[{"citation":{"short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1.","chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104."},"publication":"Nature Communications","article_type":"original","date_published":"2023-02-27T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"27","_id":"12702","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","ddc":["540"],"title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","status":"public","oa_version":"Published Version","file":[{"file_id":"12713","relation":"main_file","date_updated":"2023-03-07T10:58:00Z","date_created":"2023-03-07T10:58:00Z","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","file_name":"2023_NatComm_Cheng.pdf","access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_size":1946443}],"type":"journal_article","abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36843123"],"isi":["000939678300002"]},"oa":1,"project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-36841-1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"02","pmid":1,"year":"2023","acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","department":[{"_id":"BiCh"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Hamel, Sebastien","last_name":"Hamel","first_name":"Sebastien"},{"last_name":"Bethkenhagen","first_name":"Mandy","orcid":"0000-0002-1838-2129","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","full_name":"Bethkenhagen, Mandy"}],"volume":14,"date_created":"2023-03-05T23:01:04Z","date_updated":"2023-08-01T13:36:11Z","article_number":"1104","file_date_updated":"2023-03-07T10:58:00Z"},{"day":"28","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-02-28T00:00:00Z","publication":"Genome Medicine","citation":{"short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12."},"article_type":"original","abstract":[{"lang":"eng","text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"12722","date_updated":"2023-03-14T10:29:47Z","date_created":"2023-03-14T10:29:47Z","checksum":"833b837910c4db42fb5f0f34125f77a7","success":1,"file_name":"2023_GenomeMed_Bernabeu.pdf","access_level":"open_access","file_size":4275987,"content_type":"application/pdf","creator":"cchlebak"}],"oa_version":"Published Version","_id":"12719","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Refining epigenetic prediction of chronological and biological age","status":"public","ddc":["570"],"intvolume":" 15","month":"02","publication_identifier":{"eissn":["1756-994X"]},"doi":"10.1186/s13073-023-01161-y","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000940286600001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2023-03-14T10:29:47Z","article_number":"12","author":[{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"first_name":"Daniel L.","last_name":"Mccartney","full_name":"Mccartney, Daniel L."},{"full_name":"Gadd, Danni A.","first_name":"Danni A.","last_name":"Gadd"},{"full_name":"Hillary, Robert F.","first_name":"Robert F.","last_name":"Hillary"},{"full_name":"Lu, Ake T.","last_name":"Lu","first_name":"Ake T."},{"first_name":"Lee","last_name":"Murphy","full_name":"Murphy, Lee"},{"last_name":"Wrobel","first_name":"Nicola","full_name":"Wrobel, Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"first_name":"Sarah E.","last_name":"Harris","full_name":"Harris, Sarah E."},{"full_name":"Liewald, David","last_name":"Liewald","first_name":"David"},{"full_name":"Hayward, Caroline","last_name":"Hayward","first_name":"Caroline"},{"full_name":"Sudlow, Cathie","first_name":"Cathie","last_name":"Sudlow"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"first_name":"Steve","last_name":"Horvath","full_name":"Horvath, Steve"},{"full_name":"Mcintosh, Andrew M.","first_name":"Andrew M.","last_name":"Mcintosh"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Vallejos","first_name":"Catalina A.","full_name":"Vallejos, Catalina A."},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"}],"date_created":"2023-03-12T23:01:02Z","date_updated":"2023-08-01T13:38:12Z","volume":15,"acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature"},{"citation":{"ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602."},"publication":"IEEE Robotics and Automation Letters","page":"1595-1602","article_type":"original","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12704","intvolume":" 8","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","ddc":["000"],"status":"public","file":[{"content_type":"application/pdf","file_size":944052,"creator":"cchlebak","file_name":"2023_IEEERobAutLetters_Lechner.pdf","access_level":"open_access","date_created":"2023-03-07T12:22:23Z","date_updated":"2023-03-07T12:22:23Z","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"relation":"main_file","file_id":"12714"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2204.07373"],"isi":["000936534100012"]},"quality_controlled":"1","isi":1,"doi":"10.1109/LRA.2023.3240930","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2377-3766"]},"month":"03","year":"2023","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"11366","relation":"earlier_version","status":"public"}]},"author":[{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"volume":8,"date_created":"2023-03-05T23:01:04Z","date_updated":"2023-08-01T13:36:50Z","file_date_updated":"2023-03-07T12:22:23Z"},{"page":"4625-4636","article_type":"original","citation":{"chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057","ieee":"Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057"},"publication":"Inorganic Chemistry","date_published":"2023-03-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"08","intvolume":" 62","status":"public","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","_id":"12737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","issue":"11","abstract":[{"text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed.","lang":"eng"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000956110300001"],"pmid":["36883367"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.inorgchem.3c00057","publication_identifier":{"eissn":["1520-510X"],"issn":["0020-1669"]},"month":"03","department":[{"_id":"StFr"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","year":"2023","volume":62,"date_created":"2023-03-19T23:00:59Z","date_updated":"2023-08-01T13:42:59Z","author":[{"full_name":"García-Romero, Álvaro","last_name":"García-Romero","first_name":"Álvaro"},{"first_name":"Jessica E.","last_name":"Waters","full_name":"Waters, Jessica E."},{"full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","first_name":"Rajesh B"},{"first_name":"Andrew D.","last_name":"Bond","full_name":"Bond, Andrew D."},{"first_name":"Annie L.","last_name":"Colebatch","full_name":"Colebatch, Annie L."},{"first_name":"Raúl","last_name":"García-Rodríguez","full_name":"García-Rodríguez, Raúl"},{"full_name":"Wright, Dominic S.","first_name":"Dominic S.","last_name":"Wright"}]},{"intvolume":" 130","title":"Spin-electric coupling in lead halide perovskites","status":"public","_id":"12723","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901.","ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901"},"publication":"Physical Review Letters","date_published":"2023-03-10T00:00:00Z","keyword":["General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"10","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","year":"2023","volume":130,"date_updated":"2023-08-01T13:39:04Z","date_created":"2023-03-14T13:11:59Z","author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a"},{"full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","last_name":"Lorenc","first_name":"Dusan"},{"full_name":"Ashourishokri, Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","last_name":"Ashourishokri","first_name":"Younes"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek"}],"article_number":"106901","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.106901","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03"},{"status":"public","title":"Effective model for studying optical properties of lead halide perovskites","intvolume":" 107","_id":"12724","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.","lang":"eng"}],"issue":"12","article_type":"original","publication":"Physical Review B","citation":{"ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023)."},"date_published":"2023-03-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"year":"2023","date_created":"2023-03-14T13:13:05Z","date_updated":"2023-08-01T13:39:47Z","volume":107,"author":[{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan","last_name":"Lorenc","full_name":"Lorenc, Dusan"},{"last_name":"Ashourishokri","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes"},{"last_name":"Zhumekenov","first_name":"Ayan","full_name":"Zhumekenov, Ayan"},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"article_number":"125201","isi":1,"quality_controlled":"1","external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.107.125201","month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"doi":"10.1371/journal.pone.0277148","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001024737400001"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739","call_identifier":"FWF","name":"Structural plasticity at mossy fiber-CA3 synapses"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1932-6203"]},"month":"03","author":[{"last_name":"Rothman","first_name":"Jason Seth","full_name":"Rothman, Jason Seth"},{"full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0005-401X","first_name":"Carolina","last_name":"Borges Merjane"},{"full_name":"Holderith, Noemi","last_name":"Holderith","first_name":"Noemi"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"},{"first_name":"R.","last_name":"Angus Silver","full_name":"Angus Silver, R."}],"volume":18,"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:46:39Z","year":"2023","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","publisher":"Public Library of Science","department":[{"_id":"PeJo"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-03-27T06:51:09Z","article_number":"e0277148","date_published":"2023-03-17T00:00:00Z","citation":{"mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023).","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148","ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148"},"publication":"PLoS ONE","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"17","scopus_import":"1","file":[{"file_id":"12770","relation":"main_file","date_created":"2023-03-27T06:51:09Z","date_updated":"2023-03-27T06:51:09Z","success":1,"checksum":"2380331ec27cc87808826fc64419ac1c","file_name":"2023_PLoSOne_Rothman.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":7290413}],"oa_version":"Published Version","_id":"12759","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 18","status":"public","title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","ddc":["570"],"issue":"3 March","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"type":"journal_article"},{"article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2023-03-17T00:00:00Z","citation":{"ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224."},"publication":"Science Advances","article_type":"original","issue":"11","abstract":[{"text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","file_size":1826471,"content_type":"application/pdf","file_name":"2023_ScienceAdvances_Hurtig.pdf","access_level":"open_access","date_updated":"2023-03-27T06:24:49Z","date_created":"2023-03-27T06:24:49Z","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_id":"12768","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12756","intvolume":" 9","status":"public","ddc":["570"],"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","publication_identifier":{"eissn":["2375-2548"]},"month":"03","doi":"10.1126/sciadv.ade5224","language":[{"iso":"eng"}],"external_id":{"isi":["000968083500010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-03-27T06:24:49Z","article_number":"eade5224","author":[{"first_name":"Fredrik","last_name":"Hurtig","full_name":"Hurtig, Fredrik"},{"first_name":"Thomas C.Q.","last_name":"Burgers","full_name":"Burgers, Thomas C.Q."},{"last_name":"Cezanne","first_name":"Alice","full_name":"Cezanne, Alice"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"full_name":"Mol, Frank N.","last_name":"Mol","first_name":"Frank N."},{"last_name":"Traparić","first_name":"Jovan","full_name":"Traparić, Jovan"},{"first_name":"Andre Arashiro","last_name":"Pulschen","full_name":"Pulschen, Andre Arashiro"},{"full_name":"Nierhaus, Tim","first_name":"Tim","last_name":"Nierhaus"},{"full_name":"Tarrason-Risa, Gabriel","first_name":"Gabriel","last_name":"Tarrason-Risa"},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"full_name":"Löwe, Jan","first_name":"Jan","last_name":"Löwe"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Rifka","last_name":"Vlijm","full_name":"Vlijm, Rifka"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"}],"volume":9,"date_created":"2023-03-26T22:01:06Z","date_updated":"2023-08-01T13:45:54Z","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","year":"2023","department":[{"_id":"AnSa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published"},{"doi":"10.1371/journal.pone.0282689","language":[{"iso":"eng"}],"external_id":{"isi":["000985134400106"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"month":"03","publication_identifier":{"eissn":["1932-6203"]},"author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"first_name":"Karina A.","last_name":"Markhieva","full_name":"Markhieva, Karina A."},{"last_name":"Novikova","first_name":"Mariia S.","full_name":"Novikova, Mariia S."},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"first_name":"Ilya S.","last_name":"Vorobyev","full_name":"Vorobyev, Ilya S."},{"first_name":"Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87","full_name":"Maksimova, Ekaterina"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Ivankov, Dmitry N.","first_name":"Dmitry N.","last_name":"Ivankov"}],"date_created":"2023-03-26T22:01:07Z","date_updated":"2023-08-01T13:47:14Z","volume":18,"year":"2023","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"file_date_updated":"2023-03-27T07:09:08Z","article_number":"e0282689","date_published":"2023-03-16T00:00:00Z","publication":"PLoS ONE","citation":{"ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689","ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689."},"article_type":"original","day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","date_updated":"2023-03-27T07:09:08Z","date_created":"2023-03-27T07:09:08Z","file_id":"12771","relation":"main_file","creator":"dernst","file_size":856625,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_PLoSOne_Pak.pdf"}],"oa_version":"Published Version","_id":"12758","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","ddc":["570"],"status":"public","intvolume":" 18","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"issue":"3","type":"journal_article"},{"author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"date_updated":"2023-08-01T13:45:12Z","date_created":"2023-03-26T22:01:06Z","volume":480,"year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Portland Press","month":"03","publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"doi":"10.1042/BCJ20210285","language":[{"iso":"eng"}],"external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BCJ20210285"}],"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"lang":"eng","text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues."}],"issue":"5","type":"journal_article","oa_version":"Published Version","_id":"12757","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","ddc":["570"],"status":"public","intvolume":" 480","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-15T00:00:00Z","publication":"The Biochemical Journal","citation":{"ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285","ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.","mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333."},"article_type":"review","page":"319-333"}]