[{"publication_identifier":{"eissn":["1097-4164"],"issn":["1097-2765"]},"ec_funded":1,"publisher":"Cell Press","has_accepted_license":"1","file_date_updated":"2024-09-16T07:38:38Z","scopus_import":"1","dataavailabilitystatement":"Raw image files of all figures have been deposited at Mendeley Data and are publicly available as of the date of publication (Mendeley data: https://doi.org/10.17632/dwcpnncsyd.1). All other data reported in this paper will be shared by the lead contact upon request","file":[{"file_name":"2024_MolecularCell_HernandezArmendariz.pdf","creator":"dernst","date_updated":"2024-09-16T07:38:38Z","success":1,"access_level":"open_access","date_created":"2024-09-16T07:38:38Z","file_size":11654644,"file_id":"18075","checksum":"3f360e0287b8ec79fb2b8b02b5070360","content_type":"application/pdf","relation":"main_file"}],"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"volume":84,"acknowledgement":"We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs. This work was supported by the German Research Foundation (DFG project number 402723784) and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie Actions, COFUND grant agreement 664726).","article_type":"original","date_created":"2024-09-15T22:01:41Z","page":"P3254-3270.E9","pmid":1,"ddc":["570"],"type":"journal_article","supplementarymaterial":"yes","month":"09","related_material":{"record":[{"status":"public","id":"22987","relation":"research_data"}]},"day":"05","oa":1,"das_tickbox":"1","title":"A liquid-like coat mediates chromosome clustering during mitotic exit","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-09-24T10:43:18Z","doi":"10.1016/j.molcel.2024.07.022","quality_controlled":"1","researchdata_availability":"yes","intvolume":"        84","abstract":[{"lang":"eng","text":"The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis."}],"publication_status":"published","issue":"17","author":[{"first_name":"Alberto","full_name":"Hernandez-Armendariz, Alberto","last_name":"Hernandez-Armendariz"},{"first_name":"Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","full_name":"Sorichetti, Valerio"},{"last_name":"Hayashi","full_name":"Hayashi, Yuki","first_name":"Yuki"},{"last_name":"Koskova","full_name":"Koskova, Zuzana","first_name":"Zuzana"},{"full_name":"Brunner, Andreas","last_name":"Brunner","first_name":"Andreas"},{"first_name":"Jan","last_name":"Ellenberg","full_name":"Ellenberg, Jan"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Sara","last_name":"Cuylen-Haering","full_name":"Cuylen-Haering, Sara"}],"fulldoi":"https://doi.org/10.1016/j.molcel.2024.07.022","date_published":"2024-09-05T00:00:00Z","oa_version":"Published Version","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"isi":1,"publication":"Molecular Cell","external_id":{"pmid":["39153474"],"isi":["001309051100001"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat mediates chromosome clustering during mitotic exit. <i>Molecular Cell</i>. 2024;84(17):P3254-3270.E9. doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">10.1016/j.molcel.2024.07.022</a>","apa":"Hernandez-Armendariz, A., Sorichetti, V., Hayashi, Y., Koskova, Z., Brunner, A., Ellenberg, J., … Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome clustering during mitotic exit. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">https://doi.org/10.1016/j.molcel.2024.07.022</a>","ista":"Hernandez-Armendariz A, Sorichetti V, Hayashi Y, Koskova Z, Brunner A, Ellenberg J, Šarić A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. 84(17), P3254–3270.E9.","ieee":"A. Hernandez-Armendariz <i>et al.</i>, “A liquid-like coat mediates chromosome clustering during mitotic exit,” <i>Molecular Cell</i>, vol. 84, no. 17. Cell Press, p. P3254–3270.E9, 2024.","chicago":"Hernandez-Armendariz, Alberto, Valerio Sorichetti, Yuki Hayashi, Zuzana Koskova, Andreas Brunner, Jan Ellenberg, Anđela Šarić, and Sara Cuylen-Haering. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” <i>Molecular Cell</i>. Cell Press, 2024. <a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">https://doi.org/10.1016/j.molcel.2024.07.022</a>.","mla":"Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” <i>Molecular Cell</i>, vol. 84, no. 17, Cell Press, 2024, p. P3254–3270.E9, doi:<a href=\"https://doi.org/10.1016/j.molcel.2024.07.022\">10.1016/j.molcel.2024.07.022</a>.","short":"A. Hernandez-Armendariz, V. Sorichetti, Y. Hayashi, Z. Koskova, A. Brunner, J. Ellenberg, A. Šarić, S. Cuylen-Haering, Molecular Cell 84 (2024) P3254–3270.E9."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"18072","year":"2024"},{"citation":{"ama":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. 2024;18(28):18485-18492. doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>","ista":"Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. 2024. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 18(28), 18485–18492.","ieee":"C. Garcia-Sacristan, V. G. Gisbert, K. Klein, A. Šarić, and R. Garcia, “In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures,” <i>ACS Nano</i>, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024.","apa":"Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., &#38; Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492.","chicago":"Garcia-Sacristan, Clara, Victor G. Gisbert, Kevin Klein, Anđela Šarić, and Ricardo Garcia. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsnano.4c03839\">https://doi.org/10.1021/acsnano.4c03839</a>.","mla":"Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” <i>ACS Nano</i>, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:<a href=\"https://doi.org/10.1021/acsnano.4c03839\">10.1021/acsnano.4c03839</a>."},"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38958189"],"isi":["001263155500001"]},"publication":"ACS Nano","year":"2024","_id":"17239","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","researchdata_availability":"no","quality_controlled":"1","doi":"10.1021/acsnano.4c03839","date_published":"2024-07-16T00:00:00Z","fulldoi":"https://doi.org/10.1021/acsnano.4c03839","oa_version":"Published Version","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"isi":1,"author":[{"first_name":"Clara","full_name":"Garcia-Sacristan, Clara","last_name":"Garcia-Sacristan"},{"first_name":"Victor G.","last_name":"Gisbert","full_name":"Gisbert, Victor G."},{"id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Garcia","full_name":"Garcia, Ricardo","first_name":"Ricardo"}],"publication_status":"published","issue":"28","intvolume":"        18","abstract":[{"lang":"eng","text":"Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes."}],"oa":1,"day":"16","date_updated":"2026-09-24T10:43:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","das_tickbox":"0","OA_place":"publisher","scopus_import":"1","file_date_updated":"2025-01-09T12:06:48Z","has_accepted_license":"1","publisher":"American Chemical Society","ec_funded":1,"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"supplementarymaterial":"yes","ddc":["540"],"type":"journal_article","month":"07","pmid":1,"page":"18485-18492","date_created":"2024-07-14T22:01:12Z","volume":18,"article_type":"original","acknowledgement":"We are grateful to Nancy Forde (Simon Fraser University) for her motivating comments. Financial support from the Ministerio de Ciencia, Innovación y Universidades (PID2019-106801GB-I00 and PID2022-136851NB-I00) is acknowledged. A.Š. and K.K. acknowledge support from the Royal Society University Research Fellowship and ERC the European Union’s Horizon 2020584 Research and Innovation Programme (Grant No. 585 80296).","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"18808","file_size":10036838,"checksum":"b7e9ce718e92f568bcb3810e8e28e458","success":1,"date_updated":"2025-01-09T12:06:48Z","access_level":"open_access","date_created":"2025-01-09T12:06:48Z","file_name":"2024_ACSNano_GarciaSacristan.pdf","creator":"dernst"}]},{"publication":"Physical Review E","article_number":"064403","citation":{"ama":"Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. 2024;110(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>","short":"F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024).","mla":"Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>, vol. 110, no. 6, 064403, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">10.1103/PhysRevE.110.064403</a>.","chicago":"Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” <i>Physical Review E</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>.","apa":"Frey, F. F., &#38; Schwarz, U. S. (2024). Coat stiffening can explain invagination of clathrin-coated membranes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.110.064403\">https://doi.org/10.1103/PhysRevE.110.064403</a>","ista":"Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 110(6), 064403.","ieee":"F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of clathrin-coated membranes,” <i>Physical Review E</i>, vol. 110, no. 6. American Physical Society, 2024."},"article_processing_charge":"No","external_id":{"arxiv":["2405.02820"],"isi":["001379135100004"],"pmid":["39916158"]},"_id":"18704","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"green","year":"2024","quality_controlled":"1","doi":"10.1103/PhysRevE.110.064403","researchdata_availability":"no","publication_status":"published","issue":"6","author":[{"orcid":"0000-0001-8501-6017","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey"},{"full_name":"Schwarz, Ulrich S.","last_name":"Schwarz","first_name":"Ulrich S."}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the main pathway used by eukaryotic cells to take up extracellular material, but the dominant physical mechanisms driving this process are still elusive. Recently, several high-resolution imaging techniques have been used on different cell lines to measure the geometrical properties of clathrin-coated pits over their whole lifetime. Here, we first show that the combination of all datasets with the recently introduced cooperative curvature model defines a consensus pathway, which is characterized by a flat-to-curved transition at finite area, followed by linear growth and subsequent saturation of curvature. We then apply an energetic model for the composite of the plasma membrane and clathrin coat to this consensus pathway to show that the dominant mechanism for invagination could be coat stiffening, which might originate from cooperative interactions between the different clathrin molecules and progressively drives the system toward its intrinsic curvature. Our theory predicts that two length scales determine the invagination pathway, namely the patch size at which the flat-to-curved transition occurs and the final pit radius."}],"intvolume":"       110","oa_version":"Preprint","fulldoi":"https://doi.org/10.1103/PhysRevE.110.064403","isi":1,"date_published":"2024-12-10T00:00:00Z","day":"10","oa":1,"title":"Coat stiffening can explain invagination of clathrin-coated membranes","das_tickbox":"0","date_updated":"2026-09-24T10:43:36Z","publisher":"American Physical Society","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"scopus_import":"1","OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02820","open_access":"1"}],"department":[{"_id":"AnSa"}],"arxiv":1,"language":[{"iso":"eng"}],"month":"12","supplementarymaterial":"no","type":"journal_article","pmid":1,"date_created":"2024-12-22T23:01:48Z","acknowledgement":"We thank Markus Mund, Aline Tschanz, and Jonas Ries for helpful discussions and a critical reading of the manuscript. We also kindly acknowledge Simon Scheuring for providing the HS-AFM data for the analysis of clathrin coat invagination. We thank the reviewers of previous versions of this manuscript for useful feedback that helped us to improve this work. F.F. acknowledges financial support by the NOMIS foundation. U.S.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Project No. 240245660 (SFB 1129). Moreover, he is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg and of the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society.","article_type":"original","volume":110},{"article_processing_charge":"No","citation":{"ista":"Hernandez-Armendariz A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al., Repository, <a href=\"https://doi.org/10.17632/dwcpnncsyd.1\">10.17632/dwcpnncsyd.1</a>.","apa":"Hernandez-Armendariz, A., &#38; Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al. Repository. <a href=\"https://doi.org/10.17632/dwcpnncsyd.1\">https://doi.org/10.17632/dwcpnncsyd.1</a>","ieee":"A. Hernandez-Armendariz and S. Cuylen-Haering, “A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.” Repository, 2024.","chicago":"Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz et Al.” Repository, 2024. <a href=\"https://doi.org/10.17632/dwcpnncsyd.1\">https://doi.org/10.17632/dwcpnncsyd.1</a>.","mla":"Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. <i>A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz et Al.</i> Repository, 2024, doi:<a href=\"https://doi.org/10.17632/dwcpnncsyd.1\">10.17632/dwcpnncsyd.1</a>.","short":"A. Hernandez-Armendariz, S. Cuylen-Haering, (2024).","ama":"Hernandez-Armendariz A, Cuylen-Haering S. A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al. 2024. doi:<a href=\"https://doi.org/10.17632/dwcpnncsyd.1\">10.17632/dwcpnncsyd.1</a>"},"oa":1,"related_material":{"record":[{"relation":"used_in_publication","id":"18072","status":"public"}]},"day":"22","year":"2024","date_updated":"2026-09-24T10:43:18Z","OA_type":"green","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.","_id":"22987","OA_place":"repository","doi":"10.17632/dwcpnncsyd.1","publisher":"Repository","date_created":"2026-09-24T10:38:23Z","date_published":"2024-08-22T00:00:00Z","fulldoi":"https://doi.org/10.17632/dwcpnncsyd.1","oa_version":"None","ddc":["570"],"month":"08","type":"research_data_reference","abstract":[{"text":"Imaging data of all main and supplementary figures. The files are the raw microcopy files including all Z-slices and timepoints. ","lang":"eng"}],"department":[{"_id":"AnSa"}],"author":[{"first_name":"Alberto","last_name":"Hernandez-Armendariz","full_name":"Hernandez-Armendariz, Alberto"},{"full_name":"Cuylen-Haering, Sara","last_name":"Cuylen-Haering","first_name":"Sara"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/dwcpnncsyd.1"}]},{"_id":"22940","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2","OA_type":"green","date_updated":"2026-09-24T10:36:36Z","year":"2024","day":"15","related_material":{"record":[{"relation":"used_in_publication","id":"15401","status":"public"}]},"oa":1,"citation":{"short":"A.  Sivertsen, F. Napoli, P. Schanda, (2024).","mla":"Sivertsen, Astrid, et al. <i>Amide and A-Hydrogens Extension to the Solid-State NMR Assignment of P. Horikoshii TET2</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.13018/BMR52400\">10.13018/BMR52400</a>.","chicago":"Sivertsen, Astrid, Federico Napoli, and Paul Schanda. “Amide and A-Hydrogens Extension to the Solid-State NMR Assignment of P. Horikoshii TET2.” Repository, 2024. <a href=\"https://doi.org/10.13018/BMR52400\">https://doi.org/10.13018/BMR52400</a>.","ista":"Sivertsen A, Napoli F, Schanda P. 2024. Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2, Repository, <a href=\"https://doi.org/10.13018/BMR52400\">10.13018/BMR52400</a>.","apa":"Sivertsen, A., Napoli, F., &#38; Schanda, P. (2024). Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2. Repository. <a href=\"https://doi.org/10.13018/BMR52400\">https://doi.org/10.13018/BMR52400</a>","ieee":"A.  Sivertsen, F. Napoli, and P. Schanda, “Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2.” Repository, 2024.","ama":"Sivertsen A, Napoli F, Schanda P. Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2. 2024. doi:<a href=\"https://doi.org/10.13018/BMR52400\">10.13018/BMR52400</a>"},"article_processing_charge":"No","department":[{"_id":"PaSc"}],"main_file_link":[{"url":"https://doi.org/10.13018/BMR52400","open_access":"1"}],"author":[{"first_name":"Astrid","full_name":" Sivertsen, Astrid","last_name":" Sivertsen"},{"full_name":"Napoli, Federico","last_name":"Napoli","first_name":"Federico"},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"}],"ddc":["530"],"month":"05","type":"research_data_reference","fulldoi":"https://doi.org/10.13018/BMR52400","date_published":"2024-05-15T00:00:00Z","oa_version":"None","date_created":"2026-09-17T09:10:45Z","publisher":"Repository","doi":"10.13018/BMR52400","OA_place":"repository"},{"publisher":"Figshare","doi":"10.21942/UVA.24829896","has_accepted_license":"1","author":[{"first_name":"G.","full_name":"Giubertoni, G.","last_name":"Giubertoni"},{"first_name":"S.","last_name":"Woutersen","full_name":"Woutersen, S."}],"main_file_link":[{"url":"https://doi.org/10.21942/UVA.24829896","open_access":"1"}],"abstract":[{"text":"This zip file contains data, and analysis for the paper \"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration\".","lang":"eng"}],"fulldoi":"https://doi.org/10.21942/UVA.24829896","date_published":"2024-02-14T00:00:00Z","oa_version":"Published Version","ddc":["550"],"month":"02","type":"research_data_reference","date_created":"2024-03-19T10:47:16Z","extern":"1","day":"14","related_material":{"record":[{"relation":"used_in_publication","id":"15116","status":"public"}]},"citation":{"ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:<a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>","ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, <a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>.","apa":"Giubertoni, G., &#38; Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. <a href=\"https://doi.org/10.21942/UVA.24829896\">https://doi.org/10.21942/UVA.24829896</a>","short":"G. Giubertoni, S. Woutersen, (2024).","mla":"Giubertoni, G., and S. Woutersen. <i>Dataset Collagen Self Assembly in H2O and D2O</i>. Figshare, 2024, doi:<a href=\"https://doi.org/10.21942/UVA.24829896\">10.21942/UVA.24829896</a>.","chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. <a href=\"https://doi.org/10.21942/UVA.24829896\">https://doi.org/10.21942/UVA.24829896</a>."},"oa":1,"article_processing_charge":"No","title":"Dataset Collagen Self Assembly in H2O and D2O","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15126","date_updated":"2026-09-24T10:42:12Z","year":"2024","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"researchdata_availability":"no","quality_controlled":"1","doi":"10.1145/3641519.3657470","conference":{"start_date":"2024-07-27","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","location":"Denver, CO, United States","end_date":"2024-08-01"},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1145/3641519.3657470","isi":1,"date_published":"2024-07-13T00:00:00Z","publication_status":"published","author":[{"full_name":"Rao, Pramod","last_name":"Rao","first_name":"Pramod"},{"first_name":"Gereon","full_name":"Fox, Gereon","last_name":"Fox"},{"full_name":"Meka, Abhimitra","last_name":"Meka","first_name":"Abhimitra"},{"first_name":"B. R.","full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun"},{"last_name":"Zhan","full_name":"Zhan, Fangneng","first_name":"Fangneng"},{"first_name":"Tim","full_name":"Weyrich, Tim","last_name":"Weyrich"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"last_name":"Pfister","full_name":"Pfister, Hanspeter","first_name":"Hanspeter"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"last_name":"Elgharib","full_name":"Elgharib, Mohamed","first_name":"Mohamed"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"abstract":[{"lang":"eng","text":"Achieving photorealistic 3D view synthesis and relighting of human portraits is pivotal for advancing AR/VR applications. Existing methodologies in portrait relighting demonstrate substantial limitations in terms of generalization and 3D consistency, coupled with inaccuracies in physically realistic lighting and identity preservation. Furthermore, personalization from a single view is difficult to achieve and often requires multiview images during the testing phase or involves slow optimization processes. This paper introduces Lite2Relight , a novel technique that can predict 3D consistent head poses of portraits while performing physically plausible light editing at interactive speed. Our method uniquely extends the generative capabilities and efficient volumetric representation of EG3D, leveraging a lightstage dataset to implicitly disentangle face reflectance and perform relighting under target HDRI environment maps. By utilizing a pre-trained geometry-aware encoder and a feature alignment module, we map input images into a relightable 3D space, enhancing them with a strong face geometry and reflectance prior. Through extensive quantitative and qualitative evaluations, we show that our method outperforms the state-of-the-art methods in terms of efficacy, photorealism, and practical application. This includes producing 3D-consistent results of the full head, including hair, eyes, and expressions. Lite2Relight paves the way for large-scale adoption of photorealistic portrait editing in various domains, offering a robust, interactive solution to a previously constrained problem."}],"citation":{"ista":"Rao P, Fox G, Meka A, Mallikarjun BR, Zhan F, Weyrich T, Bickel B, Pfister H, Matusik W, Elgharib M, Theobalt C. 2024. Lite2Relight: 3D-aware single image portrait relighting. Proceedings - SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 41.","ieee":"P. Rao <i>et al.</i>, “Lite2Relight: 3D-aware single image portrait relighting,” in <i>Proceedings - SIGGRAPH 2024 Conference Papers</i>, Denver, CO, United States, 2024.","apa":"Rao, P., Fox, G., Meka, A., Mallikarjun, B. R., Zhan, F., Weyrich, T., … Theobalt, C. (2024). Lite2Relight: 3D-aware single image portrait relighting. In <i>Proceedings - SIGGRAPH 2024 Conference Papers</i>. Denver, CO, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657470\">https://doi.org/10.1145/3641519.3657470</a>","short":"P. Rao, G. Fox, A. Meka, B.R. Mallikarjun, F. Zhan, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings - SIGGRAPH 2024 Conference Papers, Association for Computing Machinery, 2024.","chicago":"Rao, Pramod, Gereon Fox, Abhimitra Meka, B. R. Mallikarjun, Fangneng Zhan, Tim Weyrich, Bernd Bickel, et al. “Lite2Relight: 3D-Aware Single Image Portrait Relighting.” In <i>Proceedings - SIGGRAPH 2024 Conference Papers</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657470\">https://doi.org/10.1145/3641519.3657470</a>.","mla":"Rao, Pramod, et al. “Lite2Relight: 3D-Aware Single Image Portrait Relighting.” <i>Proceedings - SIGGRAPH 2024 Conference Papers</i>, 41, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657470\">10.1145/3641519.3657470</a>.","ama":"Rao P, Fox G, Meka A, et al. Lite2Relight: 3D-aware single image portrait relighting. In: <i>Proceedings - SIGGRAPH 2024 Conference Papers</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657470\">10.1145/3641519.3657470</a>"},"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2407.10487"],"isi":["001282218200076"]},"publication":"Proceedings - SIGGRAPH 2024 Conference Papers","article_number":"41","year":"2024","_id":"17374","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","scopus_import":"1","file_date_updated":"2024-08-05T08:25:18Z","has_accepted_license":"1","publisher":"Association for Computing Machinery","publication_identifier":{"isbn":["9798400705250"]},"type":"conference","ddc":["000"],"month":"07","supplementarymaterial":"yes","date_created":"2024-08-04T22:01:21Z","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We extend our gratitude to Shrisha Bharadwaj for providing feedback and constant support.","department":[{"_id":"BeBi"}],"arxiv":1,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","date_created":"2024-08-05T08:25:18Z","date_updated":"2024-08-05T08:25:18Z","success":1,"creator":"dernst","file_name":"2024_SIGGRAPH_Rao.pdf","relation":"main_file","content_type":"application/pdf","checksum":"4650f6d1419e675929133e46a91ca177","file_size":59683257,"file_id":"17387"}],"oa":1,"day":"13","date_updated":"2026-09-24T11:00:21Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Lite2Relight: 3D-aware single image portrait relighting","das_tickbox":"0"},{"das_tickbox":"1","title":"Self-organization of mortal filaments and its role in bacterial division ring formation","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-09-24T10:58:39Z","APC_amount":"12348 EUR","related_material":{"record":[{"status":"public","id":"22988","relation":"research_data"}]},"day":"01","oa":1,"dataavailabilitystatement":"The simulation data presented in this work are available from the University College London public data repository at https://doi.org/10.5522/04/24754527 (ref. 74). Live-cell imaging of FtsZ rings data presented in this work are from ref. 23. High-speed atomic force microscopy data presented in this work are from ref. 9. Total internal reflection fluorescence microscopy data presented in this work are from refs. 37,75,76","file":[{"creator":"dernst","file_name":"2024_NaturePhysics_VanhilleCampos.pdf","access_level":"open_access","date_created":"2025-04-14T06:06:35Z","success":1,"date_updated":"2025-04-14T06:06:35Z","checksum":"c4842152e2b90d67f48ea8c9ed7c473b","file_size":8058249,"file_id":"19556","relation":"main_file","content_type":"application/pdf"}],"department":[{"_id":"AnSa"},{"_id":"MaLo"}],"language":[{"iso":"eng"}],"date_created":"2024-08-25T22:01:08Z","page":"1670-1678","pmid":1,"article_type":"original","acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","volume":20,"ddc":["570"],"type":"journal_article","supplementarymaterial":"yes","month":"10","ec_funded":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publisher":"Springer Nature","has_accepted_license":"1","corr_author":"1","file_date_updated":"2025-04-14T06:06:35Z","scopus_import":"1","OA_place":"publisher","OA_type":"hybrid","_id":"17460","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","publication":"Nature Physics","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001289394500005"],"pmid":["39416851"]},"citation":{"short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>.","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>.","ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., &#38; Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>","ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1670–1678, 2024.","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. 2024;20:1670-1678. doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>"},"abstract":[{"text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments.","lang":"eng"}],"intvolume":"        20","author":[{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"last_name":"Whitley","full_name":"Whitley, Kevin D.","first_name":"Kevin D."},{"first_name":"Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp"},{"first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Holden, Séamus","last_name":"Holden","first_name":"Séamus"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"publication_status":"published","oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41567-024-02597-8","popular_science":"1","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"date_published":"2024-10-01T00:00:00Z","isi":1,"quality_controlled":"1","doi":"10.1038/s41567-024-02597-8","researchdata_availability":"yes"},{"publisher":"Springer Nature","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"file_date_updated":"2024-07-22T11:07:14Z","scopus_import":"1","has_accepted_license":"1","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"dataavailabilitystatement":"Due to privacy concerns, we cannot make the dataset used in our project publicly available. However, to demonstrate the effectiveness of our proposed method, we evaluate our approach using publicly available datasets such as H3DS (Ramon et al., 2021): https://github.com/CrisalixSA/h3ds, FFHQ (Karras et al., 2021): https://github.com/NVlabs/ffhq-dataset, and CelebA (Liu et al., 2015): https://mmlab.ie.cuhk.edu.hk/projects/CelebA.html. Using these datasets allows us to evaluate the generalization ability of our proposed method on unseen data. H3DS provides high-quality 3D scans of human faces, FFHQ contains high-resolution facial images, and CelebA is a large-scale dataset of celebrity faces. We use these datasets to evaluate the performance of our proposed method in various scenarios, such as face rotation and relighting, and compare them with state-of-the-art methods.","file":[{"creator":"dernst","file_name":"2024_IJCV_Rao.pdf","access_level":"open_access","date_created":"2024-07-22T11:07:14Z","success":1,"date_updated":"2024-07-22T11:07:14Z","checksum":"5eef1d920f6fe700d7856098000d05f1","file_size":9942520,"file_id":"17304","relation":"main_file","content_type":"application/pdf"}],"ddc":["000"],"type":"journal_article","month":"04","supplementarymaterial":"no","pmid":1,"page":"1148-1166","date_created":"2023-11-05T23:00:54Z","article_type":"original","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.","volume":132,"day":"01","oa":1,"title":"A deeper analysis of volumetric relightiable faces","das_tickbox":"1","date_updated":"2026-09-24T10:59:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","doi":"10.1007/s11263-023-01899-3","researchdata_availability":"no (restricted access)","author":[{"first_name":"Pramod","last_name":"Rao","full_name":"Rao, Pramod"},{"first_name":"B. R.","last_name":"Mallikarjun","full_name":"Mallikarjun, B. R."},{"first_name":"Gereon","last_name":"Fox","full_name":"Fox, Gereon"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"},{"first_name":"Fangneng","full_name":"Zhan, Fangneng","last_name":"Zhan"},{"last_name":"Tewari","full_name":"Tewari, Ayush","first_name":"Ayush"},{"full_name":"Theobalt, Christian","last_name":"Theobalt","first_name":"Christian"},{"full_name":"Elgharib, Mohamed","last_name":"Elgharib","first_name":"Mohamed"}],"publication_status":"published","abstract":[{"text":"Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.","lang":"eng"}],"intvolume":"       132","fulldoi":"https://doi.org/10.1007/s11263-023-01899-3","oa_version":"Published Version","date_published":"2024-04-01T00:00:00Z","isi":1,"publication":"International Journal of Computer Vision","citation":{"ama":"Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable faces. <i>International Journal of Computer Vision</i>. 2024;132:1148-1166. doi:<a href=\"https://doi.org/10.1007/s11263-023-01899-3\">10.1007/s11263-023-01899-3</a>","apa":"Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H., … Elgharib, M. (2024). A deeper analysis of volumetric relightiable faces. <i>International Journal of Computer Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11263-023-01899-3\">https://doi.org/10.1007/s11263-023-01899-3</a>","ista":"Rao P, Mallikarjun BR, Fox G, Weyrich T, Bickel B, Pfister H, Matusik W, Zhan F, Tewari A, Theobalt C, Elgharib M. 2024. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. 132, 1148–1166.","ieee":"P. Rao <i>et al.</i>, “A deeper analysis of volumetric relightiable faces,” <i>International Journal of Computer Vision</i>, vol. 132. Springer Nature, pp. 1148–1166, 2024.","short":"P. Rao, B.R. Mallikarjun, G. Fox, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, F. Zhan, A. Tewari, C. Theobalt, M. Elgharib, International Journal of Computer Vision 132 (2024) 1148–1166.","chicago":"Rao, Pramod, B. R. Mallikarjun, Gereon Fox, Tim Weyrich, Bernd Bickel, Hanspeter Pfister, Wojciech Matusik, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” <i>International Journal of Computer Vision</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s11263-023-01899-3\">https://doi.org/10.1007/s11263-023-01899-3</a>.","mla":"Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” <i>International Journal of Computer Vision</i>, vol. 132, Springer Nature, 2024, pp. 1148–66, doi:<a href=\"https://doi.org/10.1007/s11263-023-01899-3\">10.1007/s11263-023-01899-3</a>."},"article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38549787"],"isi":["001091935600002"]},"_id":"14488","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024"},{"title":"Fabricable 3D wire art","das_tickbox":"0","date_updated":"2026-09-24T11:00:48Z","day":"01","language":[{"iso":"eng"}],"department":[{"_id":"BeBi"}],"month":"07","type":"conference","supplementarymaterial":"yes","acknowledgement":"The authors thank the anonymous reviewers for their valuable comments and suggestions for improving the paper. This work was supported by JSPS KAKENHI Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan. This work was partially supported by Israel Science Foundation Grant number 1390/19 and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful advice on wire selection and Takeo Igarashi for his assistance in arranging the collaboration of the authors.","date_created":"2025-01-27T13:47:35Z","publisher":"ACM","publication_identifier":{"isbn":["9798400705250"]},"scopus_import":"1","corr_author":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18912","OA_type":"closed access","year":"2024","publication":"SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers","article_number":"134","citation":{"ama":"Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>","apa":"Tojo, K., Shamir, A., Bickel, B., &#38; Umetani, N. (2024). Fabricable 3D wire art. In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. Denver, CO, United States: ACM. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 134.","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,” in <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, Denver, CO, United States, 2024.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, ACM, 2024.","mla":"Tojo, Kenji, et al. “Fabricable 3D Wire Art.” <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, 134, ACM, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>.","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable 3D Wire Art.” In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM, 2024. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>."},"external_id":{"isi":["001282218200059"]},"article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Kenji","full_name":"Tojo, Kenji","last_name":"Tojo"},{"full_name":"Shamir, Ariel","last_name":"Shamir","first_name":"Ariel"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"full_name":"Umetani, Nobuyuki","last_name":"Umetani","first_name":"Nobuyuki"}],"abstract":[{"lang":"eng","text":"This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending."}],"fulldoi":"https://doi.org/10.1145/3641519.3657453","isi":1,"oa_version":"None","date_published":"2024-07-01T00:00:00Z","doi":"10.1145/3641519.3657453","conference":{"end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28","location":"Denver, CO, United States"},"quality_controlled":"1","researchdata_availability":"no"},{"OA_place":"repository","doi":"10.5522/04/24754527","publisher":"Repository","date_created":"2026-09-24T10:56:29Z","type":"research_data_reference","month":"07","ddc":["570"],"date_published":"2024-07-11T00:00:00Z","fulldoi":"https://doi.org/10.5522/04/24754527","oa_version":"None","abstract":[{"text":"This repository contains all the necessary files to replicate the simulations and analyse the data presented in the following publication: \"Self-organization of mortal filaments and its role in bacterial division ring formation\" - C. Vanhille-Campos et al. (DOI: https://doi.org/10.1038/s41567-024-02597-8) See README files for details.\r\n\r\nABSTRACT:\r\n\r\nFilaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the formation of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments.","lang":"eng"}],"department":[{"_id":"AnSa"},{"_id":"MaLo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5522/04/24754527"}],"author":[{"first_name":"Christian","full_name":"Vanhille Campos, Christian","last_name":"Vanhille Campos"},{"last_name":"Saric","full_name":"Saric, Andela","first_name":"Andela"}],"article_processing_charge":"No","citation":{"ieee":"C. Vanhille Campos and A. Saric, “Self-organization of mortal filaments and its role in bacterial division ring formation.” Repository, 2024.","ista":"Vanhille Campos C, Saric A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation, Repository, <a href=\"https://doi.org/10.5522/04/24754527\">10.5522/04/24754527</a>.","apa":"Vanhille Campos, C., &#38; Saric, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. Repository. <a href=\"https://doi.org/10.5522/04/24754527\">https://doi.org/10.5522/04/24754527</a>","short":"C. Vanhille Campos, A. Saric, (2024).","chicago":"Vanhille Campos, Christian, and Andela Saric. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Repository, 2024. <a href=\"https://doi.org/10.5522/04/24754527\">https://doi.org/10.5522/04/24754527</a>.","mla":"Vanhille Campos, Christian, and Andela Saric. <i>Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation</i>. Repository, 2024, doi:<a href=\"https://doi.org/10.5522/04/24754527\">10.5522/04/24754527</a>.","ama":"Vanhille Campos C, Saric A. Self-organization of mortal filaments and its role in bacterial division ring formation. 2024. doi:<a href=\"https://doi.org/10.5522/04/24754527\">10.5522/04/24754527</a>"},"oa":1,"related_material":{"record":[{"id":"17460","relation":"used_in_publication","status":"public"}]},"day":"11","year":"2024","date_updated":"2026-09-24T10:58:40Z","OA_type":"green","_id":"22988","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","title":"Self-organization of mortal filaments and its role in bacterial division ring formation"},{"date_created":"2024-08-25T22:01:07Z","pmid":1,"acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","volume":151,"article_type":"original","type":"journal_article","ddc":["599"],"month":"08","supplementarymaterial":"no","file":[{"content_type":"application/pdf","relation":"main_file","file_size":2085135,"file_id":"17464","checksum":"5e428bda0440d3f957c694b315a8f2a9","success":1,"date_updated":"2024-08-28T10:32:16Z","access_level":"open_access","date_created":"2024-08-28T10:32:16Z","file_name":"2024_Development_Cecalev.pdf","creator":"cchlebak"}],"department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","file_date_updated":"2024-08-28T10:32:16Z","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"publisher":"Company of Biologists","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-09-24T11:05:40Z","das_tickbox":"0","title":"Compensation of gene dosage on the mammalian X","oa":1,"day":"14","oa_version":"Published Version","fulldoi":"https://doi.org/10.1242/dev.202891","popular_science":"1","isi":1,"date_published":"2024-08-14T00:00:00Z","abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"intvolume":"       151","publication_status":"published","issue":"15","author":[{"full_name":"Cecalev, Daniela","last_name":"Cecalev","first_name":"Daniela"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"full_name":"Galupa, Rafael","last_name":"Galupa","first_name":"Rafael"}],"researchdata_availability":"no","quality_controlled":"1","doi":"10.1242/dev.202891","year":"2024","_id":"17458","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"citation":{"chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>.","short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. Company of Biologists, 2024.","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>"},"article_number":"dev202891","publication":"Development"},{"department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"file":[{"date_created":"2024-11-04T10:29:43Z","access_level":"open_access","date_updated":"2024-11-04T10:29:43Z","success":1,"creator":"dernst","file_name":"2024_PNAS_McDonough.pdf","relation":"main_file","content_type":"application/pdf","checksum":"73db3c87b35753e0f4324417f164a35e","file_size":1299095,"file_id":"18501"}],"dataavailabilitystatement":"All study data are included in the article and/or supporting information.","ddc":["570"],"supplementarymaterial":"yes","type":"journal_article","month":"10","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2024-10-27T23:01:44Z","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.","article_type":"original","volume":121,"publisher":"National Academy of Sciences","ec_funded":1,"publication_identifier":{"eissn":["1091-6490"]},"OA_place":"publisher","file_date_updated":"2024-11-04T10:29:43Z","scopus_import":"1","has_accepted_license":"1","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","das_tickbox":"1","date_updated":"2026-09-24T11:12:56Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"29","oa":1,"issue":"44","publication_status":"published","author":[{"last_name":"Mcdonough","full_name":"Mcdonough, Yasmine","first_name":"Yasmine"},{"full_name":"Ruzicka, Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","last_name":"Ruzicka","first_name":"Filip"},{"last_name":"Connallon","full_name":"Connallon, Tim","first_name":"Tim"}],"abstract":[{"lang":"eng","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."}],"intvolume":"       121","fulldoi":"https://doi.org/10.1073/pnas.2406335121","oa_version":"Published Version","date_published":"2024-10-29T00:00:00Z","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2406335121","researchdata_availability":"yes (supplementary data)","_id":"18479","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","year":"2024","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_number":"e2406335121","citation":{"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>","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.","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.","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>.","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>.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001359216400017"],"pmid":["39436652"]}},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2025-01-05T23:01:58Z","pmid":1,"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).","article_type":"original","volume":16,"supplementarymaterial":"yes","month":"12","ddc":["570"],"type":"journal_article","file":[{"content_type":"application/pdf","relation":"main_file","file_size":795106,"file_id":"18772","checksum":"9cf8fd14580dd694dd810ccca808ad0e","success":1,"date_updated":"2025-01-08T08:28:07Z","access_level":"open_access","date_created":"2025-01-08T08:28:07Z","file_name":"2024_GBE_Fraser.pdf","creator":"dernst"}],"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)","department":[{"_id":"BeVi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","OA_place":"publisher","file_date_updated":"2025-01-08T08:28:07Z","publication_identifier":{"eissn":["1759-6653"]},"publisher":"Oxford University Press","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_updated":"2026-09-24T11:16:00Z","das_tickbox":"1","DOAJ_listed":"1","title":"Evidence for a novel X chromosome in termites","oa":1,"day":"01","fulldoi":"https://doi.org/10.1093/gbe/evae265","project":[{"_id":"26641CAC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex Determination in Termites","grant_number":"M02484"}],"isi":1,"date_published":"2024-12-01T00:00:00Z","oa_version":"Published Version","intvolume":"        16","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."}],"issue":"12","author":[{"last_name":"Fraser","full_name":"Fraser, Roxanne","first_name":"Roxanne"},{"first_name":"Ruth","full_name":"Moraa, Ruth","last_name":"Moraa"},{"first_name":"Annika","last_name":"Djolai","full_name":"Djolai, Annika"},{"first_name":"Nils","full_name":"Meisenheimer, Nils","last_name":"Meisenheimer"},{"full_name":"Laube, Sophie","last_name":"Laube","first_name":"Sophie"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans","orcid":"0000-0001-8871-4961","first_name":"Ann K"}],"publication_status":"published","researchdata_availability":"yes","quality_controlled":"1","doi":"10.1093/gbe/evae265","year":"2024","OA_type":"gold","_id":"18761","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes","external_id":{"isi":["001380841100001"],"pmid":["39658246"]},"citation":{"short":"R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K. Huylmans, Genome Biology and Evolution 16 (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>.","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>.","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>","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.","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.","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>"},"article_number":"evae265","publication":"Genome Biology and Evolution"},{"author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"file":[{"file_name":"README.txt","creator":"melkrewi","date_updated":"2024-08-05T22:24:18Z","success":1,"date_created":"2024-08-05T22:24:18Z","access_level":"open_access","file_size":2465,"file_id":"17394","checksum":"26b5d41b3103f4284dd97d56e370a5b6","content_type":"text/plain","relation":"main_file"},{"content_type":"application/x-zip-compressed","relation":"main_file","file_id":"17395","file_size":2526735400,"checksum":"95adab5e36148015da313505e3910707","success":1,"date_updated":"2024-08-05T23:28:52Z","access_level":"open_access","date_created":"2024-08-05T23:28:52Z","file_name":"Data_artemia_single_nucleus_atlas.zip","creator":"melkrewi"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/AT:ISTA:17362","date_published":"2024-08-05T00:00:00Z","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"month":"08","ddc":["576"],"type":"research_data","date_created":"2024-08-02T07:27:45Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:17362","file_date_updated":"2024-08-05T23:28:52Z","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","has_accepted_license":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","_id":"17362","date_updated":"2026-09-24T11:17:37Z","year":"2024","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"05","related_material":{"record":[{"id":"17890","relation":"used_in_publication","status":"public"}]},"oa":1,"citation":{"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>.","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.","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>","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>.","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>."},"article_processing_charge":"No"},{"department":[{"_id":"BiCh"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":10061037,"file_id":"18954","checksum":"33b8083e76564cc918182b0b0b2cc023","date_updated":"2025-01-29T11:09:48Z","success":1,"date_created":"2025-01-29T11:09:48Z","access_level":"open_access","file_name":"2024_ActaCrystallographicaB_Hunnisett.pdf","creator":"dernst"}],"ddc":["540"],"type":"journal_article","supplementarymaterial":"yes","month":"12","page":"517-547","date_created":"2025-01-29T11:07:36Z","pmid":1,"volume":80,"article_type":"original","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.","publisher":"International Union of Crystallography","publication_identifier":{"issn":["2052-5206"]},"file_date_updated":"2025-01-29T11:09:48Z","scopus_import":"1","OA_place":"publisher","has_accepted_license":"1","title":"The seventh blind test of crystal structure prediction: Structure generation methods","das_tickbox":"0","date_updated":"2026-09-24T11:31:46Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","oa":1,"publication_status":"published","issue":"6","author":[{"first_name":"Lily M.","full_name":"Hunnisett, Lily M.","last_name":"Hunnisett"},{"last_name":"Nyman","full_name":"Nyman, Jonas","first_name":"Jonas"},{"first_name":"Nicholas","last_name":"Francia","full_name":"Francia, Nicholas"},{"first_name":"Nathan S.","full_name":"Abraham, Nathan S.","last_name":"Abraham"},{"first_name":"Claire S.","full_name":"Adjiman, Claire S.","last_name":"Adjiman"},{"full_name":"Aitipamula, Srinivasulu","last_name":"Aitipamula","first_name":"Srinivasulu"},{"first_name":"Tamador","full_name":"Alkhidir, Tamador","last_name":"Alkhidir"},{"first_name":"Mubarak","full_name":"Almehairbi, 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."},{"last_name":"Arnold","full_name":"Arnold, Joseph E.","first_name":"Joseph E."},{"first_name":"Faezeh","last_name":"Bahrami","full_name":"Bahrami, Faezeh"},{"last_name":"Bellucci","full_name":"Bellucci, Michael A.","first_name":"Michael A."},{"first_name":"Rajni M.","last_name":"Bhardwaj","full_name":"Bhardwaj, Rajni M."},{"full_name":"Bier, Imanuel","last_name":"Bier","first_name":"Imanuel"},{"first_name":"Joanna A.","last_name":"Bis","full_name":"Bis, Joanna A."},{"first_name":"A. Daniel","last_name":"Boese","full_name":"Boese, A. Daniel"},{"first_name":"David H.","full_name":"Bowskill, David H.","last_name":"Bowskill"},{"full_name":"Bramley, James","last_name":"Bramley","first_name":"James"},{"last_name":"Brandenburg","full_name":"Brandenburg, Jan Gerit","first_name":"Jan Gerit"},{"first_name":"Doris E.","full_name":"Braun, Doris E.","last_name":"Braun"},{"first_name":"Patrick W. V.","last_name":"Butler","full_name":"Butler, Patrick W. V."},{"first_name":"Joseph","full_name":"Cadden, Joseph","last_name":"Cadden"},{"last_name":"Carino","full_name":"Carino, Stephen","first_name":"Stephen"},{"first_name":"Eric J.","full_name":"Chan, Eric J.","last_name":"Chan"},{"last_name":"Chang","full_name":"Chang, Chao","first_name":"Chao"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Clarke, Sarah M.","last_name":"Clarke","first_name":"Sarah M."},{"first_name":"Simon J.","last_name":"Coles","full_name":"Coles, Simon J."},{"last_name":"Cooper","full_name":"Cooper, Richard I.","first_name":"Richard I."},{"first_name":"Ricky","last_name":"Couch","full_name":"Couch, Ricky"},{"first_name":"Ramon","full_name":"Cuadrado, Ramon","last_name":"Cuadrado"},{"first_name":"Tom","last_name":"Darden","full_name":"Darden, Tom"},{"first_name":"Graeme M.","full_name":"Day, Graeme M.","last_name":"Day"},{"first_name":"Hanno","last_name":"Dietrich","full_name":"Dietrich, Hanno"},{"last_name":"Ding","full_name":"Ding, Yiming","first_name":"Yiming"},{"full_name":"DiPasquale, Antonio","last_name":"DiPasquale","first_name":"Antonio"},{"first_name":"Bhausaheb","last_name":"Dhokale","full_name":"Dhokale, Bhausaheb"},{"last_name":"van Eijck","full_name":"van Eijck, Bouke P.","first_name":"Bouke P."},{"first_name":"Mark R. J.","last_name":"Elsegood","full_name":"Elsegood, Mark R. J."},{"full_name":"Firaha, Dzmitry","last_name":"Firaha","first_name":"Dzmitry"},{"first_name":"Wenbo","last_name":"Fu","full_name":"Fu, Wenbo"},{"last_name":"Fukuzawa","full_name":"Fukuzawa, Kaori","first_name":"Kaori"},{"first_name":"Joseph","full_name":"Glover, Joseph","last_name":"Glover"},{"full_name":"Goto, Hitoshi","last_name":"Goto","first_name":"Hitoshi"},{"first_name":"Chandler","last_name":"Greenwell","full_name":"Greenwell, Chandler"},{"first_name":"Rui","last_name":"Guo","full_name":"Guo, Rui"},{"last_name":"Harter","full_name":"Harter, Jürgen","first_name":"Jürgen"},{"last_name":"Helfferich","full_name":"Helfferich, Julian","first_name":"Julian"},{"full_name":"Hofmann, Detlef W. M.","last_name":"Hofmann","first_name":"Detlef W. M."},{"first_name":"Johannes","full_name":"Hoja, Johannes","last_name":"Hoja"},{"full_name":"Hone, John","last_name":"Hone","first_name":"John"},{"first_name":"Richard","last_name":"Hong","full_name":"Hong, Richard"},{"last_name":"Hutchison","full_name":"Hutchison, Geoffrey","first_name":"Geoffrey"},{"first_name":"Yasuhiro","full_name":"Ikabata, Yasuhiro","last_name":"Ikabata"},{"last_name":"Isayev","full_name":"Isayev, Olexandr","first_name":"Olexandr"},{"full_name":"Ishaque, Ommair","last_name":"Ishaque","first_name":"Ommair"},{"last_name":"Jain","full_name":"Jain, Varsha","first_name":"Varsha"},{"last_name":"Jin","full_name":"Jin, Yingdi","first_name":"Yingdi"},{"first_name":"Aling","full_name":"Jing, Aling","last_name":"Jing"},{"first_name":"Erin R.","last_name":"Johnson","full_name":"Johnson, Erin R."},{"full_name":"Jones, Ian","last_name":"Jones","first_name":"Ian"},{"last_name":"Jose","full_name":"Jose, K. V. Jovan","first_name":"K. V. Jovan"},{"full_name":"Kabova, Elena A.","last_name":"Kabova","first_name":"Elena A."},{"full_name":"Keates, Adam","last_name":"Keates","first_name":"Adam"},{"first_name":"Paul F.","full_name":"Kelly, Paul F.","last_name":"Kelly"},{"full_name":"Khakimov, Dmitry","last_name":"Khakimov","first_name":"Dmitry"},{"first_name":"Stefanos","last_name":"Konstantinopoulos","full_name":"Konstantinopoulos, Stefanos"},{"first_name":"Liudmila N.","last_name":"Kuleshova","full_name":"Kuleshova, Liudmila N."},{"full_name":"Li, He","last_name":"Li","first_name":"He"},{"first_name":"Xiaolu","full_name":"Lin, Xiaolu","last_name":"Lin"},{"last_name":"List","full_name":"List, Alexander","first_name":"Alexander"},{"last_name":"Liu","full_name":"Liu, Congcong","first_name":"Congcong"},{"last_name":"Liu","full_name":"Liu, Yifei Michelle","first_name":"Yifei Michelle"},{"first_name":"Zenghui","full_name":"Liu, Zenghui","last_name":"Liu"},{"full_name":"Liu, Zhi-Pan","last_name":"Liu","first_name":"Zhi-Pan"},{"first_name":"Joseph W.","last_name":"Lubach","full_name":"Lubach, Joseph W."},{"first_name":"Noa","full_name":"Marom, Noa","last_name":"Marom"},{"first_name":"Alexander A.","last_name":"Maryewski","full_name":"Maryewski, Alexander A."},{"last_name":"Matsui","full_name":"Matsui, Hiroyuki","first_name":"Hiroyuki"},{"first_name":"Alessandra","full_name":"Mattei, Alessandra","last_name":"Mattei"},{"first_name":"R. Alex","full_name":"Mayo, R. Alex","last_name":"Mayo"},{"full_name":"Melkumov, John W.","last_name":"Melkumov","first_name":"John W."},{"first_name":"Sharmarke","last_name":"Mohamed","full_name":"Mohamed, Sharmarke"},{"first_name":"Zahrasadat","full_name":"Momenzadeh Abardeh, Zahrasadat","last_name":"Momenzadeh Abardeh"},{"first_name":"Hari S.","last_name":"Muddana","full_name":"Muddana, Hari S."},{"full_name":"Nakayama, Naofumi","last_name":"Nakayama","first_name":"Naofumi"},{"last_name":"Nayal","full_name":"Nayal, Kamal Singh","first_name":"Kamal Singh"},{"last_name":"Neumann","full_name":"Neumann, Marcus A.","first_name":"Marcus A."},{"first_name":"Rahul","full_name":"Nikhar, Rahul","last_name":"Nikhar"},{"last_name":"Obata","full_name":"Obata, Shigeaki","first_name":"Shigeaki"},{"full_name":"O'Connor, Dana","last_name":"O'Connor","first_name":"Dana"},{"first_name":"Artem R.","last_name":"Oganov","full_name":"Oganov, Artem R."},{"last_name":"Okuwaki","full_name":"Okuwaki, Koji","first_name":"Koji"},{"last_name":"Otero-de-la-Roza","full_name":"Otero-de-la-Roza, Alberto","first_name":"Alberto"},{"first_name":"Constantinos C.","last_name":"Pantelides","full_name":"Pantelides, Constantinos C."},{"last_name":"Parkin","full_name":"Parkin, Sean","first_name":"Sean"},{"last_name":"Pickard","full_name":"Pickard, Chris J.","first_name":"Chris J."},{"first_name":"Luca","last_name":"Pilia","full_name":"Pilia, Luca"},{"first_name":"Tatyana","last_name":"Pivina","full_name":"Pivina, Tatyana"},{"full_name":"Podeszwa, Rafał","last_name":"Podeszwa","first_name":"Rafał"},{"last_name":"Price","full_name":"Price, Alastair J. A.","first_name":"Alastair J. A."},{"full_name":"Price, Louise S.","last_name":"Price","first_name":"Louise S."},{"last_name":"Price","full_name":"Price, Sarah L.","first_name":"Sarah L."},{"first_name":"Michael R.","last_name":"Probert","full_name":"Probert, Michael R."},{"last_name":"Pulido","full_name":"Pulido, Angeles","first_name":"Angeles"},{"first_name":"Gunjan Rajendra","last_name":"Ramteke","full_name":"Ramteke, Gunjan Rajendra"},{"full_name":"Rehman, Atta Ur","last_name":"Rehman","first_name":"Atta Ur"},{"last_name":"Reutzel-Edens","full_name":"Reutzel-Edens, Susan M.","first_name":"Susan M."},{"last_name":"Rogal","full_name":"Rogal, Jutta","first_name":"Jutta"},{"first_name":"Marta J.","full_name":"Ross, Marta J.","last_name":"Ross"},{"last_name":"Rumson","full_name":"Rumson, Adrian F.","first_name":"Adrian F."},{"full_name":"Sadiq, Ghazala","last_name":"Sadiq","first_name":"Ghazala"},{"first_name":"Zeinab M.","full_name":"Saeed, Zeinab M.","last_name":"Saeed"},{"first_name":"Alireza","last_name":"Salimi","full_name":"Salimi, Alireza"},{"full_name":"Salvalaglio, Matteo","last_name":"Salvalaglio","first_name":"Matteo"},{"first_name":"Leticia","full_name":"Sanders de Almada, Leticia","last_name":"Sanders de Almada"},{"first_name":"Kiran","last_name":"Sasikumar","full_name":"Sasikumar, Kiran"},{"full_name":"Sekharan, Sivakumar","last_name":"Sekharan","first_name":"Sivakumar"},{"full_name":"Shang, Cheng","last_name":"Shang","first_name":"Cheng"},{"last_name":"Shankland","full_name":"Shankland, Kenneth","first_name":"Kenneth"},{"last_name":"Shinohara","full_name":"Shinohara, Kotaro","first_name":"Kotaro"},{"full_name":"Shi, Baimei","last_name":"Shi","first_name":"Baimei"},{"first_name":"Xuekun","full_name":"Shi, Xuekun","last_name":"Shi"},{"full_name":"Skillman, A. Geoffrey","last_name":"Skillman","first_name":"A. Geoffrey"},{"first_name":"Hongxing","last_name":"Song","full_name":"Song, Hongxing"},{"last_name":"Strasser","full_name":"Strasser, Nina","first_name":"Nina"},{"first_name":"Jacco","last_name":"van de Streek","full_name":"van de Streek, Jacco"},{"full_name":"Sugden, Isaac J.","last_name":"Sugden","first_name":"Isaac J."},{"full_name":"Sun, Guangxu","last_name":"Sun","first_name":"Guangxu"},{"last_name":"Szalewicz","full_name":"Szalewicz, Krzysztof","first_name":"Krzysztof"},{"last_name":"Tan","full_name":"Tan, Benjamin I.","first_name":"Benjamin I."},{"first_name":"Lu","full_name":"Tan, Lu","last_name":"Tan"},{"last_name":"Tarczynski","full_name":"Tarczynski, Frank","first_name":"Frank"},{"first_name":"Christopher R.","last_name":"Taylor","full_name":"Taylor, Christopher R."},{"full_name":"Tkatchenko, Alexandre","last_name":"Tkatchenko","first_name":"Alexandre"},{"full_name":"Tom, Rithwik","last_name":"Tom","first_name":"Rithwik"},{"first_name":"Mark E.","last_name":"Tuckerman","full_name":"Tuckerman, Mark E."},{"first_name":"Yohei","last_name":"Utsumi","full_name":"Utsumi, Yohei"},{"full_name":"Vogt-Maranto, Leslie","last_name":"Vogt-Maranto","first_name":"Leslie"},{"last_name":"Weatherston","full_name":"Weatherston, Jake","first_name":"Jake"},{"first_name":"Luke J.","last_name":"Wilkinson","full_name":"Wilkinson, Luke J."},{"full_name":"Willacy, Robert D.","last_name":"Willacy","first_name":"Robert D."},{"first_name":"Lukasz","last_name":"Wojtas","full_name":"Wojtas, Lukasz"},{"last_name":"Woollam","full_name":"Woollam, Grahame R.","first_name":"Grahame R."},{"full_name":"Yang, Zhuocen","last_name":"Yang","first_name":"Zhuocen"},{"first_name":"Etsuo","last_name":"Yonemochi","full_name":"Yonemochi, Etsuo"},{"last_name":"Yue","full_name":"Yue, Xin","first_name":"Xin"},{"full_name":"Zeng, Qun","last_name":"Zeng","first_name":"Qun"},{"last_name":"Zhang","full_name":"Zhang, Yizu","first_name":"Yizu"},{"first_name":"Tian","last_name":"Zhou","full_name":"Zhou, Tian"},{"first_name":"Yunfei","full_name":"Zhou, Yunfei","last_name":"Zhou"},{"first_name":"Roman","last_name":"Zubatyuk","full_name":"Zubatyuk, Roman"},{"full_name":"Cole, Jason C.","last_name":"Cole","first_name":"Jason C."}],"abstract":[{"lang":"eng","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."}],"intvolume":"        80","fulldoi":"https://doi.org/10.1107/s2052520624007492","oa_version":"Published Version","isi":1,"date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","doi":"10.1107/s2052520624007492","researchdata_availability":"no","_id":"18952","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"hybrid","year":"2024","publication":"Acta Crystallographica Section B","citation":{"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.","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.","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>","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.","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>.","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>."},"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001388840500003"],"pmid":["39405196"]}},{"day":"08","oa":1,"DOAJ_listed":"1","title":"Pushing thermal conductivity to its lower limit in crystals with simple structures","das_tickbox":"1","date_updated":"2026-09-24T11:20:55Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"ec_funded":1,"scopus_import":"1","OA_place":"publisher","file_date_updated":"2024-04-26T10:34:07Z","corr_author":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"arxiv":1,"department":[{"_id":"BiCh"}],"file":[{"file_size":3049375,"file_id":"15346","checksum":"f81bd6ba42f740d060fb446eeebc1035","content_type":"application/pdf","relation":"main_file","file_name":"2024_NatComm_Zeng.pdf","creator":"cchlebak","success":1,"date_updated":"2024-04-26T10:34:07Z","access_level":"open_access","date_created":"2024-04-26T10:34:07Z"}],"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).","month":"04","supplementarymaterial":"yes","type":"journal_article","ddc":["530"],"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.","article_type":"original","volume":15,"date_created":"2024-04-14T22:01:00Z","pmid":1,"publication":"Nature Communications","article_number":"3007","citation":{"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.","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.","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>","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>.","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>.","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).","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>"},"external_id":{"isi":["001198902100029"],"pmid":["38589376"],"arxiv":["2310.01838"]},"article_processing_charge":"Yes","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15311","OA_type":"gold","year":"2024","doi":"10.1038/s41467-024-46799-3","quality_controlled":"1","researchdata_availability":"yes","publication_status":"published","author":[{"last_name":"Zeng","full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","orcid":"0000-0001-5126-4928"},{"full_name":"Shen, Xingchen","last_name":"Shen","first_name":"Xingchen"},{"last_name":"Cheng","full_name":"Cheng, Ruihuan","first_name":"Ruihuan"},{"first_name":"Olivier","full_name":"Perez, Olivier","last_name":"Perez"},{"last_name":"Ouyang","full_name":"Ouyang, Niuchang","first_name":"Niuchang"},{"last_name":"Fan","full_name":"Fan, Zheyong","first_name":"Zheyong"},{"full_name":"Lemoine, Pierric","last_name":"Lemoine","first_name":"Pierric"},{"first_name":"Bernard","last_name":"Raveau","full_name":"Raveau, Bernard"},{"first_name":"Emmanuel","full_name":"Guilmeau, Emmanuel","last_name":"Guilmeau"},{"first_name":"Yue","full_name":"Chen, Yue","last_name":"Chen"}],"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"}],"intvolume":"        15","isi":1,"fulldoi":"https://doi.org/10.1038/s41467-024-46799-3","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"oa_version":"Published Version","date_published":"2024-04-08T00:00:00Z"},{"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"18452","OA_type":"hybrid","citation":{"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>","short":"B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.","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>.","mla":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” <i>Journal of Chemical Theory and Computation</i>, vol. 20, no. 20, American Chemical Society, 2024, pp. 9259–66, doi:<a href=\"https://doi.org/10.1021/acs.jctc.4c00998\">10.1021/acs.jctc.4c00998</a>.","ista":"Cheng B. 2024. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 20(20), 9259–9266.","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.","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>"},"external_id":{"arxiv":["2405.09057"],"isi":["001330001500001"],"pmid":["39365029"]},"article_processing_charge":"Yes (in subscription journal)","publication":"Journal of Chemical Theory and Computation","fulldoi":"https://doi.org/10.1021/acs.jctc.4c00998","date_published":"2024-10-22T00:00:00Z","oa_version":"Published Version","isi":1,"issue":"20","publication_status":"published","author":[{"orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng"}],"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."}],"intvolume":"        20","researchdata_availability":"no","doi":"10.1021/acs.jctc.4c00998","quality_controlled":"1","date_updated":"2026-09-24T11:30:58Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Response matching for generating materials and molecules","das_tickbox":"1","oa":1,"day":"22","related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/cace"}]},"month":"10","ddc":["540"],"supplementarymaterial":"no","type":"journal_article","article_type":"original","volume":20,"acknowledgement":"B.C. thanks Chris Pickard for enlightening discussions.","date_created":"2024-10-20T22:02:07Z","pmid":1,"page":"9259-9266","language":[{"iso":"eng"}],"arxiv":1,"department":[{"_id":"BiCh"}],"dataavailabilitystatement":"The training scripts, trained models, and training data are available at https://github.com/BingqingCheng/cace-rm.","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"18832","file_size":4758251,"checksum":"aca0011bba4846140809b5af583daa9a","date_updated":"2025-01-13T09:11:09Z","success":1,"access_level":"open_access","date_created":"2025-01-13T09:11:09Z","file_name":"2024_JCTC_Cheng.pdf","creator":"dernst"}],"scopus_import":"1","file_date_updated":"2025-01-13T09:11:09Z","OA_place":"publisher","corr_author":"1","has_accepted_license":"1","publisher":"American Chemical Society","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]}},{"_id":"17322","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","OA_type":"gold","year":"2024","publication":"npj Computational Materials","article_number":"157","citation":{"mla":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” <i>Npj Computational Materials</i>, vol. 10, 157, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41524-024-01332-4\">10.1038/s41524-024-01332-4</a>.","chicago":"Cheng, Bingqing. “Cartesian Atomic Cluster Expansion for Machine Learning Interatomic Potentials.” <i>Npj Computational Materials</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41524-024-01332-4\">https://doi.org/10.1038/s41524-024-01332-4</a>.","short":"B. Cheng, Npj Computational Materials 10 (2024).","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>","ieee":"B. Cheng, “Cartesian atomic cluster expansion for machine learning interatomic potentials,” <i>npj Computational Materials</i>, vol. 10. Springer Nature, 2024.","ista":"Cheng B. 2024. Cartesian atomic cluster expansion for machine learning interatomic potentials. npj Computational Materials. 10, 157.","ama":"Cheng B. Cartesian atomic cluster expansion for machine learning interatomic potentials. <i>npj Computational Materials</i>. 2024;10. doi:<a href=\"https://doi.org/10.1038/s41524-024-01332-4\">10.1038/s41524-024-01332-4</a>"},"article_processing_charge":"Yes","external_id":{"isi":["001271730700001"],"arxiv":["2402.07472"]},"author":[{"orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng"}],"publication_status":"published","intvolume":"        10","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"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41524-024-01332-4","isi":1,"date_published":"2024-07-18T00:00:00Z","quality_controlled":"1","doi":"10.1038/s41524-024-01332-4","researchdata_availability":"no","title":"Cartesian atomic cluster expansion for machine learning interatomic potentials","DOAJ_listed":"1","das_tickbox":"1","date_updated":"2026-09-24T11:30:25Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"18","oa":1,"department":[{"_id":"BiCh"}],"arxiv":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2025-01-09T12:36:48Z","access_level":"open_access","date_updated":"2025-01-09T12:36:48Z","success":1,"creator":"dernst","file_name":"2024_npjComputationalMaterials_Cheng.pdf","relation":"main_file","content_type":"application/pdf","checksum":"e6b4d1a45a9ef1e9be35b313d96ebd6f","file_id":"18813","file_size":1659509}],"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.","type":"journal_article","ddc":["000"],"month":"07","supplementarymaterial":"no","date_created":"2024-07-28T22:01:08Z","article_type":"original","volume":10,"acknowledgement":"B.C. thanks Ralf Drautz and Ngoc Cuong Nguyen for illuminating discussions.","publisher":"Springer Nature","publication_identifier":{"eissn":["2057-3960"]},"corr_author":"1","scopus_import":"1","file_date_updated":"2025-01-09T12:36:48Z","OA_place":"publisher","has_accepted_license":"1"},{"article_processing_charge":"No","external_id":{"isi":["001198615900003"]},"citation":{"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.","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>","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” <i>Physical Review B</i>, vol. 109, no. 5. American Physical Society, 2024.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevb.109.054305\">https://doi.org/10.1103/physrevb.109.054305</a>.","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” <i>Physical Review B</i>, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevb.109.054305\">10.1103/physrevb.109.054305</a>."},"article_number":"054305","publication":"Physical Review B","year":"2024","_id":"15052","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","researchdata_availability":"no","quality_controlled":"1","doi":"10.1103/physrevb.109.054305","isi":1,"fulldoi":"https://doi.org/10.1103/physrevb.109.054305","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"date_published":"2024-02-14T00:00:00Z","oa_version":"None","intvolume":"       109","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}],"author":[{"last_name":"Cheng","full_name":"Cheng, Ruihuan","first_name":"Ruihuan"},{"first_name":"Zezhu","orcid":"0000-0001-5126-4928","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","full_name":"Zeng, Zezhu"},{"first_name":"Chen","full_name":"Wang, Chen","last_name":"Wang"},{"last_name":"Ouyang","full_name":"Ouyang, Niuchang","first_name":"Niuchang"},{"last_name":"Chen","full_name":"Chen, Yue","first_name":"Yue"}],"issue":"5","publication_status":"published","day":"14","date_updated":"2026-09-24T11:19:44Z","das_tickbox":"0","title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","scopus_import":"1","ec_funded":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publisher":"American Physical Society","date_created":"2024-03-04T07:41:23Z","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.","article_type":"original","volume":109,"month":"02","supplementarymaterial":"yes","type":"journal_article","department":[{"_id":"BiCh"}],"language":[{"iso":"eng"}]}]