4. Company of Biologists, pp. 1–18, 2024.","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202316\">https://doi.org/10.1242/dev.202316</a>."},"doi":"10.1242/dev.202316","day":"01","date_published":"2024-02-01T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"das_tickbox":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"supplementarymaterial":"yes","OA_place":"publisher","has_accepted_license":"1","file_date_updated":"2024-03-04T07:34:00Z","article_processing_charge":"Yes","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/"}]},"oa":1,"dataavailabilitystatement":"All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The ICONA/O simulations were done with the ICON branch nextgems_cycle1_dpp0066 as commit 62dbfc. The source code is available here (https://doi.org/10.17617/3.1XTSR6). The ICON model is available to individuals under licenses (https://mpimet.mpg.de/en/science/modeling-with-icon/code-availability). IMERG was provided by the NASA Goddard Space Flight Center’s IMERG and PPS teams, which develop and compute IMERG as a contribution to the GPM mission, and archived at the NASA GES DISC (https://disc.gsfc.nasa.gov/datasets/GPM_3IMERGHH_V06/summary). The data and scripts for reproducing the plots are available on MPG publication repository (https://hdl.handle.net/21.11116/0000-000C-7F2B-7).","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","title":"Intensification of daily tropical precipitation extremes from more organized convection","file":[{"file_id":"15051","file_size":800926,"creator":"dernst","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","relation":"main_file","date_updated":"2024-03-04T07:34:00Z","success":1,"content_type":"application/pdf","date_created":"2024-03-04T07:34:00Z","file_name":"2024_ScienceAdv_Bao.pdf","access_level":"open_access"}],"project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"},{"call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"fulldoi":"https://doi.org/10.1126/sciadv.adj6801","isi":1,"status":"public","type":"journal_article","OA_type":"gold","ddc":["550"],"ec_funded":1,"pmid":1,"article_number":"eadj6801","issue":"8","quality_controlled":"1","publication_identifier":{"eissn":["2375-2548"]},"article_type":"original","volume":10,"researchdata_availability":"yes (supplementary data)","intvolume":"        10","external_id":{"isi":["001300045100007"],"pmid":["38394192"]},"publisher":"American Association for the Advancement of Science","month":"02","oa_version":"Published Version","department":[{"_id":"CaMu"}],"_id":"15047","acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","day":"23","DOAJ_listed":"1","date_published":"2024-02-23T00:00:00Z","doi":"10.1126/sciadv.adj6801","abstract":[{"text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling.","lang":"eng"}],"scopus_import":"1","das_tickbox":"1","date_updated":"2026-10-01T08:36:23Z","author":[{"last_name":"Bao","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei"},{"last_name":"Stevens","first_name":"Bjorn","full_name":"Stevens, Bjorn"},{"full_name":"Kluft, Lukas","first_name":"Lukas","last_name":"Kluft"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"publication":"Science Advances","citation":{"mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” <i>Science Advances</i>, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>.","apa":"Bao, J., Stevens, B., Kluft, L., &#38; Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adj6801\">https://doi.org/10.1126/sciadv.adj6801</a>","ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. <i>Science Advances</i>. 2024;10(8). doi:<a href=\"https://doi.org/10.1126/sciadv.adj6801\">10.1126/sciadv.adj6801</a>","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801."},"year":"2024","date_created":"2024-03-03T23:00:50Z"},{"oa":1,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-08-09T13:37:24Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"Data will be made available on request","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","ec_funded":1,"ddc":["550"],"type":"journal_article","publication_status":"published","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"file":[{"creator":"acasalla","checksum":"6fa476a4c08aded413844d92336b0e52","file_id":"17405","file_size":1595118,"date_created":"2024-08-09T13:37:23Z","content_type":"application/pdf","access_level":"open_access","file_name":"Fires_Galicia_SM.pdf","relation":"main_file","date_updated":"2024-08-09T13:37:23Z","success":1},{"date_updated":"2024-08-09T13:37:24Z","success":1,"relation":"main_file","file_name":"Fires_Galicia.pdf","access_level":"open_access","date_created":"2024-08-09T13:37:24Z","content_type":"application/pdf","file_size":13662676,"file_id":"17406","checksum":"859dcdef9555c383b702cf8cc7da66f2","creator":"acasalla"}],"title":"Wildfires impact on PM2.5 concentration in galicia Spain","isi":1,"fulldoi":"https://doi.org/10.1016/j.jenvman.2024.122093","publisher":"Elsevier","month":"09","oa_version":"Published Version","external_id":{"pmid":["39106804"],"isi":["001289532100001"]},"acknowledgement":"Alejandro Casallas was partially funded by a fellowship from the Abdus Salam International Centre for Theoretical Physics – ICTP. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 awarded to Alejandro Casallas. ","department":[{"_id":"CaMu"}],"_id":"17396","quality_controlled":"1","pmid":1,"article_number":"122093","intvolume":"       367","article_type":"original","publication_identifier":{"issn":["0301-4797"]},"volume":367,"researchdata_availability":"upon request","author":[{"last_name":"Quishpe-Vásquez","first_name":"César","full_name":"Quishpe-Vásquez, César"},{"full_name":"Oliva, Patricia","first_name":"Patricia","last_name":"Oliva"},{"first_name":"Ellie Anne","last_name":"López-Barrera","full_name":"López-Barrera, Ellie Anne"},{"orcid":"0000-0002-1988-5035","full_name":"Casallas Garcia, Alejandro","last_name":"Casallas Garcia","id":"92081129-2d75-11ef-a48d-b04dd7a2385a","first_name":"Alejandro"}],"date_updated":"2026-10-01T08:34:24Z","citation":{"apa":"Quishpe-Vásquez, C., Oliva, P., López-Barrera, E. A., &#38; Casallas Garcia, A. (2024). Wildfires impact on PM2.5 concentration in galicia Spain. <i>Journal of Environmental Management</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jenvman.2024.122093\">https://doi.org/10.1016/j.jenvman.2024.122093</a>","ista":"Quishpe-Vásquez C, Oliva P, López-Barrera EA, Casallas Garcia A. 2024. Wildfires impact on PM2.5 concentration in galicia Spain. Journal of Environmental Management. 367, 122093.","ama":"Quishpe-Vásquez C, Oliva P, López-Barrera EA, Casallas Garcia A. Wildfires impact on PM2.5 concentration in galicia Spain. <i>Journal of Environmental Management</i>. 2024;367. doi:<a href=\"https://doi.org/10.1016/j.jenvman.2024.122093\">10.1016/j.jenvman.2024.122093</a>","mla":"Quishpe-Vásquez, César, et al. “Wildfires Impact on PM2.5 Concentration in Galicia Spain.” <i>Journal of Environmental Management</i>, vol. 367, 122093, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.jenvman.2024.122093\">10.1016/j.jenvman.2024.122093</a>.","short":"C. Quishpe-Vásquez, P. Oliva, E.A. López-Barrera, A. Casallas Garcia, Journal of Environmental Management 367 (2024).","ieee":"C. Quishpe-Vásquez, P. Oliva, E. A. López-Barrera, and A. Casallas Garcia, “Wildfires impact on PM2.5 concentration in galicia Spain,” <i>Journal of Environmental Management</i>, vol. 367. Elsevier, 2024.","chicago":"Quishpe-Vásquez, César, Patricia Oliva, Ellie Anne López-Barrera, and Alejandro Casallas Garcia. “Wildfires Impact on PM2.5 Concentration in Galicia Spain.” <i>Journal of Environmental Management</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.jenvman.2024.122093\">https://doi.org/10.1016/j.jenvman.2024.122093</a>."},"date_created":"2024-08-06T05:54:52Z","year":"2024","publication":"Journal of Environmental Management","scopus_import":"1","abstract":[{"text":"Wildfire intensity and severity have been increasing in the Iberian Peninsula in recent years, particularly in the Galicia region, due to rising temperatures and accumulating drier combustible vegetation in unmanaged lands. This leads to substantial emissions of air pollutants, notably fine particles (PM2.5), posing a risk to public health. This study aims to assess the impact of local and regional wildfires on PM2.5 levels in Galicia's main cities and their implications for air quality and public health. Over a decade (2013–2022), PM2.5 data during wildfire seasons were analyzed using statistical methods and Lagrangian tracking to monitor smoke plume evolution. The results reveal a notable increase in PM2.5 concentration during the wildfire season (June–November) in Galicia, surpassing health guidelines during extreme events and posing a significant health risk to the population. Regional wildfire analyses indicate that smoke plumes from Northern Portugal contribute to pollution in Galician cities, influencing the seasonality of heightened PM2.5 levels. During extensive wildfires, elevated PM2.5 concentration values persisted for several days, potentially exacerbating health concerns in Galicia. These findings underscore the urgency of implementing air pollution prevention and management measures in the region, including developing effective alerts for large-scale events and improved wildfire management strategies to mitigate their impact on air quality in Galician cities.","lang":"eng"}],"date_published":"2024-09-01T00:00:00Z","day":"01","doi":"10.1016/j.jenvman.2024.122093","das_tickbox":"1"},{"article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-08-19T06:32:21Z","has_accepted_license":"1","oa":1,"dataavailabilitystatement":"The hourly precipitation variable in ERA5 reanalysis Hersbach et al. (2018) was downloaded from the Copernicus Climate Change Service (C3S) accessed in July 2022. It is freely available on C3S website. The results contain modified Copernicus Climate Change Service information 2020. Neither the European Commission nor ECMWF is responsible for any use that may be made of the Copernicus information or data it contains.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"language":[{"iso":"eng"}],"supplementarymaterial":"yes","status":"public","type":"journal_article","ddc":["550"],"ec_funded":1,"project":[{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020"}],"title":"Regimes of precipitation change over Europe and the Mediterranean","file":[{"access_level":"open_access","file_name":"2024_JGRAtmospheres_Andre.pdf","date_created":"2024-08-19T06:32:21Z","content_type":"application/pdf","success":1,"date_updated":"2024-08-19T06:32:21Z","relation":"main_file","checksum":"71d7f966318e11ce474737f4e37405ef","creator":"dernst","file_id":"17438","file_size":8126046}],"publication_status":"published","fulldoi":"https://doi.org/10.1029/2023JD040413","isi":1,"external_id":{"isi":["001285897600001"]},"oa_version":"Published Version","month":"08","publisher":"Wiley","_id":"17435","department":[{"_id":"CaMu"}],"acknowledgement":"CJM gratefully acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No 805041). The authors also thank Samuel Somot (Centre National de Recherches Météorologiques, Toulouse) and Juliette Blanchet (Institut des Géosciences de l’Environnement, Grenoble) for their fruitful discussions on the project.","article_number":"e2023JD040413","issue":"15","quality_controlled":"1","researchdata_availability":"not applicable","volume":129,"publication_identifier":{"issn":["2169-897X"],"eissn":["2169-8996"]},"article_type":"original","intvolume":"       129","date_updated":"2026-10-01T08:35:09Z","author":[{"full_name":"André, Julie","first_name":"Julie","last_name":"André"},{"first_name":"Fabio","last_name":"D'Andrea","full_name":"D'Andrea, Fabio"},{"full_name":"Drobinski, Philippe","first_name":"Philippe","last_name":"Drobinski"},{"first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"publication":"Journal of Geophysical Research: Atmospheres","date_created":"2024-08-18T22:01:04Z","year":"2024","citation":{"apa":"André, J., D’Andrea, F., Drobinski, P., &#38; Muller, C. J. (2024). Regimes of precipitation change over Europe and the Mediterranean. <i>Journal of Geophysical Research: Atmospheres</i>. Wiley. <a href=\"https://doi.org/10.1029/2023JD040413\">https://doi.org/10.1029/2023JD040413</a>","ista":"André J, D’Andrea F, Drobinski P, Muller CJ. 2024. Regimes of precipitation change over Europe and the Mediterranean. Journal of Geophysical Research: Atmospheres. 129(15), e2023JD040413.","ama":"André J, D’Andrea F, Drobinski P, Muller CJ. Regimes of precipitation change over Europe and the Mediterranean. <i>Journal of Geophysical Research: Atmospheres</i>. 2024;129(15). doi:<a href=\"https://doi.org/10.1029/2023JD040413\">10.1029/2023JD040413</a>","mla":"André, Julie, et al. “Regimes of Precipitation Change over Europe and the Mediterranean.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 15, e2023JD040413, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023JD040413\">10.1029/2023JD040413</a>.","ieee":"J. André, F. D’Andrea, P. Drobinski, and C. J. Muller, “Regimes of precipitation change over Europe and the Mediterranean,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 129, no. 15. Wiley, 2024.","short":"J. André, F. D’Andrea, P. Drobinski, C.J. Muller, Journal of Geophysical Research: Atmospheres 129 (2024).","chicago":"André, Julie, Fabio D’Andrea, Philippe Drobinski, and Caroline J Muller. “Regimes of Precipitation Change over Europe and the Mediterranean.” <i>Journal of Geophysical Research: Atmospheres</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023JD040413\">https://doi.org/10.1029/2023JD040413</a>."},"doi":"10.1029/2023JD040413","day":"16","date_published":"2024-08-16T00:00:00Z","abstract":[{"text":"The Mediterranean region is experiencing pronounced aridification and in certain areas higher occurrence of intense precipitation. In this work, we analyze the evolution of the precipitation probability distribution in terms of precipitating days (or “wet-days”) and all-days quantile trends, in Europe and the Mediterranean, using the ERA5 reanalysis. Looking at the form of wet-days quantile trends curves, we identify four regimes. Two are predominant: in most of northern Europe the precipitation quantiles all intensify, while in the Mediterranean the low-medium quantiles are mostly decreasing as extremes intensify or decrease. The wet-days distribution is then modeled by a Weibull law with two parameters, whose changes capture the four regimes. Assessing the significance of the parameters' changes over 1950–2020 shows that a signal on wet-days distribution has already emerged in northern Europe (where the distribution shifts to more intense precipitation), but not yet in the Mediterranean, where the natural variability is stronger. We extend the results by describing the all-days distribution change as the wet-days’ change plus a contribution from the dry-days frequency change, and study their relative contribution. In northern Europe, the wet-days distribution change is the dominant driver, and the contribution of dry-days frequency change can be neglected for wet-days percentiles above about 50%. In the Mediterranean, however, the change of precipitation distribution comes from the significant increase of dry-days frequency instead of an intensity change during wet-days. Therefore, in the Mediterranean the increase of dry-days frequency is crucial for all-days trends, even for heavy precipitation.","lang":"eng"}],"scopus_import":"1","das_tickbox":"1"},{"das_tickbox":"1","doi":"10.7554/elife.80803","date_published":"2024-02-07T00:00:00Z","day":"07","DOAJ_listed":"1","scopus_import":"1","abstract":[{"text":"BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan <jats:italic>Nematostella vectensis</jats:italic>, several of which were conserved in <jats:italic>Drosophila</jats:italic> and <jats:italic>Xenopus</jats:italic>. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in <jats:italic>Nematostella</jats:italic> are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is <jats:italic>zswim4-6</jats:italic>, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.","lang":"eng"}],"publication":"eLife","year":"2024","date_created":"2025-01-29T08:48:34Z","citation":{"mla":"Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” <i>ELife</i>, vol. 13, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>.","short":"P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024).","ieee":"P. Knabl <i>et al.</i>, “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","chicago":"Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>.","apa":"Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.80803\">https://doi.org/10.7554/elife.80803</a>","ista":"Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13.","ama":"Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.80803\">10.7554/elife.80803</a>"},"date_updated":"2026-10-01T08:31:50Z","author":[{"full_name":"Knabl, Paul","last_name":"Knabl","first_name":"Paul"},{"full_name":"Schauer, Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","last_name":"Schauer"},{"full_name":"Pomreinke, Autumn P","first_name":"Autumn P","last_name":"Pomreinke"},{"full_name":"Zimmermann, Bob","first_name":"Bob","last_name":"Zimmermann"},{"first_name":"Katherine W","last_name":"Rogers","full_name":"Rogers, Katherine W"},{"full_name":"Čapek, Daniel","first_name":"Daniel","last_name":"Čapek"},{"last_name":"Müller","first_name":"Patrick","full_name":"Müller, Patrick"},{"full_name":"Genikhovich, Grigory","last_name":"Genikhovich","first_name":"Grigory"}],"volume":13,"researchdata_availability":"yes","publication_identifier":{"issn":["2050-084X"]},"article_type":"original","intvolume":"        13","quality_controlled":"1","_id":"18940","department":[{"_id":"CaHe"}],"acknowledgement":"This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope.","oa_version":"Published Version","month":"02","publisher":"eLife Sciences Publications","fulldoi":"https://doi.org/10.7554/elife.80803","title":"Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator","file":[{"creator":"dernst","checksum":"24548a184215d3f4547bba535ccfd7b1","file_id":"18941","file_size":11855972,"content_type":"application/pdf","date_created":"2025-01-29T08:50:18Z","access_level":"open_access","file_name":"2024_eLife_Knabl.pdf","success":1,"date_updated":"2025-01-29T08:50:18Z","relation":"main_file"}],"publication_status":"published","OA_type":"gold","type":"journal_article","ddc":["570"],"status":"public","OA_place":"publisher","supplementarymaterial":"no","dataavailabilitystatement":"The data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 6D-F', Figure 6Q, Figure 5—figure supplement 1D, Figure 6—figure supplement 2G, Figure 6—figure supplement 3E and F. All the sequencing data are available at NCBI as an SRA project PRJNA820593.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2025-01-29T08:50:18Z","article_processing_charge":"Yes","has_accepted_license":"1","oa":1},{"title":"Matlab script for analysis of clone dispersal","file":[{"file_id":"14927","file_size":736,"checksum":"df7f358ae19a176cf710c0a802ce31b1","creator":"rhauschild","success":1,"relation":"main_file","date_updated":"2024-02-02T14:40:31Z","access_level":"open_access","file_name":"README.md","content_type":"application/octet-stream","date_created":"2024-02-02T14:40:31Z"},{"file_size":3543,"file_id":"14928","creator":"rhauschild","checksum":"10194cc11619eccd8f4b24472e465b7f","relation":"main_file","date_updated":"2024-02-02T14:40:31Z","success":1,"content_type":"application/x-zip-compressed","date_created":"2024-02-02T14:40:31Z","access_level":"open_access","file_name":"Supplementary_file_1.zip"}],"day":"02","date_published":"2024-02-02T00:00:00Z","doi":"10.15479/AT:ISTA:14926","fulldoi":"https://doi.org/10.15479/AT:ISTA:14926","author":[{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"}],"status":"public","date_updated":"2026-10-01T08:32:33Z","citation":{"chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>.","short":"R. Hauschild, (2024).","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” Institute of Science and Technology Austria, 2024.","mla":"Hauschild, Robert. <i>Matlab Script for Analysis of Clone Dispersal</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">10.15479/AT:ISTA:14926</a>.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14926\">https://doi.org/10.15479/AT:ISTA:14926</a>"},"ddc":["570"],"year":"2024","date_created":"2024-02-02T14:42:26Z","type":"software","license":"https://opensource.org/licenses/MIT","corr_author":"1","related_material":{"record":[{"relation":"used_in_publication","id":"15048","status":"public"}]},"publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","file_date_updated":"2024-02-02T14:40:31Z","has_accepted_license":"1","tmp":{"legal_code_url":"https://opensource.org/licenses/MIT","name":"The MIT License","short":"MIT"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"Bio"}],"_id":"14926"},{"supplementarymaterial":"no","dataavailabilitystatement":"Simulations were run with the ICON branch nextgems_cycle1_zstar_avr of the icon-aes repository as commit 2d18086d538ca6b80785f21b7a14808fbf50546c. This source code and run scripts are available from https://doi.org/10.17617/3.Z10MPA (Schmidt, 2023). The ICON model is available to licensed individuals (https://code.mpimet.mpg.de/projects/iconpublic/wiki/How to obtain the model code, last access: 10 July 2023). By downloading the ICON source code, the user accepts the license agreement. Scripts employed to produce the figures can be found at https://hdl.handle.net/21.11116/0000-000D-605D-F (last access: 15 December 2023). Radiosonde data are available from https://doi.org/10.5281/zenodo.7051674 (Schulz et al., 2022). CERES data are available from https://doi.org/10.5067/TERRA-AQUA-NOAA20/CERES/EBAF_L3B004.2 (NASA/LARC/SD/ASDC, 2023).","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1563-1584","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-03-13T08:59:21Z","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","id":"23015","status":"public"}]},"oa":1,"fulldoi":"https://doi.org/10.5194/gmd-17-1563-2024","isi":1,"publication_status":"published","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","file":[{"file_size":13364601,"file_id":"15111","creator":"dernst","checksum":"270d2340402729b0532f7072ea914cae","date_updated":"2024-03-13T08:59:21Z","relation":"main_file","success":1,"date_created":"2024-03-13T08:59:21Z","content_type":"application/pdf","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","access_level":"open_access"}],"type":"journal_article","ddc":["550"],"status":"public","publication_identifier":{"issn":["1991-959X"],"eissn":["1991-9603"]},"article_type":"original","volume":17,"researchdata_availability":"yes","intvolume":"        17","issue":"4","quality_controlled":"1","department":[{"_id":"CaMu"}],"_id":"15097","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","external_id":{"isi":["001190535000001"]},"publisher":"European Geosciences Union","month":"02","oa_version":"Published Version","das_tickbox":"1","day":"22","date_published":"2024-02-22T00:00:00Z","doi":"10.5194/gmd-17-1563-2024","abstract":[{"text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.","lang":"eng"}],"scopus_import":"1","publication":"Geoscientific Model Development","citation":{"chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” <i>Geoscientific Model Development</i>. European Geosciences Union, 2024. <a href=\"https://doi.org/10.5194/gmd-17-1563-2024\">https://doi.org/10.5194/gmd-17-1563-2024</a>.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","ieee":"H. Schmidt <i>et al.</i>, “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” <i>Geoscientific Model Development</i>, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” <i>Geoscientific Model Development</i>, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:<a href=\"https://doi.org/10.5194/gmd-17-1563-2024\">10.5194/gmd-17-1563-2024</a>.","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. <i>Geoscientific Model Development</i>. 2024;17(4):1563-1584. doi:<a href=\"https://doi.org/10.5194/gmd-17-1563-2024\">10.5194/gmd-17-1563-2024</a>","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. <i>Geoscientific Model Development</i>. European Geosciences Union. <a href=\"https://doi.org/10.5194/gmd-17-1563-2024\">https://doi.org/10.5194/gmd-17-1563-2024</a>"},"year":"2024","date_created":"2024-03-10T23:00:53Z","date_updated":"2026-10-01T08:55:28Z","author":[{"first_name":"Hauke","last_name":"Schmidt","full_name":"Schmidt, Hauke"},{"full_name":"Rast, Sebastian","first_name":"Sebastian","last_name":"Rast"},{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","last_name":"Bao","full_name":"Bao, Jiawei"},{"last_name":"Cassim","first_name":"Amrit","full_name":"Cassim, Amrit"},{"last_name":"Fang","first_name":"Shih Wei","full_name":"Fang, Shih Wei"},{"full_name":"Jimenez-De La Cuesta, Diego","first_name":"Diego","last_name":"Jimenez-De La Cuesta"},{"first_name":"Paul","last_name":"Keil","full_name":"Keil, Paul"},{"last_name":"Kluft","first_name":"Lukas","full_name":"Kluft, Lukas"},{"full_name":"Kroll, Clarissa","last_name":"Kroll","first_name":"Clarissa"},{"full_name":"Lang, Theresa","last_name":"Lang","first_name":"Theresa"},{"full_name":"Niemeier, Ulrike","last_name":"Niemeier","first_name":"Ulrike"},{"first_name":"Andrea","last_name":"Schneidereit","full_name":"Schneidereit, Andrea"},{"full_name":"Williams, Andrew I.L.","last_name":"Williams","first_name":"Andrew I.L."},{"full_name":"Stevens, Bjorn","first_name":"Bjorn","last_name":"Stevens"}]},{"acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","_id":"15186","department":[{"_id":"CaMu"}],"oa_version":"Published Version","month":"03","publisher":"Wiley","external_id":{"isi":["001187002300001"]},"intvolume":"        51","researchdata_availability":"yes","volume":51,"article_type":"original","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"quality_controlled":"1","issue":"6","article_number":" e2023GL106523","year":"2024","date_created":"2024-03-25T10:27:30Z","citation":{"apa":"Hwong, Y.-L., &#38; Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. <i>Geophysical Research Letters</i>. Wiley. <a href=\"https://doi.org/10.1029/2023gl106523\">https://doi.org/10.1029/2023gl106523</a>","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. <i>Geophysical Research Letters</i>. 2024;51(6). doi:<a href=\"https://doi.org/10.1029/2023gl106523\">10.1029/2023gl106523</a>","ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” <i>Geophysical Research Letters</i>, vol. 51, no. 6. Wiley, 2024.","mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” <i>Geophysical Research Letters</i>, vol. 51, no. 6, e2023GL106523, Wiley, 2024, doi:<a href=\"https://doi.org/10.1029/2023gl106523\">10.1029/2023gl106523</a>.","chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” <i>Geophysical Research Letters</i>. Wiley, 2024. <a href=\"https://doi.org/10.1029/2023gl106523\">https://doi.org/10.1029/2023gl106523</a>."},"publication":"Geophysical Research Letters","author":[{"last_name":"Hwong","first_name":"Yi-Ling","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling"},{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","last_name":"Muller"}],"date_updated":"2026-10-01T09:22:29Z","das_tickbox":"1","abstract":[{"text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain.","lang":"eng"}],"scopus_import":"1","doi":"10.1029/2023gl106523","day":"19","date_published":"2024-03-19T00:00:00Z","DOAJ_listed":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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)"},"language":[{"iso":"eng"}],"dataavailabilitystatement":"The data, scripts and model source codes and files required to reproduce the results described in this manuscript are available in Hwong and Muller (2023)\r\nHwong, Y.-L., & Muller, C. (2023). Data - The unreasonable efficiency of total rain evaporation removal in triggering convective self-aggregation (version 5) [Dataset]. Zenodo. https://doi.org/10.5281/zenodo.10687169","oa":1,"related_material":{"record":[{"id":"19307","status":"public","relation":"research_data"}]},"file_date_updated":"2024-03-25T11:28:25Z","has_accepted_license":"1","article_processing_charge":"Yes","OA_place":"publisher","keyword":["General Earth and Planetary Sciences","Geophysics"],"corr_author":"1","supplementarymaterial":"yes","ec_funded":1,"ddc":["550"],"APC_amount":"2940 EUR","OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1029/2023gl106523","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"call_identifier":"H2020","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"file":[{"checksum":"eacb011091a503b9e7b748fef639ba4c","creator":"dernst","file_size":1280108,"file_id":"15187","access_level":"open_access","file_name":"2024_GeophysResLetters_Hwong.pdf","date_created":"2024-03-25T11:28:25Z","content_type":"application/pdf","date_updated":"2024-03-25T11:28:25Z","success":1,"relation":"main_file"}],"title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","publication_status":"published"}]