[{"article_processing_charge":"No","place":"Cham","title":"Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications","publisher":"Springer Nature","abstract":[{"text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review a recent proof of the asymptotic expansion of its spectrum and eigenstates and two applications of this result, namely the derivation of an Edgeworth expansion for fluctuations of one-body operators and the computation of the binding energy of an inhomogeneous Bose gas to any order. Finally, we collect related results for the dynamics of the weakly interacting Bose gas and for the regularized Nelson model.","lang":"eng"}],"editor":[{"last_name":"Bassi","first_name":"Angelo","full_name":"Bassi, Angelo"},{"first_name":"Sheldon","last_name":"Goldstein","full_name":"Goldstein, Sheldon"},{"full_name":"Tumulka, Roderich","first_name":"Roderich","last_name":"Tumulka"},{"first_name":"Nino","last_name":"Zanghi","full_name":"Zanghi, Nino"}],"OA_place":"repository","fulldoi":"https://doi.org/10.1007/978-3-031-45434-9_22","arxiv":1,"type":"book_chapter","scopus_import":"1","_id":"18948","acknowledgement":"It is our pleasure to thank Marco Falconi, Nataša Pavlović, Peter Pickl, Robert Seiringer and Avy Soffer for the collaboration on the works [11, 13, 14, 21, 33, 39]. L.B. was supported by the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111). N.L. acknowledges support from the Swiss National Science Foundation through the NCCR SwissMap and funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101024712. S.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 512258249.","author":[{"orcid":"0000-0002-6854-1343","last_name":"Bossmann","first_name":"Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","full_name":"Bossmann, Lea"},{"full_name":"Leopold, Nikolai","first_name":"Nikolai","last_name":"Leopold"},{"first_name":"David Johannes","last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"first_name":"Sören","last_name":"Petrat","full_name":"Petrat, Sören"}],"series_title":"FTPH","page":"307-321","publication_status":"published","language":[{"iso":"eng"}],"intvolume":"       215","publication_identifier":{"issn":["0168-1222"],"isbn":["9783031454332"],"eissn":["2365-6425"],"eisbn":["9783031454349"]},"status":"public","year":"2024","publication":"Physics and the Nature of Reality","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2304.12910"]},"das_tickbox":"0","citation":{"ama":"Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Bassi A, Goldstein S, Tumulka R, Zanghi N, eds. <i>Physics and the Nature of Reality</i>. Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:<a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">10.1007/978-3-031-45434-9_22</a>","mla":"Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” <i>Physics and the Nature of Reality</i>, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024, pp. 307–21, doi:<a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">10.1007/978-3-031-45434-9_22</a>.","apa":"Bossmann, L., Leopold, N., Mitrouskas, D. J., &#38; Petrat, S. (2024). Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In A. Bassi, S. Goldstein, R. Tumulka, &#38; N. Zanghi (Eds.), <i>Physics and the Nature of Reality</i> (Vol. 215, pp. 307–321). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">https://doi.org/10.1007/978-3-031-45434-9_22</a>","chicago":"Bossmann, Lea, Nikolai Leopold, David Johannes Mitrouskas, and Sören Petrat. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” In <i>Physics and the Nature of Reality</i>, edited by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21. FTPH. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-45434-9_22\">https://doi.org/10.1007/978-3-031-45434-9_22</a>.","ista":"Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. 2024.Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications. In: Physics and the Nature of Reality. Fundamental Theories of Physics, vol. 215, 307–321.","ieee":"L. Bossmann, N. Leopold, D. J. Mitrouskas, and S. Petrat, “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications,” in <i>Physics and the Nature of Reality</i>, vol. 215, A. Bassi, S. Goldstein, R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321.","short":"L. Bossmann, N. Leopold, D.J. Mitrouskas, S. Petrat, in:, A. Bassi, S. Goldstein, R. Tumulka, N. Zanghi (Eds.), Physics and the Nature of Reality, Springer Nature, Cham, 2024, pp. 307–321."},"department":[{"_id":"RoSe"}],"alternative_title":["Fundamental Theories of Physics"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12910"}],"date_created":"2025-01-29T10:30:08Z","researchdata_availability":"no","oa_version":"Preprint","volume":215,"OA_type":"green","doi":"10.1007/978-3-031-45434-9_22","day":"04","quality_controlled":"1","oa":1,"date_updated":"2026-09-17T11:08:01Z","date_published":"2024-02-04T00:00:00Z","month":"02"},{"month":"09","date_published":"2024-09-01T00:00:00Z","date_updated":"2026-09-17T11:27:41Z","oa":1,"quality_controlled":"1","day":"01","project":[{"grant_number":"I04638","name":"LGI1 antibody-induced pathophysiology in synapses","_id":"05970B30-7A3F-11EA-A408-12923DDC885E"}],"doi":"10.1212/NXI.0000000000200284","OA_type":"gold","issue":"5","volume":11,"oa_version":"Published Version","researchdata_availability":"upon request","date_created":"2024-08-25T22:01:07Z","department":[{"_id":"RySh"}],"citation":{"ama":"Ritzau-Jost A, Gsell F, Sell J, et al. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. 2024;11(5):e200284. doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>","mla":"Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:<a href=\"https://doi.org/10.1212/NXI.0000000000200284\">10.1212/NXI.0000000000200284</a>.","apa":"Ritzau-Jost, A., Gsell, F., Sell, J., Sachs, S., Montanaro-Punzengruber, J.-C., Kirmann, T., … Hallermann, S. (2024). LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>","chicago":"Ritzau-Jost, Andreas, Felix Gsell, Josefine Sell, Stefan Sachs, Jacqueline-Claire Montanaro-Punzengruber, Toni Kirmann, Sebastian Maaß, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>. Wolters Kluwer, 2024. <a href=\"https://doi.org/10.1212/NXI.0000000000200284\">https://doi.org/10.1212/NXI.0000000000200284</a>.","ista":"Ritzau-Jost A, Gsell F, Sell J, Sachs S, Montanaro-Punzengruber J-C, Kirmann T, Maaß S, Irani SR, Werner C, Geis C, Sauer M, Shigemoto R, Hallermann S. 2024. LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening. Neurology, Neuroimmunology &#38; Neuroinflammation. 11(5), e200284.","ieee":"A. Ritzau-Jost <i>et al.</i>, “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” <i>Neurology, Neuroimmunology &#38; Neuroinflammation</i>, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024.","short":"A. Ritzau-Jost, F. Gsell, J. Sell, S. Sachs, J.-C. Montanaro-Punzengruber, T. Kirmann, S. Maaß, S.R. Irani, C. Werner, C. Geis, M. Sauer, R. Shigemoto, S. Hallermann, Neurology, Neuroimmunology &#38; Neuroinflammation 11 (2024) e200284."},"das_tickbox":"1","external_id":{"isi":["001291908600001"],"pmid":["39141878"]},"pmid":1,"publication":"Neurology, Neuroimmunology & Neuroinflammation","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","dataavailabilitystatement":"Data that support the findings of this study are available from the corresponding author on reasonable request.","related_material":{"link":[{"url":"https://doi.org/10.1101/2023.10.04.560631","relation":"earlier_version"}]},"year":"2024","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"DOAJ_listed":"1","status":"public","file_date_updated":"2025-01-09T13:42:42Z","publication_identifier":{"eissn":["2332-7812"]},"intvolume":"        11","language":[{"iso":"eng"}],"file":[{"file_size":855818,"date_updated":"2025-01-09T13:42:42Z","file_id":"18815","creator":"dernst","relation":"main_file","success":1,"file_name":"2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf","content_type":"application/pdf","date_created":"2025-01-09T13:42:42Z","access_level":"open_access","checksum":"1e6d1230e0387f72752e3268f5330c9e"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","page":"e200284","isi":1,"author":[{"full_name":"Ritzau-Jost, Andreas","last_name":"Ritzau-Jost","first_name":"Andreas"},{"full_name":"Gsell, Felix","first_name":"Felix","last_name":"Gsell"},{"full_name":"Sell, Josefine","last_name":"Sell","first_name":"Josefine"},{"full_name":"Sachs, Stefan","first_name":"Stefan","last_name":"Sachs"},{"full_name":"Montanaro-Punzengruber, Jacqueline-Claire","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","last_name":"Montanaro-Punzengruber","first_name":"Jacqueline-Claire"},{"last_name":"Kirmann","first_name":"Toni","full_name":"Kirmann, Toni"},{"full_name":"Maaß, Sebastian","last_name":"Maaß","first_name":"Sebastian"},{"full_name":"Irani, Sarosh R.","last_name":"Irani","first_name":"Sarosh R."},{"first_name":"Christian","last_name":"Werner","full_name":"Werner, Christian"},{"full_name":"Geis, Christian","last_name":"Geis","first_name":"Christian"},{"full_name":"Sauer, Markus","last_name":"Sauer","first_name":"Markus"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hallermann","first_name":"Stefan","full_name":"Hallermann, Stefan"}],"acknowledgement":"The authors thank Claudia Sommer for expert technical assistance, the Electron Microscopy Facility of IST-Austria for resources, and Tereza Belinova in the Imaging and Optics Facility of IST-Austria for 3D reconstruction. ","scopus_import":"1","_id":"17457","type":"journal_article","ddc":["570"],"fulldoi":"https://doi.org/10.1212/NXI.0000000000200284","OA_place":"publisher","abstract":[{"text":"Autoantibodies against the protein leucine-rich glioma inactivated 1 (LGI1) cause the most\r\ncommon subtype of autoimmune encephalitis with predominant involvement of the limbic\r\nsystem, associated with seizures and memory deficits. LGI1 and its receptor ADAM22 are part\r\nof a transsynaptic protein complex that includes several proteins involved in presynaptic\r\nneurotransmitter release and postsynaptic glutamate sensing. Autoantibodies against LGI1\r\nincrease excitatory synaptic strength, but studies that genetically disrupt the LGI1-ADAM22\r\ncomplex report a reduction in postsynaptic glutamate receptor-mediated responses. Thus, the\r\nmechanisms underlying the increased synaptic strength induced by LGI1 autoantibodies remain elusive, and the contributions of presynaptic molecules to the LGI1-transsynaptic complex remain unclear. We therefore investigated the presynaptic mechanisms that mediate\r\nautoantibody-induced synaptic strengthening.","lang":"eng"}],"title":"LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening","publisher":"Wolters Kluwer","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes"},{"article_type":"original","publisher":"EMS Press","abstract":[{"text":"This workshop brought together experts on the analysis of quantum many-body problems and quantum statistical mechanics, with the goal of discussing the state-of-the-art of the field, recent developments as well as challenges for the future. The main topics of discussion concerned the equilibrium and dynamical behavior of (bosonic or fermionic) quantum gases, quantum spin systems, as well as quantum field theory models like the Nelson or Fröhlich model.","lang":"eng"}],"title":"Many-body quantum systems","type":"journal_article","fulldoi":"https://doi.org/10.4171/owr/2023/39","article_processing_charge":"No","page":"2247-2302","publication_status":"published","acknowledgement":"The MFO and the workshop organizers would like to thank the National Science Foundation for supporting the participation of junior researchers in the workshop by the grant DMS-2230648, “US Junior Oberwolfach Fellows”.","_id":"18958","author":[{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"},{"last_name":"Warzel","first_name":"Simone","full_name":"Warzel, Simone"}],"year":"2024","publication":"Oberwolfach Reports","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","publication_identifier":{"eissn":["1660-8941"],"issn":["1660-8933"]},"status":"public","language":[{"iso":"eng"}],"intvolume":"        20","day":"18","doi":"10.4171/owr/2023/39","date_published":"2024-04-18T00:00:00Z","month":"04","quality_controlled":"1","date_updated":"2026-09-17T11:09:16Z","department":[{"_id":"RoSe"}],"date_created":"2025-01-29T13:09:28Z","citation":{"ama":"Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. <i>Oberwolfach Reports</i>. 2024;20(3):2247-2302. doi:<a href=\"https://doi.org/10.4171/owr/2023/39\">10.4171/owr/2023/39</a>","chicago":"Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” <i>Oberwolfach Reports</i>. EMS Press, 2024. <a href=\"https://doi.org/10.4171/owr/2023/39\">https://doi.org/10.4171/owr/2023/39</a>.","mla":"Hainzl, Christian, et al. “Many-Body Quantum Systems.” <i>Oberwolfach Reports</i>, vol. 20, no. 3, EMS Press, 2024, pp. 2247–302, doi:<a href=\"https://doi.org/10.4171/owr/2023/39\">10.4171/owr/2023/39</a>.","apa":"Hainzl, C., Schlein, B., Seiringer, R., &#38; Warzel, S. (2024). Many-body quantum systems. <i>Oberwolfach Reports</i>. EMS Press. <a href=\"https://doi.org/10.4171/owr/2023/39\">https://doi.org/10.4171/owr/2023/39</a>","ista":"Hainzl C, Schlein B, Seiringer R, Warzel S. 2024. Many-body quantum systems. Oberwolfach Reports. 20(3), 2247–2302.","short":"C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 20 (2024) 2247–2302.","ieee":"C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” <i>Oberwolfach Reports</i>, vol. 20, no. 3. EMS Press, pp. 2247–2302, 2024."},"das_tickbox":"0","oa_version":"None","researchdata_availability":"no","volume":20,"issue":"3"},{"doi":"10.1016/j.bpj.2023.12.020","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960"}],"day":"06","oa":1,"date_updated":"2026-09-24T10:26:59Z","quality_controlled":"1","month":"02","date_published":"2024-02-06T00:00:00Z","citation":{"ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical Journal</i>, vol. 123, no. 3. Elsevier, pp. 307–316, 2024.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal 123 (2024) 307–316.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. 2024. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. 123(3), 307–316.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (2024). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, vol. 123, no. 3, Elsevier, 2024, pp. 307–16, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. 2024;123(3):307-316. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>"},"das_tickbox":"0","date_created":"2024-01-21T23:00:56Z","department":[{"_id":"AnSa"}],"issue":"3","volume":123,"oa_version":"Published Version","researchdata_availability":"no","year":"2024","pmid":1,"supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Biophysical Journal","external_id":{"isi":["001185235900001"],"pmid":["38158654"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"intvolume":"       123","language":[{"iso":"eng"}],"file":[{"checksum":"1c8fe1cf950394875b65b90da86428ff","access_level":"open_access","date_created":"2024-07-16T12:09:55Z","content_type":"application/pdf","file_name":"2024_BiophysicalJournal_Azadbakht.pdf","success":1,"relation":"main_file","creator":"dernst","date_updated":"2024-07-16T12:09:55Z","file_id":"17266","file_size":3189926}],"status":"public","file_date_updated":"2024-07-16T12:09:55Z","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"isi":1,"ec_funded":1,"page":"307-316","publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","_id":"14844","acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","author":[{"last_name":"Azadbakht","first_name":"Ali","full_name":"Azadbakht, Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","first_name":"Billie","last_name":"Meadowcroft"},{"id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj","last_name":"Majek","first_name":"Juraj"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"publisher":"Elsevier","abstract":[{"text":"Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.","lang":"eng"}],"title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.1016/j.bpj.2023.12.020","type":"journal_article","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)"},{"APC_amount":"5936,71 EUR","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"eissn":["1091-6490"]},"status":"public","file_date_updated":"2024-02-26T08:20:00Z","file":[{"success":1,"content_type":"application/pdf","file_name":"2024_PNAS_Curk.pdf","access_level":"open_access","date_created":"2024-02-26T08:20:00Z","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","file_size":7699487,"date_updated":"2024-02-26T08:20:00Z","file_id":"15026","creator":"dernst","relation":"main_file"}],"language":[{"iso":"eng"}],"corr_author":"1","intvolume":"       121","related_material":{"record":[{"id":"15027","relation":"research_data","status":"public"}]},"year":"2024","dataavailabilitystatement":"Aggregation data and the source code for the coarse-grained computer model have been deposited in Figshare (https://figshare.com/s/85798bba4ebc68d822ed)","external_id":{"pmid":["38335256"],"isi":["001169063600007"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","supplementarymaterial":"no","pmid":1,"department":[{"_id":"AnSa"}],"date_created":"2024-02-18T23:01:00Z","das_tickbox":"1","citation":{"apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <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.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7, e2220075121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>.","chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <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.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(7). doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>","ieee":"S. Curk <i>et al.</i>, “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7. National Academy of Sciences, 2024.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121."},"researchdata_availability":"yes","oa_version":"Published Version","OA_type":"hybrid","volume":121,"issue":"7","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020"}],"day":"13","doi":"10.1073/pnas.2220075121","date_published":"2024-02-13T00:00:00Z","month":"02","quality_controlled":"1","oa":1,"date_updated":"2026-09-24T10:27:36Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","article_type":"original","publisher":"National Academy of Sciences","abstract":[{"text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.","lang":"eng"}],"title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","ddc":["570"],"article_number":"e2220075121","type":"journal_article","fulldoi":"https://doi.org/10.1073/pnas.2220075121","OA_place":"publisher","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","scopus_import":"1","_id":"15001","author":[{"orcid":"0000-0001-6160-9766","first_name":"Samo","last_name":"Curk","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","full_name":"Curk, Samo"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T.","last_name":"Michaels"},{"last_name":"Knowles","first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J."},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"ec_funded":1,"isi":1,"publication_status":"published"},{"publication_status":"published","isi":1,"author":[{"full_name":"Giubertoni, Giulia","first_name":"Giulia","last_name":"Giubertoni"},{"full_name":"Feng, Liru","last_name":"Feng","first_name":"Liru"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"first_name":"Guido","last_name":"Giannetti","full_name":"Giannetti, Guido"},{"last_name":"Rutten","first_name":"Luco","full_name":"Rutten, Luco"},{"full_name":"Choi, Yeji","last_name":"Choi","first_name":"Yeji"},{"full_name":"Van Der Net, Anouk","first_name":"Anouk","last_name":"Van Der Net"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"full_name":"Caporaletti, Federico","last_name":"Caporaletti","first_name":"Federico"},{"first_name":"Dimitra","last_name":"Micha","full_name":"Micha, Dimitra"},{"full_name":"Hunger, Johannes","last_name":"Hunger","first_name":"Johannes"},{"first_name":"Antoine","last_name":"Deblais","full_name":"Deblais, Antoine"},{"full_name":"Bonn, Daniel","last_name":"Bonn","first_name":"Daniel"},{"last_name":"Sommerdijk","first_name":"Nico","full_name":"Sommerdijk, Nico"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Ilie, Ioana M.","last_name":"Ilie","first_name":"Ioana M."},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"full_name":"Woutersen, Sander","last_name":"Woutersen","first_name":"Sander"}],"acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","_id":"15116","scopus_import":"1","ddc":["550"],"article_number":"e2313162121","type":"journal_article","fulldoi":"https://doi.org/10.1073/pnas.2313162121","has_accepted_license":"1","article_type":"original","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","publisher":"National Academy of Sciences","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"article_processing_charge":"Yes (in subscription journal)","date_published":"2024-03-12T00:00:00Z","month":"03","quality_controlled":"1","date_updated":"2026-09-24T10:42:11Z","oa":1,"day":"12","doi":"10.1073/pnas.2313162121","oa_version":"Published Version","researchdata_availability":"yes","issue":"11","volume":121,"department":[{"_id":"AnSa"}],"date_created":"2024-03-17T23:00:57Z","das_tickbox":"1","citation":{"mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <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.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <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.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>.","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>","ieee":"G. Giubertoni <i>et al.</i>, “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121."},"external_id":{"isi":["001206387400001"],"pmid":["38451946"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"year":"2024","related_material":{"record":[{"status":"public","id":"15126","relation":"research_data"}]},"dataavailabilitystatement":"Turbidity data; IR and 2D-IR data; TEM images; cryo-TEM images; CRM images; coarse grained simulations; molecular dynamics simulation data have been deposited in UvAauas.figshare 10.21942/uva.24829896","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","file_date_updated":"2024-03-19T10:22:42Z","file":[{"success":1,"file_name":"2024_PNAS_Giubertoni.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2024-03-19T10:22:42Z","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","file_id":"15125","creator":"dernst","relation":"main_file"}],"language":[{"iso":"eng"}],"intvolume":"       121","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"author":[{"first_name":"Ethan","last_name":"Weiner","full_name":"Weiner, Ethan"},{"full_name":"Berryman, Elizabeth","last_name":"Berryman","first_name":"Elizabeth"},{"orcid":"0000-0001-8501-6017","first_name":"Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"last_name":"Solís","first_name":"Ariadna González","full_name":"Solís, Ariadna González"},{"last_name":"Leier","first_name":"André","full_name":"Leier, André"},{"full_name":"Lago, Tatiana Marquez","last_name":"Lago","first_name":"Tatiana Marquez"},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Otegui, Marisa S.","first_name":"Marisa S.","last_name":"Otegui"}],"acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","_id":"18526","scopus_import":"1","publication_status":"published","ec_funded":1,"isi":1,"article_processing_charge":"Yes (in subscription journal)","article_number":"e2409407121","ddc":["570"],"type":"journal_article","OA_place":"publisher","fulldoi":"https://doi.org/10.1073/pnas.2409407121","has_accepted_license":"1","article_type":"original","abstract":[{"text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets.","lang":"eng"}],"title":"Endosomal membrane budding patterns in plants","publisher":"National Academy of Sciences","oa_version":"Published Version","researchdata_availability":"yes","issue":"44","OA_type":"hybrid","volume":121,"department":[{"_id":"AnSa"}],"date_created":"2024-11-10T23:01:59Z","citation":{"ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","ieee":"E. Weiner <i>et al.</i>, “Endosomal membrane budding patterns in plants,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. <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.2409407121\">10.1073/pnas.2409407121</a>","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. <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.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>.","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” <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.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>."},"das_tickbox":"1","date_published":"2024-10-29T00:00:00Z","month":"10","quality_controlled":"1","date_updated":"2026-09-24T10:41:24Z","oa":1,"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"}],"day":"29","doi":"10.1073/pnas.2409407121","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","file_date_updated":"2024-11-11T09:35:15Z","language":[{"iso":"eng"}],"file":[{"checksum":"21c82d2ab58ff99b2bd0489797be42e5","access_level":"open_access","date_created":"2024-11-11T09:35:15Z","content_type":"application/pdf","file_name":"2024_PNAS_Weiner.pdf","success":1,"relation":"main_file","creator":"dernst","file_id":"18538","date_updated":"2024-11-11T09:35:15Z","file_size":5268074}],"intvolume":"       121","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["001349500800007"],"pmid":["39441629"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Proceedings of the National Academy of Sciences of the United States of America","supplementarymaterial":"yes","pmid":1,"year":"2024","dataavailabilitystatement":"Electron tomogram files are deposited in EMPIAR under EMPIAR-12299 (54). All other data are included in the manuscript and/or supporting information"},{"related_material":{"record":[{"relation":"research_data","id":"22940","status":"public"}]},"acknowledged_ssus":[{"_id":"NMR"}],"year":"2024","external_id":{"pmid":["40384771"]},"publication":"Magnetic Resonance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"APC_amount":"1530 EUR","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2699-0016"]},"file_date_updated":"2024-05-22T07:01:15Z","status":"public","corr_author":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2024-05-22T07:01:15Z","creator":"dernst","file_id":"15413","file_size":6657865,"relation":"main_file","file_name":"2024_MagneticResonance_Napoli.pdf","content_type":"application/pdf","success":1,"checksum":"80ea50114e428461ca9530d3bd5d89e4","date_created":"2024-05-22T07:01:15Z","access_level":"open_access"}],"intvolume":"         5","project":[{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"},{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"day":"19","doi":"10.5194/mr-5-33-2024","date_published":"2024-04-19T00:00:00Z","month":"04","quality_controlled":"1","date_updated":"2026-09-24T10:36:36Z","oa":1,"department":[{"_id":"PaSc"}],"date_created":"2024-05-16T15:02:43Z","citation":{"ieee":"F. Napoli <i>et al.</i>, “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” <i>Magnetic Resonance</i>, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024.","short":"F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49.","ista":"Napoli F, Guan J-Y, Arnaud C-A, Macek P, Fraga H, Breyton C, Schanda P. 2024. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. Magnetic Resonance. 5(1), 33–49.","apa":"Napoli, F., Guan, J.-Y., Arnaud, C.-A., Macek, P., Fraga, H., Breyton, C., &#38; Schanda, P. (2024). Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>","mla":"Napoli, Federico, et al. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>.","chicago":"Napoli, Federico, Jia-Ying Guan, Charles-Adrien Arnaud, Pavel Macek, Hugo Fraga, Cécile Breyton, and Paul Schanda. “Deuteration of Proteins Boosted by Cell Lysates: High-Resolution Amide and Ha Magic-Angle-Spinning (MAS) NMR without the Reprotonation Bottleneck.” <i>Magnetic Resonance</i>. Copernicus Publications, 2024. <a href=\"https://doi.org/10.5194/mr-5-33-2024\">https://doi.org/10.5194/mr-5-33-2024</a>.","ama":"Napoli F, Guan J-Y, Arnaud C-A, et al. Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck. <i>Magnetic Resonance</i>. 2024;5(1):33-49. doi:<a href=\"https://doi.org/10.5194/mr-5-33-2024\">10.5194/mr-5-33-2024</a>"},"oa_version":"Published Version","OA_type":"gold","volume":5,"issue":"1","article_type":"original","has_accepted_license":"1","publisher":"Copernicus Publications","abstract":[{"lang":"eng","text":"Amide-proton-detected magic-angle-spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with a H2O-based culture medium doped with deuterated cell lysate allow scientists to overcome this “reprotonation bottleneck” while retaining a high level of deuteration (ca. 80 %) and narrow linewidths. We quantified coherence lifetimes of several proteins prepared with this labeling pattern over a range of magic-angle-spinning (MAS) frequencies (40–100 kHz). We demonstrate that under commonly used conditions (50–60 kHz MAS), the amide 1H linewidths with our labeling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33–50 kDa size range, many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and we show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by the de novo assignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm 100 kHz MAS experiments."}],"title":"Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck","ddc":["530"],"type":"journal_article","OA_place":"publisher","fulldoi":"https://doi.org/10.5194/mr-5-33-2024","article_processing_charge":"Yes","publication_status":"published","page":"33-49","acknowledgement":"We thank Dominique Madern (IBS Grenoble) for providing the plasmid for MalDH and feedback on the article, Alicia Vallet for excellent support at the Grenoble NMR facility, and Petra Rovo and Margarita Valhondo at the IST Austria NMR Service Unit. We thank Dorothea Anrather in the mass spectrometry facility of Max Perutz Labs for the mass spectrometry analysis using the instruments of the Vienna BioCenter Core Facilities (VBCF). We are grateful to Jean-Pierre Andrieu (Plateforme Seq3A, IBS Grenoble) for the analysis of the amino acid composition of the in-house-prepared lysates. We are grateful to Rasmus Linser (Technical University Dortmund) for sharing a paper draft describing a similar study. This work was supported by the Austrian Science Fund (FWF; project number I5812-B). We thank Tobias Schubeis (Lyon) and the reviewers for constructive input.\r\nThis research has been supported by the Austrian Science Fund (grant no. I5812-B). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for 40 Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, 45 CEA). Charles-Adrien Arnaud was funded by GRAL.","_id":"15401","scopus_import":"1","author":[{"id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","full_name":"Napoli, Federico","orcid":"0000-0002-9043-136X","first_name":"Federico","last_name":"Napoli"},{"full_name":"Guan, Jia-Ying","last_name":"Guan","first_name":"Jia-Ying"},{"last_name":"Arnaud","first_name":"Charles-Adrien","full_name":"Arnaud, Charles-Adrien"},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"full_name":"Fraga, Hugo","first_name":"Hugo","last_name":"Fraga"},{"first_name":"Cécile","last_name":"Breyton","full_name":"Breyton, Cécile"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}]},{"_id":"18072","scopus_import":"1","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).","author":[{"last_name":"Hernandez-Armendariz","first_name":"Alberto","full_name":"Hernandez-Armendariz, Alberto"},{"last_name":"Sorichetti","first_name":"Valerio","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"full_name":"Hayashi, Yuki","last_name":"Hayashi","first_name":"Yuki"},{"first_name":"Zuzana","last_name":"Koskova","full_name":"Koskova, Zuzana"},{"full_name":"Brunner, Andreas","last_name":"Brunner","first_name":"Andreas"},{"full_name":"Ellenberg, Jan","first_name":"Jan","last_name":"Ellenberg"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Cuylen-Haering, Sara","last_name":"Cuylen-Haering","first_name":"Sara"}],"isi":1,"ec_funded":1,"publication_status":"published","page":"P3254-3270.E9","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","article_type":"original","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."}],"publisher":"Cell Press","title":"A liquid-like coat mediates chromosome clustering during mitotic exit","fulldoi":"https://doi.org/10.1016/j.molcel.2024.07.022","ddc":["570"],"type":"journal_article","das_tickbox":"1","citation":{"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.","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.","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>","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>.","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>","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>."},"department":[{"_id":"AnSa"}],"date_created":"2024-09-15T22:01:41Z","researchdata_availability":"yes","oa_version":"Published Version","volume":84,"issue":"17","doi":"10.1016/j.molcel.2024.07.022","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"}],"day":"05","quality_controlled":"1","oa":1,"date_updated":"2026-09-24T10:43:18Z","date_published":"2024-09-05T00:00:00Z","month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"success":1,"content_type":"application/pdf","file_name":"2024_MolecularCell_HernandezArmendariz.pdf","access_level":"open_access","date_created":"2024-09-16T07:38:38Z","checksum":"3f360e0287b8ec79fb2b8b02b5070360","file_size":11654644,"creator":"dernst","date_updated":"2024-09-16T07:38:38Z","file_id":"18075","relation":"main_file"}],"intvolume":"        84","publication_identifier":{"issn":["1097-2765"],"eissn":["1097-4164"]},"file_date_updated":"2024-09-16T07:38:38Z","status":"public","related_material":{"record":[{"id":"22987","relation":"research_data","status":"public"}]},"year":"2024","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","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Molecular Cell","supplementarymaterial":"yes","pmid":1,"external_id":{"pmid":["39153474"],"isi":["001309051100001"]}},{"isi":1,"ec_funded":1,"page":"18485-18492","publication_status":"published","scopus_import":"1","_id":"17239","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).","author":[{"full_name":"Garcia-Sacristan, Clara","last_name":"Garcia-Sacristan","first_name":"Clara"},{"full_name":"Gisbert, Victor G.","first_name":"Victor G.","last_name":"Gisbert"},{"first_name":"Kevin","last_name":"Klein","id":"1e7ede04-9e54-11f0-9ec4-8d4d5563c398","full_name":"Klein, Kevin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Ricardo","last_name":"Garcia","full_name":"Garcia, Ricardo"}],"article_type":"original","has_accepted_license":"1","publisher":"American Chemical Society","title":"In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures","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."}],"fulldoi":"https://doi.org/10.1021/acsnano.4c03839","OA_place":"publisher","ddc":["540"],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","doi":"10.1021/acsnano.4c03839","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960"}],"day":"16","quality_controlled":"1","oa":1,"date_updated":"2026-09-24T10:43:56Z","date_published":"2024-07-16T00:00:00Z","month":"07","citation":{"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.","short":"C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 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.","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>","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>.","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>","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>."},"das_tickbox":"0","department":[{"_id":"AnSa"}],"date_created":"2024-07-14T22:01:12Z","oa_version":"Published Version","researchdata_availability":"no","volume":18,"issue":"28","OA_type":"hybrid","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"ACS Nano","supplementarymaterial":"yes","pmid":1,"external_id":{"isi":["001263155500001"],"pmid":["38958189"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_id":"18808","creator":"dernst","date_updated":"2025-01-09T12:06:48Z","file_size":10036838,"checksum":"b7e9ce718e92f568bcb3810e8e28e458","date_created":"2025-01-09T12:06:48Z","access_level":"open_access","file_name":"2024_ACSNano_GarciaSacristan.pdf","content_type":"application/pdf","success":1}],"intvolume":"        18","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"file_date_updated":"2025-01-09T12:06:48Z","status":"public"},{"language":[{"iso":"eng"}],"intvolume":"       110","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Physical Review E","supplementarymaterial":"no","pmid":1,"external_id":{"arxiv":["2405.02820"],"pmid":["39916158"],"isi":["001379135100004"]},"year":"2024","researchdata_availability":"no","oa_version":"Preprint","volume":110,"OA_type":"green","issue":"6","citation":{"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.","short":"F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024).","ista":"Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 110(6), 064403.","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>","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>.","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>"},"das_tickbox":"0","department":[{"_id":"AnSa"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2405.02820","open_access":"1"}],"date_created":"2024-12-22T23:01:48Z","quality_controlled":"1","date_updated":"2026-09-24T10:43:36Z","oa":1,"date_published":"2024-12-10T00:00:00Z","month":"12","doi":"10.1103/PhysRevE.110.064403","day":"10","article_processing_charge":"No","OA_place":"repository","fulldoi":"https://doi.org/10.1103/PhysRevE.110.064403","arxiv":1,"article_number":"064403","type":"journal_article","article_type":"original","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."}],"publisher":"American Physical Society","title":"Coat stiffening can explain invagination of clathrin-coated membranes","author":[{"orcid":"0000-0001-8501-6017","last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F"},{"first_name":"Ulrich S.","last_name":"Schwarz","full_name":"Schwarz, Ulrich S."}],"_id":"18704","scopus_import":"1","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.","publication_status":"published","isi":1},{"article_processing_charge":"No","status":"public","related_material":{"record":[{"id":"18072","relation":"used_in_publication","status":"public"}]},"year":"2024","abstract":[{"lang":"eng","text":"Imaging data of all main and supplementary figures. The files are the raw microcopy files including all Z-slices and timepoints. "}],"publisher":"Repository","title":"A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.","ddc":["570"],"type":"research_data_reference","fulldoi":"https://doi.org/10.17632/dwcpnncsyd.1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","department":[{"_id":"AnSa"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/dwcpnncsyd.1"}],"date_created":"2026-09-24T10:38:23Z","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>.","short":"A. Hernandez-Armendariz, S. Cuylen-Haering, (2024).","ieee":"A. Hernandez-Armendariz and S. Cuylen-Haering, “A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.” Repository, 2024.","ama":"Hernandez-Armendariz A, Cuylen-Haering S. A liquid-like coat mediates chromosome clustering during mitotic exit. 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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>."},"_id":"15126","oa_version":"Published Version","author":[{"full_name":"Giubertoni, G.","last_name":"Giubertoni","first_name":"G."},{"full_name":"Woutersen, S.","first_name":"S.","last_name":"Woutersen"}],"year":"2024","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"15116"}]},"has_accepted_license":"1","extern":"1","title":"Dataset Collagen Self Assembly in H2O and D2O","publisher":"Figshare","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"}],"ddc":["550"],"type":"research_data_reference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.21942/UVA.24829896","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_name":"2024_SIGGRAPH_Rao.pdf","success":1,"checksum":"4650f6d1419e675929133e46a91ca177","date_created":"2024-08-05T08:25:18Z","access_level":"open_access","creator":"dernst","date_updated":"2024-08-05T08:25:18Z","file_id":"17387","file_size":59683257,"relation":"main_file"}],"status":"public","file_date_updated":"2024-08-05T08:25:18Z","publication_identifier":{"isbn":["9798400705250"]},"year":"2024","publication":"Proceedings - SIGGRAPH 2024 Conference Papers","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2407.10487"],"isi":["001282218200076"]},"citation":{"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>.","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>. 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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.","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."},"das_tickbox":"0","date_created":"2024-08-04T22:01:21Z","department":[{"_id":"BeBi"}],"researchdata_availability":"no","oa_version":"Published Version","doi":"10.1145/3641519.3657470","day":"13","date_updated":"2026-09-24T11:00:21Z","oa":1,"quality_controlled":"1","month":"07","date_published":"2024-07-13T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","title":"Lite2Relight: 3D-aware single image portrait relighting","publisher":"Association for Computing Machinery","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."}],"has_accepted_license":"1","fulldoi":"https://doi.org/10.1145/3641519.3657470","type":"conference","article_number":"41","ddc":["000"],"arxiv":1,"scopus_import":"1","_id":"17374","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.","author":[{"full_name":"Rao, Pramod","first_name":"Pramod","last_name":"Rao"},{"last_name":"Fox","first_name":"Gereon","full_name":"Fox, Gereon"},{"full_name":"Meka, Abhimitra","last_name":"Meka","first_name":"Abhimitra"},{"full_name":"Mallikarjun, B. R.","first_name":"B. R.","last_name":"Mallikarjun"},{"first_name":"Fangneng","last_name":"Zhan","full_name":"Zhan, Fangneng"},{"last_name":"Weyrich","first_name":"Tim","full_name":"Weyrich, Tim"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"full_name":"Elgharib, Mohamed","first_name":"Mohamed","last_name":"Elgharib"},{"first_name":"Christian","last_name":"Theobalt","full_name":"Theobalt, Christian"}],"conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-27","end_date":"2024-08-01","location":"Denver, CO, United States"},"isi":1,"publication_status":"published"},{"type":"journal_article","ddc":["570"],"fulldoi":"https://doi.org/10.1038/s41567-024-02597-8","OA_place":"publisher","abstract":[{"lang":"eng","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."}],"publisher":"Springer Nature","title":"Self-organization of mortal filaments and its role in bacterial division ring formation","has_accepted_license":"1","article_type":"original","popular_science":"1","article_processing_charge":"Yes (in subscription journal)","page":"1670-1678","publication_status":"published","ec_funded":1,"isi":1,"author":[{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo"},{"full_name":"Whitley, Kevin D.","last_name":"Whitley","first_name":"Kevin D."},{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","orcid":"0000-0001-9198-2182 "},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"},{"last_name":"Holden","first_name":"Séamus","full_name":"Holden, Séamus"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"}],"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.).","_id":"17460","scopus_import":"1","external_id":{"pmid":["39416851"],"isi":["001289394500005"]},"pmid":1,"supplementarymaterial":"yes","publication":"Nature Physics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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","year":"2024","related_material":{"record":[{"status":"public","relation":"research_data","id":"22988"}]},"status":"public","file_date_updated":"2025-04-14T06:06:35Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"intvolume":"        20","corr_author":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":8058249,"file_id":"19556","creator":"dernst","date_updated":"2025-04-14T06:06:35Z","access_level":"open_access","date_created":"2025-04-14T06:06:35Z","checksum":"c4842152e2b90d67f48ea8c9ed7c473b","success":1,"file_name":"2024_NaturePhysics_VanhilleCampos.pdf","content_type":"application/pdf"}],"APC_amount":"12348 EUR","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","date_published":"2024-10-01T00:00:00Z","oa":1,"date_updated":"2026-09-24T10:58:39Z","quality_controlled":"1","day":"01","project":[{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division","grant_number":"P34607"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"}],"doi":"10.1038/s41567-024-02597-8","volume":20,"OA_type":"hybrid","oa_version":"Published Version","researchdata_availability":"yes","date_created":"2024-08-25T22:01:08Z","department":[{"_id":"AnSa"},{"_id":"MaLo"}],"citation":{"short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","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.","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.","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>.","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>","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>.","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>"},"das_tickbox":"1"},{"file_date_updated":"2024-07-22T11:07:14Z","status":"public","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"intvolume":"       132","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","date_created":"2024-07-22T11:07:14Z","checksum":"5eef1d920f6fe700d7856098000d05f1","success":1,"file_name":"2024_IJCV_Rao.pdf","content_type":"application/pdf","relation":"main_file","file_size":9942520,"date_updated":"2024-07-22T11:07:14Z","creator":"dernst","file_id":"17304"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["38549787"],"isi":["001091935600002"]},"pmid":1,"publication":"International Journal of Computer Vision","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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.","year":"2024","volume":132,"researchdata_availability":"no (restricted access)","oa_version":"Published Version","date_created":"2023-11-05T23:00:54Z","department":[{"_id":"BeBi"}],"citation":{"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.","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>","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>.","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>."},"das_tickbox":"1","month":"04","date_published":"2024-04-01T00:00:00Z","oa":1,"date_updated":"2026-09-24T10:59:50Z","quality_controlled":"1","day":"01","doi":"10.1007/s11263-023-01899-3","article_processing_charge":"Yes (via OA deal)","type":"journal_article","ddc":["000"],"fulldoi":"https://doi.org/10.1007/s11263-023-01899-3","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"}],"publisher":"Springer Nature","title":"A deeper analysis of volumetric relightiable faces","has_accepted_license":"1","article_type":"original","author":[{"full_name":"Rao, Pramod","last_name":"Rao","first_name":"Pramod"},{"last_name":"Mallikarjun","first_name":"B. R.","full_name":"Mallikarjun, B. R."},{"last_name":"Fox","first_name":"Gereon","full_name":"Fox, Gereon"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"},{"full_name":"Zhan, Fangneng","first_name":"Fangneng","last_name":"Zhan"},{"first_name":"Ayush","last_name":"Tewari","full_name":"Tewari, Ayush"},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"},{"full_name":"Elgharib, Mohamed","last_name":"Elgharib","first_name":"Mohamed"}],"acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.","_id":"14488","scopus_import":"1","page":"1148-1166","publication_status":"published","isi":1},{"publication_status":"published","conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28","end_date":"2024-08-01","location":"Denver, CO, United States"},"isi":1,"author":[{"last_name":"Tojo","first_name":"Kenji","full_name":"Tojo, Kenji"},{"full_name":"Shamir, Ariel","first_name":"Ariel","last_name":"Shamir"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"}],"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.","scopus_import":"1","_id":"18912","type":"conference","article_number":"134","fulldoi":"https://doi.org/10.1145/3641519.3657453","title":"Fabricable 3D wire art","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."}],"publisher":"ACM","article_processing_charge":"No","month":"07","date_published":"2024-07-01T00:00:00Z","date_updated":"2026-09-24T11:00:48Z","quality_controlled":"1","day":"01","doi":"10.1145/3641519.3657453","OA_type":"closed access","oa_version":"None","researchdata_availability":"no","date_created":"2025-01-27T13:47:35Z","department":[{"_id":"BeBi"}],"das_tickbox":"0","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>","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>.","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."},"external_id":{"isi":["001282218200059"]},"publication":"SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers","supplementarymaterial":"yes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","status":"public","publication_identifier":{"isbn":["9798400705250"]},"language":[{"iso":"eng"}],"corr_author":"1"},{"article_processing_charge":"No","status":"public","title":"Self-organization of mortal filaments and its role in bacterial division ring formation","abstract":[{"lang":"eng","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."}],"publisher":"Repository","related_material":{"record":[{"relation":"used_in_publication","id":"17460","status":"public"}]},"year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.5522/04/24754527","OA_place":"repository","type":"research_data_reference","ddc":["570"],"_id":"22988","citation":{"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>","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>.","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>","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>.","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>.","ieee":"C. Vanhille Campos and A. Saric, “Self-organization of mortal filaments and its role in bacterial division ring formation.” Repository, 2024.","short":"C. Vanhille Campos, A. Saric, (2024)."},"date_created":"2026-09-24T10:56:29Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5522/04/24754527"}],"department":[{"_id":"AnSa"},{"_id":"MaLo"}],"author":[{"full_name":"Vanhille Campos, Christian","last_name":"Vanhille Campos","first_name":"Christian"},{"full_name":"Saric, Andela","last_name":"Saric","first_name":"Andela"}],"OA_type":"green","oa_version":"None","doi":"10.5522/04/24754527","day":"11","oa":1,"date_updated":"2026-09-24T10:58:40Z","month":"07","date_published":"2024-07-11T00:00:00Z"},{"publication_status":"published","isi":1,"author":[{"last_name":"Cecalev","first_name":"Daniela","full_name":"Cecalev, Daniela"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"},{"first_name":"Rafael","last_name":"Galupa","full_name":"Galupa, Rafael"}],"scopus_import":"1","_id":"17458","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.","fulldoi":"https://doi.org/10.1242/dev.202891","type":"journal_article","article_number":"dev202891","ddc":["599"],"abstract":[{"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.","lang":"eng"}],"title":"Compensation of gene dosage on the mammalian X","publisher":"Company of Biologists","article_type":"original","has_accepted_license":"1","popular_science":"1","article_processing_charge":"Yes (in subscription journal)","oa":1,"date_updated":"2026-09-24T11:05:40Z","quality_controlled":"1","month":"08","date_published":"2024-08-14T00:00:00Z","doi":"10.1242/dev.202891","day":"14","volume":151,"issue":"15","researchdata_availability":"no","oa_version":"Published Version","citation":{"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>.","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>","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>.","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>","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.","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."},"das_tickbox":"0","date_created":"2024-08-25T22:01:07Z","department":[{"_id":"BeVi"}],"pmid":1,"publication":"Development","supplementarymaterial":"no","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"year":"2024","intvolume":"       151","language":[{"iso":"eng"}],"file":[{"file_id":"17464","date_updated":"2024-08-28T10:32:16Z","creator":"cchlebak","file_size":2085135,"relation":"main_file","file_name":"2024_Development_Cecalev.pdf","content_type":"application/pdf","success":1,"checksum":"5e428bda0440d3f957c694b315a8f2a9","date_created":"2024-08-28T10:32:16Z","access_level":"open_access"}],"status":"public","file_date_updated":"2024-08-28T10:32:16Z","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}]