[{"OA_type":"gold","day":"24","status":"public","citation":{"mla":"Sunko, Veronika, et al. “Controlled Introduction of Defects to Delafossite Metals by Electron Irradiation.” <i>Physical Review X</i>, vol. 10, no. 2, 021018, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevx.10.021018\">10.1103/physrevx.10.021018</a>.","chicago":"Sunko, Veronika, P. H. McGuinness, C. S. Chang, E. Zhakina, S. Khim, C. E. Dreyer, M. Konczykowski, et al. “Controlled Introduction of Defects to Delafossite Metals by Electron Irradiation.” <i>Physical Review X</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevx.10.021018\">https://doi.org/10.1103/physrevx.10.021018</a>.","apa":"Sunko, V., McGuinness, P. H., Chang, C. S., Zhakina, E., Khim, S., Dreyer, C. E., … Mackenzie, A. P. (2020). Controlled introduction of defects to delafossite metals by electron irradiation. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.10.021018\">https://doi.org/10.1103/physrevx.10.021018</a>","ista":"Sunko V, McGuinness PH, Chang CS, Zhakina E, Khim S, Dreyer CE, Konczykowski M, Borrmann H, Moll PJW, König M, Muller DA, Mackenzie AP. 2020. Controlled introduction of defects to delafossite metals by electron irradiation. Physical Review X. 10(2), 021018.","ama":"Sunko V, McGuinness PH, Chang CS, et al. Controlled introduction of defects to delafossite metals by electron irradiation. <i>Physical Review X</i>. 2020;10(2). doi:<a href=\"https://doi.org/10.1103/physrevx.10.021018\">10.1103/physrevx.10.021018</a>","short":"V. Sunko, P.H. McGuinness, C.S. Chang, E. Zhakina, S. Khim, C.E. Dreyer, M. Konczykowski, H. Borrmann, P.J.W. Moll, M. König, D.A. Muller, A.P. Mackenzie, Physical Review X 10 (2020).","ieee":"V. Sunko <i>et al.</i>, “Controlled introduction of defects to delafossite metals by electron irradiation,” <i>Physical Review X</i>, vol. 10, no. 2. American Physical Society, 2020."},"article_type":"original","oa_version":"Published Version","intvolume":"        10","type":"journal_article","_id":"19823","scopus_import":"1","oa":1,"DOAJ_listed":"1","language":[{"iso":"eng"}],"month":"04","date_published":"2020-04-24T00:00:00Z","publisher":"American Physical Society","arxiv":1,"date_updated":"2025-06-10T13:08:51Z","year":"2020","date_created":"2025-06-10T09:21:11Z","article_number":"021018","issue":"2","doi":"10.1103/physrevx.10.021018","publication_identifier":{"eissn":["2160-3308"]},"publication":"Physical Review X","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1103/PhysRevX.10.021018"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Veronika","last_name":"Sunko","full_name":"Sunko, Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3"},{"first_name":"P. H.","last_name":"McGuinness","full_name":"McGuinness, P. H."},{"full_name":"Chang, C. S.","last_name":"Chang","first_name":"C. S."},{"first_name":"E.","last_name":"Zhakina","full_name":"Zhakina, E."},{"last_name":"Khim","first_name":"S.","full_name":"Khim, S."},{"full_name":"Dreyer, C. E.","last_name":"Dreyer","first_name":"C. E."},{"first_name":"M.","last_name":"Konczykowski","full_name":"Konczykowski, M."},{"first_name":"H.","last_name":"Borrmann","full_name":"Borrmann, H."},{"first_name":"P. J. W.","last_name":"Moll","full_name":"Moll, P. J. W."},{"first_name":"M.","last_name":"König","full_name":"König, M."},{"full_name":"Muller, D. A.","last_name":"Muller","first_name":"D. A."},{"full_name":"Mackenzie, A. P.","last_name":"Mackenzie","first_name":"A. P."}],"OA_place":"publisher","volume":10,"article_processing_charge":"Yes","abstract":[{"text":"The delafossite metals PdCoO2, PtCoO2, and PdCrO2 are among the highest conductivity materials known, with low-temperature mean free paths of tens of microns in the best as-grown single crystals. A key question is whether these very low resistive scattering rates result from strongly suppressed backscattering due to special features of the electronic structure or are a consequence of highly unusual levels of crystalline perfection. We report the results of experiments in which high-energy electron irradiation was used to introduce point disorder to the Pd and Pt layers in which the conduction occurs. We obtain the cross section for formation of Frenkel pairs in absolute units, and cross-check our analysis with first-principles calculations of the relevant atomic displacement energies. We observe an increase of resistivity that is linear in defect density with a slope consistent with scattering in the unitary limit. Our results enable us to deduce that the as-grown crystals contain extremely low levels of in-plane defects of approximately 0.001%. This confirms that crystalline perfection is the most important factor in realizing the long mean free paths and highlights how unusual these delafossite metals are in comparison with the vast majority of other multicomponent oxides and alloys. We discuss the implications of our findings for future materials research.","lang":"eng"}],"external_id":{"arxiv":["2001.01471"]},"publication_status":"published","title":"Controlled introduction of defects to delafossite metals by electron irradiation"},{"quality_controlled":"1","file":[{"access_level":"open_access","checksum":"28ece115e8d2d9263e253a598e7caef2","relation":"main_file","file_size":316681,"date_updated":"2025-09-23T12:03:09Z","file_id":"20380","success":1,"creator":"dernst","date_created":"2025-09-23T12:03:09Z","file_name":"2020_ProbProgramming_Chatterjee.pdf","content_type":"application/pdf"}],"corr_author":"1","ddc":["000"],"has_accepted_license":"1","date_created":"2025-07-10T13:28:51Z","year":"2020","publication":"Foundations of Probabilistic Programming","doi":"10.1017/9781108770750.008","publication_identifier":{"eisbn":["9781108770750"],"isbn":["9781108488518"]},"publication_status":"published","abstract":[{"text":"For non-probabilistic programs, a key question in static analysis is termination, which asks whether a given program terminates under a given initial condition. In the presence of probabilistic behaviour, there are two fundamental extensions of the termination question: (a) the almost-sure termination question, which asks whether the termination probability is 1; and (b) the bounded-time termination question, which asks whether the expected termination time is bounded. There are many active research directions to address these two questions; one important such direction is the use of martingale theory for termination analysis. In this chapter, we survey the main techniques of the martingale-based approach to the termination analysis of probabilistic programs.","lang":"eng"}],"article_processing_charge":"No","page":"221-258","title":"Termination Analysis of Probabilistic Programs with Martingales","OA_place":"publisher","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hongfei","last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei"},{"last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"K. Chatterjee, H. Fu, and P. Novotný, “Termination Analysis of Probabilistic Programs with Martingales,” in <i>Foundations of Probabilistic Programming</i>, Cambridge University Press, 2020, pp. 221–258.","short":"K. Chatterjee, H. Fu, P. Novotný, in:, Foundations of Probabilistic Programming, Cambridge University Press, 2020, pp. 221–258.","ista":"Chatterjee K, Fu H, Novotný P. 2020.Termination Analysis of Probabilistic Programs with Martingales. In: Foundations of Probabilistic Programming. , 221–258.","ama":"Chatterjee K, Fu H, Novotný P. Termination Analysis of Probabilistic Programs with Martingales. In: <i>Foundations of Probabilistic Programming</i>. Cambridge University Press; 2020:221-258. doi:<a href=\"https://doi.org/10.1017/9781108770750.008\">10.1017/9781108770750.008</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Petr Novotný. “Termination Analysis of Probabilistic Programs with Martingales.” In <i>Foundations of Probabilistic Programming</i>, 221–58. Cambridge University Press, 2020. <a href=\"https://doi.org/10.1017/9781108770750.008\">https://doi.org/10.1017/9781108770750.008</a>.","apa":"Chatterjee, K., Fu, H., &#38; Novotný, P. (2020). Termination Analysis of Probabilistic Programs with Martingales. In <i>Foundations of Probabilistic Programming</i> (pp. 221–258). Cambridge University Press. <a href=\"https://doi.org/10.1017/9781108770750.008\">https://doi.org/10.1017/9781108770750.008</a>","mla":"Chatterjee, Krishnendu, et al. “Termination Analysis of Probabilistic Programs with Martingales.” <i>Foundations of Probabilistic Programming</i>, Cambridge University Press, 2020, pp. 221–58, doi:<a href=\"https://doi.org/10.1017/9781108770750.008\">10.1017/9781108770750.008</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"18","file_date_updated":"2025-09-23T12:03:09Z","oa":1,"date_updated":"2025-09-23T12:10:25Z","publisher":"Cambridge University Press","department":[{"_id":"KrCh"}],"date_published":"2020-11-18T00:00:00Z","month":"11","language":[{"iso":"eng"}],"acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN\r\nGrant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Hongfei Fu\r\nis supported by the National Natural Science Foundation of China (NSFC) Grant\r\nNo. 61802254. Petr Novotný is supported by the Czech Science Foundation grant\r\nNo. GJ19-15134Y.","type":"book_chapter","oa_version":"Published Version","_id":"19986"},{"publication":"Journal of the American Chemical Society","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"doi":"10.1021/jacs.0c03184","issue":"25","date_created":"2025-12-09T14:25:37Z","year":"2020","main_file_link":[{"url":"10.26434/chemrxiv.11931633.v1","open_access":"1"}],"quality_controlled":"1","pmid":1,"volume":142,"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bhawal","first_name":"Benjamin N.","full_name":"Bhawal, Benjamin N."},{"last_name":"Reisenbauer","first_name":"Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","full_name":"Reisenbauer, Julia"},{"last_name":"Ehinger","first_name":"Christian","full_name":"Ehinger, Christian"},{"first_name":"Bill","last_name":"Morandi","full_name":"Morandi, Bill"}],"extern":"1","title":"Overcoming selectivity issues in reversible catalysis: A transfer hydrocyanation exhibiting high kinetic control","publication_status":"published","external_id":{"pmid":["32478515"]},"abstract":[{"lang":"eng","text":"Reversible catalytic reactions operate under thermodynamic control, and thus, establishing a selective catalytic system poses a considerable challenge. Herein, we report a reversible transfer hydrocyanation protocol that exhibits high selectivity for the thermodynamically less favorable branched isomer. Selectivity is achieved by exploiting the lower barrier for C–CN oxidative addition and reductive elimination at benzylic positions in the absence of a cocatalytic Lewis acid. Through the design of a novel type of HCN donor, a practical, branched-selective, HCN-free transfer hydrocyanation was realized. The synthetically useful resolution of a mixture of branched and linear nitrile isomers was also demonstrated to underline the value of reversible and selective transfer reactions. In a broader context, this work demonstrates that high kinetic selectivity can be achieved in reversible transfer reactions, thus opening new horizons for their synthetic applications."}],"article_processing_charge":"No","page":"10914-10920","status":"public","day":"01","OA_type":"green","citation":{"ista":"Bhawal BN, Reisenbauer J, Ehinger C, Morandi B. 2020. Overcoming selectivity issues in reversible catalysis: A transfer hydrocyanation exhibiting high kinetic control. Journal of the American Chemical Society. 142(25), 10914–10920.","ama":"Bhawal BN, Reisenbauer J, Ehinger C, Morandi B. Overcoming selectivity issues in reversible catalysis: A transfer hydrocyanation exhibiting high kinetic control. <i>Journal of the American Chemical Society</i>. 2020;142(25):10914-10920. doi:<a href=\"https://doi.org/10.1021/jacs.0c03184\">10.1021/jacs.0c03184</a>","short":"B.N. Bhawal, J. Reisenbauer, C. Ehinger, B. Morandi, Journal of the American Chemical Society 142 (2020) 10914–10920.","ieee":"B. N. Bhawal, J. Reisenbauer, C. Ehinger, and B. Morandi, “Overcoming selectivity issues in reversible catalysis: A transfer hydrocyanation exhibiting high kinetic control,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 25. American Chemical Society, pp. 10914–10920, 2020.","mla":"Bhawal, Benjamin N., et al. “Overcoming Selectivity Issues in Reversible Catalysis: A Transfer Hydrocyanation Exhibiting High Kinetic Control.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 25, American Chemical Society, 2020, pp. 10914–20, doi:<a href=\"https://doi.org/10.1021/jacs.0c03184\">10.1021/jacs.0c03184</a>.","apa":"Bhawal, B. N., Reisenbauer, J., Ehinger, C., &#38; Morandi, B. (2020). Overcoming selectivity issues in reversible catalysis: A transfer hydrocyanation exhibiting high kinetic control. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c03184\">https://doi.org/10.1021/jacs.0c03184</a>","chicago":"Bhawal, Benjamin N., Julia Reisenbauer, Christian Ehinger, and Bill Morandi. “Overcoming Selectivity Issues in Reversible Catalysis: A Transfer Hydrocyanation Exhibiting High Kinetic Control.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c03184\">https://doi.org/10.1021/jacs.0c03184</a>."},"scopus_import":"1","_id":"20766","type":"journal_article","oa_version":"Preprint","intvolume":"       142","article_type":"original","date_updated":"2025-12-16T12:10:08Z","publisher":"American Chemical Society","date_published":"2020-06-01T00:00:00Z","language":[{"iso":"eng"}],"month":"06","oa":1},{"citation":{"short":"L. Doubravská, V. Dostál, F. Knop, L. Libusová, M. Macůrková, Experimental Cell Research 386 (2020).","ieee":"L. Doubravská, V. Dostál, F. Knop, L. Libusová, and M. Macůrková, “Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion,” <i>Experimental Cell Research</i>, vol. 386, no. 1. Elsevier, 2020.","ama":"Doubravská L, Dostál V, Knop F, Libusová L, Macůrková M. Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion. <i>Experimental Cell Research</i>. 2020;386(1). doi:<a href=\"https://doi.org/10.1016/j.yexcr.2019.111709\">10.1016/j.yexcr.2019.111709</a>","ista":"Doubravská L, Dostál V, Knop F, Libusová L, Macůrková M. 2020. Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion. Experimental Cell Research. 386(1), 111709.","apa":"Doubravská, L., Dostál, V., Knop, F., Libusová, L., &#38; Macůrková, M. (2020). Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion. <i>Experimental Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.yexcr.2019.111709\">https://doi.org/10.1016/j.yexcr.2019.111709</a>","chicago":"Doubravská, Lenka, Vojtěch Dostál, Filip Knop, Lenka Libusová, and Marie Macůrková. “Human Myotubularin-Related Protein 9 Regulates ER-to-Golgi Trafficking and Modulates WNT3A Secretion.” <i>Experimental Cell Research</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.yexcr.2019.111709\">https://doi.org/10.1016/j.yexcr.2019.111709</a>.","mla":"Doubravská, Lenka, et al. “Human Myotubularin-Related Protein 9 Regulates ER-to-Golgi Trafficking and Modulates WNT3A Secretion.” <i>Experimental Cell Research</i>, vol. 386, no. 1, 111709, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.yexcr.2019.111709\">10.1016/j.yexcr.2019.111709</a>."},"status":"public","day":"01","OA_type":"closed access","month":"01","language":[{"iso":"eng"}],"date_published":"2020-01-01T00:00:00Z","publisher":"Elsevier","date_updated":"2025-12-15T10:17:13Z","_id":"20806","scopus_import":"1","article_type":"original","oa_version":"None","intvolume":"       386","type":"journal_article","quality_controlled":"1","issue":"1","publication_identifier":{"issn":["0014-4827"]},"doi":"10.1016/j.yexcr.2019.111709","publication":"Experimental Cell Research","year":"2020","date_created":"2025-12-12T09:03:03Z","article_number":"111709","title":"Human myotubularin-related protein 9 regulates ER-to-Golgi trafficking and modulates WNT3A secretion","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Regulation of phosphatidylinositol phosphates plays a crucial role in signal transduction, membrane trafficking or autophagy. Members of the myotubularin family of lipid phosphatases contribute to phosphoinositide metabolism by counteracting the activity of phosphoinositide kinases. The mechanisms determining their subcellular localization and targeting to specific membrane compartments are still poorly understood.\r\nWe show here that the inactive phosphatase MTMR9 localizes to the intermediate compartment and to the Golgi apparatus and is able to recruit its active phosphatase partners MTMR6 and MTMR8 to these locations. Furthermore, MTMR8 and MTMR9 co-localize with the small GTPase RAB1A and regulate its localization. Loss of MTMR9 expression compromises the integrity of the Golgi apparatus and results in altered distribution of RAB1A and actin nucleation-promoting factor WHAMM. Loss or overexpression of MTMR9 leads to decreased rate of protein secretion. We demonstrate that secretion of physiologically relevant cargo exemplified by the WNT3A protein is affected after perturbation of MTMR9 levels."}],"external_id":{"pmid":["31704058 "]},"publication_status":"published","pmid":1,"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Doubravská, Lenka","last_name":"Doubravská","first_name":"Lenka"},{"full_name":"Dostál, Vojtěch","last_name":"Dostál","first_name":"Vojtěch"},{"full_name":"Knop, Filip","orcid":"0000-0002-3845-3465","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","first_name":"Filip","last_name":"Knop"},{"full_name":"Libusová, Lenka","last_name":"Libusová","first_name":"Lenka"},{"last_name":"Macůrková","first_name":"Marie","full_name":"Macůrková, Marie"}],"volume":386},{"status":"public","publication":"arXiv","day":"11","doi":"10.48550/arXiv.2003.05478","article_number":"2003.05478","ec_funded":1,"date_created":"2021-09-13T12:17:11Z","year":"2020","main_file_link":[{"url":"https://arxiv.org/abs/2003.05478","open_access":"1"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"citation":{"ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” <i>arXiv</i>. .","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2003.05478\">10.48550/arXiv.2003.05478</a>","chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2003.05478\">https://doi.org/10.48550/arXiv.2003.05478</a>.","apa":"Fischer, J. L., Hensel, S., Laux, T., &#38; Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2003.05478\">https://doi.org/10.48550/arXiv.2003.05478</a>","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” <i>ArXiv</i>, 2003.05478, doi:<a href=\"https://doi.org/10.48550/arXiv.2003.05478\">10.48550/arXiv.2003.05478</a>."},"_id":"10012","related_material":{"record":[{"status":"public","id":"10007","relation":"dissertation_contains"}]},"acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L"},{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","first_name":"Sebastian","last_name":"Hensel"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"},{"full_name":"Simon, Thilo","first_name":"Thilo","last_name":"Simon"}],"oa_version":"Preprint","date_updated":"2026-04-08T07:01:01Z","department":[{"_id":"JuFi"}],"arxiv":1,"date_published":"2020-03-11T00:00:00Z","month":"03","title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","language":[{"iso":"eng"}],"publication_status":"draft","external_id":{"arxiv":["2003.05478"]},"oa":1,"abstract":[{"text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable.","lang":"eng"}],"article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.10962"}],"corr_author":"1","doi":"10.48550/arXiv.2008.10962","publication":"arXiv","year":"2020","date_created":"2021-09-17T10:57:27Z","article_number":"2008.10962","title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","article_processing_charge":"No","abstract":[{"text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.","lang":"eng"}],"external_id":{"arxiv":["2008.10962"]},"publication_status":"draft","related_material":{"record":[{"id":"11739","relation":"later_version","status":"public"},{"id":"10030","relation":"dissertation_contains","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","first_name":"Dominik L"},{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"}],"citation":{"chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2008.10962\">https://doi.org/10.48550/arXiv.2008.10962</a>.","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2008.10962\">https://doi.org/10.48550/arXiv.2008.10962</a>","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>ArXiv</i>, 2008.10962, doi:<a href=\"https://doi.org/10.48550/arXiv.2008.10962\">10.48550/arXiv.2008.10962</a>.","short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>arXiv</i>. .","ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2008.10962\">10.48550/arXiv.2008.10962</a>","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962."},"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"status":"public","day":"25","ec_funded":1,"language":[{"iso":"eng"}],"month":"08","date_published":"2020-08-25T00:00:00Z","department":[{"_id":"JaMa"}],"arxiv":1,"date_updated":"2026-04-08T07:00:03Z","oa":1,"_id":"10022","oa_version":"Preprint","acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","type":"preprint"},{"day":"01","status":"public","publication":"OSA Quantum 2.0 Conference","alternative_title":["OSA Technical Digest"],"publication_identifier":{"isbn":["9-781-5575-2820-9"]},"doi":"10.1364/QUANTUM.2020.QTu8A.1","article_number":"QTu8A.1","year":"2020","date_created":"2021-11-21T23:01:31Z","conference":{"name":"OSA: Optical Society of America","start_date":"2020-09-14","end_date":"2020-09-17","location":"Washington, DC, United States"},"quality_controlled":"1","citation":{"chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group, 2020. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., &#38; Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In <i>OSA Quantum 2.0 Conference</i>. Washington, DC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” <i>OSA Quantum 2.0 Conference</i>, QTu8A.1, Optica Publishing Group, 2020, doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in <i>OSA Quantum 2.0 Conference</i>, Washington, DC, United States, 2020.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group; 2020. doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1."},"_id":"10328","scopus_import":"1","type":"conference","author":[{"full_name":"Lambert, Nicholas J.","first_name":"Nicholas J.","last_name":"Lambert"},{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"date_updated":"2023-10-18T08:32:34Z","month":"01","language":[{"iso":"eng"}],"title":"New designs and noise channels in electro-optic microwave to optical up-conversion","date_published":"2020-01-01T00:00:00Z","abstract":[{"text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No"},{"citation":{"mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>.","apa":"Krausser, J., Knowles, T. P. J., &#38; Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>","ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098.","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(52):33090-33098. doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020.","short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098."},"day":"16","status":"public","oa":1,"date_updated":"2021-11-25T15:35:58Z","publisher":"National Academy of Sciences","date_published":"2020-12-16T00:00:00Z","month":"12","language":[{"iso":"eng"}],"acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","type":"journal_article","oa_version":"Published Version","intvolume":"       117","article_type":"original","scopus_import":"1","_id":"10336","quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2","open_access":"1"}],"date_created":"2021-11-25T15:07:09Z","year":"2020","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2007694117","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"issue":"52","publication_status":"published","external_id":{"pmid":["33328273"]},"abstract":[{"lang":"eng","text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context."}],"article_processing_charge":"No","page":"33090-33098","title":"Physical mechanisms of amyloid nucleation on fluid membranes","volume":117,"author":[{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","pmid":1},{"OA_type":"hybrid","day":"06","status":"public","citation":{"ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” <i>Soft Matter</i>, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. 2020;16(47):10628-10639. doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>.","apa":"Debets, V. E., Janssen, L. M. C., &#38; Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>."},"article_type":"original","oa_version":"Published Version","intvolume":"        16","acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).","type":"journal_article","_id":"10341","scopus_import":"1","oa":1,"language":[{"iso":"eng"}],"month":"10","date_published":"2020-10-06T00:00:00Z","publisher":"Royal Society of Chemistry","date_updated":"2024-10-16T12:53:17Z","year":"2020","date_created":"2021-11-26T06:29:41Z","issue":"47","publication_identifier":{"issn":["1744-683X","1744-6848"]},"doi":"10.1039/d0sm00712a","publication":"Soft Matter","quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1","open_access":"1"}],"extern":"1","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","author":[{"first_name":"V. E.","last_name":"Debets","full_name":"Debets, V. E."},{"last_name":"Janssen","first_name":"L. M. C.","full_name":"Janssen, L. M. C."},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"OA_place":"publisher","volume":16,"pmid":1,"page":"10628-10639","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes."}],"publication_status":"published","external_id":{"pmid":["33084724"]},"title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","keyword":["condensed matter physics","general chemistry"]},{"scopus_import":"1","_id":"10342","intvolume":"         6","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.","date_published":"2020-11-27T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2024-10-16T12:56:52Z","publisher":"American Association for the Advancement of Science","DOAJ_listed":"1","file_date_updated":"2021-11-26T06:50:09Z","oa":1,"day":"27","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","citation":{"chicago":"Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>.","apa":"Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>.","ieee":"X. Tian <i>et al.</i>, “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” <i>Science Advances</i>, vol. 6, no. 48. American Association for the Advancement of Science, 2020.","short":"X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020).","ista":"Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.","ama":"Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. 2020;6(48). doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>"},"pmid":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","author":[{"full_name":"Tian, Xiaohe","last_name":"Tian","first_name":"Xiaohe"},{"first_name":"Diana M.","last_name":"Leite","full_name":"Leite, Diana M."},{"first_name":"Edoardo","last_name":"Scarpa","full_name":"Scarpa, Edoardo"},{"first_name":"Sophie","last_name":"Nyberg","full_name":"Nyberg, Sophie"},{"full_name":"Fullstone, Gavin","last_name":"Fullstone","first_name":"Gavin"},{"first_name":"Joe","last_name":"Forth","full_name":"Forth, Joe"},{"full_name":"Matias, Diana","first_name":"Diana","last_name":"Matias"},{"full_name":"Apriceno, Azzurra","last_name":"Apriceno","first_name":"Azzurra"},{"full_name":"Poma, Alessandro","first_name":"Alessandro","last_name":"Poma"},{"full_name":"Duro-Castano, Aroa","last_name":"Duro-Castano","first_name":"Aroa"},{"full_name":"Vuyyuru, Manish","last_name":"Vuyyuru","first_name":"Manish"},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Zhang, Zhongping","first_name":"Zhongping","last_name":"Zhang"},{"first_name":"Pan","last_name":"Xiang","full_name":"Xiang, Pan"},{"first_name":"Bin","last_name":"Fang","full_name":"Fang, Bin"},{"full_name":"Tian, Yupeng","first_name":"Yupeng","last_name":"Tian"},{"full_name":"Luo, Lei","last_name":"Luo","first_name":"Lei"},{"last_name":"Rizzello","first_name":"Loris","full_name":"Rizzello, Loris"},{"last_name":"Battaglia","first_name":"Giuseppe","full_name":"Battaglia, Giuseppe"}],"extern":"1","volume":6,"OA_place":"publisher","keyword":["multidisciplinary"],"title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","article_processing_charge":"No","external_id":{"pmid":["33246953"]},"publication_status":"published","abstract":[{"lang":"eng","text":"The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across."}],"doi":"10.1126/sciadv.abc4397","publication_identifier":{"issn":["2375-2548"]},"issue":"48","publication":"Science Advances","date_created":"2021-11-26T06:40:28Z","year":"2020","article_number":"eabc4397 ","has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1"}],"ddc":["611"],"file":[{"file_name":"2020_SciAdv_Tian.pdf","content_type":"application/pdf","date_created":"2021-11-26T06:50:09Z","success":1,"creator":"cchlebak","file_id":"10343","file_size":10381298,"date_updated":"2021-11-26T06:50:09Z","access_level":"open_access","checksum":"3ba2eca975930cdb0b1ce1ae876885a7","relation":"main_file"}],"quality_controlled":"1"},{"file":[{"creator":"cchlebak","success":1,"content_type":"application/pdf","file_name":"2020_PhysRevLett_Forster.pdf","date_created":"2021-11-26T07:16:49Z","date_updated":"2021-11-26T07:16:49Z","file_size":844353,"relation":"main_file","checksum":"fbf2e1415e332d6add90222d60401a1d","access_level":"open_access","file_id":"10345"}],"quality_controlled":"1","ddc":["530"],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1","open_access":"1"}],"has_accepted_license":"1","article_number":"228101","year":"2020","date_created":"2021-11-26T07:10:43Z","publication":"Physical Review Letters","issue":"22","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"doi":"10.1103/physrevlett.125.228101","abstract":[{"lang":"eng","text":"In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry."}],"publication_status":"published","external_id":{"pmid":["33315453"]},"article_processing_charge":"No","title":"Exploring the design rules for efficient membrane-reshaping nanostructures","volume":125,"OA_place":"publisher","extern":"1","author":[{"last_name":"Forster","first_name":"Joel C.","full_name":"Forster, Joel C."},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"full_name":"Vuyyuru, Manish R.","first_name":"Manish R.","last_name":"Vuyyuru"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","pmid":1,"citation":{"ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” <i>Physical Review Letters</i>, vol. 125, no. 22. American Physical Society, 2020.","short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020).","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. 2020;125(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>","ista":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101.","apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., &#38; Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>","chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>.","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>."},"OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"23","oa":1,"file_date_updated":"2021-11-26T07:16:49Z","publisher":"American Physical Society","date_updated":"2024-10-16T12:59:57Z","language":[{"iso":"eng"}],"month":"11","date_published":"2020-11-23T00:00:00Z","acknowledgement":"We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1).","type":"journal_article","article_type":"original","intvolume":"       125","oa_version":"Published Version","_id":"10344","scopus_import":"1"},{"oa":1,"date_updated":"2024-10-16T13:05:34Z","publisher":"Cell Press","date_published":"2020-09-23T00:00:00Z","month":"09","language":[{"iso":"eng"}],"acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","type":"journal_article","oa_version":"Published Version","intvolume":"       119","article_type":"original","scopus_import":"1","_id":"10346","citation":{"ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. 2020;119(9):1791-1799. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” <i>Biophysical Journal</i>, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>.","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>.","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., &#38; Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>"},"OA_type":"hybrid","day":"23","status":"public","publication_status":"published","external_id":{"pmid":["33049216"]},"abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"article_processing_charge":"No","page":"1791-1799","keyword":["biophysics"],"title":"Modeling fibrillogenesis of collagen-mimetic molecules","OA_place":"publisher","volume":119,"author":[{"full_name":"Hafner, Anne E.","first_name":"Anne E.","last_name":"Hafner"},{"full_name":"Gyori, Noemi G.","first_name":"Noemi G.","last_name":"Gyori"},{"full_name":"Bench, Ciaran A.","last_name":"Bench","first_name":"Ciaran A."},{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","extern":"1","pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1"}],"date_created":"2021-11-26T07:27:24Z","year":"2020","publication":"Biophysical Journal","doi":"10.1016/j.bpj.2020.09.013","publication_identifier":{"issn":["0006-3495"]},"issue":"9"},{"oa":1,"date_updated":"2021-11-26T08:59:06Z","publisher":"National Academy of Sciences","date_published":"2020-09-14T00:00:00Z","language":[{"iso":"eng"}],"month":"09","type":"journal_article","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","intvolume":"       117","oa_version":"Published Version","article_type":"original","scopus_import":"1","_id":"10347","citation":{"mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>.","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>","chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>.","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(39):24251-24257. doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>","ieee":"T. C. T. Michaels <i>et al.</i>, “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257."},"status":"public","day":"14","publication_status":"published","external_id":{"pmid":["32929030"]},"abstract":[{"lang":"eng","text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors."}],"article_processing_charge":"No","page":"24251-24257","keyword":["multidisciplinary"],"title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","volume":117,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"full_name":"Heller, Gabriella T.","first_name":"Gabriella T.","last_name":"Heller"},{"first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"extern":"1","pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716"}],"date_created":"2021-11-26T07:48:27Z","year":"2020","publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2006684117","issue":"39"},{"pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner","first_name":"Anna-Katharina"},{"full_name":"Mercier, Vincent","first_name":"Vincent","last_name":"Mercier"},{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"last_name":"Moser von Filseck","first_name":"Joachim","full_name":"Moser von Filseck, Joachim"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"}],"extern":"1","volume":182,"keyword":["general biochemistry","genetics and molecular biology"],"title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","article_processing_charge":"No","page":"1140-1155.e18","publication_status":"published","external_id":{"pmid":["32814015"]},"abstract":[{"lang":"eng","text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity."}],"publication_identifier":{"issn":["0092-8674"]},"doi":"10.1016/j.cell.2020.07.021","issue":"5","publication":"Cell","date_created":"2021-11-26T08:02:27Z","year":"2020","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"quality_controlled":"1","scopus_import":"1","_id":"10348","oa_version":"Published Version","intvolume":"       182","article_type":"original","type":"journal_article","acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]).","date_published":"2020-08-18T00:00:00Z","language":[{"iso":"eng"}],"month":"08","date_updated":"2021-11-26T08:58:37Z","publisher":"Elsevier","oa":1,"status":"public","day":"18","citation":{"mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>.","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., &#38; Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>","chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>.","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. 2020;182(5):1140-1155.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18.","ieee":"A.-K. Pfitzner <i>et al.</i>, “An ESCRT-III polymerization sequence drives membrane deformation and fission,” <i>Cell</i>, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020."}},{"oa":1,"date_published":"2020-08-07T00:00:00Z","month":"08","language":[{"iso":"eng"}],"date_updated":"2021-11-26T08:58:33Z","publisher":"American Association for the Advancement of Science","intvolume":"       369","oa_version":"Preprint","article_type":"original","type":"journal_article","acknowledgement":"We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice.","scopus_import":"1","_id":"10349","citation":{"ista":"Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).","ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. 2020;369(6504). doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>","short":"G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020).","ieee":"G. Tarrason Risa <i>et al.</i>, “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” <i>Science</i>, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>.","chicago":"Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>.","apa":"Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>"},"status":"public","day":"07","article_processing_charge":"No","publication_status":"published","external_id":{"pmid":["32764038"]},"abstract":[{"text":"Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.","lang":"eng"}],"keyword":["multidisciplinary"],"title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Tarrason Risa, Gabriel","first_name":"Gabriel","last_name":"Tarrason Risa"},{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Bray, Sian","first_name":"Sian","last_name":"Bray"},{"first_name":"Anne E.","last_name":"Hafner","full_name":"Hafner, Anne E."},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"first_name":"Peter","last_name":"Faull","full_name":"Faull, Peter"},{"last_name":"Davis","first_name":"Colin","full_name":"Davis, Colin"},{"last_name":"Papatziamou","first_name":"Dimitra","full_name":"Papatziamou, Dimitra"},{"full_name":"Mutavchiev, Delyan R.","last_name":"Mutavchiev","first_name":"Delyan R."},{"full_name":"Fan, Catherine","last_name":"Fan","first_name":"Catherine"},{"full_name":"Meneguello, Leticia","first_name":"Leticia","last_name":"Meneguello"},{"full_name":"Arashiro Pulschen, Andre","first_name":"Andre","last_name":"Arashiro Pulschen"},{"last_name":"Dey","first_name":"Gautam","full_name":"Dey, Gautam"},{"full_name":"Culley, Siân","last_name":"Culley","first_name":"Siân"},{"full_name":"Kilkenny, Mairi","first_name":"Mairi","last_name":"Kilkenny"},{"full_name":"Souza, Diorge P.","last_name":"Souza","first_name":"Diorge P."},{"full_name":"Pellegrini, Luca","last_name":"Pellegrini","first_name":"Luca"},{"first_name":"Robertus A. M.","last_name":"de Bruin","full_name":"de Bruin, Robertus A. M."},{"first_name":"Ricardo","last_name":"Henriques","full_name":"Henriques, Ricardo"},{"full_name":"Snijders, Ambrosius P.","first_name":"Ambrosius P.","last_name":"Snijders"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Lindås, Ann-Christin","first_name":"Ann-Christin","last_name":"Lindås"},{"first_name":"Nicholas P.","last_name":"Robinson","full_name":"Robinson, Nicholas P."},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"}],"extern":"1","volume":369,"pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/774273v1"}],"date_created":"2021-11-26T08:21:34Z","year":"2020","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"doi":"10.1126/science.aaz2532","issue":"6504","publication":"Science"},{"tmp":{"short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"status":"public","day":"08","citation":{"chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>.","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., &#38; Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>","mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>.","ieee":"A. J. Dear <i>et al.</i>, “Identification of on- and off-pathway oligomers in amyloid fibril formation,” <i>Chemical Science</i>, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247.","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. 2020;11(24):6236-6247. doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>"},"oa_version":"Published Version","intvolume":"        11","article_type":"original","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","type":"journal_article","scopus_import":"1","_id":"10350","oa":1,"date_published":"2020-06-08T00:00:00Z","month":"06","language":[{"iso":"eng"}],"date_updated":"2021-11-26T11:21:20Z","publisher":"Royal Society of Chemistry","date_created":"2021-11-26T09:08:19Z","year":"2020","doi":"10.1039/c9sc06501f","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"issue":"24","publication":"Chemical Science","quality_controlled":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f","open_access":"1"}],"author":[{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"first_name":"Magnus","last_name":"Kjaergaard","full_name":"Kjaergaard, Magnus"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","volume":11,"pmid":1,"article_processing_charge":"No","page":"6236-6247","external_id":{"pmid":["32953019"]},"publication_status":"published","abstract":[{"text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.","lang":"eng"}],"keyword":["general chemistry"],"title":"Identification of on- and off-pathway oligomers in amyloid fibril formation"},{"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488","open_access":"1"}],"quality_controlled":"1","issue":"5","doi":"10.1038/s41557-020-0452-1","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"publication":"Nature Chemistry","year":"2020","date_created":"2021-11-26T09:15:13Z","title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide","keyword":["general chemical engineering","general chemistry"],"page":"445-451","article_processing_charge":"No","abstract":[{"text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["32303714"]},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41557-020-0468-6"}]},"pmid":1,"extern":"1","author":[{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"full_name":"Bernfur, Katja","last_name":"Bernfur","first_name":"Katja"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"last_name":"Cohen","first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A."},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":12,"citation":{"short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451.","ieee":"T. C. T. Michaels <i>et al.</i>, “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” <i>Nature Chemistry</i>, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. 2020;12(5):445-451. doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>","apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>","chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>.","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>."},"status":"public","day":"13","language":[{"iso":"eng"}],"month":"04","date_published":"2020-04-13T00:00:00Z","publisher":"Springer Nature","date_updated":"2021-11-26T11:21:08Z","oa":1,"_id":"10351","scopus_import":"1","article_type":"original","intvolume":"        12","oa_version":"None","acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","type":"journal_article"},{"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/571687"}],"quality_controlled":"1","publication":"Physical Review E","issue":"2","doi":"10.1103/physreve.101.022420","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"article_number":"022420","year":"2020","date_created":"2021-11-26T09:41:04Z","title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","abstract":[{"lang":"eng","text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events."}],"publication_status":"published","external_id":{"pmid":["32168597"]},"article_processing_charge":"No","pmid":1,"volume":101,"extern":"1","author":[{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"last_name":"Ford","first_name":"Ian J.","full_name":"Ford, Ian J."},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"full_name":"Hoogenboom, Bart W.","last_name":"Hoogenboom","first_name":"Bart W."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” <i>Physical Review E</i>, vol. 101, no. 2. American Physical Society, 2020.","ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>","ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>.","apa":"Davis, L. K., Ford, I. J., Šarić, A., &#38; Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>."},"status":"public","day":"28","publisher":"American Physical Society","date_updated":"2021-11-26T11:21:16Z","language":[{"iso":"eng"}],"month":"02","date_published":"2020-02-28T00:00:00Z","oa":1,"_id":"10352","scopus_import":"1","type":"journal_article","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.).","article_type":"original","intvolume":"       101","oa_version":"Preprint"},{"external_id":{"pmid":["32058787"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content."}],"article_processing_charge":"No","keyword":["general physics and astronomy"],"title":"Dynamic clustering regulates activity of mechanosensitive membrane channels","volume":124,"author":[{"full_name":"Paraschiv, Alexandru","last_name":"Paraschiv","first_name":"Alexandru"},{"full_name":"Hegde, Smitha","last_name":"Hegde","first_name":"Smitha"},{"first_name":"Raman","last_name":"Ganti","full_name":"Ganti, Raman"},{"full_name":"Pilizota, Teuta","first_name":"Teuta","last_name":"Pilizota"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","pmid":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/553248"}],"article_number":"048102","date_created":"2021-11-26T09:57:01Z","year":"2020","publication":"Physical Review Letters","doi":"10.1103/physrevlett.124.048102","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"issue":"4","oa":1,"date_updated":"2021-11-26T11:21:12Z","publisher":"American Physical Society","date_published":"2020-01-31T00:00:00Z","language":[{"iso":"eng"}],"month":"01","type":"journal_article","acknowledgement":"We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.).","oa_version":"Preprint","intvolume":"       124","article_type":"original","scopus_import":"1","_id":"10353","citation":{"chicago":"Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.124.048102\">https://doi.org/10.1103/physrevlett.124.048102</a>.","apa":"Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., &#38; Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.124.048102\">https://doi.org/10.1103/physrevlett.124.048102</a>","mla":"Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” <i>Physical Review Letters</i>, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.124.048102\">10.1103/physrevlett.124.048102</a>.","short":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020).","ieee":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” <i>Physical Review Letters</i>, vol. 124, no. 4. American Physical Society, 2020.","ama":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. <i>Physical Review Letters</i>. 2020;124(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.124.048102\">10.1103/physrevlett.124.048102</a>","ista":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102."},"status":"public","day":"31"},{"publication":"Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security","publication_identifier":{"isbn":["978-1-4503-7089-9"]},"doi":"10.1145/3372297.3423364","year":"2020","date_created":"2021-12-16T13:23:27Z","conference":{"name":"CCS: Conference on Computer and Communications Security","start_date":"2020-11-09","end_date":"2020-11-13","location":"Virtual, United States"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Malkhi, Dahlia","last_name":"Malkhi","first_name":"Dahlia"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"title":"Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures","abstract":[{"text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1<k łe 2f+1, which is of independent interest. Our High-threshold-AVSS (HAVSS) uses an asymmetric bivariate polynomial to encode the secret. This enables the reconstruction of the secret only if a set of k nodes contribute while allowing an honest node that did not participate in the sharing phase to recover his share with the help of f+1 honest parties. Once we have HAVSS we can use it to bootstrap scalable partially synchronous consensus protocols, but the question on how to get a DKG in asynchrony remains as we need a way to produce common randomness. The solution comes from a novel Eventually Perfect Common Coin (EPCC) abstraction that enables the generation of a common coin from n concurrent HAVSS invocations. EPCC's key property is that it is eventually reliable, as it might fail to agree at most f times (even if invoked a polynomial number of times). Using EPCC we implement an Eventually Efficient Asynchronous Binary Agreement (EEABA) which is optimal when the EPCC agrees and protects safety when EPCC fails. Finally, using EEABA we construct the first ADKG which has the same overhead and expected runtime as the best partially-synchronous DKG (O(n4) words, O(f) rounds). As a corollary of our ADKG, we can also create the first Validated Asynchronous Byzantine Agreement (VABA) that does not need a trusted dealer to setup threshold signatures of degree n-f. Our VABA has an overhead of expected O(n2) words and O(1) time per instance, after an initial O(n4) words and O(f) time bootstrap via ADKG.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["000768470400104"]},"page":"1751–1767","article_processing_charge":"No","status":"public","day":"30","citation":{"ista":"Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1751–1767.","ama":"Kokoris Kogias E, Malkhi D, Spiegelman A. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In: <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>. Association for Computing Machinery; 2020:1751–1767. doi:<a href=\"https://doi.org/10.1145/3372297.3423364\">10.1145/3372297.3423364</a>","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, Virtual, United States, 2020, pp. 1751–1767.","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, Association for Computing Machinery, 2020, pp. 1751–1767, doi:<a href=\"https://doi.org/10.1145/3372297.3423364\">10.1145/3372297.3423364</a>.","chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i>, 1751–1767. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3372297.3423364\">https://doi.org/10.1145/3372297.3423364</a>.","apa":"Kokoris Kogias, E., Malkhi, D., &#38; Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In <i>Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security</i> (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3372297.3423364\">https://doi.org/10.1145/3372297.3423364</a>"},"_id":"10556","scopus_import":"1","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","type":"conference","oa_version":"Preprint","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"date_updated":"2025-07-10T11:49:52Z","language":[{"iso":"eng"}],"month":"10","date_published":"2020-10-30T00:00:00Z","oa":1,"isi":1}]