[{"abstract":[{"text":"The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance.","lang":"eng"}],"scopus_import":"1","doi":"10.1073/pnas.2406335121","date_published":"2024-10-29T00:00:00Z","day":"29","das_tickbox":"1","author":[{"full_name":"Mcdonough, Yasmine","first_name":"Yasmine","last_name":"Mcdonough"},{"full_name":"Ruzicka, Filip","last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","first_name":"Filip"},{"first_name":"Tim","last_name":"Connallon","full_name":"Connallon, Tim"}],"date_updated":"2026-09-24T11:12:56Z","year":"2024","date_created":"2024-10-27T23:01:44Z","citation":{"mla":"Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>.","ieee":"Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>.","apa":"Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>","ista":"Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2406335121.","ama":"Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","issue":"44","article_number":"e2406335121","pmid":1,"intvolume":"       121","volume":121,"researchdata_availability":"yes (supplementary data)","publication_identifier":{"eissn":["1091-6490"]},"article_type":"original","month":"10","oa_version":"Published Version","publisher":"National Academy of Sciences","external_id":{"isi":["001359216400017"],"pmid":["39436652"]},"acknowledgement":"This work was supported by funds from the Australian Research Council and The School of Biological Sciences at Monash University. F.R. was funded by a H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous reviewers for suggestions that substantially improved the paper and breadth of the analysis.","_id":"18479","department":[{"_id":"BeVi"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","file":[{"date_updated":"2024-11-04T10:29:43Z","success":1,"relation":"main_file","content_type":"application/pdf","date_created":"2024-11-04T10:29:43Z","access_level":"open_access","file_name":"2024_PNAS_McDonough.pdf","file_size":1299095,"file_id":"18501","creator":"dernst","checksum":"73db3c87b35753e0f4324417f164a35e"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1073/pnas.2406335121","status":"public","ddc":["570"],"ec_funded":1,"OA_type":"hybrid","type":"journal_article","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","OA_place":"publisher","oa":1,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","file_date_updated":"2024-11-04T10:29:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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)"},"dataavailabilitystatement":"All study data are included in the article and/or supporting information."},{"ddc":["570"],"OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1093/gbe/evae265","title":"Evidence for a novel X chromosome in termites","project":[{"name":"Sex Determination in Termites","_id":"26641CAC-B435-11E9-9278-68D0E5697425","grant_number":"M02484","call_identifier":"FWF"}],"file":[{"file_id":"18772","file_size":795106,"checksum":"9cf8fd14580dd694dd810ccca808ad0e","creator":"dernst","date_updated":"2025-01-08T08:28:07Z","success":1,"relation":"main_file","file_name":"2024_GBE_Fraser.pdf","access_level":"open_access","date_created":"2025-01-08T08:28:07Z","content_type":"application/pdf"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"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"},"dataavailabilitystatement":"Male and female DNAseq reads for the termites C. secundus, M. natalensis, and R. flavipes can be found in the NCBI SRA under accession codes SRR30467421-SRR30467422, SRR30467423-SRR30467424, and SRR30467425-SRR30467426, respectively (all BioProject PRJNA1153745)","oa":1,"has_accepted_license":"1","file_date_updated":"2025-01-08T08:28:07Z","article_processing_charge":"Yes","OA_place":"publisher","corr_author":"1","supplementarymaterial":"yes","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2024","date_created":"2025-01-05T23:01:58Z","citation":{"chicago":"Fraser, Roxanne, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, and Ann K Huylmans. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>.","short":"R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K. Huylmans, Genome Biology and Evolution 16 (2024).","ieee":"R. Fraser <i>et al.</i>, “Evidence for a novel X chromosome in termites,” <i>Genome Biology and Evolution</i>, vol. 16, no. 12. Oxford University Press, 2024.","mla":"Fraser, Roxanne, et al. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>, vol. 16, no. 12, evae265, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>.","ama":"Fraser R, Moraa R, Djolai A, et al. Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. 2024;16(12). doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>","ista":"Fraser R, Moraa R, Djolai A, Meisenheimer N, Laube S, Vicoso B, Huylmans AK. 2024. Evidence for a novel X chromosome in termites. Genome Biology and Evolution. 16(12), evae265.","apa":"Fraser, R., Moraa, R., Djolai, A., Meisenheimer, N., Laube, S., Vicoso, B., &#38; Huylmans, A. K. (2024). Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>"},"publication":"Genome Biology and Evolution","author":[{"full_name":"Fraser, Roxanne","last_name":"Fraser","first_name":"Roxanne"},{"full_name":"Moraa, Ruth","last_name":"Moraa","first_name":"Ruth"},{"full_name":"Djolai, Annika","last_name":"Djolai","first_name":"Annika"},{"last_name":"Meisenheimer","first_name":"Nils","full_name":"Meisenheimer, Nils"},{"full_name":"Laube, Sophie","last_name":"Laube","first_name":"Sophie"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"}],"date_updated":"2026-09-24T11:16:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"das_tickbox":"1","abstract":[{"lang":"eng","text":"Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution."}],"scopus_import":"1","doi":"10.1093/gbe/evae265","DOAJ_listed":"1","date_published":"2024-12-01T00:00:00Z","day":"01","acknowledgement":"urthermore, we thank all lab members and collaborators for feedback on the project. Specifically, Dino McMahon provided R. flavipes males and females, Judith Korb provided C. secundus males and females, gave feedback on the project and discussed questions on termite reproduction, Mireille Vasseur-Cognet provided M. natalensis males and females, Ariana Macon performed the lab work for sequencing and the Vicoso group gave critical feedback on the project. We furthermore thank the HPC group at IST Austria and Christian Meesters at JGU Mainz for their technical support.\r\nThis work was supported by a Österreichischer Wissenschaftsfonds (FWF) grant of the Meitner Programme to A.K.H. (project number M 2484), funding by the Deutsche Forschungsgemeinschaft (DFG) of the Research Training Group GenEvo (project number 407023052) to A.K.H., R.F., and A.D., and funding of the DFG within the Schwerpunktprogramm Gevol to A.K.H. and R.M. (project number 503256468).","_id":"18761","department":[{"_id":"BeVi"}],"oa_version":"Published Version","month":"12","publisher":"Oxford University Press","external_id":{"pmid":["39658246"],"isi":["001380841100001"]},"intvolume":"        16","volume":16,"researchdata_availability":"yes","article_type":"original","publication_identifier":{"eissn":["1759-6653"]},"quality_controlled":"1","issue":"12","pmid":1,"article_number":"evae265"},{"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","file":[{"access_level":"open_access","file_name":"README.txt","date_created":"2024-08-05T22:24:18Z","content_type":"text/plain","date_updated":"2024-08-05T22:24:18Z","relation":"main_file","success":1,"checksum":"26b5d41b3103f4284dd97d56e370a5b6","creator":"melkrewi","file_id":"17394","file_size":2465},{"relation":"main_file","date_updated":"2024-08-05T23:28:52Z","success":1,"date_created":"2024-08-05T23:28:52Z","content_type":"application/x-zip-compressed","file_name":"Data_artemia_single_nucleus_atlas.zip","access_level":"open_access","file_size":2526735400,"file_id":"17395","creator":"melkrewi","checksum":"95adab5e36148015da313505e3910707"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:17362","status":"public","type":"research_data","ddc":["576"],"license":"https://creativecommons.org/licenses/by/4.0/","corr_author":"1","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2024-08-05T23:28:52Z","oa":1,"related_material":{"record":[{"status":"public","id":"17890","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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)"},"doi":"10.15479/AT:ISTA:17362","date_published":"2024-08-05T00:00:00Z","day":"05","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-09-24T11:17:37Z","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"year":"2024","date_created":"2024-08-02T07:27:45Z","citation":{"apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. <i>Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","short":"M.N. Elkrewi, B. Vicoso, (2024).","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>."},"month":"08","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","_id":"17362","department":[{"_id":"GradSch"},{"_id":"BeVi"}]},{"publication":"Acta Crystallographica Section B","date_created":"2025-01-29T11:07:36Z","year":"2024","citation":{"apa":"Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S., Aitipamula, S., … Cole, J. C. (2024). The seventh blind test of crystal structure prediction: Structure generation methods. <i>Acta Crystallographica Section B</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/s2052520624007492\">https://doi.org/10.1107/s2052520624007492</a>","ama":"Hunnisett LM, Nyman J, Francia N, et al. The seventh blind test of crystal structure prediction: Structure generation methods. <i>Acta Crystallographica Section B</i>. 2024;80(6):517-547. doi:<a href=\"https://doi.org/10.1107/s2052520624007492\">10.1107/s2052520624007492</a>","ista":"Hunnisett LM et al. 2024. The seventh blind test of crystal structure prediction: Structure generation methods. Acta Crystallographica Section B. 80(6), 517–547.","mla":"Hunnisett, Lily M., et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” <i>Acta Crystallographica Section B</i>, vol. 80, no. 6, International Union of Crystallography, 2024, pp. 517–47, doi:<a href=\"https://doi.org/10.1107/s2052520624007492\">10.1107/s2052520624007492</a>.","ieee":"L. M. Hunnisett <i>et al.</i>, “The seventh blind test of crystal structure prediction: Structure generation methods,” <i>Acta Crystallographica Section B</i>, vol. 80, no. 6. International Union of Crystallography, pp. 517–547, 2024.","short":"L.M. Hunnisett, J. Nyman, N. Francia, N.S. Abraham, C.S. Adjiman, S. Aitipamula, T. Alkhidir, M. Almehairbi, A. Anelli, D.M. Anstine, J.E. Anthony, J.E. Arnold, F. Bahrami, M.A. Bellucci, R.M. Bhardwaj, I. Bier, J.A. Bis, A.D. Boese, D.H. Bowskill, J. Bramley, J.G. Brandenburg, D.E. Braun, P.W.V. Butler, J. Cadden, S. Carino, E.J. Chan, C. Chang, B. Cheng, S.M. Clarke, S.J. Coles, R.I. Cooper, R. Couch, R. Cuadrado, T. Darden, G.M. Day, H. Dietrich, Y. Ding, A. DiPasquale, B. Dhokale, B.P. van Eijck, M.R.J. Elsegood, D. Firaha, W. Fu, K. Fukuzawa, J. Glover, H. Goto, C. Greenwell, R. Guo, J. Harter, J. Helfferich, D.W.M. Hofmann, J. Hoja, J. Hone, R. Hong, G. Hutchison, Y. Ikabata, O. Isayev, O. Ishaque, V. Jain, Y. Jin, A. Jing, E.R. Johnson, I. Jones, K.V.J. Jose, E.A. Kabova, A. Keates, P.F. Kelly, D. Khakimov, S. Konstantinopoulos, L.N. Kuleshova, H. Li, X. Lin, A. List, C. Liu, Y.M. Liu, Z. Liu, Z.-P. Liu, J.W. Lubach, N. Marom, A.A. Maryewski, H. Matsui, A. Mattei, R.A. Mayo, J.W. Melkumov, S. Mohamed, Z. Momenzadeh Abardeh, H.S. Muddana, N. Nakayama, K.S. Nayal, M.A. Neumann, R. Nikhar, S. Obata, D. O’Connor, A.R. Oganov, K. Okuwaki, A. Otero-de-la-Roza, C.C. Pantelides, S. Parkin, C.J. Pickard, L. Pilia, T. Pivina, R. Podeszwa, A.J.A. Price, L.S. Price, S.L. Price, M.R. Probert, A. Pulido, G.R. Ramteke, A.U. Rehman, S.M. Reutzel-Edens, J. Rogal, M.J. Ross, A.F. Rumson, G. Sadiq, Z.M. Saeed, A. Salimi, M. Salvalaglio, L. Sanders de Almada, K. Sasikumar, S. Sekharan, C. Shang, K. Shankland, K. Shinohara, B. Shi, X. Shi, A.G. Skillman, H. Song, N. Strasser, J. van de Streek, I.J. Sugden, G. Sun, K. Szalewicz, B.I. Tan, L. Tan, F. Tarczynski, C.R. Taylor, A. Tkatchenko, R. Tom, M.E. Tuckerman, Y. Utsumi, L. Vogt-Maranto, J. Weatherston, L.J. Wilkinson, R.D. Willacy, L. Wojtas, G.R. Woollam, Z. Yang, E. Yonemochi, X. Yue, Q. Zeng, Y. Zhang, T. Zhou, Y. Zhou, R. Zubatyuk, J.C. Cole, Acta Crystallographica Section B 80 (2024) 517–547.","chicago":"Hunnisett, Lily M., Jonas Nyman, Nicholas Francia, Nathan S. Abraham, Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, et al. “The Seventh Blind Test of Crystal Structure Prediction: Structure Generation Methods.” <i>Acta Crystallographica Section B</i>. International Union of Crystallography, 2024. <a href=\"https://doi.org/10.1107/s2052520624007492\">https://doi.org/10.1107/s2052520624007492</a>."},"date_updated":"2026-09-24T11:31:46Z","author":[{"last_name":"Hunnisett","first_name":"Lily M.","full_name":"Hunnisett, Lily M."},{"first_name":"Jonas","last_name":"Nyman","full_name":"Nyman, Jonas"},{"full_name":"Francia, Nicholas","first_name":"Nicholas","last_name":"Francia"},{"full_name":"Abraham, Nathan S.","last_name":"Abraham","first_name":"Nathan S."},{"last_name":"Adjiman","first_name":"Claire S.","full_name":"Adjiman, Claire S."},{"full_name":"Aitipamula, Srinivasulu","last_name":"Aitipamula","first_name":"Srinivasulu"},{"first_name":"Tamador","last_name":"Alkhidir","full_name":"Alkhidir, Tamador"},{"full_name":"Almehairbi, Mubarak","first_name":"Mubarak","last_name":"Almehairbi"},{"full_name":"Anelli, Andrea","last_name":"Anelli","first_name":"Andrea"},{"first_name":"Dylan M.","last_name":"Anstine","full_name":"Anstine, Dylan M."},{"full_name":"Anthony, John E.","last_name":"Anthony","first_name":"John E."},{"first_name":"Joseph E.","last_name":"Arnold","full_name":"Arnold, Joseph E."},{"last_name":"Bahrami","first_name":"Faezeh","full_name":"Bahrami, Faezeh"},{"last_name":"Bellucci","first_name":"Michael A.","full_name":"Bellucci, Michael A."},{"first_name":"Rajni M.","last_name":"Bhardwaj","full_name":"Bhardwaj, Rajni M."},{"full_name":"Bier, Imanuel","first_name":"Imanuel","last_name":"Bier"},{"full_name":"Bis, Joanna A.","first_name":"Joanna A.","last_name":"Bis"},{"full_name":"Boese, A. Daniel","first_name":"A. Daniel","last_name":"Boese"},{"first_name":"David H.","last_name":"Bowskill","full_name":"Bowskill, David H."},{"full_name":"Bramley, James","first_name":"James","last_name":"Bramley"},{"full_name":"Brandenburg, Jan Gerit","last_name":"Brandenburg","first_name":"Jan Gerit"},{"full_name":"Braun, Doris E.","last_name":"Braun","first_name":"Doris E."},{"first_name":"Patrick W. V.","last_name":"Butler","full_name":"Butler, Patrick W. 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Geoffrey","last_name":"Skillman"},{"first_name":"Hongxing","last_name":"Song","full_name":"Song, Hongxing"},{"last_name":"Strasser","first_name":"Nina","full_name":"Strasser, Nina"},{"first_name":"Jacco","last_name":"van de Streek","full_name":"van de Streek, Jacco"},{"first_name":"Isaac J.","last_name":"Sugden","full_name":"Sugden, Isaac J."},{"full_name":"Sun, Guangxu","first_name":"Guangxu","last_name":"Sun"},{"full_name":"Szalewicz, Krzysztof","first_name":"Krzysztof","last_name":"Szalewicz"},{"first_name":"Benjamin I.","last_name":"Tan","full_name":"Tan, Benjamin I."},{"full_name":"Tan, Lu","first_name":"Lu","last_name":"Tan"},{"full_name":"Tarczynski, Frank","first_name":"Frank","last_name":"Tarczynski"},{"first_name":"Christopher R.","last_name":"Taylor","full_name":"Taylor, Christopher R."},{"full_name":"Tkatchenko, Alexandre","first_name":"Alexandre","last_name":"Tkatchenko"},{"last_name":"Tom","first_name":"Rithwik","full_name":"Tom, Rithwik"},{"first_name":"Mark E.","last_name":"Tuckerman","full_name":"Tuckerman, Mark E."},{"last_name":"Utsumi","first_name":"Yohei","full_name":"Utsumi, Yohei"},{"first_name":"Leslie","last_name":"Vogt-Maranto","full_name":"Vogt-Maranto, Leslie"},{"full_name":"Weatherston, Jake","last_name":"Weatherston","first_name":"Jake"},{"last_name":"Wilkinson","first_name":"Luke J.","full_name":"Wilkinson, Luke J."},{"first_name":"Robert D.","last_name":"Willacy","full_name":"Willacy, Robert D."},{"last_name":"Wojtas","first_name":"Lukasz","full_name":"Wojtas, Lukasz"},{"last_name":"Woollam","first_name":"Grahame R.","full_name":"Woollam, Grahame R."},{"full_name":"Yang, Zhuocen","last_name":"Yang","first_name":"Zhuocen"},{"last_name":"Yonemochi","first_name":"Etsuo","full_name":"Yonemochi, Etsuo"},{"last_name":"Yue","first_name":"Xin","full_name":"Yue, Xin"},{"first_name":"Qun","last_name":"Zeng","full_name":"Zeng, Qun"},{"full_name":"Zhang, Yizu","last_name":"Zhang","first_name":"Yizu"},{"last_name":"Zhou","first_name":"Tian","full_name":"Zhou, Tian"},{"last_name":"Zhou","first_name":"Yunfei","full_name":"Zhou, Yunfei"},{"full_name":"Zubatyuk, Roman","first_name":"Roman","last_name":"Zubatyuk"},{"full_name":"Cole, Jason C.","first_name":"Jason C.","last_name":"Cole"}],"das_tickbox":"0","doi":"10.1107/s2052520624007492","day":"01","date_published":"2024-12-01T00:00:00Z","abstract":[{"text":"A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.","lang":"eng"}],"scopus_import":"1","_id":"18952","department":[{"_id":"BiCh"}],"acknowledgement":"The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett, J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge numerous CCDC colleagues for\r\ntheir helpful feedback and suggestions on the manuscript (P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python knowledge (A. Moldovan), providing and maintaining internal compute resources (K. Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind test meeting (E. Clarke),and improvements to the Crystal Packing Similarity tool (M.\r\nRead). Data analysis was performed using resources provided by the Cambridge Service for Data Driven Discovery (CSD3) operated by the University of Cambridge Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel using Tier-2 funding from the Engineering and Physical Sciences Research Council (capital grant EP/T022159/1), and DiRAC funding from the Science and Technology Facilities Council (www.dirac.ac.uk). N. Francia  thanks M. Salvalaglio for advice on the metadynamics simulations and the University College London for providing access to the Kathleen High Performance Computing Facility Kathleen@UCL) on which simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson for counselling on crystal structure similarity. I. Sugden and N. Francia participated in the blind test as members of Groups 1 and 24, respectively. They were involved in the analysis of the results.\r\nand in writing this paper only after all results were made\r\navailable to participants.","external_id":{"isi":["001388840500003"],"pmid":["39405196"]},"oa_version":"Published Version","month":"12","publisher":"International Union of Crystallography","researchdata_availability":"no","volume":80,"article_type":"original","publication_identifier":{"issn":["2052-5206"]},"intvolume":"        80","issue":"6","pmid":1,"quality_controlled":"1","OA_type":"hybrid","type":"journal_article","ddc":["540"],"status":"public","fulldoi":"https://doi.org/10.1107/s2052520624007492","isi":1,"title":"The seventh blind test of crystal structure prediction: Structure generation methods","file":[{"date_created":"2025-01-29T11:09:48Z","content_type":"application/pdf","file_name":"2024_ActaCrystallographicaB_Hunnisett.pdf","access_level":"open_access","relation":"main_file","success":1,"date_updated":"2025-01-29T11:09:48Z","creator":"dernst","checksum":"33b8083e76564cc918182b0b0b2cc023","file_id":"18954","file_size":10061037}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"517-547","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"}],"has_accepted_license":"1","file_date_updated":"2025-01-29T11:09:48Z","article_processing_charge":"Yes (in subscription journal)","oa":1,"OA_place":"publisher","supplementarymaterial":"yes"},{"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":"All necessary source data files generated for this study are available in the SI repository https://github.com/ZengZezhu/Thermal-conductivity-AgTlI2 see ref 72.\r\n72. Zeng, Z. et al. Source data for pushing thermal conductivity to its lower limit in crystals with simple structures. Zenodo (2024).","oa":1,"article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-04-26T10:34:07Z","OA_place":"publisher","corr_author":"1","supplementarymaterial":"yes","ddc":["530"],"ec_funded":1,"OA_type":"gold","type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1038/s41467-024-46799-3","arxiv":1,"title":"Pushing thermal conductivity to its lower limit in crystals with simple structures","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"file":[{"creator":"cchlebak","checksum":"f81bd6ba42f740d060fb446eeebc1035","file_id":"15346","file_size":3049375,"content_type":"application/pdf","date_created":"2024-04-26T10:34:07Z","file_name":"2024_NatComm_Zeng.pdf","access_level":"open_access","success":1,"date_updated":"2024-04-26T10:34:07Z","relation":"main_file"}],"publication_status":"published","acknowledgement":"We thank Bingqing Cheng (IST Austria) and Terumasa Tadano (NIMS\r\nJapan) for reading the manuscript and providing insightful comments.\r\nThis work is supported by the Research Grants Council of Hong Kong\r\n(C7002-22Y and 17318122). ZZ acknowledges the European Union’s\r\nHorizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 101034413. XS acknowledges\r\nfunding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement\r\nNo. 101034329, and the WINNING Normandy Programme supported by\r\nthe Normandy Region. The computations were performed using\r\nresearch computing facilities offered by Information Technology Services, at the University of Hong Kong.","_id":"15311","department":[{"_id":"BiCh"}],"oa_version":"Published Version","month":"04","publisher":"Springer Nature","external_id":{"pmid":["38589376"],"arxiv":["2310.01838"],"isi":["001198902100029"]},"intvolume":"        15","volume":15,"researchdata_availability":"yes","publication_identifier":{"eissn":["2041-1723"]},"article_type":"original","quality_controlled":"1","article_number":"3007","pmid":1,"year":"2024","date_created":"2024-04-14T22:01:00Z","citation":{"apa":"Zeng, Z., Shen, X., Cheng, R., Perez, O., Ouyang, N., Fan, Z., … Chen, Y. (2024). Pushing thermal conductivity to its lower limit in crystals with simple structures. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-46799-3\">https://doi.org/10.1038/s41467-024-46799-3</a>","ista":"Zeng Z, Shen X, Cheng R, Perez O, Ouyang N, Fan Z, Lemoine P, Raveau B, Guilmeau E, Chen Y. 2024. Pushing thermal conductivity to its lower limit in crystals with simple structures. Nature Communications. 15, 3007.","ama":"Zeng Z, Shen X, Cheng R, et al. Pushing thermal conductivity to its lower limit in crystals with simple structures. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-46799-3\">10.1038/s41467-024-46799-3</a>","ieee":"Z. Zeng <i>et al.</i>, “Pushing thermal conductivity to its lower limit in crystals with simple structures,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"Z. Zeng, X. Shen, R. Cheng, O. Perez, N. Ouyang, Z. Fan, P. Lemoine, B. Raveau, E. Guilmeau, Y. Chen, Nature Communications 15 (2024).","mla":"Zeng, Zezhu, et al. “Pushing Thermal Conductivity to Its Lower Limit in Crystals with Simple Structures.” <i>Nature Communications</i>, vol. 15, 3007, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-46799-3\">10.1038/s41467-024-46799-3</a>.","chicago":"Zeng, Zezhu, Xingchen Shen, Ruihuan Cheng, Olivier Perez, Niuchang Ouyang, Zheyong Fan, Pierric Lemoine, Bernard Raveau, Emmanuel Guilmeau, and Yue Chen. “Pushing Thermal Conductivity to Its Lower Limit in Crystals with Simple Structures.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-46799-3\">https://doi.org/10.1038/s41467-024-46799-3</a>."},"publication":"Nature Communications","author":[{"orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu","last_name":"Zeng","first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7"},{"first_name":"Xingchen","last_name":"Shen","full_name":"Shen, Xingchen"},{"full_name":"Cheng, Ruihuan","last_name":"Cheng","first_name":"Ruihuan"},{"first_name":"Olivier","last_name":"Perez","full_name":"Perez, Olivier"},{"first_name":"Niuchang","last_name":"Ouyang","full_name":"Ouyang, Niuchang"},{"first_name":"Zheyong","last_name":"Fan","full_name":"Fan, Zheyong"},{"last_name":"Lemoine","first_name":"Pierric","full_name":"Lemoine, Pierric"},{"first_name":"Bernard","last_name":"Raveau","full_name":"Raveau, Bernard"},{"full_name":"Guilmeau, Emmanuel","last_name":"Guilmeau","first_name":"Emmanuel"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"date_updated":"2026-09-24T11:20:55Z","das_tickbox":"1","scopus_import":"1","abstract":[{"text":"Materials with low thermal conductivity usually have complex crystal structures. Herein we experimentally find that a simple crystal structure material AgTlI2 (I4/mcm) owns an extremely low thermal conductivity of 0.25 W/mK at room temperature. To understand this anomaly, we perform in-depth theoretical studies based on ab initio molecular dynamics simulations and anharmonic lattice dynamics. We find that the unique atomic arrangement and weak chemical bonding provide a permissive environment for strong oscillations of Ag atoms, leading to a considerable rattling behaviour and giant lattice anharmonicity. This feature is also verified by the experimental probability density function refinement of single-crystal diffraction. The particularly strong anharmonicity breaks down the conventional phonon gas model, giving rise to non-negligible wavelike phonon behaviours in AgTlI2 at 300 K. Intriguingly, unlike many strongly anharmonic materials where a small propagative thermal conductivity is often accompanied by a large diffusive thermal conductivity, we find an unusual coexistence of ultralow propagative and diffusive thermal conductivities in AgTlI2 based on the thermal transport unified theory. This study underscores the potential of simple crystal structures in achieving low thermal conductivity and encourages further experimental research to enrich the family of materials with ultralow thermal conductivity.","lang":"eng"}],"doi":"10.1038/s41467-024-46799-3","date_published":"2024-04-08T00:00:00Z","day":"08","DOAJ_listed":"1"},{"fulldoi":"https://doi.org/10.1021/acs.jctc.4c00998","arxiv":1,"isi":1,"title":"Response matching for generating materials and molecules","file":[{"date_updated":"2025-01-13T09:11:09Z","success":1,"relation":"main_file","access_level":"open_access","file_name":"2024_JCTC_Cheng.pdf","content_type":"application/pdf","date_created":"2025-01-13T09:11:09Z","file_id":"18832","file_size":4758251,"checksum":"aca0011bba4846140809b5af583daa9a","creator":"dernst"}],"publication_status":"published","OA_type":"hybrid","type":"journal_article","ddc":["540"],"status":"public","OA_place":"publisher","corr_author":"1","supplementarymaterial":"no","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)"},"file_date_updated":"2025-01-13T09:11:09Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/cace"}]},"das_tickbox":"1","doi":"10.1021/acs.jctc.4c00998","day":"22","date_published":"2024-10-22T00:00:00Z","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","publication":"Journal of Chemical Theory and Computation","date_created":"2024-10-20T22:02:07Z","year":"2024","citation":{"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>","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>","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.","short":"B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.","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>.","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>."},"date_updated":"2026-09-24T11:30:58Z","author":[{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng"}],"volume":20,"researchdata_availability":"no","article_type":"original","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"intvolume":"        20","pmid":1,"issue":"20","quality_controlled":"1","_id":"18452","department":[{"_id":"BiCh"}],"acknowledgement":"B.C. thanks Chris Pickard for enlightening discussions.","external_id":{"isi":["001330001500001"],"arxiv":["2405.09057"],"pmid":["39365029"]},"oa_version":"Published Version","month":"10","publisher":"American Chemical Society"},{"citation":{"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>","ista":"Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 10, 157.","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>","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>.","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>.","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."},"year":"2024","date_created":"2024-07-28T22:01:08Z","publication":"npj Computational Materials","author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"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","day":"18","date_published":"2024-07-18T00:00:00Z","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","oa_version":"Published Version","month":"07","external_id":{"arxiv":["2402.07472"],"isi":["001271730700001"]},"intvolume":"        10","article_type":"original","publication_identifier":{"eissn":["2057-3960"]},"researchdata_availability":"no","volume":10,"quality_controlled":"1","article_number":"157","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","file":[{"relation":"main_file","success":1,"date_updated":"2025-01-09T12:36:48Z","file_name":"2024_npjComputationalMaterials_Cheng.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-09T12:36:48Z","file_id":"18813","file_size":1659509,"checksum":"e6b4d1a45a9ef1e9be35b313d96ebd6f","creator":"dernst"}],"title":"Cartesian atomic cluster expansion for machine learning interatomic potentials","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","file_date_updated":"2025-01-09T12:36:48Z","has_accepted_license":"1","corr_author":"1","OA_place":"publisher","supplementarymaterial":"no"},{"status":"public","type":"journal_article","ec_funded":1,"publication_status":"published","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","fulldoi":"https://doi.org/10.1103/physrevb.109.054305","isi":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"yes","date_updated":"2026-09-24T11:19:44Z","author":[{"last_name":"Cheng","first_name":"Ruihuan","full_name":"Cheng, Ruihuan"},{"orcid":"0000-0001-5126-4928","full_name":"Zeng, Zezhu","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu"},{"first_name":"Chen","last_name":"Wang","full_name":"Wang, Chen"},{"last_name":"Ouyang","first_name":"Niuchang","full_name":"Ouyang, Niuchang"},{"full_name":"Chen, Yue","first_name":"Yue","last_name":"Chen"}],"publication":"Physical Review B","citation":{"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>","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>","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.","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>.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","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.","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>."},"date_created":"2024-03-04T07:41:23Z","year":"2024","day":"14","date_published":"2024-02-14T00:00:00Z","doi":"10.1103/physrevb.109.054305","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"das_tickbox":"0","external_id":{"isi":["001198615900003"]},"publisher":"American Physical Society","oa_version":"None","month":"02","department":[{"_id":"BiCh"}],"_id":"15052","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.","issue":"5","article_number":"054305","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"researchdata_availability":"no","volume":109,"intvolume":"       109"},{"related_material":{"record":[{"status":"public","id":"23013","relation":"research_data"}]},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2025-01-13T11:17:35Z","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":"4740-4757.e12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"],"type":"journal_article","OA_type":"hybrid","publication_status":"published","title":"STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment","file":[{"checksum":"e051e2766b2d424983778f742cb7c5ed","creator":"dernst","file_id":"18844","file_size":25071994,"file_name":"2024_MolecularCell_Ramadhin.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-13T11:17:35Z","date_updated":"2025-01-13T11:17:35Z","success":1,"relation":"main_file"}],"isi":1,"fulldoi":"https://doi.org/10.1016/j.molcel.2024.10.030","publisher":"Elsevier","oa_version":"Published Version","month":"12","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.","department":[{"_id":"CaBe"}],"_id":"18553","quality_controlled":"1","issue":"24","pmid":1,"intvolume":"        84","publication_identifier":{"issn":["1097-2765"]},"article_type":"original","researchdata_availability":"yes","volume":84,"author":[{"full_name":"Ramadhin, Anisha R.","last_name":"Ramadhin","first_name":"Anisha R."},{"first_name":"Shun-Hsiao","last_name":"Lee","full_name":"Lee, Shun-Hsiao"},{"first_name":"Di","last_name":"Zhou","full_name":"Zhou, Di"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"last_name":"Gonzalo-Hansen","first_name":"Camila","full_name":"Gonzalo-Hansen, Camila"},{"first_name":"Marjolein","last_name":"van Sluis","full_name":"van Sluis, Marjolein"},{"full_name":"Blom, Cindy M.A.","last_name":"Blom","first_name":"Cindy M.A."},{"full_name":"Janssens, Roel C.","last_name":"Janssens","first_name":"Roel C."},{"last_name":"Raams","first_name":"Anja","full_name":"Raams, Anja"},{"first_name":"Dick","last_name":"Dekkers","full_name":"Dekkers, Dick"},{"first_name":"Karel","last_name":"Bezstarosti","full_name":"Bezstarosti, Karel"},{"full_name":"Slade, Dea","first_name":"Dea","last_name":"Slade"},{"full_name":"Vermeulen, Wim","first_name":"Wim","last_name":"Vermeulen"},{"full_name":"Pines, Alex","first_name":"Alex","last_name":"Pines"},{"full_name":"Demmers, Jeroen A.A.","last_name":"Demmers","first_name":"Jeroen A.A."},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"full_name":"Sixma, Titia K.","last_name":"Sixma","first_name":"Titia K."},{"full_name":"Marteijn, Jurgen A.","first_name":"Jurgen A.","last_name":"Marteijn"}],"date_updated":"2026-10-01T08:20:39Z","citation":{"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>","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>.","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>.","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.","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."},"date_created":"2024-11-15T12:12:54Z","year":"2024","publication":"Molecular Cell","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"day":"19","date_published":"2024-12-19T00:00:00Z","doi":"10.1016/j.molcel.2024.10.030","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"}],"das_tickbox":"1"},{"OA_type":"closed access","type":"journal_article","status":"public","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","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).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"8609-8629","language":[{"iso":"eng"}],"article_processing_charge":"No","supplementarymaterial":"yes","publication":"Journal of Medicinal Chemistry","year":"2024","date_created":"2025-01-29T09:14:19Z","citation":{"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>.","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.","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.","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>","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.","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>"},"date_updated":"2026-10-01T08:26:28Z","author":[{"full_name":"de Souza Gama, Fernando H.","last_name":"de Souza Gama","first_name":"Fernando H."},{"first_name":"Luiz A.","last_name":"Dutra","full_name":"Dutra, Luiz A."},{"full_name":"Hawgood, Michael","last_name":"Hawgood","first_name":"Michael"},{"last_name":"dos Reis","first_name":"Caio Vinícius","full_name":"dos Reis, Caio Vinícius"},{"first_name":"Ricardo A. M.","last_name":"Serafim","full_name":"Serafim, Ricardo A. M."},{"full_name":"Ferreira, Marcos A.","last_name":"Ferreira","first_name":"Marcos A."},{"first_name":"Bruno V. M.","last_name":"Teodoro","full_name":"Teodoro, Bruno V. M."},{"first_name":"Jéssica Emi","last_name":"Takarada","full_name":"Takarada, Jéssica Emi"},{"full_name":"Santiago, André S.","last_name":"Santiago","first_name":"André S."},{"full_name":"Balourdas, Dimitrios-Ilias","last_name":"Balourdas","first_name":"Dimitrios-Ilias"},{"last_name":"Nilsson","first_name":"Ann-Sofie","full_name":"Nilsson, Ann-Sofie"},{"first_name":"Bruno","last_name":"Urien","full_name":"Urien, Bruno"},{"full_name":"Almeida, Vitor M.","first_name":"Vitor M.","last_name":"Almeida"},{"full_name":"Gileadi, Carina","first_name":"Carina","last_name":"Gileadi"},{"full_name":"Ramos, Priscila Z.","first_name":"Priscila Z.","last_name":"Ramos"},{"full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vasconcelos, Stanley N. S.","last_name":"Vasconcelos","first_name":"Stanley N. S."},{"first_name":"Micael R.","last_name":"Cunha","full_name":"Cunha, Micael R."},{"full_name":"Mueller, Susanne","last_name":"Mueller","first_name":"Susanne"},{"last_name":"Knapp","first_name":"Stefan","full_name":"Knapp, Stefan"},{"first_name":"Katlin B.","last_name":"Massirer","full_name":"Massirer, Katlin B."},{"first_name":"Jonathan M.","last_name":"Elkins","full_name":"Elkins, Jonathan M."},{"full_name":"Gileadi, Opher","first_name":"Opher","last_name":"Gileadi"},{"last_name":"Mascarello","first_name":"Alessandra","full_name":"Mascarello, Alessandra"},{"full_name":"Lemmens, Bennie B. L. G.","last_name":"Lemmens","first_name":"Bennie B. L. G."},{"full_name":"Guimarães, Cristiano R. W.","first_name":"Cristiano R. W.","last_name":"Guimarães"},{"full_name":"Azevedo, Hatylas","first_name":"Hatylas","last_name":"Azevedo"},{"full_name":"Couñago, Rafael M.","last_name":"Couñago","first_name":"Rafael M."}],"das_tickbox":"1","doi":"10.1021/acs.jmedchem.3c02250","day":"23","date_published":"2024-05-23T00:00:00Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"_id":"18945","department":[{"_id":"CaBe"}],"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.","external_id":{"pmid":["38780468"]},"oa_version":"None","month":"05","publisher":"American Chemical Society","researchdata_availability":"yes","volume":67,"article_type":"original","publication_identifier":{"issn":["0022-2623"],"eissn":["1520-4804"]},"intvolume":"        67","pmid":1,"issue":"11","quality_controlled":"1"},{"external_id":{"arxiv":["2404.15101"]},"publisher":"Springer Nature","month":"08","oa_version":"Published Version","department":[{"_id":"CaGo"}],"_id":"17407","acknowledgement":"We thank M. Lechner for helpful discussions.","article_number":"141","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["2662-4443"]},"researchdata_availability":"yes (supplementary data)","volume":5,"intvolume":"         5","date_updated":"2026-10-01T08:28:59Z","author":[{"full_name":"Zu, Mengjie","first_name":"Mengjie","id":"26dd9e7c-e86a-11eb-a854-82ac731c9ae2","last_name":"Zu"},{"orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"}],"publication":"Communications Materials","citation":{"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>","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.","ieee":"M. Zu and C. P. Goodrich, “Designing athermal disordered solids with automatic differentiation,” <i>Communications Materials</i>, vol. 5. Springer Nature, 2024.","short":"M. Zu, C.P. Goodrich, Communications Materials 5 (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>.","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>."},"date_created":"2024-08-11T22:01:11Z","year":"2024","date_published":"2024-08-01T00:00:00Z","day":"01","doi":"10.1038/s43246-024-00583-4","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","das_tickbox":"1","article_processing_charge":"Yes","has_accepted_license":"1","file_date_updated":"2024-08-12T07:56:38Z","oa":1,"dataavailabilitystatement":"The authors declare that the data supporting the findings of this study are available within the paper and its Supplementary Information files","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","supplementarymaterial":"yes","corr_author":"1","OA_place":"publisher","status":"public","type":"journal_article","OA_type":"gold","APC_amount":"3534 EUR","ddc":["530"],"publication_status":"published","title":"Designing athermal disordered solids with automatic differentiation","file":[{"relation":"main_file","success":1,"date_updated":"2024-08-12T07:56:38Z","file_name":"2024_CommMaterials_Zu.pdf","access_level":"open_access","date_created":"2024-08-12T07:56:38Z","content_type":"application/pdf","file_id":"17416","file_size":9824134,"checksum":"d6f74e242db5f46bb0e380ee23a268af","creator":"dernst"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"arxiv":1,"fulldoi":"https://doi.org/10.1038/s43246-024-00583-4"},{"publication_status":"published","file":[{"success":1,"relation":"main_file","date_updated":"2024-07-29T10:56:01Z","file_name":"2024_AnnualReviewBiophys_Lo.pdf","access_level":"open_access","date_created":"2024-07-29T10:56:01Z","content_type":"application/pdf","file_size":1276645,"file_id":"17339","checksum":"e0505553b3cee624fa865f0cc5a99ecc","creator":"dernst"}],"project":[{"name":"Bacterial cytoplasm glass transition: passive physiological switch or active survival strategy","_id":"eb872896-77a9-11ec-83b8-f59a38ec17f8","grant_number":"ALTF 44-2021"}],"title":"Bacterial Electrophysiology","isi":1,"fulldoi":"https://doi.org/10.1146/annurev-biophys-030822-032215","status":"public","ddc":["570"],"type":"journal_article","supplementarymaterial":"unclear","oa":1,"file_date_updated":"2024-07-29T10:56:01Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","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","page":"487-510","abstract":[{"lang":"eng","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."}],"scopus_import":"1","date_published":"2024-07-01T00:00:00Z","day":"01","doi":"10.1146/annurev-biophys-030822-032215","das_tickbox":"0","author":[{"full_name":"Lo, Wei Chang","first_name":"Wei Chang","last_name":"Lo"},{"full_name":"Krasnopeeva, Ekaterina","last_name":"Krasnopeeva","id":"1F1EE44A-BF83-11EA-B3C1-BB9CC619BF3A","first_name":"Ekaterina"},{"full_name":"Pilizota, Teuta","first_name":"Teuta","last_name":"Pilizota"}],"date_updated":"2026-10-01T08:29:37Z","citation":{"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>.","short":"W.C. Lo, E. Krasnopeeva, T. Pilizota, Annual Review of Biophysics 53 (2024) 487–510.","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.","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>.","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>","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>","ista":"Lo WC, Krasnopeeva E, Pilizota T. 2024. Bacterial Electrophysiology. Annual Review of Biophysics. 53, 487–510."},"date_created":"2024-07-28T22:01:09Z","year":"2024","publication":"Annual Review of Biophysics","quality_controlled":"1","pmid":1,"intvolume":"        53","article_type":"original","publication_identifier":{"eissn":["1936-1238"],"issn":["1936-122X"]},"volume":53,"researchdata_availability":"no","publisher":"Annual Reviews","month":"07","oa_version":"Published Version","external_id":{"pmid":["38382113"],"isi":["001278237500021"]},"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.","department":[{"_id":"CaGu"}],"_id":"17325"},{"supplementarymaterial":"yes","corr_author":"1","article_processing_charge":"No","related_material":{"record":[{"id":"23012","status":"public","relation":"research_data"}]},"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":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"}],"fulldoi":"https://doi.org/10.1038/s41567-024-02513-0","isi":1,"status":"public","type":"journal_article","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"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":[{"last_name":"Lemoult","first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M"},{"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"},{"full_name":"Linga, Gaute","first_name":"Gaute","last_name":"Linga"},{"first_name":"Joachim","last_name":"Mathiesen","full_name":"Mathiesen, Joachim"},{"first_name":"Nigel","last_name":"Goldenfeld","full_name":"Goldenfeld, Nigel"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"}],"publication":"Nature Physics","citation":{"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.","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>","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>","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>.","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>.","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."},"year":"2024","date_created":"2024-06-09T22:01:03Z"},{"das_tickbox":"0","scopus_import":"1","abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.cub.2024.10.065","day":"16","date_published":"2024-12-16T00:00:00Z","date_created":"2024-12-15T23:01:49Z","year":"2024","citation":{"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>","ista":"Hino N, Santos Fernandes Lasbarrères Camelo C, Heisenberg C-PJ. 2024. Development: Turing mechanics. Current Biology. 34(24), R1230–R1232.","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>","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>.","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>.","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.","short":"N. Hino, C. Santos Fernandes Lasbarrères Camelo, C.-P.J. Heisenberg, Current Biology 34 (2024) R1230–R1232."},"publication":"Current Biology","author":[{"first_name":"Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","last_name":"Hino","full_name":"Hino, Naoya"},{"full_name":"Santos Fernandes Lasbarrères Camelo, Carolina","last_name":"Santos Fernandes Lasbarrères Camelo","id":"6347dca5-074c-11ed-af92-a80f860d9d5b","first_name":"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","intvolume":"        34","researchdata_availability":"no","volume":34,"article_type":"letter_note","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"quality_controlled":"1","issue":"24","pmid":1,"_id":"18651","department":[{"_id":"CaHe"}],"month":"12","oa_version":"None","publisher":"Elsevier","external_id":{"isi":["001392077000001"],"pmid":["39689690"]},"isi":1,"fulldoi":"https://doi.org/10.1016/j.cub.2024.10.065","title":"Development: Turing mechanics","publication_status":"published","OA_type":"closed access","type":"journal_article","status":"public","corr_author":"1","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"R1230-R1232","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"OA_place":"repository","_id":"23013","department":[{"_id":"CaBe"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","oa_version":"None","oa":1,"month":"10","publisher":"Mendeley Data","related_material":{"record":[{"id":"18553","status":"public","relation":"used_in_publication"}]},"fulldoi":"https://doi.org/10.17632/wp9sf6sp4z.1","doi":"10.17632/wp9sf6sp4z.1","date_published":"2024-10-01T00:00:00Z","day":"01","title":"Study of STK19 drives Transcription-Coupled Repair by stimulating repair complex stability, Pol II ubiquitylation and TFIIH recruitment by Ramadhin et al.","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. "}],"OA_type":"green","main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/wp9sf6sp4z.1"}],"type":"research_data_reference","ddc":["570"],"date_created":"2026-10-01T08:20:32Z","year":"2024","citation":{"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>","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>","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).","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>.","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>."},"date_updated":"2026-10-01T08:20:39Z","status":"public","author":[{"full_name":"Marteijn,  Jurgen","last_name":"Marteijn","first_name":" Jurgen"}]},{"supplementarymaterial":"yes","corr_author":"1","oa":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/","relation":"press_release","description":"News on ISTA Website"}]},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-07-16T12:12:43Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"310-321","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":"Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on request","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","file":[{"file_size":9897883,"file_id":"17267","checksum":"7891ebe7c900ae47469ab127031dd1ec","creator":"dernst","date_updated":"2024-07-16T12:12:43Z","success":1,"relation":"main_file","access_level":"open_access","file_name":"2024_NaturePhysics_CaballeroMancebo.pdf","date_created":"2024-07-16T12:12:43Z","content_type":"application/pdf"}],"project":[{"call_identifier":"FWF","name":"Control of embryonic cleavage pattern","_id":"2646861A-B435-11E9-9278-68D0E5697425","grant_number":"I03601"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1038/s41567-023-02302-1","status":"public","ddc":["530"],"type":"journal_article","quality_controlled":"1","pmid":1,"intvolume":"        20","researchdata_availability":"yes","volume":20,"article_type":"original","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"02","oa_version":"Published Version","publisher":"Springer Nature","external_id":{"pmid":["38370025"],"isi":["001138880800005"]},"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).","_id":"14846","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"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"}],"scopus_import":"1","doi":"10.1038/s41567-023-02302-1","day":"01","date_published":"2024-02-01T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"das_tickbox":"1","author":[{"first_name":"Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","full_name":"Caballero Mancebo, Silvia","orcid":"0000-0002-5223-3346"},{"first_name":"Rushikesh","last_name":"Shinde","full_name":"Shinde, Rushikesh"},{"full_name":"Bolger-Munro, Madison","orcid":"0000-0002-8176-4824","first_name":"Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","last_name":"Bolger-Munro"},{"last_name":"Peruzzo","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory","full_name":"Szep, Gregory"},{"full_name":"Steccari, Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene","last_name":"Steccari"},{"full_name":"Labrousse Arias, David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425","first_name":"David","last_name":"Labrousse Arias"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"full_name":"Callan-Jones, Andrew","first_name":"Andrew","last_name":"Callan-Jones"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"},{"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"}],"date_updated":"2026-10-01T08:33:51Z","year":"2024","date_created":"2024-01-21T23:00:57Z","citation":{"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>","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>","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.","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.","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>."},"publication":"Nature Physics"},{"corr_author":"1","supplementarymaterial":"yes","page":"171-182.e8","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":"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","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-01-16T10:53:31Z","isi":1,"fulldoi":"https://doi.org/10.1016/j.cub.2023.11.067","file":[{"creator":"dernst","checksum":"51220b76d72a614208f84bdbfbaf9b72","file_id":"14813","file_size":5183861,"content_type":"application/pdf","date_created":"2024-01-16T10:53:31Z","access_level":"open_access","file_name":"2024_CurrentBiology_Arslan.pdf","relation":"main_file","success":1,"date_updated":"2024-01-16T10:53:31Z"}],"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"}],"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","publication_status":"published","ddc":["570"],"ec_funded":1,"type":"journal_article","status":"public","intvolume":"        34","volume":34,"researchdata_availability":"upon request","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"article_type":"original","quality_controlled":"1","pmid":1,"issue":"1","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.","_id":"14795","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"oa_version":"Published Version","month":"01","publisher":"Elsevier","external_id":{"isi":["001154500400001"],"pmid":["38134934"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"das_tickbox":"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"}],"scopus_import":"1","doi":"10.1016/j.cub.2023.11.067","date_published":"2024-01-08T00:00:00Z","day":"08","year":"2024","date_created":"2024-01-14T23:00:56Z","citation":{"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>","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.","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>","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>.","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","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.","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>."},"publication":"Current Biology","author":[{"last_name":"Arslan","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-10-01T08:33:05Z"},{"file_date_updated":"2024-03-04T07:24:43Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","related_material":{"record":[{"id":"14926","status":"public","relation":"research_data"}]},"oa":1,"dataavailabilitystatement":"A custom MATLAB script for analyzing cell dispersal has been deposited in the ISTA library (doi:10.15479/AT:ISTA:14926)","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","page":"1-18","supplementarymaterial":"yes","corr_author":"1","status":"public","type":"journal_article","ddc":["570"],"ec_funded":1,"publication_status":"published","title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling","file":[{"creator":"dernst","checksum":"6961ea10012bf0d266681f9628bb8f13","file_size":14839986,"file_id":"15050","date_created":"2024-03-04T07:24:43Z","content_type":"application/pdf","access_level":"open_access","file_name":"2024_Development_Schauer.pdf","relation":"main_file","date_updated":"2024-03-04T07:24:43Z","success":1}],"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"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1242/dev.202316","isi":1,"external_id":{"pmid":["38372390"],"isi":["001170580200001"]},"publisher":"Company of Biologists","month":"02","oa_version":"Published Version","department":[{"_id":"CaHe"},{"_id":"Bio"}],"_id":"15048","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","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"article_type":"original","volume":151,"researchdata_availability":"yes","intvolume":"       151","date_updated":"2026-10-01T08:32:34Z","author":[{"orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra","last_name":"Schauer","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","full_name":"Pranjic-Ferscha, Kornelija"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publication":"Development","citation":{"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>.","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>.","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.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 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>","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.","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>"},"year":"2024","date_created":"2024-03-03T23:00:50Z","day":"01","date_published":"2024-02-01T00:00:00Z","doi":"10.1242/dev.202316","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","das_tickbox":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"das_tickbox":"1","doi":"10.1126/sciadv.adj6801","day":"23","date_published":"2024-02-23T00:00:00Z","DOAJ_listed":"1","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","publication":"Science Advances","year":"2024","date_created":"2024-03-03T23:00:50Z","citation":{"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>.","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.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","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>.","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.","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>"},"date_updated":"2026-10-01T08:36:23Z","author":[{"last_name":"Bao","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","first_name":"Jiawei","full_name":"Bao, Jiawei"},{"full_name":"Stevens, Bjorn","last_name":"Stevens","first_name":"Bjorn"},{"full_name":"Kluft, Lukas","last_name":"Kluft","first_name":"Lukas"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350"}],"volume":10,"researchdata_availability":"yes (supplementary data)","article_type":"original","publication_identifier":{"eissn":["2375-2548"]},"intvolume":"        10","article_number":"eadj6801","pmid":1,"issue":"8","quality_controlled":"1","_id":"15047","department":[{"_id":"CaMu"}],"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).","external_id":{"isi":["001300045100007"],"pmid":["38394192"]},"month":"02","oa_version":"Published Version","publisher":"American Association for the Advancement of Science","fulldoi":"https://doi.org/10.1126/sciadv.adj6801","isi":1,"title":"Intensification of daily tropical precipitation extremes from more organized convection","file":[{"creator":"dernst","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","file_id":"15051","file_size":800926,"date_created":"2024-03-04T07:34:00Z","content_type":"application/pdf","file_name":"2024_ScienceAdv_Bao.pdf","access_level":"open_access","date_updated":"2024-03-04T07:34:00Z","relation":"main_file","success":1}],"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"publication_status":"published","OA_type":"gold","type":"journal_article","ddc":["550"],"ec_funded":1,"status":"public","OA_place":"publisher","supplementarymaterial":"yes","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).","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":"2024-03-04T07:34:00Z","article_processing_charge":"Yes","has_accepted_license":"1","oa":1,"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/","relation":"press_release"}]}},{"dataavailabilitystatement":"Data will be made available on request","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"}],"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-08-09T13:37:24Z","oa":1,"supplementarymaterial":"yes","type":"journal_article","ddc":["550"],"ec_funded":1,"status":"public","fulldoi":"https://doi.org/10.1016/j.jenvman.2024.122093","isi":1,"title":"Wildfires impact on PM2.5 concentration in galicia Spain","file":[{"file_size":1595118,"file_id":"17405","checksum":"6fa476a4c08aded413844d92336b0e52","creator":"acasalla","date_updated":"2024-08-09T13:37:23Z","relation":"main_file","success":1,"file_name":"Fires_Galicia_SM.pdf","access_level":"open_access","content_type":"application/pdf","date_created":"2024-08-09T13:37:23Z"},{"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_id":"17406","file_size":13662676,"checksum":"859dcdef9555c383b702cf8cc7da66f2","creator":"acasalla"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"publication_status":"published","_id":"17396","department":[{"_id":"CaMu"}],"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. ","external_id":{"isi":["001289532100001"],"pmid":["39106804"]},"month":"09","oa_version":"Published Version","publisher":"Elsevier","researchdata_availability":"upon request","volume":367,"article_type":"original","publication_identifier":{"issn":["0301-4797"]},"intvolume":"       367","article_number":"122093","pmid":1,"quality_controlled":"1","publication":"Journal of Environmental Management","year":"2024","date_created":"2024-08-06T05:54:52Z","citation":{"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.","short":"C. Quishpe-Vásquez, P. Oliva, E.A. López-Barrera, A. Casallas Garcia, Journal of Environmental Management 367 (2024).","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>.","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>.","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>"},"date_updated":"2026-10-01T08:34:24Z","author":[{"first_name":"César","last_name":"Quishpe-Vásquez","full_name":"Quishpe-Vásquez, César"},{"full_name":"Oliva, Patricia","first_name":"Patricia","last_name":"Oliva"},{"full_name":"López-Barrera, Ellie Anne","last_name":"López-Barrera","first_name":"Ellie Anne"},{"orcid":"0000-0002-1988-5035","full_name":"Casallas Garcia, Alejandro","last_name":"Casallas Garcia","first_name":"Alejandro","id":"92081129-2d75-11ef-a48d-b04dd7a2385a"}],"das_tickbox":"1","doi":"10.1016/j.jenvman.2024.122093","date_published":"2024-09-01T00:00:00Z","day":"01","abstract":[{"lang":"eng","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."}],"scopus_import":"1"}]