--- _id: '15318' abstract: - lang: eng text: We consider a gas of N weakly interacting bosons in the ground state. Such gases exhibit Bose–Einstein condensation. The binding energy is defined as the energy it takes to remove one particle from the gas. In this article, we prove an asymptotic expansion for the binding energy, and compute the first orders explicitly for the homogeneous gas. Our result addresses in particular a conjecture by Nam (Lett Math Phys 108(1):141–159, 2018), and provides an asymptotic expansion of the ionization energy of bosonic atoms. acknowledgement: "It is a pleasure to thank Phan Thành Nam for helpful discussions on bosonic atoms. L.B. was supported by the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111). N.L. gratefully 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.\r\nOpen Access funding enabled and organized by Projekt DEAL." article_number: '48' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Sören P full_name: Petrat, Sören P id: 40AC02DC-F248-11E8-B48F-1D18A9856A87 last_name: Petrat orcid: 0000-0002-9166-5889 citation: ama: Bossmann L, Leopold NK, Mitrouskas DJ, Petrat SP. A note on the binding energy for Bosons in the mean-field limit. Journal of Statistical Physics. 2024;191(4). doi:10.1007/s10955-024-03260-5 apa: Bossmann, L., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2024). A note on the binding energy for Bosons in the mean-field limit. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-024-03260-5 chicago: Bossmann, Lea, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “A Note on the Binding Energy for Bosons in the Mean-Field Limit.” Journal of Statistical Physics. Springer Nature, 2024. https://doi.org/10.1007/s10955-024-03260-5. ieee: L. Bossmann, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “A note on the binding energy for Bosons in the mean-field limit,” Journal of Statistical Physics, vol. 191, no. 4. Springer Nature, 2024. ista: Bossmann L, Leopold NK, Mitrouskas DJ, Petrat SP. 2024. A note on the binding energy for Bosons in the mean-field limit. Journal of Statistical Physics. 191(4), 48. mla: Bossmann, Lea, et al. “A Note on the Binding Energy for Bosons in the Mean-Field Limit.” Journal of Statistical Physics, vol. 191, no. 4, 48, Springer Nature, 2024, doi:10.1007/s10955-024-03260-5. short: L. Bossmann, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Journal of Statistical Physics 191 (2024). das_tickbox: '1' dataavailabilitystatement: Data sharing not applicable to this article as no datasets were generated or analyzed during the current study. date_created: 2024-04-14T22:01:02Z date_published: 2024-04-06T00:00:00Z date_updated: 2026-09-17T11:05:18Z day: '06' ddc: - '510' department: - _id: RoSe doi: 10.1007/s10955-024-03260-5 external_id: arxiv: - '2307.13115' isi: - '001197663100002' file: - access_level: open_access checksum: 839242a9ec1c01158112de25f196e60d content_type: application/pdf creator: dernst date_created: 2024-04-16T11:09:37Z date_updated: 2024-04-16T11:09:37Z file_id: '15325' file_name: 2024_JourStatPhysics_Bossmann.pdf file_size: 398665 relation: main_file success: 1 file_date_updated: 2024-04-16T11:09:37Z fulldoi: https://doi.org/10.1007/s10955-024-03260-5 has_accepted_license: '1' intvolume: ' 191' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Journal of Statistical Physics publication_identifier: eissn: - 1572-9613 issn: - 0022-4715 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: not applicable scopus_import: '1' status: public supplementarymaterial: no title: A note on the binding energy for Bosons in the mean-field limit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 191 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17478' abstract: - lang: eng text: "We study the Fröhlich polaron model in R3, and prove a lower bound on its ground state energy as a function of the total momentum. The bound is asymptotically sharp at large coupling. In combination with a corresponding upper bound proved earlier (Mitrouskas et al. in Forum Math. Sigma 11:1–52, 2023), it shows that the energy is approximately parabolic below the continuum threshold, and that the polaron’s effective mass (defined as the semi-latus rectum of the\r\nparabola) is given by the celebrated Landau–Pekar formula. In particular, it diverges as α4 for large coupling constant α." article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Morris full_name: Brooks, Morris id: B7ECF9FC-AA38-11E9-AC9A-0930E6697425 last_name: Brooks orcid: 0000-0002-6249-0928 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Brooks M, Seiringer R. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques. 2024;140:271-309. doi:10.1007/s10240-024-00150-0' apa: 'Brooks, M., & Seiringer, R. (2024). The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques. Springer Nature. https://doi.org/10.1007/s10240-024-00150-0' chicago: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques. Springer Nature, 2024. https://doi.org/10.1007/s10240-024-00150-0.' ieee: 'M. Brooks and R. Seiringer, “The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass,” Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques, vol. 140. Springer Nature, pp. 271–309, 2024.' ista: 'Brooks M, Seiringer R. 2024. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques. 140, 271–309.' mla: 'Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques, vol. 140, Springer Nature, 2024, pp. 271–309, doi:10.1007/s10240-024-00150-0.' short: M. Brooks, R. Seiringer, Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques 140 (2024) 271–309. corr_author: '1' das_tickbox: '0' date_created: 2024-09-01T22:01:08Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-09-17T11:07:19Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s10240-024-00150-0 external_id: arxiv: - '2211.03353' isi: - '001297785000001' file: - access_level: open_access checksum: af3becc50f7534c9409d3ff8b5c47ed6 content_type: application/pdf creator: dernst date_created: 2025-01-13T08:13:42Z date_updated: 2025-01-13T08:13:42Z file_id: '18824' file_name: 2024_PublicMathIHES_Brooks.pdf file_size: 924342 relation: main_file success: 1 file_date_updated: 2025-01-13T08:13:42Z fulldoi: https://doi.org/10.1007/s10240-024-00150-0 has_accepted_license: '1' intvolume: ' 140' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 271-309 publication: Publications Mathematiques de l'Institut des Hautes Etudes Scientifiques publication_identifier: eissn: - 1618-1913 issn: - 0073-8301 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 140 year: '2024' ... --- OA_place: repository OA_type: green _id: '18948' abstract: - lang: eng 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. 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. alternative_title: - Fundamental Theories of Physics article_processing_charge: No arxiv: 1 author: - first_name: Lea full_name: Bossmann, Lea id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425 last_name: Bossmann orcid: 0000-0002-6854-1343 - first_name: Nikolai full_name: Leopold, Nikolai last_name: Leopold - first_name: David Johannes full_name: Mitrouskas, David Johannes id: cbddacee-2b11-11eb-a02e-a2e14d04e52d last_name: Mitrouskas - first_name: Sören full_name: Petrat, Sören last_name: Petrat 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. Physics and the Nature of Reality. Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:10.1007/978-3-031-45434-9_22' apa: 'Bossmann, L., Leopold, N., Mitrouskas, D. J., & 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, & N. Zanghi (Eds.), Physics and the Nature of Reality (Vol. 215, pp. 307–321). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-45434-9_22' 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 Physics and the Nature of Reality, edited by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21. FTPH. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-45434-9_22.' 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 Physics and the Nature of Reality, vol. 215, A. Bassi, S. Goldstein, R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321.' 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.' mla: 'Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.” Physics and the Nature of Reality, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024, pp. 307–21, doi:10.1007/978-3-031-45434-9_22.' 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. das_tickbox: '0' date_created: 2025-01-29T10:30:08Z date_published: 2024-02-04T00:00:00Z date_updated: 2026-09-17T11:08:01Z day: '04' department: - _id: RoSe doi: 10.1007/978-3-031-45434-9_22 editor: - first_name: Angelo full_name: Bassi, Angelo last_name: Bassi - first_name: Sheldon full_name: Goldstein, Sheldon last_name: Goldstein - first_name: Roderich full_name: Tumulka, Roderich last_name: Tumulka - first_name: Nino full_name: Zanghi, Nino last_name: Zanghi external_id: arxiv: - '2304.12910' fulldoi: https://doi.org/10.1007/978-3-031-45434-9_22 intvolume: ' 215' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.12910 month: '02' oa: 1 oa_version: Preprint page: 307-321 place: Cham publication: Physics and the Nature of Reality publication_identifier: eisbn: - '9783031454349' eissn: - 2365-6425 isbn: - '9783031454332' issn: - 0168-1222 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no scopus_import: '1' series_title: FTPH status: public supplementarymaterial: no title: 'Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications' type: book_chapter user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 215 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17457' abstract: - lang: eng 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." acknowledged_ssus: - _id: Bio - _id: EM-Fac 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. ' article_processing_charge: Yes article_type: original author: - first_name: Andreas full_name: Ritzau-Jost, Andreas last_name: Ritzau-Jost - first_name: Felix full_name: Gsell, Felix last_name: Gsell - first_name: Josefine full_name: Sell, Josefine last_name: Sell - first_name: Stefan full_name: Sachs, Stefan last_name: Sachs - first_name: Jacqueline-Claire full_name: Montanaro-Punzengruber, Jacqueline-Claire id: 3786AB44-F248-11E8-B48F-1D18A9856A87 last_name: Montanaro-Punzengruber - first_name: Toni full_name: Kirmann, Toni last_name: Kirmann - first_name: Sebastian full_name: Maaß, Sebastian last_name: Maaß - first_name: Sarosh R. full_name: Irani, Sarosh R. last_name: Irani - first_name: Christian full_name: Werner, Christian last_name: Werner - first_name: Christian full_name: Geis, Christian last_name: Geis - first_name: Markus full_name: Sauer, Markus last_name: Sauer - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Stefan full_name: Hallermann, Stefan last_name: Hallermann 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. Neurology, Neuroimmunology & Neuroinflammation. 2024;11(5):e200284. doi:10.1212/NXI.0000000000200284 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. Neurology, Neuroimmunology & Neuroinflammation. Wolters Kluwer. https://doi.org/10.1212/NXI.0000000000200284 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.” Neurology, Neuroimmunology & Neuroinflammation. Wolters Kluwer, 2024. https://doi.org/10.1212/NXI.0000000000200284. ieee: A. Ritzau-Jost et al., “LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening,” Neurology, Neuroimmunology & Neuroinflammation, vol. 11, no. 5. Wolters Kluwer, p. e200284, 2024. 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 & Neuroinflammation. 11(5), e200284. mla: Ritzau-Jost, Andreas, et al. “LGI1 Autoantibodies Enhance Synaptic Transmission by Presynaptic Kv1 Loss and Increased Action Potential Broadening.” Neurology, Neuroimmunology & Neuroinflammation, vol. 11, no. 5, Wolters Kluwer, 2024, p. e200284, doi:10.1212/NXI.0000000000200284. 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 & Neuroinflammation 11 (2024) e200284. das_tickbox: '1' dataavailabilitystatement: Data that support the findings of this study are available from the corresponding author on reasonable request. date_created: 2024-08-25T22:01:07Z date_published: 2024-09-01T00:00:00Z date_updated: 2026-09-17T11:27:41Z day: '01' ddc: - '570' department: - _id: RySh doi: 10.1212/NXI.0000000000200284 external_id: isi: - '001291908600001' pmid: - '39141878' file: - access_level: open_access checksum: 1e6d1230e0387f72752e3268f5330c9e content_type: application/pdf creator: dernst date_created: 2025-01-09T13:42:42Z date_updated: 2025-01-09T13:42:42Z file_id: '18815' file_name: 2024_NeurologyNeuroimmNeuroinflamm_RitzauJost.pdf file_size: 855818 relation: main_file success: 1 file_date_updated: 2025-01-09T13:42:42Z fulldoi: https://doi.org/10.1212/NXI.0000000000200284 has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: e200284 pmid: 1 project: - _id: 05970B30-7A3F-11EA-A408-12923DDC885E grant_number: I04638 name: LGI1 antibody-induced pathophysiology in synapses publication: Neurology, Neuroimmunology & Neuroinflammation publication_identifier: eissn: - 2332-7812 publication_status: published publisher: Wolters Kluwer quality_controlled: '1' related_material: link: - relation: earlier_version url: https://doi.org/10.1101/2023.10.04.560631 researchdata_availability: upon request scopus_import: '1' status: public supplementarymaterial: yes title: LGI1 autoantibodies enhance synaptic transmission by presynaptic Kv1 loss and increased action potential broadening tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 11 year: '2024' ... --- _id: '18958' abstract: - lang: eng 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. 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”. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Simone full_name: Warzel, Simone last_name: Warzel citation: ama: Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach Reports. 2024;20(3):2247-2302. doi:10.4171/owr/2023/39 apa: Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2024). Many-body quantum systems. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2023/39 chicago: Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel. “Many-Body Quantum Systems.” Oberwolfach Reports. EMS Press, 2024. https://doi.org/10.4171/owr/2023/39. ieee: C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,” Oberwolfach Reports, vol. 20, no. 3. EMS Press, pp. 2247–2302, 2024. ista: Hainzl C, Schlein B, Seiringer R, Warzel S. 2024. Many-body quantum systems. Oberwolfach Reports. 20(3), 2247–2302. mla: Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports, vol. 20, no. 3, EMS Press, 2024, pp. 2247–302, doi:10.4171/owr/2023/39. short: C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 20 (2024) 2247–2302. das_tickbox: '0' date_created: 2025-01-29T13:09:28Z date_published: 2024-04-18T00:00:00Z date_updated: 2026-09-17T11:09:16Z day: '18' department: - _id: RoSe doi: 10.4171/owr/2023/39 fulldoi: https://doi.org/10.4171/owr/2023/39 intvolume: ' 20' issue: '3' language: - iso: eng month: '04' oa_version: None page: 2247-2302 publication: Oberwolfach Reports publication_identifier: eissn: - 1660-8941 issn: - 1660-8933 publication_status: published publisher: EMS Press quality_controlled: '1' researchdata_availability: no status: public supplementarymaterial: no title: Many-body quantum systems type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- _id: '14844' abstract: - lang: eng 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.' 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). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ali full_name: Azadbakht, Ali last_name: Azadbakht - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Daniela J. full_name: Kraft, Daniela J. last_name: Kraft citation: ama: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. 2024;123(3):307-316. doi:10.1016/j.bpj.2023.12.020 apa: Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (2024). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020 chicago: Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal. Elsevier, 2024. https://doi.org/10.1016/j.bpj.2023.12.020. ieee: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” Biophysical Journal, vol. 123, no. 3. Elsevier, pp. 307–316, 2024. 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. mla: Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal, vol. 123, no. 3, Elsevier, 2024, pp. 307–16, doi:10.1016/j.bpj.2023.12.020. short: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal 123 (2024) 307–316. das_tickbox: '0' date_created: 2024-01-21T23:00:56Z date_published: 2024-02-06T00:00:00Z date_updated: 2026-09-24T10:26:59Z day: '06' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.bpj.2023.12.020 ec_funded: 1 external_id: isi: - '001185235900001' pmid: - '38158654' file: - access_level: open_access checksum: 1c8fe1cf950394875b65b90da86428ff content_type: application/pdf creator: dernst date_created: 2024-07-16T12:09:55Z date_updated: 2024-07-16T12:09:55Z file_id: '17266' file_name: 2024_BiophysicalJournal_Azadbakht.pdf file_size: 3189926 relation: main_file success: 1 file_date_updated: 2024-07-16T12:09:55Z fulldoi: https://doi.org/10.1016/j.bpj.2023.12.020 has_accepted_license: '1' intvolume: ' 123' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '02' oa: 1 oa_version: Published Version page: 307-316 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Biophysical Journal publication_identifier: eissn: - 1542-0086 issn: - 0006-3495 publication_status: published publisher: Elsevier quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Nonadditivity in interactions between three membrane-wrapped colloidal spheres tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2024' ... --- APC_amount: 5936,71 EUR OA_place: publisher OA_type: hybrid _id: '15001' abstract: - lang: eng 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." 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.). article_number: e2220075121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Samo full_name: Curk, Samo id: 031eff0d-d481-11ee-8508-cd12a7a86e5b last_name: Curk orcid: 0000-0001-6160-9766 - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Daan full_name: Frenkel, Daan last_name: Frenkel - first_name: Sara full_name: Linse, Sara last_name: Linse - first_name: Thomas C.T. full_name: Michaels, Thomas C.T. last_name: Michaels - first_name: Tuomas P.J. full_name: Knowles, Tuomas P.J. last_name: Knowles - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Curk S, Krausser J, Meisl G, et al. 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. 2024;121(7). doi:10.1073/pnas.2220075121 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. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121 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.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121. ieee: S. Curk et al., “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, vol. 121, no. 7. National Academy of Sciences, 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. mla: Curk, Samo, et al. “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, vol. 121, no. 7, e2220075121, National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121. 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). corr_author: '1' das_tickbox: '1' dataavailabilitystatement: Aggregation data and the source code for the coarse-grained computer model have been deposited in Figshare (https://figshare.com/s/85798bba4ebc68d822ed) date_created: 2024-02-18T23:01:00Z date_published: 2024-02-13T00:00:00Z date_updated: 2026-09-24T10:27:36Z day: '13' ddc: - '570' department: - _id: AnSa doi: 10.1073/pnas.2220075121 ec_funded: 1 external_id: isi: - '001169063600007' pmid: - '38335256' file: - access_level: open_access checksum: 5aeb65bcc0dd829b1f9ab307c5031d4b content_type: application/pdf creator: dernst date_created: 2024-02-26T08:20:00Z date_updated: 2024-02-26T08:20:00Z file_id: '15026' file_name: 2024_PNAS_Curk.pdf file_size: 7699487 relation: main_file success: 1 file_date_updated: 2024-02-26T08:20:00Z fulldoi: https://doi.org/10.1073/pnas.2220075121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: record: - id: '15027' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- DOAJ_listed: '1' _id: '17050' abstract: - lang: eng text: The process of polymer condensation, i.e., the formation of bonds between reactive end groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing polymer condensation in competition with cyclization. Using a generalized Smoluchowski theory, molecular dynamics simulations and experiments with DNA and ATP-consuming T4 ligase, we find that this system displays a transition, from a ring-dominated regime with finite-length chains at infinite time to a linear-polymers-dominated one with chains that keep growing in time. Finally, we show that fluids prepared close to the transition may have widely different compositions and rheology at large condensation times. acknowledgement: D.M. acknowledges the support of the Royal Society via a University Research Fellowship. This project has received support from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 947918 to D.M. and No. 677532 to M.L.). The authors acknowledge insightful discussions with Daan Noordermeer and Antonio Valdes, who also kindly gifted us with the 1288 plasmid. article_number: '023189' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Maria full_name: Panoukidou, Maria last_name: Panoukidou - first_name: Simon full_name: Weir, Simon last_name: Weir - first_name: Valerio full_name: Sorichetti, Valerio id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b last_name: Sorichetti orcid: 0000-0002-9645-6576 - first_name: Yair Gutierrez full_name: Fosado, Yair Gutierrez last_name: Fosado - first_name: Martin full_name: Lenz, Martin last_name: Lenz - first_name: Davide full_name: Michieletto, Davide last_name: Michieletto citation: ama: Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. Runaway transition in irreversible polymer condensation with cyclization. Physical Review Research. 2024;6(2). doi:10.1103/PhysRevResearch.6.023189 apa: Panoukidou, M., Weir, S., Sorichetti, V., Fosado, Y. G., Lenz, M., & Michieletto, D. (2024). Runaway transition in irreversible polymer condensation with cyclization. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.023189 chicago: Panoukidou, Maria, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado, Martin Lenz, and Davide Michieletto. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.023189. ieee: M. Panoukidou, S. Weir, V. Sorichetti, Y. G. Fosado, M. Lenz, and D. Michieletto, “Runaway transition in irreversible polymer condensation with cyclization,” Physical Review Research, vol. 6, no. 2. American Physical Society, 2024. ista: Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. 2024. Runaway transition in irreversible polymer condensation with cyclization. Physical Review Research. 6(2), 023189. mla: Panoukidou, Maria, et al. “Runaway Transition in Irreversible Polymer Condensation with Cyclization.” Physical Review Research, vol. 6, no. 2, 023189, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.023189. short: M. Panoukidou, S. Weir, V. Sorichetti, Y.G. Fosado, M. Lenz, D. Michieletto, Physical Review Research 6 (2024). das_tickbox: '0' date_created: 2024-05-26T22:00:58Z date_published: 2024-05-01T00:00:00Z date_updated: 2026-09-24T10:26:36Z day: '01' ddc: - '530' department: - _id: AnSa doi: 10.1103/PhysRevResearch.6.023189 external_id: arxiv: - '2210.14010' file: - access_level: open_access checksum: 63a962d49ef1e21a3367d265784df14b content_type: application/pdf creator: dernst date_created: 2024-05-27T06:37:01Z date_updated: 2024-05-27T06:37:01Z file_id: '17055' file_name: 2024_PhysicalReviewResearch_Panoukidou.pdf file_size: 1409416 relation: main_file success: 1 file_date_updated: 2024-05-27T06:37:01Z fulldoi: https://doi.org/10.1103/PhysRevResearch.6.023189 has_accepted_license: '1' intvolume: ' 6' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Physical Review Research publication_identifier: eissn: - 2643-1564 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Runaway transition in irreversible polymer condensation with cyclization tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2024' ... --- _id: '15116' abstract: - lang: eng 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. 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. article_number: e2313162121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Giulia full_name: Giubertoni, Giulia last_name: Giubertoni - first_name: Liru full_name: Feng, Liru last_name: Feng - first_name: Kevin full_name: Klein, Kevin last_name: Klein - first_name: Guido full_name: Giannetti, Guido last_name: Giannetti - first_name: Luco full_name: Rutten, Luco last_name: Rutten - first_name: Yeji full_name: Choi, Yeji last_name: Choi - first_name: Anouk full_name: Van Der Net, Anouk last_name: Van Der Net - first_name: Gerard full_name: Castro-Linares, Gerard last_name: Castro-Linares - first_name: Federico full_name: Caporaletti, Federico last_name: Caporaletti - first_name: Dimitra full_name: Micha, Dimitra last_name: Micha - first_name: Johannes full_name: Hunger, Johannes last_name: Hunger - first_name: Antoine full_name: Deblais, Antoine last_name: Deblais - first_name: Daniel full_name: Bonn, Daniel last_name: Bonn - first_name: Nico full_name: Sommerdijk, Nico last_name: Sommerdijk - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Ioana M. full_name: Ilie, Ioana M. last_name: Ilie - first_name: Gijsje H. full_name: Koenderink, Gijsje H. last_name: Koenderink - first_name: Sander full_name: Woutersen, Sander last_name: Woutersen citation: ama: Giubertoni G, Feng L, Klein K, et al. 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. 2024;121(11). doi:10.1073/pnas.2313162121 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. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121 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.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121. ieee: G. Giubertoni et al., “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, vol. 121, no. 11. National Academy of Sciences, 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. mla: Giubertoni, Giulia, et al. “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, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121. 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). das_tickbox: '1' 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 date_created: 2024-03-17T23:00:57Z date_published: 2024-03-12T00:00:00Z date_updated: 2026-09-24T10:42:11Z day: '12' ddc: - '550' department: - _id: AnSa doi: 10.1073/pnas.2313162121 external_id: isi: - '001206387400001' pmid: - '38451946' file: - access_level: open_access checksum: a3f7fdc29dd9f0a38952ab4e322b3a05 content_type: application/pdf creator: dernst date_created: 2024-03-19T10:22:42Z date_updated: 2024-03-19T10:22:42Z file_id: '15125' file_name: 2024_PNAS_Giubertoni.pdf file_size: 12952586 relation: main_file success: 1 file_date_updated: 2024-03-19T10:22:42Z fulldoi: https://doi.org/10.1073/pnas.2313162121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '11' language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: record: - id: '15126' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18526' abstract: - lang: eng 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. 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. article_number: e2409407121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ethan full_name: Weiner, Ethan last_name: Weiner - first_name: Elizabeth full_name: Berryman, Elizabeth last_name: Berryman - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Ariadna González full_name: Solís, Ariadna González last_name: Solís - first_name: André full_name: Leier, André last_name: Leier - first_name: Tatiana Marquez full_name: Lago, Tatiana Marquez last_name: Lago - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Marisa S. full_name: Otegui, Marisa S. last_name: Otegui citation: ama: Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(44). doi:10.1073/pnas.2409407121 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. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2409407121 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.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2409407121. ieee: E. Weiner et al., “Endosomal membrane budding patterns in plants,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44. National Academy of Sciences, 2024. 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. mla: Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:10.1073/pnas.2409407121. 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). das_tickbox: '1' dataavailabilitystatement: Electron tomogram files are deposited in EMPIAR under EMPIAR-12299 (54). All other data are included in the manuscript and/or supporting information date_created: 2024-11-10T23:01:59Z date_published: 2024-10-29T00:00:00Z date_updated: 2026-09-24T10:41:24Z day: '29' ddc: - '570' department: - _id: AnSa doi: 10.1073/pnas.2409407121 ec_funded: 1 external_id: isi: - '001349500800007' pmid: - '39441629' file: - access_level: open_access checksum: 21c82d2ab58ff99b2bd0489797be42e5 content_type: application/pdf creator: dernst date_created: 2024-11-11T09:35:15Z date_updated: 2024-11-11T09:35:15Z file_id: '18538' file_name: 2024_PNAS_Weiner.pdf file_size: 5268074 relation: main_file success: 1 file_date_updated: 2024-11-11T09:35:15Z fulldoi: https://doi.org/10.1073/pnas.2409407121 has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '44' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Endosomal membrane budding patterns in plants tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- APC_amount: 1530 EUR OA_place: publisher OA_type: gold _id: '15401' 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. acknowledged_ssus: - _id: NMR 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." article_processing_charge: Yes article_type: original author: - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Jia-Ying full_name: Guan, Jia-Ying last_name: Guan - first_name: Charles-Adrien full_name: Arnaud, Charles-Adrien last_name: Arnaud - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Cécile full_name: Breyton, Cécile last_name: Breyton - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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. Magnetic Resonance. 2024;5(1):33-49. doi:10.5194/mr-5-33-2024' apa: '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. Copernicus Publications. https://doi.org/10.5194/mr-5-33-2024' 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.” Magnetic Resonance. Copernicus Publications, 2024. https://doi.org/10.5194/mr-5-33-2024.' ieee: 'F. Napoli et al., “Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck,” Magnetic Resonance, vol. 5, no. 1. Copernicus Publications, pp. 33–49, 2024.' 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.' 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.” Magnetic Resonance, vol. 5, no. 1, Copernicus Publications, 2024, pp. 33–49, doi:10.5194/mr-5-33-2024.' short: F. Napoli, J.-Y. Guan, C.-A. Arnaud, P. Macek, H. Fraga, C. Breyton, P. Schanda, Magnetic Resonance 5 (2024) 33–49. corr_author: '1' date_created: 2024-05-16T15:02:43Z date_published: 2024-04-19T00:00:00Z date_updated: 2026-09-24T10:36:36Z day: '19' ddc: - '530' department: - _id: PaSc doi: 10.5194/mr-5-33-2024 external_id: pmid: - '40384771' file: - access_level: open_access checksum: 80ea50114e428461ca9530d3bd5d89e4 content_type: application/pdf creator: dernst date_created: 2024-05-22T07:01:15Z date_updated: 2024-05-22T07:01:15Z file_id: '15413' file_name: 2024_MagneticResonance_Napoli.pdf file_size: 6657865 relation: main_file success: 1 file_date_updated: 2024-05-22T07:01:15Z fulldoi: https://doi.org/10.5194/mr-5-33-2024 has_accepted_license: '1' intvolume: ' 5' issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 33-49 pmid: 1 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Magnetic Resonance publication_identifier: issn: - 2699-0016 publication_status: published publisher: Copernicus Publications quality_controlled: '1' related_material: record: - id: '22940' relation: research_data status: public scopus_import: '1' status: public title: 'Deuteration of proteins boosted by cell lysates: High-resolution amide and Ha magic-angle-spinning (MAS) NMR without the reprotonation bottleneck' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '18072' 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. acknowledgement: We thank Daniel W. Gerlich for providing cell lines, the EMBL Advanced Light Microscopy Facility (ALMF) for support, Christian H. Haering and Thomas Quail for input on the manuscript, and Martina Dees for cloning several Ki-67 constructs. This work was supported by the German Research Foundation (DFG project number 402723784) and the Human Frontier Science Program (CDA00045/2019). A.H.-A. and A.B. have received PhD fellowships from the Boehringer Ingelheim Fonds, V.S. and A.Š. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960), and Y.H. was supported by a fellowship from the EMBL interdisciplinary Postdoc (EIPOD) program (Marie Sklodowska-Curie Actions, COFUND grant agreement 664726). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Alberto full_name: Hernandez-Armendariz, Alberto last_name: Hernandez-Armendariz - first_name: Valerio full_name: Sorichetti, Valerio id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b last_name: Sorichetti orcid: 0000-0002-9645-6576 - first_name: Yuki full_name: Hayashi, Yuki last_name: Hayashi - first_name: Zuzana full_name: Koskova, Zuzana last_name: Koskova - first_name: Andreas full_name: Brunner, Andreas last_name: Brunner - first_name: Jan full_name: Ellenberg, Jan last_name: Ellenberg - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Sara full_name: Cuylen-Haering, Sara last_name: Cuylen-Haering citation: ama: Hernandez-Armendariz A, Sorichetti V, Hayashi Y, et al. A liquid-like coat mediates chromosome clustering during mitotic exit. Molecular Cell. 2024;84(17):P3254-3270.E9. doi:10.1016/j.molcel.2024.07.022 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. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2024.07.022 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.” Molecular Cell. Cell Press, 2024. https://doi.org/10.1016/j.molcel.2024.07.022. ieee: A. Hernandez-Armendariz et al., “A liquid-like coat mediates chromosome clustering during mitotic exit,” Molecular Cell, vol. 84, no. 17. Cell Press, p. P3254–3270.E9, 2024. 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. mla: Hernandez-Armendariz, Alberto, et al. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit.” Molecular Cell, vol. 84, no. 17, Cell Press, 2024, p. P3254–3270.E9, doi:10.1016/j.molcel.2024.07.022. 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. das_tickbox: '1' dataavailabilitystatement: 'Raw image files of all figures have been deposited at Mendeley Data and are publicly available as of the date of publication (Mendeley data: https://doi.org/10.17632/dwcpnncsyd.1). All other data reported in this paper will be shared by the lead contact upon request' date_created: 2024-09-15T22:01:41Z date_published: 2024-09-05T00:00:00Z date_updated: 2026-09-24T10:43:18Z day: '05' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.molcel.2024.07.022 ec_funded: 1 external_id: isi: - '001309051100001' pmid: - '39153474' file: - access_level: open_access checksum: 3f360e0287b8ec79fb2b8b02b5070360 content_type: application/pdf creator: dernst date_created: 2024-09-16T07:38:38Z date_updated: 2024-09-16T07:38:38Z file_id: '18075' file_name: 2024_MolecularCell_HernandezArmendariz.pdf file_size: 11654644 relation: main_file success: 1 file_date_updated: 2024-09-16T07:38:38Z fulldoi: https://doi.org/10.1016/j.molcel.2024.07.022 has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '17' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: P3254-3270.E9 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Molecular Cell publication_identifier: eissn: - 1097-4164 issn: - 1097-2765 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '22987' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: A liquid-like coat mediates chromosome clustering during mitotic exit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 84 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17239' 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. 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). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Clara full_name: Garcia-Sacristan, Clara last_name: Garcia-Sacristan - first_name: Victor G. full_name: Gisbert, Victor G. last_name: Gisbert - first_name: Kevin full_name: Klein, Kevin id: 1e7ede04-9e54-11f0-9ec4-8d4d5563c398 last_name: Klein - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Ricardo full_name: Garcia, Ricardo last_name: Garcia citation: ama: Garcia-Sacristan C, Gisbert VG, Klein K, Šarić A, Garcia R. In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. 2024;18(28):18485-18492. doi:10.1021/acsnano.4c03839 apa: Garcia-Sacristan, C., Gisbert, V. G., Klein, K., Šarić, A., & Garcia, R. (2024). In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.4c03839 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.” ACS Nano. American Chemical Society, 2024. https://doi.org/10.1021/acsnano.4c03839. 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,” ACS Nano, vol. 18, no. 28. American Chemical Society, pp. 18485–18492, 2024. 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. mla: Garcia-Sacristan, Clara, et al. “In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures.” ACS Nano, vol. 18, no. 28, American Chemical Society, 2024, pp. 18485–92, doi:10.1021/acsnano.4c03839. short: C. Garcia-Sacristan, V.G. Gisbert, K. Klein, A. Šarić, R. Garcia, ACS Nano 18 (2024) 18485–18492. das_tickbox: '0' date_created: 2024-07-14T22:01:12Z date_published: 2024-07-16T00:00:00Z date_updated: 2026-09-24T10:43:56Z day: '16' ddc: - '540' department: - _id: AnSa doi: 10.1021/acsnano.4c03839 ec_funded: 1 external_id: isi: - '001263155500001' pmid: - '38958189' file: - access_level: open_access checksum: b7e9ce718e92f568bcb3810e8e28e458 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:06:48Z date_updated: 2025-01-09T12:06:48Z file_id: '18808' file_name: 2024_ACSNano_GarciaSacristan.pdf file_size: 10036838 relation: main_file success: 1 file_date_updated: 2025-01-09T12:06:48Z fulldoi: https://doi.org/10.1021/acsnano.4c03839 has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '28' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 18485-18492 pmid: 1 project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: In operando imaging electrostatic-driven disassembly and reassembly of collagen nanostructures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 18 year: '2024' ... --- OA_place: repository OA_type: green _id: '18704' 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. acknowledgement: We thank Markus Mund, Aline Tschanz, and Jonas Ries for helpful discussions and a critical reading of the manuscript. We also kindly acknowledge Simon Scheuring for providing the HS-AFM data for the analysis of clathrin coat invagination. We thank the reviewers of previous versions of this manuscript for useful feedback that helped us to improve this work. F.F. acknowledges financial support by the NOMIS foundation. U.S.S. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Project No. 240245660 (SFB 1129). Moreover, he is a member of the Interdisciplinary Center for Scientific Computing (IWR) at Heidelberg and of the Max Planck School Matter to Life supported by the German Federal Ministry of Education and Research (BMBF) in collaboration with the Max Planck Society. article_number: '064403' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Ulrich S. full_name: Schwarz, Ulrich S. last_name: Schwarz citation: ama: Frey FF, Schwarz US. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 2024;110(6). doi:10.1103/PhysRevE.110.064403 apa: Frey, F. F., & Schwarz, U. S. (2024). Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.064403 chicago: Frey, Felix F, and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.064403. ieee: F. F. Frey and U. S. Schwarz, “Coat stiffening can explain invagination of clathrin-coated membranes,” Physical Review E, vol. 110, no. 6. American Physical Society, 2024. ista: Frey FF, Schwarz US. 2024. Coat stiffening can explain invagination of clathrin-coated membranes. Physical Review E. 110(6), 064403. mla: Frey, Felix F., and Ulrich S. Schwarz. “Coat Stiffening Can Explain Invagination of Clathrin-Coated Membranes.” Physical Review E, vol. 110, no. 6, 064403, American Physical Society, 2024, doi:10.1103/PhysRevE.110.064403. short: F.F. Frey, U.S. Schwarz, Physical Review E 110 (2024). das_tickbox: '0' date_created: 2024-12-22T23:01:48Z date_published: 2024-12-10T00:00:00Z date_updated: 2026-09-24T10:43:36Z day: '10' department: - _id: AnSa doi: 10.1103/PhysRevE.110.064403 external_id: arxiv: - '2405.02820' isi: - '001379135100004' pmid: - '39916158' fulldoi: https://doi.org/10.1103/PhysRevE.110.064403 intvolume: ' 110' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.02820 month: '12' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: no title: Coat stiffening can explain invagination of clathrin-coated membranes type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 110 year: '2024' ... --- OA_place: repository OA_type: green _id: '22987' 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. ' article_processing_charge: No author: - first_name: Alberto full_name: Hernandez-Armendariz, Alberto last_name: Hernandez-Armendariz - first_name: Sara full_name: Cuylen-Haering, Sara last_name: Cuylen-Haering citation: ama: Hernandez-Armendariz A, Cuylen-Haering S. A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al. 2024. doi:10.17632/dwcpnncsyd.1 apa: Hernandez-Armendariz, A., & Cuylen-Haering, S. (2024). A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al. Repository. https://doi.org/10.17632/dwcpnncsyd.1 chicago: Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. “A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz et Al.” Repository, 2024. https://doi.org/10.17632/dwcpnncsyd.1. ieee: A. Hernandez-Armendariz and S. Cuylen-Haering, “A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al.” Repository, 2024. ista: Hernandez-Armendariz A, Cuylen-Haering S. 2024. A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al., Repository, 10.17632/dwcpnncsyd.1. mla: Hernandez-Armendariz, Alberto, and Sara Cuylen-Haering. A Liquid-like Coat Mediates Chromosome Clustering during Mitotic Exit. Hernandez-Armendariz et Al. Repository, 2024, doi:10.17632/dwcpnncsyd.1. short: A. Hernandez-Armendariz, S. Cuylen-Haering, (2024). date_created: 2026-09-24T10:38:23Z date_published: 2024-08-22T00:00:00Z date_updated: 2026-09-24T10:43:18Z day: '22' ddc: - '570' department: - _id: AnSa doi: 10.17632/dwcpnncsyd.1 fulldoi: https://doi.org/10.17632/dwcpnncsyd.1 main_file_link: - open_access: '1' url: https://doi.org/10.17632/dwcpnncsyd.1 month: '08' oa: 1 oa_version: None publisher: Repository related_material: record: - id: '18072' relation: used_in_publication status: public status: public title: A liquid-like coat mediates chromosome clustering during mitotic exit. Hernandez-Armendariz et al. type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository OA_type: green _id: '22940' article_processing_charge: No author: - first_name: Astrid full_name: ' Sivertsen, Astrid' last_name: ' Sivertsen' - first_name: Federico full_name: Napoli, Federico last_name: Napoli - first_name: Paul full_name: Schanda, Paul last_name: Schanda citation: ama: Sivertsen A, Napoli F, Schanda P. Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2. 2024. doi:10.13018/BMR52400 apa: Sivertsen, A., Napoli, F., & Schanda, P. (2024). Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2. Repository. https://doi.org/10.13018/BMR52400 chicago: Sivertsen, Astrid, Federico Napoli, and Paul Schanda. “Amide and A-Hydrogens Extension to the Solid-State NMR Assignment of P. Horikoshii TET2.” Repository, 2024. https://doi.org/10.13018/BMR52400. ieee: A. Sivertsen, F. Napoli, and P. Schanda, “Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2.” Repository, 2024. ista: Sivertsen A, Napoli F, Schanda P. 2024. Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2, Repository, 10.13018/BMR52400. mla: Sivertsen, Astrid, et al. Amide and A-Hydrogens Extension to the Solid-State NMR Assignment of P. Horikoshii TET2. Repository, 2024, doi:10.13018/BMR52400. short: A. Sivertsen, F. Napoli, P. Schanda, (2024). date_created: 2026-09-17T09:10:45Z date_published: 2024-05-15T00:00:00Z date_updated: 2026-09-24T10:36:36Z day: '15' ddc: - '530' department: - _id: PaSc doi: 10.13018/BMR52400 fulldoi: https://doi.org/10.13018/BMR52400 main_file_link: - open_access: '1' url: https://doi.org/10.13018/BMR52400 month: '05' oa: 1 oa_version: None publisher: Repository related_material: record: - id: '15401' relation: used_in_publication status: public status: public title: Amide and a-hydrogens extension to the Solid-state NMR assignment of P. horikoshii TET2 type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '15126' abstract: - lang: eng 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". article_processing_charge: No author: - first_name: G. full_name: Giubertoni, G. last_name: Giubertoni - first_name: S. full_name: Woutersen, S. last_name: Woutersen citation: ama: Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:10.21942/UVA.24829896 apa: Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896 chicago: Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896. ieee: G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. ista: Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, 10.21942/UVA.24829896. mla: Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O and D2O. Figshare, 2024, doi:10.21942/UVA.24829896. short: G. Giubertoni, S. Woutersen, (2024). date_created: 2024-03-19T10:47:16Z date_published: 2024-02-14T00:00:00Z date_updated: 2026-09-24T10:42:12Z day: '14' ddc: - '550' doi: 10.21942/UVA.24829896 extern: '1' fulldoi: https://doi.org/10.21942/UVA.24829896 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.21942/UVA.24829896 month: '02' oa: 1 oa_version: Published Version publisher: Figshare related_material: record: - id: '15116' relation: used_in_publication status: public status: public title: Dataset Collagen Self Assembly in H2O and D2O tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '17374' 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. 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. article_number: '41' article_processing_charge: Yes (in subscription journal) arxiv: 1 author: - first_name: Pramod full_name: Rao, Pramod last_name: Rao - first_name: Gereon full_name: Fox, Gereon last_name: Fox - first_name: Abhimitra full_name: Meka, Abhimitra last_name: Meka - first_name: B. R. full_name: Mallikarjun, B. R. last_name: Mallikarjun - first_name: Fangneng full_name: Zhan, Fangneng last_name: Zhan - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Mohamed full_name: Elgharib, Mohamed last_name: Elgharib - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt citation: ama: 'Rao P, Fox G, Meka A, et al. Lite2Relight: 3D-aware single image portrait relighting. In: Proceedings - SIGGRAPH 2024 Conference Papers. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657470' 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 Proceedings - SIGGRAPH 2024 Conference Papers. Denver, CO, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657470' 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 Proceedings - SIGGRAPH 2024 Conference Papers. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657470.' ieee: 'P. Rao et al., “Lite2Relight: 3D-aware single image portrait relighting,” in Proceedings - SIGGRAPH 2024 Conference Papers, 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.' mla: 'Rao, Pramod, et al. “Lite2Relight: 3D-Aware Single Image Portrait Relighting.” Proceedings - SIGGRAPH 2024 Conference Papers, 41, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657470.' short: P. Rao, G. Fox, A. Meka, B.R. Mallikarjun, F. Zhan, T. Weyrich, B. Bickel, H. Pfister, W. Matusik, M. Elgharib, C. Theobalt, in:, Proceedings - SIGGRAPH 2024 Conference Papers, Association for Computing Machinery, 2024. conference: end_date: 2024-08-01 location: Denver, CO, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2024-07-27 das_tickbox: '0' date_created: 2024-08-04T22:01:21Z date_published: 2024-07-13T00:00:00Z date_updated: 2026-09-24T11:00:21Z day: '13' ddc: - '000' department: - _id: BeBi doi: 10.1145/3641519.3657470 external_id: arxiv: - '2407.10487' isi: - '001282218200076' file: - access_level: open_access checksum: 4650f6d1419e675929133e46a91ca177 content_type: application/pdf creator: dernst date_created: 2024-08-05T08:25:18Z date_updated: 2024-08-05T08:25:18Z file_id: '17387' file_name: 2024_SIGGRAPH_Rao.pdf file_size: 59683257 relation: main_file success: 1 file_date_updated: 2024-08-05T08:25:18Z fulldoi: https://doi.org/10.1145/3641519.3657470 has_accepted_license: '1' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Proceedings - SIGGRAPH 2024 Conference Papers publication_identifier: isbn: - '9798400705250' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' researchdata_availability: no scopus_import: '1' status: public supplementarymaterial: yes title: 'Lite2Relight: 3D-aware single image portrait relighting' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- APC_amount: 12348 EUR OA_place: publisher OA_type: hybrid _id: '17460' 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. 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.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Christian Eduardo full_name: Vanhille-Campos, Christian Eduardo id: 3adeca52-9313-11ed-b1ac-c170b2505714 last_name: Vanhille-Campos - first_name: Kevin D. full_name: Whitley, Kevin D. last_name: Whitley - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Séamus full_name: Holden, Séamus last_name: Holden - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: 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. Nature Physics. 2024;20:1670-1678. doi:10.1038/s41567-024-02597-8 apa: Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., & Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02597-8 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.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02597-8. 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,” Nature Physics, 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. mla: Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:10.1038/s41567-024-02597-8. short: C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678. corr_author: '1' das_tickbox: '1' dataavailabilitystatement: The simulation data presented in this work are available from the University College London public data repository at https://doi.org/10.5522/04/24754527 (ref. 74). Live-cell imaging of FtsZ rings data presented in this work are from ref. 23. High-speed atomic force microscopy data presented in this work are from ref. 9. Total internal reflection fluorescence microscopy data presented in this work are from refs. 37,75,76 date_created: 2024-08-25T22:01:08Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-09-24T10:58:39Z day: '01' ddc: - '570' department: - _id: AnSa - _id: MaLo doi: 10.1038/s41567-024-02597-8 ec_funded: 1 external_id: isi: - '001289394500005' pmid: - '39416851' file: - access_level: open_access checksum: c4842152e2b90d67f48ea8c9ed7c473b content_type: application/pdf creator: dernst date_created: 2025-04-14T06:06:35Z date_updated: 2025-04-14T06:06:35Z file_id: '19556' file_name: 2024_NaturePhysics_VanhilleCampos.pdf file_size: 8058249 relation: main_file success: 1 file_date_updated: 2025-04-14T06:06:35Z fulldoi: https://doi.org/10.1038/s41567-024-02597-8 has_accepted_license: '1' intvolume: ' 20' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1670-1678 pmid: 1 popular_science: '1' project: - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: In vitro reconstitution of bacterial cell division - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '22988' relation: research_data status: public researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: yes title: Self-organization of mortal filaments and its role in bacterial division ring formation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 20 year: '2024' ... --- _id: '14488' abstract: - lang: eng 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.' acknowledgement: Open Access funding enabled and organized by Projekt DEAL. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Pramod full_name: Rao, Pramod last_name: Rao - first_name: B. R. full_name: Mallikarjun, B. R. last_name: Mallikarjun - first_name: Gereon full_name: Fox, Gereon last_name: Fox - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Fangneng full_name: Zhan, Fangneng last_name: Zhan - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt - first_name: Mohamed full_name: Elgharib, Mohamed last_name: Elgharib citation: ama: Rao P, Mallikarjun BR, Fox G, et al. A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. 2024;132:1148-1166. doi:10.1007/s11263-023-01899-3 apa: Rao, P., Mallikarjun, B. R., Fox, G., Weyrich, T., Bickel, B., Pfister, H., … Elgharib, M. (2024). A deeper analysis of volumetric relightiable faces. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-023-01899-3 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.” International Journal of Computer Vision. Springer Nature, 2024. https://doi.org/10.1007/s11263-023-01899-3. ieee: P. Rao et al., “A deeper analysis of volumetric relightiable faces,” International Journal of Computer Vision, vol. 132. Springer Nature, pp. 1148–1166, 2024. 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. mla: Rao, Pramod, et al. “A Deeper Analysis of Volumetric Relightiable Faces.” International Journal of Computer Vision, vol. 132, Springer Nature, 2024, pp. 1148–66, doi:10.1007/s11263-023-01899-3. 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. das_tickbox: '1' 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.' date_created: 2023-11-05T23:00:54Z date_published: 2024-04-01T00:00:00Z date_updated: 2026-09-24T10:59:50Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1007/s11263-023-01899-3 external_id: isi: - '001091935600002' pmid: - '38549787' file: - access_level: open_access checksum: 5eef1d920f6fe700d7856098000d05f1 content_type: application/pdf creator: dernst date_created: 2024-07-22T11:07:14Z date_updated: 2024-07-22T11:07:14Z file_id: '17304' file_name: 2024_IJCV_Rao.pdf file_size: 9942520 relation: main_file success: 1 file_date_updated: 2024-07-22T11:07:14Z fulldoi: https://doi.org/10.1007/s11263-023-01899-3 has_accepted_license: '1' intvolume: ' 132' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1148-1166 pmid: 1 publication: International Journal of Computer Vision publication_identifier: eissn: - 1573-1405 issn: - 0920-5691 publication_status: published publisher: Springer Nature quality_controlled: '1' researchdata_availability: no (restricted access) scopus_import: '1' status: public supplementarymaterial: no title: A deeper analysis of volumetric relightiable faces tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 132 year: '2024' ...